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Folder iconhiCLIP reveals mRNA secondary structures

Rahul Arora
June 13, 2019
mRNA structure is important for post-transcriptional regulation, largely because it affects binding of trans-acting factors. However, little is known about the in vivo structure of full-length mRNAs. Here we present hiCLIP, a high-throughput technique to identify RNA secondary structures interacting with RNA-binding proteins (RBPs) in vivo. Using this technique to investigate RNA structures bound by Staufen 1 (STAU1), we uncover a dominance of intra-molecular RNA duplexes, a depletion of duplexes from coding regions of highly translated mRNAs, an unforeseen prevalence of long-range duplexes in 3′ untranslated regions (UTRs), and a decreased incidence of SNPs in duplex-forming regions. We also discover a duplex spanning 858nts in the 3′ UTR of the X-box binding Protein 1 (XBP1) mRNA that regulates its cytoplasmic splicing and stability. Our study reveals the fundamental role of mRNA secondary structures in gene regulation and introduces hiCLIP as a widely applicable method for discovering novel, especially long-range, RNA duplexes.

20120628_LUs14_SLX_4942.fq.gz

FASTQ file (single-end)
fastqc
Directory
20120628_LUs14_SLX_4942_fastqc.zip
493.42 kB
stderr.txt
1.11 kB
20120628_LUs14_SLX_4942.fastq.gz
493.95 MB

LUs27_ae.fastq.gz

FASTQ file (single-end)
fastqc
Directory
LUs27_ae.fastq.gz
1.16 GB
LUs27_ae_fastqc.zip
475.88 kB
stderr.txt
835 B

demux_nomatch.fastq.gz

FASTQ file (single-end)
demux_nomatch.fastq.gz
26.95 MB
fastqc
Directory
demux_nomatch_fastqc.zip
430.14 kB
stderr.txt
935 B

demux_nomatch.fastq.gz

FASTQ file (single-end)
fastqc
Directory
stderr.txt
935 B
demux_nomatch_fastqc.zip
430.85 kB
demux_nomatch.fastq.gz
44.43 MB

STAU1_293Flp_denature_STAU1_20120628_LUs14_2

FASTQ file (single-end)
fastqc
Directory
stau1-293flp-denature-stau1-20120628-lus14-2.fastq.gz
59.63 MB
stau1-293flp-denature-stau1-20120628-lus14-2_fastqc.zip
328.13 kB
stderr.txt
1.52 kB
Cutadapt (single-end)
fastqc
Directory
stau1-293flp-denature-stau1-20120628-lus14-2_trimmed.fastq.gz
61.59 MB
report.txt
679 B
STAR
stau1-293flp-denature-stau1-20120628-lus14-2_trimmed_unmapped.out.mate1.fastq.gz
11.07 MB
stau1-293flp-denature-stau1-20120628-lus14-2_trimmed.bam.bai
4.33 MB
stau1-293flp-denature-stau1-20120628-lus14-2_trimmed_SJ.out.tab
289.55 kB
stau1-293flp-denature-stau1-20120628-lus14-2_trimmed_stats.txt
1.80 kB
stau1-293flp-denature-stau1-20120628-lus14-2_trimmed.bw
54.41 kB
stau1-293flp-denature-stau1-20120628-lus14-2_trimmed.bam
146.04 MB
iCount xlsites
stau1-293flp-denature-stau1-20120628-lus14-2_trimmed_reads_single.bed.gz
3.85 MB
stau1-293flp-denature-stau1-20120628-lus14-2_trimmed_single.bed.gz
3.51 MB
stau1-293flp-denature-stau1-20120628-lus14-2_trimmed_singleAndMulti.bed.gz
9.16 MB
stau1-293flp-denature-stau1-20120628-lus14-2_trimmed_single.bedgraph
15.98 MB
stau1-293flp-denature-stau1-20120628-lus14-2_trimmed_skipped.bam
2.90 kB
iCount summary
stau1-293flp-denature-stau1-20120628-lus14-2_trimmed_single_summary_type.tsv
433 B
stau1-293flp-denature-stau1-20120628-lus14-2_trimmed_single_summary_gene.tsv
1.39 MB
stau1-293flp-denature-stau1-20120628-lus14-2_trimmed_single_summary_subtype.tsv
1014 B
iCount RNA-maps
stau1-293flp-denature-stau1-20120628-lus14-2_trimmed_single.tar.gz
725.91 kB
Paraclu
stau1-293flp-denature-stau1-20120628-lus14-2_trimmed_single_peaks.bed.gz
11.35 kB
K-mers
stau1-293flp-denature-stau1-20120628-lus14-2.tar.gz
363.74 kB

STAU1_293Flp_denature_STAU1_20120628_LUs14_1

FASTQ file (single-end)
fastqc
Directory
stau1-293flp-denature-stau1-20120628-lus14-1.fastq.gz
152.61 MB
stderr.txt
1.52 kB
stau1-293flp-denature-stau1-20120628-lus14-1_fastqc.zip
324.69 kB
Cutadapt (single-end)
fastqc
Directory
report.txt
680 B
stau1-293flp-denature-stau1-20120628-lus14-1_trimmed.fastq.gz
157.42 MB
STAR
stau1-293flp-denature-stau1-20120628-lus14-1_trimmed_unmapped.out.mate1.fastq.gz
26.50 MB
stau1-293flp-denature-stau1-20120628-lus14-1_trimmed.bam.bai
4.23 MB
stau1-293flp-denature-stau1-20120628-lus14-1_trimmed_SJ.out.tab
657.14 kB
stau1-293flp-denature-stau1-20120628-lus14-1_trimmed_stats.txt
1.81 kB
stau1-293flp-denature-stau1-20120628-lus14-1_trimmed.bam
357.06 MB
iCount xlsites
stau1-293flp-denature-stau1-20120628-lus14-1_trimmed_skipped.bam
3.39 kB
stau1-293flp-denature-stau1-20120628-lus14-1_trimmed_reads_single.bed.gz
10.09 MB
stau1-293flp-denature-stau1-20120628-lus14-1_trimmed_single.bed.gz
9.26 MB
stau1-293flp-denature-stau1-20120628-lus14-1_trimmed_single.bedgraph
43.25 MB
stau1-293flp-denature-stau1-20120628-lus14-1_trimmed_singleAndMulti.bed.gz
22.27 MB
iCount RNA-maps
stau1-293flp-denature-stau1-20120628-lus14-1_trimmed_single.tar.gz
1.02 MB
Paraclu
stau1-293flp-denature-stau1-20120628-lus14-1_trimmed_single_peaks.bed.gz
68.19 kB
K-mers
stau1-293flp-denature-stau1-20120628-lus14-1.tar.gz
427.74 kB
iCount summary
stau1-293flp-denature-stau1-20120628-lus14-1_trimmed_single_summary_gene.tsv
1.68 MB
stau1-293flp-denature-stau1-20120628-lus14-1_trimmed_single_summary_type.tsv
439 B
stau1-293flp-denature-stau1-20120628-lus14-1_trimmed_single_summary_subtype.tsv
1.00 kB

STAU1_293Flp_denature_STAU1_20120628_LUs14

FASTQ file (single-end)
fastqc
Directory
stau1-293flp-denature-stau1-20120628-lus14.fastq.gz
48.00 MB
stderr.txt
1.55 kB
stau1-293flp-denature-stau1-20120628-lus14_fastqc.zip
334.15 kB
K-mers
stau1-293flp-denature-stau1-20120628-lus14.tar.gz
354.20 kB
Cutadapt (single-end)
report.txt
677 B
fastqc
Directory
stau1-293flp-denature-stau1-20120628-lus14_trimmed.fastq.gz
49.34 MB
STAR
stau1-293flp-denature-stau1-20120628-lus14_trimmed.bam.bai
4.25 MB
stau1-293flp-denature-stau1-20120628-lus14_trimmed_unmapped.out.mate1.fastq.gz
8.64 MB
stau1-293flp-denature-stau1-20120628-lus14_trimmed_SJ.out.tab
271.04 kB
stau1-293flp-denature-stau1-20120628-lus14_trimmed.bam
119.85 MB
stau1-293flp-denature-stau1-20120628-lus14_trimmed.bw
47.93 kB
stau1-293flp-denature-stau1-20120628-lus14_trimmed_stats.txt
1.80 kB
iCount xlsites
stau1-293flp-denature-stau1-20120628-lus14_trimmed_skipped.bam
2.90 kB
stau1-293flp-denature-stau1-20120628-lus14_trimmed_single.bed.gz
2.85 MB
stau1-293flp-denature-stau1-20120628-lus14_trimmed_reads_single.bed.gz
3.11 MB
stau1-293flp-denature-stau1-20120628-lus14_trimmed_singleAndMulti.bed.gz
7.28 MB
stau1-293flp-denature-stau1-20120628-lus14_trimmed_single.bedgraph
12.86 MB
iCount summary
stau1-293flp-denature-stau1-20120628-lus14_trimmed_single_summary_subtype.tsv
1007 B
stau1-293flp-denature-stau1-20120628-lus14_trimmed_single_summary_type.tsv
431 B
stau1-293flp-denature-stau1-20120628-lus14_trimmed_single_summary_gene.tsv
1.35 MB
iCount RNA-maps
stau1-293flp-denature-stau1-20120628-lus14_trimmed_single.tar.gz
734.48 kB
Paraclu
stau1-293flp-denature-stau1-20120628-lus14_trimmed_single_peaks.bed.gz
7.81 kB

STAU1_293Flp_Low_Rnase_LUs27

Cutadapt (single-end)
report.txt
665 B
fastqc
Directory
stau1-293flp-low-rnase-lus27_trimmed.fastq.gz
134.78 MB
K-mers
stau1-293flp-low-rnase-lus27.tar.gz
362.18 kB
iCount summary
stau1-293flp-low-rnase-lus27_trimmed_single_summary_subtype.tsv
1008 B
stau1-293flp-low-rnase-lus27_trimmed_single_summary_type.tsv
434 B
stau1-293flp-low-rnase-lus27_trimmed_single_summary_gene.tsv
1.19 MB
iCount RNA-maps
stau1-293flp-low-rnase-lus27_trimmed_single.tar.gz
1015.76 kB
FASTQ file (single-end)
stau1-293flp-low-rnase-lus27.fastq.gz
147.63 MB
fastqc
Directory
stau1-293flp-low-rnase-lus27_fastqc.zip
412.84 kB
stderr.txt
1.21 kB
STAR
stau1-293flp-low-rnase-lus27_trimmed.bam.bai
2.56 MB
stau1-293flp-low-rnase-lus27_trimmed_unmapped.out.mate1.fastq.gz
41.38 MB
stau1-293flp-low-rnase-lus27_trimmed.bam
414.67 MB
stau1-293flp-low-rnase-lus27_trimmed_stats.txt
1.81 kB
stau1-293flp-low-rnase-lus27_trimmed_SJ.out.tab
1.04 MB
Paraclu
stau1-293flp-low-rnase-lus27_trimmed_single_peaks.bed.gz
19.22 kB
iCount xlsites
stau1-293flp-low-rnase-lus27_trimmed_single.bed.gz
1.55 MB
stau1-293flp-low-rnase-lus27_trimmed_singleAndMulti.bed.gz
2.67 MB
stau1-293flp-low-rnase-lus27_trimmed_reads_single.bed.gz
1.72 MB
stau1-293flp-low-rnase-lus27_trimmed_skipped.bam
4.15 kB
stau1-293flp-low-rnase-lus27_trimmed_single.bedgraph
7.18 MB

STAU1_293Flp_High_RNAse_LUs27

FASTQ file (single-end)
fastqc
Directory
stau1-293flp-high-rnase-lus27.fastq.gz
160.14 MB
stau1-293flp-high-rnase-lus27_fastqc.zip
397.77 kB
stderr.txt
1.23 kB
K-mers
stau1-293flp-high-rnase-lus27.tar.gz
356.15 kB
Cutadapt (single-end)
fastqc
Directory
stau1-293flp-high-rnase-lus27_trimmed.fastq.gz
150.89 MB
report.txt
665 B
STAR
stau1-293flp-high-rnase-lus27_trimmed.bam.bai
2.45 MB
stau1-293flp-high-rnase-lus27_trimmed.bam
342.86 MB
stau1-293flp-high-rnase-lus27_trimmed_unmapped.out.mate1.fastq.gz
48.69 MB
stau1-293flp-high-rnase-lus27_trimmed_SJ.out.tab
867.96 kB
stau1-293flp-high-rnase-lus27_trimmed_stats.txt
1.81 kB
iCount RNA-maps
stau1-293flp-high-rnase-lus27_trimmed_single.tar.gz
908.44 kB
Paraclu
stau1-293flp-high-rnase-lus27_trimmed_single_peaks.bed.gz
14.43 kB
iCount xlsites
stau1-293flp-high-rnase-lus27_trimmed_skipped.bam
3.32 kB
stau1-293flp-high-rnase-lus27_trimmed_reads_single.bed.gz
1.38 MB
stau1-293flp-high-rnase-lus27_trimmed_single.bed.gz
1.20 MB
stau1-293flp-high-rnase-lus27_trimmed_single.bedgraph
5.47 MB
stau1-293flp-high-rnase-lus27_trimmed_singleAndMulti.bed.gz
2.12 MB
iCount summary
stau1-293flp-high-rnase-lus27_trimmed_single_summary_type.tsv
436 B
stau1-293flp-high-rnase-lus27_trimmed_single_summary_gene.tsv
1.13 MB
stau1-293flp-high-rnase-lus27_trimmed_single_summary_subtype.tsv
1004 B

STAU1_293Flp_denature_Low_20120628_LUs14_3

Cutadapt (single-end)
fastqc
Directory
report.txt
677 B
stau1-293flp-denature-low-20120628-lus14-3_trimmed.fastq.gz
31.37 MB
iCount RNA-maps
stau1-293flp-denature-low-20120628-lus14-3_trimmed_single.tar.gz
681.51 kB
FASTQ file (single-end)
fastqc
Directory
stau1-293flp-denature-low-20120628-lus14-3.fastq.gz
30.61 MB
stau1-293flp-denature-low-20120628-lus14-3_fastqc.zip
340.71 kB
stderr.txt
1.48 kB
STAR
stau1-293flp-denature-low-20120628-lus14-3_trimmed_unmapped.out.mate1.fastq.gz
3.89 MB
stau1-293flp-denature-low-20120628-lus14-3_trimmed.bam
86.67 MB
stau1-293flp-denature-low-20120628-lus14-3_trimmed.bam.bai
3.81 MB
stau1-293flp-denature-low-20120628-lus14-3_trimmed_stats.txt
1.80 kB
stau1-293flp-denature-low-20120628-lus14-3_trimmed_SJ.out.tab
167.26 kB
stau1-293flp-denature-low-20120628-lus14-3_trimmed.bw
37.83 kB
iCount xlsites
stau1-293flp-denature-low-20120628-lus14-3_trimmed_skipped.bam
2.90 kB
stau1-293flp-denature-low-20120628-lus14-3_trimmed_single.bedgraph
8.69 MB
stau1-293flp-denature-low-20120628-lus14-3_trimmed_singleAndMulti.bed.gz
4.07 MB
stau1-293flp-denature-low-20120628-lus14-3_trimmed_reads_single.bed.gz
2.14 MB
stau1-293flp-denature-low-20120628-lus14-3_trimmed_single.bed.gz
1.96 MB
iCount summary
stau1-293flp-denature-low-20120628-lus14-3_trimmed_single_summary_gene.tsv
1.26 MB
stau1-293flp-denature-low-20120628-lus14-3_trimmed_single_summary_subtype.tsv
1007 B
stau1-293flp-denature-low-20120628-lus14-3_trimmed_single_summary_type.tsv
430 B
Paraclu
stau1-293flp-denature-low-20120628-lus14-3_trimmed_single_peaks.bed.gz
4.32 kB
K-mers
stau1-293flp-denature-low-20120628-lus14-3.tar.gz
322.43 kB

STAU1_293Flp_denature_Low_20120628_LUs14_4

FASTQ file (single-end)
fastqc
Directory
stau1-293flp-denature-low-20120628-lus14-4.fastq.gz
45.16 MB
stau1-293flp-denature-low-20120628-lus14-4_fastqc.zip
336.64 kB
stderr.txt
1.48 kB
Cutadapt (single-end)
fastqc
Directory
report.txt
677 B
stau1-293flp-denature-low-20120628-lus14-4_trimmed.fastq.gz
45.96 MB
STAR
stau1-293flp-denature-low-20120628-lus14-4_trimmed_unmapped.out.mate1.fastq.gz
5.89 MB
stau1-293flp-denature-low-20120628-lus14-4_trimmed.bam
112.19 MB
stau1-293flp-denature-low-20120628-lus14-4_trimmed.bam.bai
4.14 MB
stau1-293flp-denature-low-20120628-lus14-4_trimmed_stats.txt
1.80 kB
stau1-293flp-denature-low-20120628-lus14-4_trimmed_SJ.out.tab
195.78 kB
stau1-293flp-denature-low-20120628-lus14-4_trimmed.bw
45.80 kB
iCount xlsites
stau1-293flp-denature-low-20120628-lus14-4_trimmed_single.bed.gz
3.11 MB
stau1-293flp-denature-low-20120628-lus14-4_trimmed_singleAndMulti.bed.gz
6.29 MB
stau1-293flp-denature-low-20120628-lus14-4_trimmed_skipped.bam
3.07 kB
stau1-293flp-denature-low-20120628-lus14-4_trimmed_reads_single.bed.gz
3.41 MB
stau1-293flp-denature-low-20120628-lus14-4_trimmed_single.bedgraph
14.06 MB
Paraclu
stau1-293flp-denature-low-20120628-lus14-4_trimmed_single_peaks.bed.gz
9.42 kB
iCount summary
stau1-293flp-denature-low-20120628-lus14-4_trimmed_single_summary_type.tsv
430 B
stau1-293flp-denature-low-20120628-lus14-4_trimmed_single_summary_subtype.tsv
1008 B
stau1-293flp-denature-low-20120628-lus14-4_trimmed_single_summary_gene.tsv
1.36 MB
iCount RNA-maps
stau1-293flp-denature-low-20120628-lus14-4_trimmed_single.tar.gz
744.70 kB
K-mers
stau1-293flp-denature-low-20120628-lus14-4.tar.gz
347.24 kB

STAU1_293Flp_denature_Low_20120628_LUs14_5

FASTQ file (single-end)
fastqc
Directory
stau1-293flp-denature-low-20120628-lus14-5.fastq.gz
9.41 MB
stderr.txt
1.48 kB
stau1-293flp-denature-low-20120628-lus14-5_fastqc.zip
332.49 kB
Cutadapt (single-end)
report.txt
677 B
fastqc
Directory
stau1-293flp-denature-low-20120628-lus14-5_trimmed.fastq.gz
9.61 MB
STAR
stau1-293flp-denature-low-20120628-lus14-5_trimmed.bam.bai
2.94 MB
stau1-293flp-denature-low-20120628-lus14-5_trimmed.bam
24.97 MB
stau1-293flp-denature-low-20120628-lus14-5_trimmed_unmapped.out.mate1.fastq.gz
1.32 MB
stau1-293flp-denature-low-20120628-lus14-5_trimmed_stats.txt
1.79 kB
stau1-293flp-denature-low-20120628-lus14-5_trimmed.bw
27.80 kB
stau1-293flp-denature-low-20120628-lus14-5_trimmed_SJ.out.tab
48.61 kB
iCount xlsites
stau1-293flp-denature-low-20120628-lus14-5_trimmed_skipped.bam
3.09 kB
stau1-293flp-denature-low-20120628-lus14-5_trimmed_singleAndMulti.bed.gz
1.47 MB
stau1-293flp-denature-low-20120628-lus14-5_trimmed_single.bed.gz
677.42 kB
stau1-293flp-denature-low-20120628-lus14-5_trimmed_single.bedgraph
2.78 MB
stau1-293flp-denature-low-20120628-lus14-5_trimmed_reads_single.bed.gz
739.46 kB
iCount RNA-maps
stau1-293flp-denature-low-20120628-lus14-5_trimmed_single.tar.gz
500.54 kB
Paraclu
stau1-293flp-denature-low-20120628-lus14-5_trimmed_single_peaks.bed.gz
819 B
K-mers
stau1-293flp-denature-low-20120628-lus14-5.tar.gz
210.25 kB
iCount summary
stau1-293flp-denature-low-20120628-lus14-5_trimmed_single_summary_type.tsv
423 B
stau1-293flp-denature-low-20120628-lus14-5_trimmed_single_summary_gene.tsv
958.46 kB
stau1-293flp-denature-low-20120628-lus14-5_trimmed_single_summary_subtype.tsv
990 B

No Sample

FASTQ file (single-end)
stderr.txt
1.55 kB
fastqc
Directory
stau1-293flp-denature-stau1-20120628-lus14.fastq.gz
48.00 MB
stau1-293flp-denature-stau1-20120628-lus14_fastqc.zip
334.15 kB
Cutadapt (single-end)
fastqc
Directory
stau1-293flp-low-rnase-lus27_trimmed.fastq.gz
134.78 MB
report.txt
665 B
K-mers
stau1-293flp-low-rnase-lus27.tar.gz
362.18 kB
FASTQ file (single-end)
fastqc
Directory
stau1-293flp-high-rnase-lus27.fastq.gz
160.14 MB
stau1-293flp-high-rnase-lus27_fastqc.zip
397.77 kB
stderr.txt
1.23 kB
iCount RNA-maps
stau1-293flp-minus-stau1-induction-lus27_trimmed_single.tar.gz
204.97 kB
Cutadapt (single-end)
fastqc
Directory
report.txt
677 B
stau1-293flp-denature-low-20120628-lus14-3_trimmed.fastq.gz
31.37 MB
iCount demultiplex (from annotation file)
demultiplexing_stats.txt
562 B
iCount demultiplex (from annotation file)
demultiplexing_stats.txt
385 B
FASTQ file (single-end)
fastqc
Directory
stau1-293flp-denature-low-20120628-lus14-4.fastq.gz
45.16 MB
stau1-293flp-denature-low-20120628-lus14-4_fastqc.zip
336.64 kB
stderr.txt
1.48 kB
Paraclu
stau1-293flp-minus-2nd-ligation-lus27_trimmed_single_peaks.bed.gz
31.35 kB
iCount summary
stau1-293flp-low-rnase-lus27_trimmed_single_summary_subtype.tsv
1008 B
stau1-293flp-low-rnase-lus27_trimmed_single_summary_type.tsv
434 B
stau1-293flp-low-rnase-lus27_trimmed_single_summary_gene.tsv
1.19 MB
STAR
stau1-293flp-minus-stau1-induction-lus27_trimmed.bam
30.88 kB
stau1-293flp-minus-stau1-induction-lus27_trimmed_unmapped.out.mate1.fastq.gz
3.63 kB
stau1-293flp-minus-stau1-induction-lus27_trimmed.bam.bai
1.16 MB
stau1-293flp-minus-stau1-induction-lus27_trimmed_stats.txt
1.77 kB
stau1-293flp-minus-stau1-induction-lus27_trimmed_SJ.out.tab
401 B
stau1-293flp-minus-stau1-induction-lus27_trimmed.bw
16.06 kB
iCount RNA-maps
stau1-293flp-denature-low-20120628-lus14-3_trimmed_single.tar.gz
681.51 kB
iCount RNA-maps
stau1-293flp-minus-2nd-ligation-lus27_trimmed_single.tar.gz
1.18 MB
iCount RNA-maps
stau1-293flp-low-rnase-lus27_trimmed_single.tar.gz
1015.76 kB
FASTQ file (single-end)
demux_nomatch.fastq.gz
26.95 MB
fastqc
Directory
demux_nomatch_fastqc.zip
430.14 kB
stderr.txt
935 B
FASTQ file (single-end)
fastqc
Directory
stau1-293flp-denature-low-20120628-lus14-5.fastq.gz
9.41 MB
stderr.txt
1.48 kB
stau1-293flp-denature-low-20120628-lus14-5_fastqc.zip
332.49 kB
FASTQ file (single-end)
fastqc
Directory
stau1-293flp-denature-low-20120628-lus14-3.fastq.gz
30.61 MB
stau1-293flp-denature-low-20120628-lus14-3_fastqc.zip
340.71 kB
stderr.txt
1.48 kB
FASTQ file (single-end)
fastqc
Directory
stau1-293flp-denature-stau1-20120628-lus14-2.fastq.gz
59.63 MB
stau1-293flp-denature-stau1-20120628-lus14-2_fastqc.zip
328.13 kB
stderr.txt
1.52 kB
FASTQ file (single-end)
fastqc
Directory
stau1-293flp-denature-stau1-20120628-lus14-1.fastq.gz
152.61 MB
stderr.txt
1.52 kB
stau1-293flp-denature-stau1-20120628-lus14-1_fastqc.zip
324.69 kB
K-mers
stau1-293flp-denature-stau1-20120628-lus14.tar.gz
354.20 kB
FASTQ file (single-end)
stau1-293flp-low-rnase-lus27.fastq.gz
147.63 MB
fastqc
Directory
stau1-293flp-low-rnase-lus27_fastqc.zip
412.84 kB
stderr.txt
1.21 kB
FASTQ file (single-end)
fastqc
Directory
stau1-293flp-minus-stau1-induction-lus27.fastq.gz
17.78 kB
stau1-293flp-minus-stau1-induction-lus27_fastqc.zip
496.71 kB
stderr.txt
70 B
FASTQ file (single-end)
stau1-293flp-minus-2nd-ligation-lus27.fastq.gz
133.21 MB
fastqc
Directory
stderr.txt
1.38 kB
stau1-293flp-minus-2nd-ligation-lus27_fastqc.zip
401.24 kB
FASTQ file (single-end)
fastqc
Directory
stderr.txt
935 B
demux_nomatch_fastqc.zip
430.85 kB
demux_nomatch.fastq.gz
44.43 MB
K-mers
stau1-293flp-high-rnase-lus27.tar.gz
356.15 kB
Cutadapt (single-end)
report.txt
677 B
fastqc
Directory
stau1-293flp-denature-low-20120628-lus14-5_trimmed.fastq.gz
9.61 MB
Cutadapt (single-end)
fastqc
Directory
report.txt
677 B
stau1-293flp-denature-low-20120628-lus14-4_trimmed.fastq.gz
45.96 MB
Cutadapt (single-end)
fastqc
Directory
stau1-293flp-denature-stau1-20120628-lus14-2_trimmed.fastq.gz
61.59 MB
report.txt
679 B
Cutadapt (single-end)
fastqc
Directory
report.txt
680 B
stau1-293flp-denature-stau1-20120628-lus14-1_trimmed.fastq.gz
157.42 MB
Cutadapt (single-end)
report.txt
677 B
fastqc
Directory
stau1-293flp-denature-stau1-20120628-lus14_trimmed.fastq.gz
49.34 MB
Cutadapt (single-end)
report.txt
676 B
fastqc
Directory
stau1-293flp-minus-stau1-induction-lus27_trimmed.fastq.gz
16.08 kB
Cutadapt (single-end)
fastqc
Directory
report.txt
673 B
stau1-293flp-minus-2nd-ligation-lus27_trimmed.fastq.gz
124.68 MB
Cutadapt (single-end)
fastqc
Directory
stau1-293flp-high-rnase-lus27_trimmed.fastq.gz
150.89 MB
report.txt
665 B
STAR
stau1-293flp-denature-low-20120628-lus14-4_trimmed_unmapped.out.mate1.fastq.gz
5.89 MB
stau1-293flp-denature-low-20120628-lus14-4_trimmed.bam
112.19 MB
stau1-293flp-denature-low-20120628-lus14-4_trimmed.bam.bai
4.14 MB
stau1-293flp-denature-low-20120628-lus14-4_trimmed_stats.txt
1.80 kB
stau1-293flp-denature-low-20120628-lus14-4_trimmed_SJ.out.tab
195.78 kB
stau1-293flp-denature-low-20120628-lus14-4_trimmed.bw
45.80 kB
STAR
stau1-293flp-denature-low-20120628-lus14-5_trimmed.bam.bai
2.94 MB
stau1-293flp-denature-low-20120628-lus14-5_trimmed.bam
24.97 MB
stau1-293flp-denature-low-20120628-lus14-5_trimmed_unmapped.out.mate1.fastq.gz
1.32 MB
stau1-293flp-denature-low-20120628-lus14-5_trimmed_stats.txt
1.79 kB
stau1-293flp-denature-low-20120628-lus14-5_trimmed.bw
27.80 kB
stau1-293flp-denature-low-20120628-lus14-5_trimmed_SJ.out.tab
48.61 kB
STAR
stau1-293flp-denature-low-20120628-lus14-3_trimmed_unmapped.out.mate1.fastq.gz
3.89 MB
stau1-293flp-denature-low-20120628-lus14-3_trimmed.bam
86.67 MB
stau1-293flp-denature-low-20120628-lus14-3_trimmed.bam.bai
3.81 MB
stau1-293flp-denature-low-20120628-lus14-3_trimmed_stats.txt
1.80 kB
stau1-293flp-denature-low-20120628-lus14-3_trimmed_SJ.out.tab
167.26 kB
stau1-293flp-denature-low-20120628-lus14-3_trimmed.bw
37.83 kB
STAR
stau1-293flp-denature-stau1-20120628-lus14-2_trimmed_unmapped.out.mate1.fastq.gz
11.07 MB
stau1-293flp-denature-stau1-20120628-lus14-2_trimmed.bam.bai
4.33 MB
stau1-293flp-denature-stau1-20120628-lus14-2_trimmed_SJ.out.tab
289.55 kB
stau1-293flp-denature-stau1-20120628-lus14-2_trimmed_stats.txt
1.80 kB
stau1-293flp-denature-stau1-20120628-lus14-2_trimmed.bw
54.41 kB
stau1-293flp-denature-stau1-20120628-lus14-2_trimmed.bam
146.04 MB
STAR
stau1-293flp-high-rnase-lus27_trimmed.bam.bai
2.45 MB
stau1-293flp-high-rnase-lus27_trimmed.bam
342.86 MB
stau1-293flp-high-rnase-lus27_trimmed_unmapped.out.mate1.fastq.gz
48.69 MB
stau1-293flp-high-rnase-lus27_trimmed_SJ.out.tab
867.96 kB
stau1-293flp-high-rnase-lus27_trimmed_stats.txt
1.81 kB
STAR
stau1-293flp-denature-stau1-20120628-lus14-1_trimmed_unmapped.out.mate1.fastq.gz
26.50 MB
stau1-293flp-denature-stau1-20120628-lus14-1_trimmed.bam.bai
4.23 MB
stau1-293flp-denature-stau1-20120628-lus14-1_trimmed_SJ.out.tab
657.14 kB
stau1-293flp-denature-stau1-20120628-lus14-1_trimmed_stats.txt
1.81 kB
stau1-293flp-denature-stau1-20120628-lus14-1_trimmed.bam
357.06 MB
STAR
stau1-293flp-denature-stau1-20120628-lus14_trimmed.bam.bai
4.25 MB
stau1-293flp-denature-stau1-20120628-lus14_trimmed_unmapped.out.mate1.fastq.gz
8.64 MB
stau1-293flp-denature-stau1-20120628-lus14_trimmed_SJ.out.tab
271.04 kB
stau1-293flp-denature-stau1-20120628-lus14_trimmed.bam
119.85 MB
stau1-293flp-denature-stau1-20120628-lus14_trimmed.bw
47.93 kB
stau1-293flp-denature-stau1-20120628-lus14_trimmed_stats.txt
1.80 kB
STAR
stau1-293flp-low-rnase-lus27_trimmed.bam.bai
2.56 MB
stau1-293flp-low-rnase-lus27_trimmed_unmapped.out.mate1.fastq.gz
41.38 MB
stau1-293flp-low-rnase-lus27_trimmed.bam
414.67 MB
stau1-293flp-low-rnase-lus27_trimmed_stats.txt
1.81 kB
stau1-293flp-low-rnase-lus27_trimmed_SJ.out.tab
1.04 MB
STAR
stau1-293flp-minus-2nd-ligation-lus27_trimmed_unmapped.out.mate1.fastq.gz
29.20 MB
stau1-293flp-minus-2nd-ligation-lus27_trimmed.bam.bai
2.33 MB
stau1-293flp-minus-2nd-ligation-lus27_trimmed.bam
305.22 MB
stau1-293flp-minus-2nd-ligation-lus27_trimmed_stats.txt
1.81 kB
stau1-293flp-minus-2nd-ligation-lus27_trimmed_SJ.out.tab
1.34 MB
stau1-293flp-minus-2nd-ligation-lus27_trimmed.bw
28.92 kB
iCount xlsites
stau1-293flp-denature-low-20120628-lus14-5_trimmed_skipped.bam
3.09 kB
stau1-293flp-denature-low-20120628-lus14-5_trimmed_singleAndMulti.bed.gz
1.47 MB
stau1-293flp-denature-low-20120628-lus14-5_trimmed_single.bed.gz
677.42 kB
stau1-293flp-denature-low-20120628-lus14-5_trimmed_single.bedgraph
2.78 MB
stau1-293flp-denature-low-20120628-lus14-5_trimmed_reads_single.bed.gz
739.46 kB
Paraclu
stau1-293flp-low-rnase-lus27_trimmed_single_peaks.bed.gz
19.22 kB
iCount RNA-maps
stau1-293flp-denature-low-20120628-lus14-5_trimmed_single.tar.gz
500.54 kB
Paraclu
stau1-293flp-denature-low-20120628-lus14-5_trimmed_single_peaks.bed.gz
819 B
iCount xlsites
stau1-293flp-denature-low-20120628-lus14-4_trimmed_single.bed.gz
3.11 MB
stau1-293flp-denature-low-20120628-lus14-4_trimmed_singleAndMulti.bed.gz
6.29 MB
stau1-293flp-denature-low-20120628-lus14-4_trimmed_skipped.bam
3.07 kB
stau1-293flp-denature-low-20120628-lus14-4_trimmed_reads_single.bed.gz
3.41 MB
stau1-293flp-denature-low-20120628-lus14-4_trimmed_single.bedgraph
14.06 MB
Upload iCount sample annotation
iCLIP_annotation_sheet_20120628_LUs14.xlsx
15.14 kB
iCLIP_annotation_sheet_20120628_LUs14.tab.gz
1.03 kB
Paraclu
stau1-293flp-denature-low-20120628-lus14-4_trimmed_single_peaks.bed.gz
9.42 kB
iCount xlsites
stau1-293flp-denature-low-20120628-lus14-3_trimmed_skipped.bam
2.90 kB
stau1-293flp-denature-low-20120628-lus14-3_trimmed_single.bedgraph
8.69 MB
stau1-293flp-denature-low-20120628-lus14-3_trimmed_singleAndMulti.bed.gz
4.07 MB
stau1-293flp-denature-low-20120628-lus14-3_trimmed_reads_single.bed.gz
2.14 MB
stau1-293flp-denature-low-20120628-lus14-3_trimmed_single.bed.gz
1.96 MB
iCount summary
stau1-293flp-denature-low-20120628-lus14-3_trimmed_single_summary_gene.tsv
1.26 MB
stau1-293flp-denature-low-20120628-lus14-3_trimmed_single_summary_subtype.tsv
1007 B
stau1-293flp-denature-low-20120628-lus14-3_trimmed_single_summary_type.tsv
430 B
Paraclu
stau1-293flp-denature-low-20120628-lus14-3_trimmed_single_peaks.bed.gz
4.32 kB
iCount xlsites
stau1-293flp-denature-stau1-20120628-lus14-2_trimmed_reads_single.bed.gz
3.85 MB
stau1-293flp-denature-stau1-20120628-lus14-2_trimmed_single.bed.gz
3.51 MB
stau1-293flp-denature-stau1-20120628-lus14-2_trimmed_singleAndMulti.bed.gz
9.16 MB
stau1-293flp-denature-stau1-20120628-lus14-2_trimmed_single.bedgraph
15.98 MB
stau1-293flp-denature-stau1-20120628-lus14-2_trimmed_skipped.bam
2.90 kB
iCount summary
stau1-293flp-denature-stau1-20120628-lus14-2_trimmed_single_summary_type.tsv
433 B
stau1-293flp-denature-stau1-20120628-lus14-2_trimmed_single_summary_gene.tsv
1.39 MB
stau1-293flp-denature-stau1-20120628-lus14-2_trimmed_single_summary_subtype.tsv
1014 B
iCount RNA-maps
stau1-293flp-denature-stau1-20120628-lus14-2_trimmed_single.tar.gz
725.91 kB
Paraclu
stau1-293flp-denature-stau1-20120628-lus14-2_trimmed_single_peaks.bed.gz
11.35 kB
iCount xlsites
stau1-293flp-denature-stau1-20120628-lus14_trimmed_skipped.bam
2.90 kB
stau1-293flp-denature-stau1-20120628-lus14_trimmed_single.bed.gz
2.85 MB
stau1-293flp-denature-stau1-20120628-lus14_trimmed_reads_single.bed.gz
3.11 MB
stau1-293flp-denature-stau1-20120628-lus14_trimmed_singleAndMulti.bed.gz
7.28 MB
stau1-293flp-denature-stau1-20120628-lus14_trimmed_single.bedgraph
12.86 MB
iCount xlsites
stau1-293flp-minus-2nd-ligation-lus27_trimmed_skipped.bam
2.90 kB
stau1-293flp-minus-2nd-ligation-lus27_trimmed_single.bed.gz
2.19 MB
stau1-293flp-minus-2nd-ligation-lus27_trimmed_reads_single.bed.gz
2.42 MB
stau1-293flp-minus-2nd-ligation-lus27_trimmed_single.bedgraph
10.42 MB
stau1-293flp-minus-2nd-ligation-lus27_trimmed_singleAndMulti.bed.gz
3.28 MB
iCount summary
stau1-293flp-denature-stau1-20120628-lus14_trimmed_single_summary_subtype.tsv
1007 B
stau1-293flp-denature-stau1-20120628-lus14_trimmed_single_summary_type.tsv
431 B
stau1-293flp-denature-stau1-20120628-lus14_trimmed_single_summary_gene.tsv
1.35 MB
iCount RNA-maps
stau1-293flp-denature-stau1-20120628-lus14_trimmed_single.tar.gz
734.48 kB
Paraclu
stau1-293flp-denature-stau1-20120628-lus14_trimmed_single_peaks.bed.gz
7.81 kB
iCount xlsites
stau1-293flp-minus-stau1-induction-lus27_trimmed_singleAndMulti.bed.gz
1.94 kB
stau1-293flp-minus-stau1-induction-lus27_trimmed_skipped.bam
2.90 kB
stau1-293flp-minus-stau1-induction-lus27_trimmed_single.bed.gz
687 B
stau1-293flp-minus-stau1-induction-lus27_trimmed_reads_single.bed.gz
751 B
stau1-293flp-minus-stau1-induction-lus27_trimmed_single.bedgraph
2.02 kB
iCount xlsites
stau1-293flp-low-rnase-lus27_trimmed_single.bed.gz
1.55 MB
stau1-293flp-low-rnase-lus27_trimmed_singleAndMulti.bed.gz
2.67 MB
stau1-293flp-low-rnase-lus27_trimmed_reads_single.bed.gz
1.72 MB
stau1-293flp-low-rnase-lus27_trimmed_skipped.bam
4.15 kB
stau1-293flp-low-rnase-lus27_trimmed_single.bedgraph
7.18 MB
iCount RNA-maps
stau1-293flp-high-rnase-lus27_trimmed_single.tar.gz
908.44 kB
iCount summary
stau1-293flp-minus-stau1-induction-lus27_trimmed_single_summary_subtype.tsv
595 B
stau1-293flp-minus-stau1-induction-lus27_trimmed_single_summary_type.tsv
363 B
stau1-293flp-minus-stau1-induction-lus27_trimmed_single_summary_gene.tsv
4.06 kB
Paraclu
stau1-293flp-minus-stau1-induction-lus27_trimmed_single_peaks.bed.gz
91 B
iCount xlsites
stau1-293flp-denature-stau1-20120628-lus14-1_trimmed_skipped.bam
3.39 kB
stau1-293flp-denature-stau1-20120628-lus14-1_trimmed_reads_single.bed.gz
10.09 MB
stau1-293flp-denature-stau1-20120628-lus14-1_trimmed_single.bed.gz
9.26 MB
stau1-293flp-denature-stau1-20120628-lus14-1_trimmed_single.bedgraph
43.25 MB
stau1-293flp-denature-stau1-20120628-lus14-1_trimmed_singleAndMulti.bed.gz
22.27 MB
FASTQ file (single-end)
fastqc
Directory
20120628_LUs14_SLX_4942_fastqc.zip
493.42 kB
stderr.txt
1.11 kB
20120628_LUs14_SLX_4942.fastq.gz
493.95 MB
FASTQ file (single-end)
fastqc
Directory
LUs27_ae.fastq.gz
1.16 GB
LUs27_ae_fastqc.zip
475.88 kB
stderr.txt
835 B
iCount RNA-maps
stau1-293flp-denature-stau1-20120628-lus14-1_trimmed_single.tar.gz
1.02 MB
Paraclu
stau1-293flp-denature-stau1-20120628-lus14-1_trimmed_single_peaks.bed.gz
68.19 kB
Upload iCount sample annotation
20120628_LUs27_annotation_sheet.tab.gz
1019 B
20120628_LUs27_annotation_sheet.xlsx
15.07 kB
Paraclu
stau1-293flp-high-rnase-lus27_trimmed_single_peaks.bed.gz
14.43 kB
iCount xlsites
stau1-293flp-high-rnase-lus27_trimmed_skipped.bam
3.32 kB
stau1-293flp-high-rnase-lus27_trimmed_reads_single.bed.gz
1.38 MB
stau1-293flp-high-rnase-lus27_trimmed_single.bed.gz
1.20 MB
stau1-293flp-high-rnase-lus27_trimmed_single.bedgraph
5.47 MB
stau1-293flp-high-rnase-lus27_trimmed_singleAndMulti.bed.gz
2.12 MB
iCount summary
stau1-293flp-high-rnase-lus27_trimmed_single_summary_type.tsv
436 B
stau1-293flp-high-rnase-lus27_trimmed_single_summary_gene.tsv
1.13 MB
stau1-293flp-high-rnase-lus27_trimmed_single_summary_subtype.tsv
1004 B
K-mers
stau1-293flp-denature-stau1-20120628-lus14-1.tar.gz
427.74 kB
iCount summary
stau1-293flp-denature-low-20120628-lus14-4_trimmed_single_summary_type.tsv
430 B
stau1-293flp-denature-low-20120628-lus14-4_trimmed_single_summary_subtype.tsv
1008 B
stau1-293flp-denature-low-20120628-lus14-4_trimmed_single_summary_gene.tsv
1.36 MB
iCount summary
stau1-293flp-minus-2nd-ligation-lus27_trimmed_single_summary_type.tsv
438 B
stau1-293flp-minus-2nd-ligation-lus27_trimmed_single_summary_subtype.tsv
1007 B
stau1-293flp-minus-2nd-ligation-lus27_trimmed_single_summary_gene.tsv
1.22 MB
K-mers
stau1-293flp-denature-low-20120628-lus14-5.tar.gz
210.25 kB
K-mers
stau1-293flp-denature-low-20120628-lus14-3.tar.gz
322.43 kB
K-mers
stau1-293flp-minus-stau1-induction-lus27.tar.gz
141 B
K-mers
stau1-293flp-denature-stau1-20120628-lus14-2.tar.gz
363.74 kB
iCount RNA-maps
stau1-293flp-denature-low-20120628-lus14-4_trimmed_single.tar.gz
744.70 kB
iCount summary
stau1-293flp-denature-stau1-20120628-lus14-1_trimmed_single_summary_gene.tsv
1.68 MB
stau1-293flp-denature-stau1-20120628-lus14-1_trimmed_single_summary_type.tsv
439 B
stau1-293flp-denature-stau1-20120628-lus14-1_trimmed_single_summary_subtype.tsv
1.00 kB
K-mers
stau1-293flp-minus-2nd-ligation-lus27.tar.gz
377.21 kB
K-mers
stau1-293flp-denature-low-20120628-lus14-4.tar.gz
347.24 kB
iCount summary
stau1-293flp-denature-low-20120628-lus14-5_trimmed_single_summary_type.tsv
423 B
stau1-293flp-denature-low-20120628-lus14-5_trimmed_single_summary_gene.tsv
958.46 kB
stau1-293flp-denature-low-20120628-lus14-5_trimmed_single_summary_subtype.tsv
990 B

STAU1_293Flp_minus 2nd ligation_LUs27

Paraclu
stau1-293flp-minus-2nd-ligation-lus27_trimmed_single_peaks.bed.gz
31.35 kB
iCount RNA-maps
stau1-293flp-minus-2nd-ligation-lus27_trimmed_single.tar.gz
1.18 MB
FASTQ file (single-end)
stau1-293flp-minus-2nd-ligation-lus27.fastq.gz
133.21 MB
fastqc
Directory
stderr.txt
1.38 kB
stau1-293flp-minus-2nd-ligation-lus27_fastqc.zip
401.24 kB
Cutadapt (single-end)
fastqc
Directory
report.txt
673 B
stau1-293flp-minus-2nd-ligation-lus27_trimmed.fastq.gz
124.68 MB
STAR
stau1-293flp-minus-2nd-ligation-lus27_trimmed_unmapped.out.mate1.fastq.gz
29.20 MB
stau1-293flp-minus-2nd-ligation-lus27_trimmed.bam.bai
2.33 MB
stau1-293flp-minus-2nd-ligation-lus27_trimmed.bam
305.22 MB
stau1-293flp-minus-2nd-ligation-lus27_trimmed_stats.txt
1.81 kB
stau1-293flp-minus-2nd-ligation-lus27_trimmed_SJ.out.tab
1.34 MB
stau1-293flp-minus-2nd-ligation-lus27_trimmed.bw
28.92 kB
iCount xlsites
stau1-293flp-minus-2nd-ligation-lus27_trimmed_skipped.bam
2.90 kB
stau1-293flp-minus-2nd-ligation-lus27_trimmed_single.bed.gz
2.19 MB
stau1-293flp-minus-2nd-ligation-lus27_trimmed_reads_single.bed.gz
2.42 MB
stau1-293flp-minus-2nd-ligation-lus27_trimmed_single.bedgraph
10.42 MB
stau1-293flp-minus-2nd-ligation-lus27_trimmed_singleAndMulti.bed.gz
3.28 MB
iCount summary
stau1-293flp-minus-2nd-ligation-lus27_trimmed_single_summary_type.tsv
438 B
stau1-293flp-minus-2nd-ligation-lus27_trimmed_single_summary_subtype.tsv
1007 B
stau1-293flp-minus-2nd-ligation-lus27_trimmed_single_summary_gene.tsv
1.22 MB
K-mers
stau1-293flp-minus-2nd-ligation-lus27.tar.gz
377.21 kB

STAU1_293Flp_minus STAU1 induction_LUs27

iCount RNA-maps
stau1-293flp-minus-stau1-induction-lus27_trimmed_single.tar.gz
204.97 kB
STAR
stau1-293flp-minus-stau1-induction-lus27_trimmed.bam
30.88 kB
stau1-293flp-minus-stau1-induction-lus27_trimmed_unmapped.out.mate1.fastq.gz
3.63 kB
stau1-293flp-minus-stau1-induction-lus27_trimmed.bam.bai
1.16 MB
stau1-293flp-minus-stau1-induction-lus27_trimmed_stats.txt
1.77 kB
stau1-293flp-minus-stau1-induction-lus27_trimmed_SJ.out.tab
401 B
stau1-293flp-minus-stau1-induction-lus27_trimmed.bw
16.06 kB
FASTQ file (single-end)
fastqc
Directory
stau1-293flp-minus-stau1-induction-lus27.fastq.gz
17.78 kB
stau1-293flp-minus-stau1-induction-lus27_fastqc.zip
496.71 kB
stderr.txt
70 B
Cutadapt (single-end)
report.txt
676 B
fastqc
Directory
stau1-293flp-minus-stau1-induction-lus27_trimmed.fastq.gz
16.08 kB
iCount xlsites
stau1-293flp-minus-stau1-induction-lus27_trimmed_singleAndMulti.bed.gz
1.94 kB
stau1-293flp-minus-stau1-induction-lus27_trimmed_skipped.bam
2.90 kB
stau1-293flp-minus-stau1-induction-lus27_trimmed_single.bed.gz
687 B
stau1-293flp-minus-stau1-induction-lus27_trimmed_reads_single.bed.gz
751 B
stau1-293flp-minus-stau1-induction-lus27_trimmed_single.bedgraph
2.02 kB
iCount summary
stau1-293flp-minus-stau1-induction-lus27_trimmed_single_summary_subtype.tsv
595 B
stau1-293flp-minus-stau1-induction-lus27_trimmed_single_summary_type.tsv
363 B
stau1-293flp-minus-stau1-induction-lus27_trimmed_single_summary_gene.tsv
4.06 kB
Paraclu
stau1-293flp-minus-stau1-induction-lus27_trimmed_single_peaks.bed.gz
91 B
K-mers
stau1-293flp-minus-stau1-induction-lus27.tar.gz
141 B