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Folder iconDual splicing effects of TIA-RNA interactions

Rahul Arora
Feb. 4, 2020
The regulation of alternative splicing involves interactions between RNA-binding proteins and pre-mRNA positions close to the splice sites. T-cell intracellular antigen 1 (TIA1) and TIA1-like 1 (TIAL1) locally enhance exon inclusion by recruiting U1 snRNP to 5' splice sites. However, effects of TIA proteins on splicing of distal exons have not yet been explored. We used UV-crosslinking and immunoprecipitation (iCLIP) to find that TIA1 and TIAL1 bind at the same positions on human RNAs. Binding downstream of 5' splice sites was used to predict the effects of TIA proteins in enhancing inclusion of proximal exons and silencing inclusion of distal exons. The predictions were validated in an unbiased manner using splice-junction microarrays, RT-PCR, and minigene constructs, which showed that TIA proteins maintain splicing fidelity and regulate alternative splicing by binding exclusively downstream of 5' splice sites. Surprisingly, TIA binding at 5' splice sites silenced distal cassette and variable-length exons without binding in proximity to the regulated alternative 3' splice sites. Using transcriptome-wide high-resolution mapping of TIA-RNA interactions we evaluated the distal splicing effects of TIA proteins. These data are consistent with a model where TIA proteins shorten the time available for definition of an alternative exon by enhancing recognition of the preceding 5' splice site. Thus, our findings indicate that changes in splicing kinetics could mediate the distal regulation of alternative splicing.

20090724_LUd2_090715_42L2VAAXX_s_6.fq.gz

FASTQ file (single-end)
stderr.txt
1.32 kB
fastqc
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20090724_LUd2_090715_42L2VAAXX_s_6_fastqc.zip
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20090724_LUd2_090715_42L2VAAXX_s_6.fastq.gz
190.51 MB

20090724_LUd3_090715_42L2VAAXX_s_7.fq.gz

FASTQ file (single-end)
fastqc
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20090724_LUd3_090715_42L2VAAXX_s_7.fastq.gz
290.31 MB
20090724_LUd3_090715_42L2VAAXX_s_7_fastqc.zip
445.83 kB
stderr.txt
1.32 kB

20090724_LUd4_090715_42L7HAAXX_s_1.fq.gz

FASTQ file (single-end)
fastqc
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20090724_LUd4_090715_42L7HAAXX_s_1_fastqc.zip
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stderr.txt
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20090724_LUd4_090715_42L7HAAXX_s_1.fastq.gz
294.83 MB

20091004_LUd15_090831_42KYHAAXX_s_6.fq.gz

FASTQ file (single-end)
fastqc
Directory
stderr.txt
1.34 kB
20091004_LUd15_090831_42KYHAAXX_s_6_fastqc.zip
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20091004_LUd15_090831_42KYHAAXX_s_6.fastq.gz
317.52 MB

20090724_LUe4_090715_42L7HAAXX_s_2.fq.gz

FASTQ file (single-end)
fastqc
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stderr.txt
1.32 kB
20090724_LUe4_090715_42L7HAAXX_s_2_fastqc.zip
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20090724_LUe4_090715_42L7HAAXX_s_2.fastq.gz
87.65 MB

TIA1_Hela_pA_beads_Hg_noAB_aL_20090724_LUd2

STAR
tia1-hela-pa-beads-hg-noab-al-20090724-lud2_trimmed.bam.bai
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tia1-hela-pa-beads-hg-noab-al-20090724-lud2_trimmed_unmapped.out.mate1.fastq.gz
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tia1-hela-pa-beads-hg-noab-al-20090724-lud2_trimmed_stats.txt
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tia1-hela-pa-beads-hg-noab-al-20090724-lud2_trimmed.bam
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tia1-hela-pa-beads-hg-noab-al-20090724-lud2_trimmed_SJ.out.tab
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tia1-hela-pa-beads-hg-noab-al-20090724-lud2_trimmed.bw
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Cutadapt (single-end)
tia1-hela-pa-beads-hg-noab-al-20090724-lud2_trimmed.fastq.gz
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fastqc
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report.txt
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Paraclu
tia1-hela-pa-beads-hg-noab-al-20090724-lud2_trimmed_single_peaks.bed.gz
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iCount xlsites
tia1-hela-pa-beads-hg-noab-al-20090724-lud2_trimmed_single.bed.gz
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tia1-hela-pa-beads-hg-noab-al-20090724-lud2_trimmed_skipped.bam
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tia1-hela-pa-beads-hg-noab-al-20090724-lud2_trimmed_singleAndMulti.bed.gz
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tia1-hela-pa-beads-hg-noab-al-20090724-lud2_trimmed_single.bedgraph
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tia1-hela-pa-beads-hg-noab-al-20090724-lud2_trimmed_reads_single.bed.gz
6.57 kB
FASTQ file (single-end)
fastqc
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tia1-hela-pa-beads-hg-noab-al-20090724-lud2.fastq.gz
1.44 MB
tia1-hela-pa-beads-hg-noab-al-20090724-lud2_fastqc.zip
411.05 kB
stderr.txt
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iCount summary
tia1-hela-pa-beads-hg-noab-al-20090724-lud2_trimmed_single_summary_subtype.tsv
698 B
tia1-hela-pa-beads-hg-noab-al-20090724-lud2_trimmed_single_summary_type.tsv
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tia1-hela-pa-beads-hg-noab-al-20090724-lud2_trimmed_single_summary_gene.tsv
35.22 kB
iCount RNA-maps
tia1-hela-pa-beads-hg-noab-al-20090724-lud2_trimmed_single.tar.gz
236.59 kB
K-mers
tia1-hela-pa-beads-hg-noab-al-20090724-lud2.tar.gz
145 B

demux_nomatch.fastq.gz

FASTQ file (single-end)
fastqc
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stderr.txt
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demux_nomatch.fastq.gz
163.00 MB
demux_nomatch_fastqc.zip
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demux_nomatch.fastq.gz

FASTQ file (single-end)
fastqc
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stderr.txt
935 B
demux_nomatch_fastqc.zip
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demux_nomatch.fastq.gz
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demux_nomatch.fastq.gz

FASTQ file (single-end)
demux_nomatch.fastq.gz
88.94 MB
fastqc
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demux_nomatch_fastqc.zip
507.14 kB
stderr.txt
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TIAL1_Hela_PEG+_20090724_LUd3

K-mers
tial1-hela-peg-20090724-lud3
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tial1-hela-peg-20090724-lud3.tar.gz
383.01 kB
FASTQ file (single-end)
fastqc
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tial1-hela-peg-20090724-lud3.fastq.gz
39.17 MB
stderr.txt
1.32 kB
tial1-hela-peg-20090724-lud3_fastqc.zip
342.11 kB
iCount summary
tial1-hela-peg-20090724-lud3_trimmed_single_summary_type.tsv
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tial1-hela-peg-20090724-lud3_trimmed_single_summary_subtype.tsv
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tial1-hela-peg-20090724-lud3_trimmed_single_summary_gene.tsv
1.25 MB
Paraclu
tial1-hela-peg-20090724-lud3_trimmed_single_peaks.bed.gz
19.84 kB
iCount RNA-maps
tial1-hela-peg-20090724-lud3_trimmed_single.tar.gz
1.03 MB
Cutadapt (single-end)
tial1-hela-peg-20090724-lud3_trimmed.fastq.gz
39.90 MB
fastqc
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report.txt
663 B
STAR
tial1-hela-peg-20090724-lud3_trimmed_unmapped.out.mate1.fastq.gz
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tial1-hela-peg-20090724-lud3_trimmed.bam
69.80 MB
tial1-hela-peg-20090724-lud3_trimmed.bam.bai
3.71 MB
tial1-hela-peg-20090724-lud3_trimmed_stats.txt
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tial1-hela-peg-20090724-lud3_trimmed.bw
38.54 kB
tial1-hela-peg-20090724-lud3_trimmed_SJ.out.tab
171.04 kB
iCount xlsites
tial1-hela-peg-20090724-lud3_trimmed_skipped.bam
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tial1-hela-peg-20090724-lud3_trimmed_single.bed.gz
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tial1-hela-peg-20090724-lud3_trimmed_singleAndMulti.bed.gz
4.23 MB
tial1-hela-peg-20090724-lud3_trimmed_reads_single.bed.gz
2.75 MB
tial1-hela-peg-20090724-lud3_trimmed_single.bedgraph
11.46 MB

demux_nomatch.fastq.gz

FASTQ file (single-end)
fastqc
Directory
demux_nomatch.fastq.gz
28.75 MB
demux_nomatch_fastqc.zip
468.56 kB
stderr.txt
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TIA1_Hela_pG_20091004_LUd15

STAR
tia1-hela-pg-20091004-lud15_trimmed_stats.txt
1.80 kB
tia1-hela-pg-20091004-lud15_trimmed_SJ.out.tab
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tia1-hela-pg-20091004-lud15_trimmed.bam.bai
4.36 MB
tia1-hela-pg-20091004-lud15_trimmed_unmapped.out.mate1.fastq.gz
9.76 MB
tia1-hela-pg-20091004-lud15_trimmed.bw
42.69 kB
tia1-hela-pg-20091004-lud15_trimmed.bam
126.48 MB
iCount RNA-maps
tia1-hela-pg-20091004-lud15_trimmed_single.tar.gz
1.02 MB
Paraclu
tia1-hela-pg-20091004-lud15_trimmed_single_peaks.bed.gz
20.63 kB
Cutadapt (single-end)
fastqc
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tia1-hela-pg-20091004-lud15_trimmed.fastq.gz
63.30 MB
report.txt
662 B
K-mers
tia1-hela-pg-20091004-lud15
Directory
tia1-hela-pg-20091004-lud15.tar.gz
378.78 kB
FASTQ file (single-end)
fastqc
Directory
tia1-hela-pg-20091004-lud15.fastq.gz
64.82 MB
stderr.txt
1.30 kB
tia1-hela-pg-20091004-lud15_fastqc.zip
376.05 kB
iCount summary
tia1-hela-pg-20091004-lud15_trimmed_single_summary_subtype.tsv
1003 B
tia1-hela-pg-20091004-lud15_trimmed_single_summary_type.tsv
431 B
tia1-hela-pg-20091004-lud15_trimmed_single_summary_gene.tsv
1.38 MB
iCount xlsites
tia1-hela-pg-20091004-lud15_trimmed_single.bed.gz
2.50 MB
tia1-hela-pg-20091004-lud15_trimmed_singleAndMulti.bed.gz
4.99 MB
tia1-hela-pg-20091004-lud15_trimmed_skipped.bam
3.13 kB
tia1-hela-pg-20091004-lud15_trimmed_reads_single.bed.gz
2.80 MB
tia1-hela-pg-20091004-lud15_trimmed_single.bedgraph
11.08 MB

TIAL1_Hela_pG_20091004_LUd15_1

FASTQ file (single-end)
fastqc
Directory
tial1-hela-pg-20091004-lud15-1.fastq.gz
64.07 MB
stderr.txt
1.36 kB
tial1-hela-pg-20091004-lud15-1_fastqc.zip
347.70 kB
Cutadapt (single-end)
report.txt
665 B
fastqc
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tial1-hela-pg-20091004-lud15-1_trimmed.fastq.gz
63.75 MB
STAR
tial1-hela-pg-20091004-lud15-1_trimmed_unmapped.out.mate1.fastq.gz
7.77 MB
tial1-hela-pg-20091004-lud15-1_trimmed.bam
106.77 MB
tial1-hela-pg-20091004-lud15-1_trimmed.bam.bai
4.30 MB
tial1-hela-pg-20091004-lud15-1_trimmed_stats.txt
1.80 kB
tial1-hela-pg-20091004-lud15-1_trimmed.bw
53.57 kB
tial1-hela-pg-20091004-lud15-1_trimmed_SJ.out.tab
281.98 kB
iCount RNA-maps
tial1-hela-pg-20091004-lud15-1_trimmed_single.tar.gz
1.34 MB
Paraclu
tial1-hela-pg-20091004-lud15-1_trimmed_single_peaks.bed.gz
25.83 kB
K-mers
tial1-hela-pg-20091004-lud15-1.tar.gz
385.04 kB
tial1-hela-pg-20091004-lud15-1
Directory
iCount summary
tial1-hela-pg-20091004-lud15-1_trimmed_single_summary_subtype.tsv
1013 B
tial1-hela-pg-20091004-lud15-1_trimmed_single_summary_type.tsv
434 B
tial1-hela-pg-20091004-lud15-1_trimmed_single_summary_gene.tsv
1.48 MB
iCount xlsites
tial1-hela-pg-20091004-lud15-1_trimmed_skipped.bam
2.90 kB
tial1-hela-pg-20091004-lud15-1_trimmed_single.bed.gz
4.27 MB
tial1-hela-pg-20091004-lud15-1_trimmed_singleAndMulti.bed.gz
7.47 MB
tial1-hela-pg-20091004-lud15-1_trimmed_reads_single.bed.gz
4.69 MB
tial1-hela-pg-20091004-lud15-1_trimmed_single.bedgraph
19.43 MB

No Sample

iCount summary
tial1-hela-peg-20090724-lue4_trimmed_single_summary_subtype.tsv
1004 B
tial1-hela-peg-20090724-lue4_trimmed_single_summary_type.tsv
432 B
tial1-hela-peg-20090724-lue4_trimmed_single_summary_gene.tsv
1.20 MB
STAR
tia1-hela-pa-beads-hg-noab-al-20090724-lud2_trimmed.bam.bai
1.48 MB
tia1-hela-pa-beads-hg-noab-al-20090724-lud2_trimmed_unmapped.out.mate1.fastq.gz
181.83 kB
tia1-hela-pa-beads-hg-noab-al-20090724-lud2_trimmed_stats.txt
1.78 kB
tia1-hela-pa-beads-hg-noab-al-20090724-lud2_trimmed.bam
990.00 kB
tia1-hela-pa-beads-hg-noab-al-20090724-lud2_trimmed_SJ.out.tab
1015 B
tia1-hela-pa-beads-hg-noab-al-20090724-lud2_trimmed.bw
16.95 kB
iCount RNA-maps
tial1-hela-peg-20090724-lue4_trimmed_single.tar.gz
950.17 kB
FASTQ file (single-end)
fastqc
Directory
stderr.txt
1.34 kB
20091004_LUd15_090831_42KYHAAXX_s_6_fastqc.zip
484.92 kB
20091004_LUd15_090831_42KYHAAXX_s_6.fastq.gz
317.52 MB
FASTQ file (single-end)
fastqc
Directory
stderr.txt
935 B
demux_nomatch.fastq.gz
163.00 MB
demux_nomatch_fastqc.zip
538.57 kB
Cutadapt (single-end)
tia1-hela-pa-beads-hg-noab-al-20090724-lud2_trimmed.fastq.gz
435.41 kB
fastqc
Directory
report.txt
679 B
Paraclu
tia1-hela-pa-beads-hg-noab-al-20090724-lud2_trimmed_single_peaks.bed.gz
94 B
iCount summary
tial1-hela-peg-20090724-lud3-1_trimmed_single_summary_subtype.tsv
1016 B
tial1-hela-peg-20090724-lud3-1_trimmed_single_summary_gene.tsv
1.40 MB
tial1-hela-peg-20090724-lud3-1_trimmed_single_summary_type.tsv
438 B
Paraclu
tial1-hela-peg-20090724-lud3-1_trimmed_single_peaks.bed.gz
39.00 kB
FASTQ file (single-end)
fastqc
Directory
tial1-hela-pg-20091004-lud15-1.fastq.gz
64.07 MB
stderr.txt
1.36 kB
tial1-hela-pg-20091004-lud15-1_fastqc.zip
347.70 kB
FASTQ file (single-end)
fastqc
Directory
demux_nomatch.fastq.gz
28.75 MB
demux_nomatch_fastqc.zip
468.56 kB
stderr.txt
935 B
Cutadapt (single-end)
report.txt
662 B
fastqc
Directory
tia1-hela-peg-20090724-lud3_trimmed.fastq.gz
36.63 MB
Cutadapt (single-end)
report.txt
665 B
fastqc
Directory
tial1-hela-pg-20091004-lud15-1_trimmed.fastq.gz
63.75 MB
Cutadapt (single-end)
fastqc
Directory
report.txt
663 B
tial1-hela-pg-20091004-lud15_trimmed.fastq.gz
36.52 MB
STAR
tial1-hela-peg-20090724-lud3-1_trimmed_unmapped.out.mate1.fastq.gz
8.75 MB
tial1-hela-peg-20090724-lud3-1_trimmed.bam.bai
3.96 MB
tial1-hela-peg-20090724-lud3-1_trimmed_SJ.out.tab
291.63 kB
tial1-hela-peg-20090724-lud3-1_trimmed_stats.txt
1.80 kB
tial1-hela-peg-20090724-lud3-1_trimmed.bam
116.36 MB
tial1-hela-peg-20090724-lud3-1_trimmed.bw
50.20 kB
STAR
tial1-hela-pg-20091004-lud15-1_trimmed_unmapped.out.mate1.fastq.gz
7.77 MB
tial1-hela-pg-20091004-lud15-1_trimmed.bam
106.77 MB
tial1-hela-pg-20091004-lud15-1_trimmed.bam.bai
4.30 MB
tial1-hela-pg-20091004-lud15-1_trimmed_stats.txt
1.80 kB
tial1-hela-pg-20091004-lud15-1_trimmed.bw
53.57 kB
tial1-hela-pg-20091004-lud15-1_trimmed_SJ.out.tab
281.98 kB
STAR
tia1-hela-pg-20091004-lud15_trimmed_stats.txt
1.80 kB
tia1-hela-pg-20091004-lud15_trimmed_SJ.out.tab
171.15 kB
tia1-hela-pg-20091004-lud15_trimmed.bam.bai
4.36 MB
tia1-hela-pg-20091004-lud15_trimmed_unmapped.out.mate1.fastq.gz
9.76 MB
tia1-hela-pg-20091004-lud15_trimmed.bw
42.69 kB
tia1-hela-pg-20091004-lud15_trimmed.bam
126.48 MB
STAR
tial1-hela-pg-20091004-lud15_trimmed_unmapped.out.mate1.fastq.gz
5.27 MB
tial1-hela-pg-20091004-lud15_trimmed_stats.txt
1.80 kB
tial1-hela-pg-20091004-lud15_trimmed.bam.bai
4.07 MB
tial1-hela-pg-20091004-lud15_trimmed.bam
83.91 MB
tial1-hela-pg-20091004-lud15_trimmed_SJ.out.tab
142.84 kB
tial1-hela-pg-20091004-lud15_trimmed.bw
39.99 kB
iCount xlsites
tia1-hela-pa-beads-hg-noab-al-20090724-lud2_trimmed_single.bed.gz
6.04 kB
tia1-hela-pa-beads-hg-noab-al-20090724-lud2_trimmed_skipped.bam
2.90 kB
tia1-hela-pa-beads-hg-noab-al-20090724-lud2_trimmed_singleAndMulti.bed.gz
22.84 kB
tia1-hela-pa-beads-hg-noab-al-20090724-lud2_trimmed_single.bedgraph
19.59 kB
tia1-hela-pa-beads-hg-noab-al-20090724-lud2_trimmed_reads_single.bed.gz
6.57 kB
FASTQ file (single-end)
fastqc
Directory
stderr.txt
935 B
demux_nomatch_fastqc.zip
476.54 kB
demux_nomatch.fastq.gz
96.18 MB
iCount RNA-maps
tial1-hela-peg-20090724-lud3-1_trimmed_single.tar.gz
1.33 MB
Paraclu
tia1-hela-peg-20090724-lud3_trimmed_single_peaks.bed.gz
9.98 kB
iCount RNA-maps
tial1-hela-pg-20091004-lud15-1_trimmed_single.tar.gz
1.34 MB
Paraclu
tial1-hela-pg-20091004-lud15-1_trimmed_single_peaks.bed.gz
25.83 kB
Paraclu
tial1-hela-pg-20091004-lud15_trimmed_single_peaks.bed.gz
14.20 kB
iCount RNA-maps
tia1-hela-pg-20091004-lud15_trimmed_single.tar.gz
1.02 MB
Paraclu
tia1-hela-pg-20091004-lud15_trimmed_single_peaks.bed.gz
20.63 kB
iCount xlsites
tial1-hela-pg-20091004-lud15_trimmed_singleAndMulti.bed.gz
4.08 MB
tial1-hela-pg-20091004-lud15_trimmed_reads_single.bed.gz
2.43 MB
tial1-hela-pg-20091004-lud15_trimmed_single.bed.gz
2.24 MB
tial1-hela-pg-20091004-lud15_trimmed_skipped.bam
3.04 kB
tial1-hela-pg-20091004-lud15_trimmed_single.bedgraph
9.93 MB
Cutadapt (single-end)
fastqc
Directory
tia1-hela-pg-20091004-lud15_trimmed.fastq.gz
63.30 MB
report.txt
662 B
Paraclu
tial1-hela-peg-20090724-lue4_trimmed_single_peaks.bed.gz
14.41 kB
Upload iCount sample annotation
20090724_LUd4_annotation_sheet.xlsx
14.85 kB
20090724_LUd4_annotation_sheet.tab.gz
910 B
iCount xlsites
tial1-hela-peg-20090724-lue4_trimmed_single.bed.gz
2.14 MB
tial1-hela-peg-20090724-lue4_trimmed_reads_single.bed.gz
2.31 MB
tial1-hela-peg-20090724-lue4_trimmed_skipped.bam
2.90 kB
tial1-hela-peg-20090724-lue4_trimmed_single.bedgraph
9.58 MB
tial1-hela-peg-20090724-lue4_trimmed_singleAndMulti.bed.gz
3.47 MB
K-mers
tial1-hela-peg-20090724-lud3
Directory
tial1-hela-peg-20090724-lud3.tar.gz
383.01 kB
K-mers
tia1-hela-peg-20090724-lud3
Directory
tia1-hela-peg-20090724-lud3.tar.gz
352.40 kB
K-mers
tial1-hela-peg-20090724-lud3-1
Directory
tial1-hela-peg-20090724-lud3-1.tar.gz
411.22 kB
K-mers
tial1-hela-pg-20091004-lud15
Directory
tial1-hela-pg-20091004-lud15.tar.gz
359.02 kB
iCount summary
tial1-hela-pg-beads-peg-20090724-lue4_trimmed_single_summary_subtype.tsv
976 B
tial1-hela-pg-beads-peg-20090724-lue4_trimmed_single_summary_type.tsv
424 B
tial1-hela-pg-beads-peg-20090724-lue4_trimmed_single_summary_gene.tsv
435.31 kB
iCount RNA-maps
tial1-hela-pg-beads-peg-20090724-lue4_trimmed_single.tar.gz
413.48 kB
K-mers
tial1-hela-pg-20091004-lud15-1.tar.gz
385.04 kB
tial1-hela-pg-20091004-lud15-1
Directory
Paraclu
tial1-hela-pg-beads-peg-20090724-lue4_trimmed_single_peaks.bed.gz
495 B
K-mers
tia1-hela-pg-20091004-lud15
Directory
tia1-hela-pg-20091004-lud15.tar.gz
378.78 kB
iCount demultiplex (from annotation file)
demultiplexing_stats.txt
269 B
K-mers
tial1-hela-peg-20090724-lue4
Directory
tial1-hela-peg-20090724-lue4.tar.gz
356.32 kB
K-mers
tial1-hela-pg-beads-peg-20090724-lue4.tar.gz
61.73 kB
tial1-hela-pg-beads-peg-20090724-lue4
Directory
Upload iCount sample annotation
20090724_LUd4_annotation_sheet.tab.gz
910 B
20090724_LUd4_annotation_sheet.xlsx
14.85 kB
Upload iCount sample annotation
20090724_LUd2_annotation_sheet.xlsx
14.51 kB
20090724_LUd2_annotation_sheet.tab.gz
831 B
Upload iCount sample annotation
20090724_LUd3_annotation_sheet.xlsx
14.84 kB
20090724_LUd3_annotation_sheet.tab.gz
907 B
FASTQ file (single-end)
stderr.txt
1.32 kB
fastqc
Directory
20090724_LUd2_090715_42L2VAAXX_s_6_fastqc.zip
541.09 kB
20090724_LUd2_090715_42L2VAAXX_s_6.fastq.gz
190.51 MB
Upload iCount sample annotation
20090724_LUe4_annotation_sheet.xlsx
14.66 kB
20090724_LUe4_annotation_sheet.tab.gz
884 B
Upload iCount sample annotation
20091004_LUd15_annotation_sheet.xlsx
14.82 kB
20091004_LUd15_annotation_sheet.tab.gz
896 B
FASTQ file (single-end)
fastqc
Directory
20090724_LUd3_090715_42L2VAAXX_s_7.fastq.gz
290.31 MB
20090724_LUd3_090715_42L2VAAXX_s_7_fastqc.zip
445.83 kB
stderr.txt
1.32 kB
FASTQ file (single-end)
fastqc
Directory
20090724_LUd4_090715_42L7HAAXX_s_1_fastqc.zip
465.84 kB
stderr.txt
1.32 kB
20090724_LUd4_090715_42L7HAAXX_s_1.fastq.gz
294.83 MB
iCount demultiplex (from annotation file)
demultiplexing_stats.txt
221 B
iCount demultiplex (from annotation file)
demultiplexing_stats.txt
317 B
iCount demultiplex (from annotation file)
demultiplexing_stats.txt
317 B
FASTQ file (single-end)
fastqc
Directory
stderr.txt
1.32 kB
20090724_LUe4_090715_42L7HAAXX_s_2_fastqc.zip
476.87 kB
20090724_LUe4_090715_42L7HAAXX_s_2.fastq.gz
87.65 MB
FASTQ file (single-end)
fastqc
Directory
tia1-hela-pg-20091004-lud15.fastq.gz
64.82 MB
stderr.txt
1.30 kB
tia1-hela-pg-20091004-lud15_fastqc.zip
376.05 kB
FASTQ file (single-end)
demux_nomatch.fastq.gz
88.94 MB
fastqc
Directory
demux_nomatch_fastqc.zip
507.14 kB
stderr.txt
983 B
FASTQ file (single-end)
tial1-hela-pg-20091004-lud15.fastq.gz
36.28 MB
fastqc
Directory
stderr.txt
1.32 kB
tial1-hela-pg-20091004-lud15_fastqc.zip
386.50 kB
FASTQ file (single-end)
fastqc
Directory
tia1-hela-pa-beads-hg-noab-al-20090724-lud2.fastq.gz
1.44 MB
tia1-hela-pa-beads-hg-noab-al-20090724-lud2_fastqc.zip
411.05 kB
stderr.txt
1.61 kB
iCount summary
tia1-hela-pa-beads-hg-noab-al-20090724-lud2_trimmed_single_summary_subtype.tsv
698 B
tia1-hela-pa-beads-hg-noab-al-20090724-lud2_trimmed_single_summary_type.tsv
404 B
tia1-hela-pa-beads-hg-noab-al-20090724-lud2_trimmed_single_summary_gene.tsv
35.22 kB
iCount RNA-maps
tia1-hela-pa-beads-hg-noab-al-20090724-lud2_trimmed_single.tar.gz
236.59 kB
K-mers
tia1-hela-pa-beads-hg-noab-al-20090724-lud2.tar.gz
145 B
FASTQ file (single-end)
tia1-hela-peg-20090724-lud3.fastq.gz
36.27 MB
fastqc
Directory
stderr.txt
1.30 kB
tia1-hela-peg-20090724-lud3_fastqc.zip
356.70 kB
FASTQ file (single-end)
fastqc
Directory
tial1-hela-peg-20090724-lud3.fastq.gz
39.17 MB
stderr.txt
1.32 kB
tial1-hela-peg-20090724-lud3_fastqc.zip
342.11 kB
FASTQ file (single-end)
tial1-hela-peg-20090724-lud3-1.fastq.gz
70.45 MB
fastqc
Directory
stderr.txt
1.36 kB
tial1-hela-peg-20090724-lud3-1_fastqc.zip
342.54 kB
iCount summary
tial1-hela-peg-20090724-lud3_trimmed_single_summary_type.tsv
431 B
tial1-hela-peg-20090724-lud3_trimmed_single_summary_subtype.tsv
1009 B
tial1-hela-peg-20090724-lud3_trimmed_single_summary_gene.tsv
1.25 MB
Paraclu
tial1-hela-peg-20090724-lud3_trimmed_single_peaks.bed.gz
19.84 kB
iCount RNA-maps
tial1-hela-peg-20090724-lud3_trimmed_single.tar.gz
1.03 MB
iCount summary
tia1-hela-peg-20090724-lud3_trimmed_single_summary_gene.tsv
1.10 MB
tia1-hela-peg-20090724-lud3_trimmed_single_summary_type.tsv
431 B
tia1-hela-peg-20090724-lud3_trimmed_single_summary_subtype.tsv
1008 B
iCount RNA-maps
tia1-hela-peg-20090724-lud3_trimmed_single.tar.gz
782.98 kB
iCount summary
tial1-hela-pg-20091004-lud15-1_trimmed_single_summary_subtype.tsv
1013 B
tial1-hela-pg-20091004-lud15-1_trimmed_single_summary_type.tsv
434 B
tial1-hela-pg-20091004-lud15-1_trimmed_single_summary_gene.tsv
1.48 MB
iCount summary
tial1-hela-pg-20091004-lud15_trimmed_single_summary_subtype.tsv
1000 B
tial1-hela-pg-20091004-lud15_trimmed_single_summary_gene.tsv
1.32 MB
tial1-hela-pg-20091004-lud15_trimmed_single_summary_type.tsv
433 B
iCount RNA-maps
tial1-hela-pg-20091004-lud15_trimmed_single.tar.gz
1.00 MB
iCount summary
tia1-hela-pg-20091004-lud15_trimmed_single_summary_subtype.tsv
1003 B
tia1-hela-pg-20091004-lud15_trimmed_single_summary_type.tsv
431 B
tia1-hela-pg-20091004-lud15_trimmed_single_summary_gene.tsv
1.38 MB
Cutadapt (single-end)
fastqc
Directory
tial1-hela-peg-20090724-lud3-1_trimmed.fastq.gz
70.54 MB
report.txt
665 B
Cutadapt (single-end)
tial1-hela-peg-20090724-lud3_trimmed.fastq.gz
39.90 MB
fastqc
Directory
report.txt
663 B
FASTQ file (single-end)
fastqc
Directory
tial1-hela-pg-beads-peg-20090724-lue4.fastq.gz
12.95 MB
tial1-hela-pg-beads-peg-20090724-lue4_fastqc.zip
351.69 kB
stderr.txt
1.49 kB
FASTQ file (single-end)
fastqc
Directory
tial1-hela-peg-20090724-lue4.fastq.gz
31.04 MB
stderr.txt
1.32 kB
tial1-hela-peg-20090724-lue4_fastqc.zip
360.30 kB
iCount xlsites
tial1-hela-pg-beads-peg-20090724-lue4_trimmed_singleAndMulti.bed.gz
457.94 kB
tial1-hela-pg-beads-peg-20090724-lue4_trimmed_skipped.bam
2.90 kB
tial1-hela-pg-beads-peg-20090724-lue4_trimmed_reads_single.bed.gz
147.61 kB
tial1-hela-pg-beads-peg-20090724-lue4_trimmed_single.bedgraph
479.29 kB
tial1-hela-pg-beads-peg-20090724-lue4_trimmed_single.bed.gz
133.98 kB
STAR
tial1-hela-peg-20090724-lud3_trimmed_unmapped.out.mate1.fastq.gz
4.99 MB
tial1-hela-peg-20090724-lud3_trimmed.bam
69.80 MB
tial1-hela-peg-20090724-lud3_trimmed.bam.bai
3.71 MB
tial1-hela-peg-20090724-lud3_trimmed_stats.txt
1.80 kB
tial1-hela-peg-20090724-lud3_trimmed.bw
38.54 kB
tial1-hela-peg-20090724-lud3_trimmed_SJ.out.tab
171.04 kB
STAR
tia1-hela-peg-20090724-lud3_trimmed_unmapped.out.mate1.fastq.gz
4.62 MB
tia1-hela-peg-20090724-lud3_trimmed.bam.bai
3.34 MB
tia1-hela-peg-20090724-lud3_trimmed_SJ.out.tab
92.95 kB
tia1-hela-peg-20090724-lud3_trimmed.bw
30.99 kB
tia1-hela-peg-20090724-lud3_trimmed_stats.txt
1.80 kB
tia1-hela-peg-20090724-lud3_trimmed.bam
68.63 MB
Cutadapt (single-end)
fastqc
Directory
tial1-hela-peg-20090724-lue4_trimmed.fastq.gz
31.42 MB
report.txt
663 B
Cutadapt (single-end)
report.txt
673 B
fastqc
Directory
tial1-hela-pg-beads-peg-20090724-lue4_trimmed.fastq.gz
11.99 MB
iCount xlsites
tial1-hela-peg-20090724-lud3_trimmed_skipped.bam
2.90 kB
tial1-hela-peg-20090724-lud3_trimmed_single.bed.gz
2.55 MB
tial1-hela-peg-20090724-lud3_trimmed_singleAndMulti.bed.gz
4.23 MB
tial1-hela-peg-20090724-lud3_trimmed_reads_single.bed.gz
2.75 MB
tial1-hela-peg-20090724-lud3_trimmed_single.bedgraph
11.46 MB
iCount xlsites
tial1-hela-peg-20090724-lud3-1_trimmed_single.bed.gz
4.53 MB
tial1-hela-peg-20090724-lud3-1_trimmed_reads_single.bed.gz
4.89 MB
tial1-hela-peg-20090724-lud3-1_trimmed_skipped.bam
2.90 kB
tial1-hela-peg-20090724-lud3-1_trimmed_single.bedgraph
20.78 MB
tial1-hela-peg-20090724-lud3-1_trimmed_singleAndMulti.bed.gz
7.60 MB
iCount xlsites
tia1-hela-peg-20090724-lud3_trimmed_skipped.bam
2.90 kB
tia1-hela-peg-20090724-lud3_trimmed_singleAndMulti.bed.gz
2.27 MB
tia1-hela-peg-20090724-lud3_trimmed_single.bed.gz
1.28 MB
tia1-hela-peg-20090724-lud3_trimmed_single.bedgraph
5.59 MB
tia1-hela-peg-20090724-lud3_trimmed_reads_single.bed.gz
1.44 MB
iCount xlsites
tial1-hela-pg-20091004-lud15-1_trimmed_skipped.bam
2.90 kB
tial1-hela-pg-20091004-lud15-1_trimmed_single.bed.gz
4.27 MB
tial1-hela-pg-20091004-lud15-1_trimmed_singleAndMulti.bed.gz
7.47 MB
tial1-hela-pg-20091004-lud15-1_trimmed_reads_single.bed.gz
4.69 MB
tial1-hela-pg-20091004-lud15-1_trimmed_single.bedgraph
19.43 MB
iCount xlsites
tia1-hela-pg-20091004-lud15_trimmed_single.bed.gz
2.50 MB
tia1-hela-pg-20091004-lud15_trimmed_singleAndMulti.bed.gz
4.99 MB
tia1-hela-pg-20091004-lud15_trimmed_skipped.bam
3.13 kB
tia1-hela-pg-20091004-lud15_trimmed_reads_single.bed.gz
2.80 MB
tia1-hela-pg-20091004-lud15_trimmed_single.bedgraph
11.08 MB
STAR
tial1-hela-peg-20090724-lue4_trimmed_unmapped.out.mate1.fastq.gz
3.46 MB
tial1-hela-peg-20090724-lue4_trimmed.bam
62.41 MB
tial1-hela-peg-20090724-lue4_trimmed.bam.bai
3.51 MB
tial1-hela-peg-20090724-lue4_trimmed_stats.txt
1.80 kB
tial1-hela-peg-20090724-lue4_trimmed_SJ.out.tab
142.62 kB
tial1-hela-peg-20090724-lue4_trimmed.bw
36.02 kB
STAR
tial1-hela-pg-beads-peg-20090724-lue4_trimmed.bam.bai
2.05 MB
tial1-hela-pg-beads-peg-20090724-lue4_trimmed_unmapped.out.mate1.fastq.gz
7.53 MB
tial1-hela-pg-beads-peg-20090724-lue4_trimmed_stats.txt
1.80 kB
tial1-hela-pg-beads-peg-20090724-lue4_trimmed.bam
21.13 MB
tial1-hela-pg-beads-peg-20090724-lue4_trimmed_SJ.out.tab
78.88 kB
tial1-hela-pg-beads-peg-20090724-lue4_trimmed.bw
21.01 kB

TIAL1_Hela_pG_beads_PEG+_20090724_LUe4

iCount summary
tial1-hela-pg-beads-peg-20090724-lue4_trimmed_single_summary_subtype.tsv
976 B
tial1-hela-pg-beads-peg-20090724-lue4_trimmed_single_summary_type.tsv
424 B
tial1-hela-pg-beads-peg-20090724-lue4_trimmed_single_summary_gene.tsv
435.31 kB
iCount RNA-maps
tial1-hela-pg-beads-peg-20090724-lue4_trimmed_single.tar.gz
413.48 kB
Paraclu
tial1-hela-pg-beads-peg-20090724-lue4_trimmed_single_peaks.bed.gz
495 B
K-mers
tial1-hela-pg-beads-peg-20090724-lue4.tar.gz
61.73 kB
tial1-hela-pg-beads-peg-20090724-lue4
Directory
FASTQ file (single-end)
fastqc
Directory
tial1-hela-pg-beads-peg-20090724-lue4.fastq.gz
12.95 MB
tial1-hela-pg-beads-peg-20090724-lue4_fastqc.zip
351.69 kB
stderr.txt
1.49 kB
iCount xlsites
tial1-hela-pg-beads-peg-20090724-lue4_trimmed_singleAndMulti.bed.gz
457.94 kB
tial1-hela-pg-beads-peg-20090724-lue4_trimmed_skipped.bam
2.90 kB
tial1-hela-pg-beads-peg-20090724-lue4_trimmed_reads_single.bed.gz
147.61 kB
tial1-hela-pg-beads-peg-20090724-lue4_trimmed_single.bedgraph
479.29 kB
tial1-hela-pg-beads-peg-20090724-lue4_trimmed_single.bed.gz
133.98 kB
Cutadapt (single-end)
report.txt
673 B
fastqc
Directory
tial1-hela-pg-beads-peg-20090724-lue4_trimmed.fastq.gz
11.99 MB
STAR
tial1-hela-pg-beads-peg-20090724-lue4_trimmed.bam.bai
2.05 MB
tial1-hela-pg-beads-peg-20090724-lue4_trimmed_unmapped.out.mate1.fastq.gz
7.53 MB
tial1-hela-pg-beads-peg-20090724-lue4_trimmed_stats.txt
1.80 kB
tial1-hela-pg-beads-peg-20090724-lue4_trimmed.bam
21.13 MB
tial1-hela-pg-beads-peg-20090724-lue4_trimmed_SJ.out.tab
78.88 kB
tial1-hela-pg-beads-peg-20090724-lue4_trimmed.bw
21.01 kB

TIA1_Hela_PEG+_20090724_LUd3

Cutadapt (single-end)
report.txt
662 B
fastqc
Directory
tia1-hela-peg-20090724-lud3_trimmed.fastq.gz
36.63 MB
Paraclu
tia1-hela-peg-20090724-lud3_trimmed_single_peaks.bed.gz
9.98 kB
K-mers
tia1-hela-peg-20090724-lud3
Directory
tia1-hela-peg-20090724-lud3.tar.gz
352.40 kB
FASTQ file (single-end)
tia1-hela-peg-20090724-lud3.fastq.gz
36.27 MB
fastqc
Directory
stderr.txt
1.30 kB
tia1-hela-peg-20090724-lud3_fastqc.zip
356.70 kB
iCount summary
tia1-hela-peg-20090724-lud3_trimmed_single_summary_gene.tsv
1.10 MB
tia1-hela-peg-20090724-lud3_trimmed_single_summary_type.tsv
431 B
tia1-hela-peg-20090724-lud3_trimmed_single_summary_subtype.tsv
1008 B
iCount RNA-maps
tia1-hela-peg-20090724-lud3_trimmed_single.tar.gz
782.98 kB
STAR
tia1-hela-peg-20090724-lud3_trimmed_unmapped.out.mate1.fastq.gz
4.62 MB
tia1-hela-peg-20090724-lud3_trimmed.bam.bai
3.34 MB
tia1-hela-peg-20090724-lud3_trimmed_SJ.out.tab
92.95 kB
tia1-hela-peg-20090724-lud3_trimmed.bw
30.99 kB
tia1-hela-peg-20090724-lud3_trimmed_stats.txt
1.80 kB
tia1-hela-peg-20090724-lud3_trimmed.bam
68.63 MB
iCount xlsites
tia1-hela-peg-20090724-lud3_trimmed_skipped.bam
2.90 kB
tia1-hela-peg-20090724-lud3_trimmed_singleAndMulti.bed.gz
2.27 MB
tia1-hela-peg-20090724-lud3_trimmed_single.bed.gz
1.28 MB
tia1-hela-peg-20090724-lud3_trimmed_single.bedgraph
5.59 MB
tia1-hela-peg-20090724-lud3_trimmed_reads_single.bed.gz
1.44 MB

TIAL1_Hela_PEG+_20090724_LUd3_1

iCount summary
tial1-hela-peg-20090724-lud3-1_trimmed_single_summary_subtype.tsv
1016 B
tial1-hela-peg-20090724-lud3-1_trimmed_single_summary_gene.tsv
1.40 MB
tial1-hela-peg-20090724-lud3-1_trimmed_single_summary_type.tsv
438 B
Paraclu
tial1-hela-peg-20090724-lud3-1_trimmed_single_peaks.bed.gz
39.00 kB
STAR
tial1-hela-peg-20090724-lud3-1_trimmed_unmapped.out.mate1.fastq.gz
8.75 MB
tial1-hela-peg-20090724-lud3-1_trimmed.bam.bai
3.96 MB
tial1-hela-peg-20090724-lud3-1_trimmed_SJ.out.tab
291.63 kB
tial1-hela-peg-20090724-lud3-1_trimmed_stats.txt
1.80 kB
tial1-hela-peg-20090724-lud3-1_trimmed.bam
116.36 MB
tial1-hela-peg-20090724-lud3-1_trimmed.bw
50.20 kB
iCount RNA-maps
tial1-hela-peg-20090724-lud3-1_trimmed_single.tar.gz
1.33 MB
K-mers
tial1-hela-peg-20090724-lud3-1
Directory
tial1-hela-peg-20090724-lud3-1.tar.gz
411.22 kB
FASTQ file (single-end)
tial1-hela-peg-20090724-lud3-1.fastq.gz
70.45 MB
fastqc
Directory
stderr.txt
1.36 kB
tial1-hela-peg-20090724-lud3-1_fastqc.zip
342.54 kB
Cutadapt (single-end)
fastqc
Directory
tial1-hela-peg-20090724-lud3-1_trimmed.fastq.gz
70.54 MB
report.txt
665 B
iCount xlsites
tial1-hela-peg-20090724-lud3-1_trimmed_single.bed.gz
4.53 MB
tial1-hela-peg-20090724-lud3-1_trimmed_reads_single.bed.gz
4.89 MB
tial1-hela-peg-20090724-lud3-1_trimmed_skipped.bam
2.90 kB
tial1-hela-peg-20090724-lud3-1_trimmed_single.bedgraph
20.78 MB
tial1-hela-peg-20090724-lud3-1_trimmed_singleAndMulti.bed.gz
7.60 MB

TIAL1_Hela_pG_20091004_LUd15

Cutadapt (single-end)
fastqc
Directory
report.txt
663 B
tial1-hela-pg-20091004-lud15_trimmed.fastq.gz
36.52 MB
STAR
tial1-hela-pg-20091004-lud15_trimmed_unmapped.out.mate1.fastq.gz
5.27 MB
tial1-hela-pg-20091004-lud15_trimmed_stats.txt
1.80 kB
tial1-hela-pg-20091004-lud15_trimmed.bam.bai
4.07 MB
tial1-hela-pg-20091004-lud15_trimmed.bam
83.91 MB
tial1-hela-pg-20091004-lud15_trimmed_SJ.out.tab
142.84 kB
tial1-hela-pg-20091004-lud15_trimmed.bw
39.99 kB
Paraclu
tial1-hela-pg-20091004-lud15_trimmed_single_peaks.bed.gz
14.20 kB
iCount xlsites
tial1-hela-pg-20091004-lud15_trimmed_singleAndMulti.bed.gz
4.08 MB
tial1-hela-pg-20091004-lud15_trimmed_reads_single.bed.gz
2.43 MB
tial1-hela-pg-20091004-lud15_trimmed_single.bed.gz
2.24 MB
tial1-hela-pg-20091004-lud15_trimmed_skipped.bam
3.04 kB
tial1-hela-pg-20091004-lud15_trimmed_single.bedgraph
9.93 MB
K-mers
tial1-hela-pg-20091004-lud15
Directory
tial1-hela-pg-20091004-lud15.tar.gz
359.02 kB
FASTQ file (single-end)
tial1-hela-pg-20091004-lud15.fastq.gz
36.28 MB
fastqc
Directory
stderr.txt
1.32 kB
tial1-hela-pg-20091004-lud15_fastqc.zip
386.50 kB
iCount summary
tial1-hela-pg-20091004-lud15_trimmed_single_summary_subtype.tsv
1000 B
tial1-hela-pg-20091004-lud15_trimmed_single_summary_gene.tsv
1.32 MB
tial1-hela-pg-20091004-lud15_trimmed_single_summary_type.tsv
433 B
iCount RNA-maps
tial1-hela-pg-20091004-lud15_trimmed_single.tar.gz
1.00 MB

TIAL1_Hela_PEG+_20090724_LUe4

iCount summary
tial1-hela-peg-20090724-lue4_trimmed_single_summary_type.tsv
432 B
tial1-hela-peg-20090724-lue4_trimmed_single_summary_subtype.tsv
1004 B
tial1-hela-peg-20090724-lue4_trimmed_single_summary_gene.tsv
1.20 MB
iCount RNA-maps
tial1-hela-peg-20090724-lue4_trimmed_single.tar.gz
950.17 kB
Paraclu
tial1-hela-peg-20090724-lue4_trimmed_single_peaks.bed.gz
14.41 kB
iCount xlsites
tial1-hela-peg-20090724-lue4_trimmed_single.bed.gz
2.14 MB
tial1-hela-peg-20090724-lue4_trimmed_reads_single.bed.gz
2.31 MB
tial1-hela-peg-20090724-lue4_trimmed_skipped.bam
2.90 kB
tial1-hela-peg-20090724-lue4_trimmed_single.bedgraph
9.58 MB
tial1-hela-peg-20090724-lue4_trimmed_singleAndMulti.bed.gz
3.47 MB
K-mers
tial1-hela-peg-20090724-lue4
Directory
tial1-hela-peg-20090724-lue4.tar.gz
356.32 kB
FASTQ file (single-end)
fastqc
Directory
tial1-hela-peg-20090724-lue4.fastq.gz
31.04 MB
stderr.txt
1.32 kB
tial1-hela-peg-20090724-lue4_fastqc.zip
360.30 kB
Cutadapt (single-end)
fastqc
Directory
tial1-hela-peg-20090724-lue4_trimmed.fastq.gz
31.42 MB
report.txt
663 B
STAR
tial1-hela-peg-20090724-lue4_trimmed_unmapped.out.mate1.fastq.gz
3.46 MB
tial1-hela-peg-20090724-lue4_trimmed.bam
62.41 MB
tial1-hela-peg-20090724-lue4_trimmed.bam.bai
3.51 MB
tial1-hela-peg-20090724-lue4_trimmed_stats.txt
1.80 kB
tial1-hela-peg-20090724-lue4_trimmed_SJ.out.tab
142.62 kB
tial1-hela-peg-20090724-lue4_trimmed.bw
36.02 kB