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GSE213867

GSE GEO
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Skipper analysis of RNA-protein interactions highlights depletion of genetic variation in translation factor binding sites

Organism: Homo sapiens
Platform: GPL24676
Samples: 36
Experiment Types:
Expression profiling by high throughput sequencing Other
Submitted: Sep 21 2022
Last Updated: Sep 11 2023
Status: Public on Oct 08 2022
Contact: Gene,W,Yeo (University of California San Diego)

Relations

BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA882819

Summary

Technology for crosslinking and immunoprecipitation followed by sequencing (CLIP-seq) has identified the transcriptomic targets of hundreds of RNA-binding proteins in cells. To improve the power of existing and future CLIP-seq datasets, we introduce Skipper, an end-to-end workflow that converts unprocessed reads into annotated binding sites using an improved statistical framework. Compared to existing methods, Skipper on average calls 3.1-4.2 times more transcriptomic binding sites and sometimes >10 times more sites, providing deeper insight into post-transcriptional gene regulation. Skipper also calls binding to annotated repetitive elements and identifies bound elements for 99% of enhanced CLIP experiments. We perform nine translation factor enhanced CLIPs and apply Skipper to learn determinants of translation factor occupancy including transcript region, sequence, and subcellular localization. Furthermore, we observe depletion of genetic variation in occupied sites and nominate transcripts subject to selective constraint because of translation factor occupancy. Skipper offers fast, easy, customizable analysis of CLIP-seq data.

Overall Design

eCLIP of ribosome proteins and EIFs in K562 cells, in duplicate

Analysis (5 steps)

View Data Processing
Processing steps for GSE213867
  1. Data was processed using Skipper, available at: http://github.com/yeolab/skipper
  2. Reads were trimmed for adapter sequences and barcode sequences (eCLIP samples) using skewer.
  3. Unique Molecular Identifiers (UMIs) were extracted from raw sequencing reads with fastp
  4. Extracted reads were aligned using STAR: --alignEndsType EndToEnd --genomeDir {params.star_sjdb} --genomeLoad NoSharedMemory --outBAMcompression 10 --outFileNamePrefix {params.outprefix} --winAnchorMultimapNmax 100 --outFilterMultimapNmax 100 --outFilterMultimapScoreRange 1 --outSAMmultNmax 1 --outMultimapperOrder Random --outFilterScoreMin 10 --outFilterType BySJout --limitOutSJcollapsed 5000000 --outReadsUnmapped None --outSAMattrRGline ID:{wildcards.replicate_label} --outSAMattributes All --outSAMmode Full --outSAMtype BAM Unsorted --outSAMunmapped Within --readFilesCommand zcat --outStd Log --readFilesIn {input.fq} --runMode alignReads --runThreadN {threads}
  5. Custom scripts called reproducible enriched windows and repetitive elements as part of Skipper

Supplementary Files (19)

GSE213867_EIF2B5.reproducible_enriched_re.tsv.gz Download
GSE213867_EIF2B5.reproducible_enriched_windows.tsv.gz Download
GSE213867_EIF2D.reproducible_enriched_re.tsv.gz Download
GSE213867_EIF2D.reproducible_enriched_windows.tsv.gz Download
GSE213867_EIF2S2.reproducible_enriched_re.tsv.gz Download
GSE213867_EIF2S2.reproducible_enriched_windows.tsv.gz Download
GSE213867_EIF3J.reproducible_enriched_re.tsv.gz Download
GSE213867_EIF3J.reproducible_enriched_windows.tsv.gz Download
GSE213867_RPL29.reproducible_enriched_re.tsv.gz Download
GSE213867_RPL29.reproducible_enriched_windows.tsv.gz Download
GSE213867_RPL35A.reproducible_enriched_re.tsv.gz Download
GSE213867_RPL35A.reproducible_enriched_windows.tsv.gz Download
GSE213867_RPS14.reproducible_enriched_re.tsv.gz Download
GSE213867_RPS14.reproducible_enriched_windows.tsv.gz Download
GSE213867_RPS19.reproducible_enriched_re.tsv.gz Download
GSE213867_RPS19.reproducible_enriched_windows.tsv.gz Download
GSE213867_RPS3A.reproducible_enriched_re.tsv.gz Download
GSE213867_RPS3A.reproducible_enriched_windows.tsv.gz Download
GSE213867_all.75nt_recentered_windows.bed.gz Download
GEO Samples (36)
GSM6595532 GSM6595533 GSM6595534 GSM6595535 GSM6595536 GSM6595537 GSM6595538 GSM6595539 GSM6595540 GSM6595541 GSM6595542 GSM6595543 GSM6595544 GSM6595545 GSM6595546 GSM6595547 GSM6595548 GSM6595549 GSM6595550 GSM6595551 GSM6595552 GSM6595553 GSM6595554 GSM6595555 GSM6595556 GSM6595557 GSM6595558 GSM6595559 GSM6595560 GSM6595561 GSM6595562 GSM6595563 GSM6595564 GSM6595565 GSM6595566 GSM6595567

Dataset Citations (1)

Skipper analysis of eCLIP datasets enables sensitive detection of constrained translation factor binding sites.
PMID 37388912 · 2023 · Cell genomics
Evan A Boyle, Hsuan-Lin Her, Jasmine R Mueller, Jack T Naritomi, Grady G Nguyen, Gene W Yeo

SRA Experiments (36) and Runs (48)

Total: 29002 MB
SRX17658726 SRP398437 RNA-Seq SINGLE
GSM6595532: Crosslinked K562, RPS14 IP, rep1; Homo sapiens; RNA-Seq
Sample: SRS15190993
BioProject: PRJNA882819
BioSample: SAMN30952273
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: K562
cell line: K562
Original files (1)
K562
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR21659002 30924922 3123417122 958.06 IP1_RPS14_S24_L001_R1_001.fastq.gz, SRR21659002, SRR21659002.lite SRA
SRX17658727 SRP398437 RNA-Seq SINGLE
GSM6595533: Crosslinked K562, RPS14 IP, rep2; Homo sapiens; RNA-Seq
Sample: SRS15190994
BioProject: PRJNA882819
BioSample: SAMN30952272
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: K562
cell line: K562
Original files (1)
K562
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR21659001 8276475 835923975 256.43 IP2_RPS14_S25_L001_R1_001.fastq.gz, SRR21659001, SRR21659001.lite SRA
SRX17658728 SRP398437 RNA-Seq SINGLE
GSM6595534: Crosslinked K562, RPL35A IP, rep1; Homo sapiens; RNA-Seq
Sample: SRS15190995
BioProject: PRJNA882819
BioSample: SAMN30952271
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: K562
cell line: K562
Original files (1)
K562
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR21659000 90869232 9177792432 2663.45 RPL35A_IP1_S31_L001_R1_001.fastq.gz, SRR21659000, SRR21659000.lite SRA
SRX17658729 SRP398437 RNA-Seq SINGLE
GSM6595535: Crosslinked K562, RPL35A IP, rep2; Homo sapiens; RNA-Seq
Sample: SRS15190996
BioProject: PRJNA882819
BioSample: SAMN30952270
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: K562
cell line: K562
Original files (1)
K562
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR21658999 48323739 4880697639 1428.2 RPL35A_IP2_S32_L001_R1_001.fastq.gz, SRR21658999, SRR21658999.lite SRA
SRX17658730 SRP398437 RNA-Seq SINGLE
GSM6595536: Crosslinked K562, RPS3A IP, rep1; Homo sapiens; RNA-Seq
Sample: SRS15190997
BioProject: PRJNA882819
BioSample: SAMN30952269
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: K562
cell line: K562
Original files (1)
K562
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR21658998 31825001 3214325101 941.6 RPS3A_IP1_S27_L001_R1_001.fastq.gz, SRR21658998, SRR21658998.lite SRA
SRX17658731 SRP398437 RNA-Seq SINGLE
GSM6595537: Crosslinked K562, RPS3A IP, rep2; Homo sapiens; RNA-Seq
Sample: SRS15190998
BioProject: PRJNA882819
BioSample: SAMN30952268
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: K562
cell line: K562
Original files (1)
K562
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR21658997 45678213 4613499513 1382.44 RPS3A_IP2_S28_L001_R1_001.fastq.gz, SRR21658997, SRR21658997.lite SRA
SRX17658732 SRP398437 RNA-Seq SINGLE
GSM6595538: Crosslinked K562, RPL29 IP, rep1; Homo sapiens; RNA-Seq
Sample: SRS15190999
BioProject: PRJNA882819
BioSample: SAMN30952267
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: K562
cell line: K562
Original files (1)
K562
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR21658996 53389071 5392296171 1580.45 RPL29_IP1_S23_L001_R1_001.fastq.gz, SRR21658996, SRR21658996.lite SRA
SRX17658733 SRP398437 RNA-Seq SINGLE
GSM6595539: Crosslinked K562, RPL29 IP, rep2; Homo sapiens; RNA-Seq
Sample: SRS15191000
BioProject: PRJNA882819
BioSample: SAMN30952266
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: K562
cell line: K562
Original files (1)
K562
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR21658995 51339318 5185271118 1522.41 RPL29_IP2_S24_L001_R1_001.fastq.gz, SRR21658995, SRR21658995.lite SRA
SRX17658734 SRP398437 RNA-Seq SINGLE
GSM6595540: Crosslinked K562, RPS19 IP, rep1; Homo sapiens; RNA-Seq
Sample: SRS15191001
BioProject: PRJNA882819
BioSample: SAMN30952265
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: K562
cell line: K562
Original files (1)
K562
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR21658994 20612465 2081858965 634.08 RPS19_IP1_S13_L001_R1_001.fastq.gz, SRR21658994, SRR21658994.lite SRA
SRX17658735 SRP398437 RNA-Seq SINGLE
GSM6595541: Crosslinked K562, RPS19 IP, rep2; Homo sapiens; RNA-Seq
Sample: SRS15191002
BioProject: PRJNA882819
BioSample: SAMN30952264
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: K562
cell line: K562
Original files (1)
K562
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR21658993 16225096 1638734696 505.0 RPS19_IP2_S14_L001_R1_001.fastq.gz, SRR21658993, SRR21658993.lite SRA
SRX17658736 SRP398437 RNA-Seq SINGLE
GSM6595542: Crosslinked K562, EIF2B5 IP, rep1; Homo sapiens; RNA-Seq
Sample: SRS15191003
BioProject: PRJNA882819
BioSample: SAMN30952263
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: K562
cell line: K562
Original files (1)
K562
Runs (2)
Run Spots Bases Size (MB) Files Link
SRR21658991 4117235 411723500 136.68 EIF2B5-IP1-_S3_L001_R1_001.fastq.gz, SRR21658991, SRR21658991.lite SRA
SRR21658992 4050055 405005500 135.23 EIF2B5-IP1-_S3_L002_R1_001.fastq.gz, SRR21658992, SRR21658992.lite SRA
SRX17658737 SRP398437 RNA-Seq SINGLE
GSM6595543: Crosslinked K562, EIF2B5 IP, rep2; Homo sapiens; RNA-Seq
Sample: SRS15191004
BioProject: PRJNA882819
BioSample: SAMN30952262
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: K562
cell line: K562
Original files (1)
K562
Runs (2)
Run Spots Bases Size (MB) Files Link
SRR21658989 3695551 369555100 122.67 EIF2B5-IP2-_S4_L001_R1_001.fastq.gz, SRR21658989, SRR21658989.lite SRA
SRR21658990 3639288 363928800 121.53 EIF2B5-IP2-_S4_L002_R1_001.fastq.gz, SRR21658990, SRR21658990.lite SRA
SRX17658738 SRP398437 RNA-Seq SINGLE
GSM6595544: Crosslinked K562, EIF2D IP, rep1; Homo sapiens; RNA-Seq
Sample: SRS15191005
BioProject: PRJNA882819
BioSample: SAMN30952261
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: K562
cell line: K562
Original files (1)
K562
Runs (2)
Run Spots Bases Size (MB) Files Link
SRR21658987 7125063 712506300 234.54 EIF2D--IP1-_S11_L001_R1_001.fastq.gz, SRR21658987, SRR21658987.lite SRA
SRR21658988 7048685 704868500 233.6 EIF2D--IP1-_S11_L002_R1_001.fastq.gz, SRR21658988, SRR21658988.lite SRA
SRX17658739 SRP398437 RNA-Seq SINGLE
GSM6595545: Crosslinked K562, EIF2D IP, rep2; Homo sapiens; RNA-Seq
Sample: SRS15191006
BioProject: PRJNA882819
BioSample: SAMN30952260
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: K562
cell line: K562
Original files (1)
K562
Runs (2)
Run Spots Bases Size (MB) Files Link
SRR21658985 5947550 594755000 196.63 EIF2D--IP2-_S12_L001_R1_001.fastq.gz, SRR21658985, SRR21658985.lite SRA
SRR21658986 5875788 587578800 195.56 EIF2D--IP2-_S12_L002_R1_001.fastq.gz, SRR21658986, SRR21658986.lite SRA
SRX17658740 SRP398437 RNA-Seq SINGLE
GSM6595546: Crosslinked K562, EIF2S2 IP, rep1; Homo sapiens; RNA-Seq
Sample: SRS15191007
BioProject: PRJNA882819
BioSample: SAMN30952259
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: K562
cell line: K562
Original files (1)
K562
Runs (2)
Run Spots Bases Size (MB) Files Link
SRR21658983 4013144 401314400 134.58 EIF2S4-IP1-_S15_L001_R1_001.fastq.gz, SRR21658983, SRR21658983.lite SRA
SRR21658984 3948710 394871000 133.26 EIF2S4-IP1-_S15_L002_R1_001.fastq.gz, SRR21658984, SRR21658984.lite SRA
SRX17658741 SRP398437 RNA-Seq SINGLE
GSM6595547: Crosslinked K562, EIF2S2 IP, rep2; Homo sapiens; RNA-Seq
Sample: SRS15191008
BioProject: PRJNA882819
BioSample: SAMN30952258
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: K562
cell line: K562
Original files (1)
K562
Runs (2)
Run Spots Bases Size (MB) Files Link
SRR21658981 6243771 624377100 208.28 EIF2S5-IP2-_S16_L001_R1_001.fastq.gz, SRR21658981, SRR21658981.lite SRA
SRR21658982 6139344 613934400 206.17 EIF2S5-IP2-_S16_L002_R1_001.fastq.gz, SRR21658982, SRR21658982.lite SRA
SRX17658742 SRP398437 RNA-Seq SINGLE
GSM6595548: Crosslinked K562, EIF3J IP, rep1; Homo sapiens; RNA-Seq
Sample: SRS15191009
BioProject: PRJNA882819
BioSample: SAMN30952257
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: K562
cell line: K562
Original files (1)
K562
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR21658980 25172777 1887958275 654.15 EIF3J-IP1_S45_L002_R1_001.fastq.gz, SRR21658980, SRR21658980.lite SRA
SRX17658743 SRP398437 RNA-Seq SINGLE
GSM6595549: Crosslinked K562, EIF3J IP, rep2; Homo sapiens; RNA-Seq
Sample: SRS15191010
BioProject: PRJNA882819
BioSample: SAMN30952256
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: K562
cell line: K562
Original files (1)
K562
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR21658979 31331596 2349869700 808.53 EIF3J-IP2_S46_L002_R1_001.fastq.gz, SRR21658979, SRR21658979.lite SRA
SRX17658744 SRP398437 RNA-Seq SINGLE
GSM6595550: Crosslinked K562, RPS14 Input, rep1; Homo sapiens; RNA-Seq
Sample: SRS15191011
BioProject: PRJNA882819
BioSample: SAMN30952255
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: K562
cell line: K562
Original files (1)
K562
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR21658978 16227328 1638960128 513.86 IN1_RPS14_S22_L001_R1_001.fastq.gz, SRR21658978, SRR21658978.lite SRA
SRX17658745 SRP398437 RNA-Seq SINGLE
GSM6595551: Crosslinked K562, RPS14 Input, rep2; Homo sapiens; RNA-Seq
Sample: SRS15191012
BioProject: PRJNA882819
BioSample: SAMN30952254
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: K562
cell line: K562
Original files (1)
K562
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR21658977 19540156 1973555756 617.76 IN2_RPS14_S23_L001_R1_001.fastq.gz, SRR21658977, SRR21658977.lite SRA
SRX17658746 SRP398437 RNA-Seq SINGLE
GSM6595552: Crosslinked K562, RPL35A Input, rep1; Homo sapiens; RNA-Seq
Sample: SRS15191013
BioProject: PRJNA882819
BioSample: SAMN30952253
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: K562
cell line: K562
Original files (1)
K562
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR21658976 45450110 4590461110 1363.92 RPL35A_IN1_S29_L001_R1_001.fastq.gz, SRR21658976, SRR21658976.lite SRA
SRX17658747 SRP398437 RNA-Seq SINGLE
GSM6595553: Crosslinked K562, RPL35A Input, rep2; Homo sapiens; RNA-Seq
Sample: SRS15191014
BioProject: PRJNA882819
BioSample: SAMN30952252
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: K562
cell line: K562
Original files (1)
K562
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR21658975 40185545 4058740045 1215.89 RPL35A_IN2_S30_L001_R1_001.fastq.gz, SRR21658975, SRR21658975.lite SRA
SRX17658748 SRP398437 RNA-Seq SINGLE
GSM6595554: Crosslinked K562, RPS3A Input, rep1; Homo sapiens; RNA-Seq
Sample: SRS15191015
BioProject: PRJNA882819
BioSample: SAMN30952251
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: K562
cell line: K562
Original files (1)
K562
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR21658974 45884156 4634299756 1384.22 RPS3A_IN1_S25_L001_R1_001.fastq.gz, SRR21658974, SRR21658974.lite SRA
SRX17658749 SRP398437 RNA-Seq SINGLE
GSM6595555: Crosslinked K562, RPS3A Input, rep2; Homo sapiens; RNA-Seq
Sample: SRS15191016
BioProject: PRJNA882819
BioSample: SAMN30952250
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: K562
cell line: K562
Original files (1)
K562
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR21658973 39740063 4013746363 1213.77 RPS3A_IN2_S26_L001_R1_001.fastq.gz, SRR21658973, SRR21658973.lite SRA
SRX17658750 SRP398437 RNA-Seq SINGLE
GSM6595556: Crosslinked K562, RPL29 Input, rep1; Homo sapiens; RNA-Seq
Sample: SRS15191017
BioProject: PRJNA882819
BioSample: SAMN30952249
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: K562
cell line: K562
Original files (1)
K562
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR21658972 60578416 6118420016 1813.94 RPL29_IN1_S21_L001_R1_001.fastq.gz, SRR21658972, SRR21658972.lite SRA
SRX17658751 SRP398437 RNA-Seq SINGLE
GSM6595557: Crosslinked K562, RPL29 Input, rep2; Homo sapiens; RNA-Seq
Sample: SRS15191018
BioProject: PRJNA882819
BioSample: SAMN30952248
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: K562
cell line: K562
Original files (1)
K562
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR21658971 60597477 6120345177 1814.59 RPL29_IN2_S22_L001_R1_001.fastq.gz, SRR21658971, SRR21658971.lite SRA
SRX17658752 SRP398437 RNA-Seq SINGLE
GSM6595558: Crosslinked K562, RPS19 Input, rep1; Homo sapiens; RNA-Seq
Sample: SRS15191019
BioProject: PRJNA882819
BioSample: SAMN30952247
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: K562
cell line: K562
Original files (1)
K562
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR21658970 15945373 1610482673 511.15 RPS19_IN1_S5_L001_R1_001.fastq.gz, SRR21658970, SRR21658970.lite SRA
SRX17658753 SRP398437 RNA-Seq SINGLE
GSM6595559: Crosslinked K562, RPS19 Input, rep2; Homo sapiens; RNA-Seq
Sample: SRS15191020
BioProject: PRJNA882819
BioSample: SAMN30952246
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: K562
cell line: K562
Original files (1)
K562
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR21658969 18924701 1911394801 592.9 RPS19_IN2_S6_L001_R1_001.fastq.gz, SRR21658969, SRR21658969.lite SRA
SRX17658754 SRP398437 RNA-Seq SINGLE
GSM6595560: Crosslinked K562, EIF2B5 Input, rep1; Homo sapiens; RNA-Seq
Sample: SRS15191021
BioProject: PRJNA882819
BioSample: SAMN30952245
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: K562
cell line: K562
Original files (1)
K562
Runs (2)
Run Spots Bases Size (MB) Files Link
SRR21658967 3626718 362671800 121.25 EIF2B5-IN1_S1_L001_R1_001.fastq.gz, SRR21658967, SRR21658967.lite SRA
SRR21658968 3607737 360773700 121.36 EIF2B5-IN1_S1_L002_R1_001.fastq.gz, SRR21658968, SRR21658968.lite SRA
SRX17658755 SRP398437 RNA-Seq SINGLE
GSM6595561: Crosslinked K562, EIF2B5 Input, rep2; Homo sapiens; RNA-Seq
Sample: SRS15191022
BioProject: PRJNA882819
BioSample: SAMN30952244
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: K562
cell line: K562
Original files (1)
K562
Runs (2)
Run Spots Bases Size (MB) Files Link
SRR21658965 2069646 206964600 69.73 EIF2B5-IN2_S2_L001_R1_001.fastq.gz, SRR21658965, SRR21658965.lite SRA
SRR21658966 2077071 207707100 70.39 EIF2B5-IN2_S2_L002_R1_001.fastq.gz, SRR21658966, SRR21658966.lite SRA
SRX17658756 SRP398437 RNA-Seq SINGLE
GSM6595562: Crosslinked K562, EIF2D Input, rep1; Homo sapiens; RNA-Seq
Sample: SRS15191023
BioProject: PRJNA882819
BioSample: SAMN30952243
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: K562
cell line: K562
Original files (1)
K562
Runs (2)
Run Spots Bases Size (MB) Files Link
SRR21658963 5693918 569391800 189.9 EIF2D--IN1-_S9_L001_R1_001.fastq.gz, SRR21658963, SRR21658963.lite SRA
SRR21658964 5663242 566324200 190.03 EIF2D--IN1-_S9_L002_R1_001.fastq.gz, SRR21658964, SRR21658964.lite SRA
SRX17658757 SRP398437 RNA-Seq SINGLE
GSM6595563: Crosslinked K562, EIF2D Input, rep2; Homo sapiens; RNA-Seq
Sample: SRS15191024
BioProject: PRJNA882819
BioSample: SAMN30952242
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: K562
cell line: K562
Original files (1)
K562
Runs (2)
Run Spots Bases Size (MB) Files Link
SRR21658961 4345891 434589100 145.26 EIF2D--IN2_S10_L001_R1_001.fastq.gz, SRR21658961, SRR21658961.lite SRA
SRR21658962 4359919 435991900 146.57 EIF2D--IN2_S10_L002_R1_001.fastq.gz, SRR21658962, SRR21658962.lite SRA
SRX17658758 SRP398437 RNA-Seq SINGLE
GSM6595564: Crosslinked K562, EIF2S2 Input, rep1; Homo sapiens; RNA-Seq
Sample: SRS15191025
BioProject: PRJNA882819
BioSample: SAMN30952241
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: K562
cell line: K562
Original files (1)
K562
Runs (2)
Run Spots Bases Size (MB) Files Link
SRR21658959 3879319 387931900 129.77 EIF2S2--IN1-_S13_L001_R1_001.fastq.gz, SRR21658959, SRR21658959.lite SRA
SRR21658960 3843762 384376200 129.38 EIF2S2--IN1-_S13_L002_R1_001.fastq.gz, SRR21658960, SRR21658960.lite SRA
SRX17658759 SRP398437 RNA-Seq SINGLE
GSM6595565: Crosslinked K562, EIF2S2 Input, rep2; Homo sapiens; RNA-Seq
Sample: SRS15191026
BioProject: PRJNA882819
BioSample: SAMN30952240
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: K562
cell line: K562
Original files (1)
K562
Runs (2)
Run Spots Bases Size (MB) Files Link
SRR21658957 3491508 349150800 117.05 EIF2S3-IN2-_S14_L001_R1_001.fastq.gz, SRR21658957, SRR21658957.lite SRA
SRR21658958 3471338 347133800 117.09 EIF2S3-IN2-_S14_L002_R1_001.fastq.gz, SRR21658958, SRR21658958.lite SRA
SRX17658760 SRP398437 RNA-Seq SINGLE
GSM6595566: Crosslinked K562, EIF3J Input, rep1; Homo sapiens; RNA-Seq
Sample: SRS15191027
BioProject: PRJNA882819
BioSample: SAMN30952239
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: K562
cell line: K562
Original files (1)
K562
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR21658956 13745508 1030913100 360.4 EIF3J-In1_S43_L002_R1_001.fastq.gz, SRR21658956, SRR21658956.lite SRA
SRX17658761 SRP398437 RNA-Seq SINGLE
GSM6595567: Crosslinked K562, EIF3J Input, rep2; Homo sapiens; RNA-Seq
Sample: SRS15191028
BioProject: PRJNA882819
BioSample: SAMN30952238
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: K562
cell line: K562
Original files (1)
K562
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR21658955 25277663 1895824725 658.41 EIF3J-In2_S44_L002_R1_001.fastq.gz, SRR21658955, SRR21658955.lite SRA

Linked Publications (2)

Skipper analysis of eCLIP datasets enables sensitive detection of constrained translation factor binding sites.
Cell genomics · 2023
Skipper analysis of eCLIP datasets enables sensitive detection of constrained translation factor binding sites.
Cell genomics · 2023

Data Files (48)

Accession File Name Stored Type Output Type Mapping Assembly Size Download
— EIF2B5-IN1_S1_L001_R1_001.fastq.gz RNA-Seq 121.2 MB link
— EIF2B5-IN1_S1_L002_R1_001.fastq.gz RNA-Seq 121.4 MB link
— EIF2B5-IN2_S2_L001_R1_001.fastq.gz RNA-Seq 69.7 MB link
— EIF2B5-IN2_S2_L002_R1_001.fastq.gz RNA-Seq 70.4 MB link
— EIF2B5-IP1-_S3_L001_R1_001.fastq.gz RNA-Seq 136.7 MB link
— EIF2B5-IP1-_S3_L002_R1_001.fastq.gz RNA-Seq 135.2 MB link
— EIF2B5-IP2-_S4_L001_R1_001.fastq.gz RNA-Seq 122.7 MB link
— EIF2B5-IP2-_S4_L002_R1_001.fastq.gz RNA-Seq 121.5 MB link
— EIF2D--IN1-_S9_L001_R1_001.fastq.gz RNA-Seq 189.9 MB link
— EIF2D--IN1-_S9_L002_R1_001.fastq.gz RNA-Seq 190.0 MB link
— EIF2D--IN2_S10_L001_R1_001.fastq.gz RNA-Seq 145.3 MB link
— EIF2D--IN2_S10_L002_R1_001.fastq.gz RNA-Seq 146.6 MB link
— EIF2D--IP1-_S11_L001_R1_001.fastq.gz RNA-Seq 234.5 MB link
— EIF2D--IP1-_S11_L002_R1_001.fastq.gz RNA-Seq 233.6 MB link
— EIF2D--IP2-_S12_L001_R1_001.fastq.gz RNA-Seq 196.6 MB link
— EIF2D--IP2-_S12_L002_R1_001.fastq.gz RNA-Seq 195.6 MB link
— EIF2S2--IN1-_S13_L001_R1_001.fastq.gz RNA-Seq 129.8 MB link
— EIF2S2--IN1-_S13_L002_R1_001.fastq.gz RNA-Seq 129.4 MB link
— EIF2S3-IN2-_S14_L001_R1_001.fastq.gz RNA-Seq 117.0 MB link
— EIF2S3-IN2-_S14_L002_R1_001.fastq.gz RNA-Seq 117.1 MB link
— EIF2S4-IP1-_S15_L001_R1_001.fastq.gz RNA-Seq 134.6 MB link
— EIF2S4-IP1-_S15_L002_R1_001.fastq.gz RNA-Seq 133.3 MB link
— EIF2S5-IP2-_S16_L001_R1_001.fastq.gz RNA-Seq 208.3 MB link
— EIF2S5-IP2-_S16_L002_R1_001.fastq.gz RNA-Seq 206.2 MB link
— EIF3J-In1_S43_L002_R1_001.fastq.gz RNA-Seq 360.4 MB link
— EIF3J-In2_S44_L002_R1_001.fastq.gz RNA-Seq 658.4 MB link
— EIF3J-IP1_S45_L002_R1_001.fastq.gz RNA-Seq 654.1 MB link
— EIF3J-IP2_S46_L002_R1_001.fastq.gz RNA-Seq 808.5 MB link
— IN1_RPS14_S22_L001_R1_001.fastq.gz RNA-Seq 513.9 MB link
— IN2_RPS14_S23_L001_R1_001.fastq.gz RNA-Seq 617.8 MB link
— IP1_RPS14_S24_L001_R1_001.fastq.gz RNA-Seq 958.1 MB link
— IP2_RPS14_S25_L001_R1_001.fastq.gz RNA-Seq 256.4 MB link
— RPL29_IN1_S21_L001_R1_001.fastq.gz RNA-Seq 1.8 GB link
— RPL29_IN2_S22_L001_R1_001.fastq.gz RNA-Seq 1.8 GB link
— RPL29_IP1_S23_L001_R1_001.fastq.gz RNA-Seq 1.5 GB link
— RPL29_IP2_S24_L001_R1_001.fastq.gz RNA-Seq 1.5 GB link
— RPL35A_IN1_S29_L001_R1_001.fastq.gz RNA-Seq 1.3 GB link
— RPL35A_IN2_S30_L001_R1_001.fastq.gz RNA-Seq 1.2 GB link
— RPL35A_IP1_S31_L001_R1_001.fastq.gz RNA-Seq 2.6 GB link
— RPL35A_IP2_S32_L001_R1_001.fastq.gz RNA-Seq 1.4 GB link
— RPS19_IN1_S5_L001_R1_001.fastq.gz RNA-Seq 511.1 MB link
— RPS19_IN2_S6_L001_R1_001.fastq.gz RNA-Seq 592.9 MB link
— RPS19_IP1_S13_L001_R1_001.fastq.gz RNA-Seq 634.1 MB link
— RPS19_IP2_S14_L001_R1_001.fastq.gz RNA-Seq 505.0 MB link
— RPS3A_IN1_S25_L001_R1_001.fastq.gz RNA-Seq 1.4 GB link
— RPS3A_IN2_S26_L001_R1_001.fastq.gz RNA-Seq 1.2 GB link
— RPS3A_IP1_S27_L001_R1_001.fastq.gz RNA-Seq 941.6 MB link
— RPS3A_IP2_S28_L001_R1_001.fastq.gz RNA-Seq 1.4 GB link