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ENCSR712CSN

ENCSR ENCODE
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RNA-seq on K562 cells treated with an shRNA knockdown against EIF4G1. (EIF4G1_BGKLV24)

Organism: Homo sapiens
Experiment Types:
shRNA RNA-seq
Status: released
Contact: Brenton Graveley, UConn

Summary

shRNA RNA-seq of EIF4G1 in Homo sapiens K562 expressing RNAi targeting H. sapiens EIF4G1

Overall Design

RNA-seq on K562 cells treated with an shRNA knockdown against EIF4G1. (EIF4G1_BGKLV24)

Analysis

View Data Processing
Analysis page is available for ENCSR712CSN.

Dataset Citations (3)

PubMed citation (PMID 32728046)
PubMed citation (PMID 32727537)
A large-scale binding and functional map of human RNA-binding proteins.
PMID 32728246 · 2020 · Nature
Eric L Van Nostrand, Peter Freese, Gabriel A Pratt, Xiaofeng Wang, Xintao Wei, Rui Xiao, Steven M Blue, Jia-Yu Chen, Neal A L Cody, Daniel Dominguez, Sara Olson, Balaji Sundararaman, Lijun Zhan, Cassandra Bazile, Louis Philip Benoit Bouvrette, Julie Bergalet, Michael O Duff, Keri E Garcia, Chelsea Gelboin-Burkhart, Myles Hochman, Nicole J Lambert, Hairi Li, Michael P McGurk, Thai B Nguyen, Tsultrim Palden, Ines Rabano, Shashank Sathe, Rebecca Stanton, Amanda Su, Ruth Wang, Brian A Yee, Bing Zhou, Ashley L Louie, Stefan Aigner, Xiang-Dong Fu, Eric Lécuyer, Christopher B Burge, Brenton R Graveley, Gene W Yeo

ENCODE Metadata

Total file size: 71.9 GB
Assay: shRNA RNA-seq
Target: EIF4G1
Biosample: Homo sapiens K562 expressing RNAi targeting H. sapiens EIF4G1
Files: 92
Unique ENC file IDs: 92
File Formats
bigWig (48) tsv (19) bam (18) fastq (4) tar (3)
Output types (11)
alignments (12) minus strand signal of all reads (12) minus strand signal of unique reads (12) plus strand signal of all reads (12) plus strand signal of unique reads (12) transcript quantifications (8) gene quantifications (6) transcriptome alignments (6) differential expression quantifications (5) reads (4) differential splicing quantifications (3)

Linked Publications (1)

A large-scale binding and functional map of human RNA-binding proteins.
Nature · 2020

Data Files (92)

Accession File Name Stored Type Output Type Mapping Assembly Size Download
ENCFF171TTJ ENCFF171TTJ.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 3.3 GB link
ENCFF411VYW ENCFF411VYW.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 2.7 GB link
ENCFF451WIR ENCFF451WIR.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 3.5 GB link
ENCFF586KAI ENCFF586KAI.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 2.9 GB link
ENCFF473KWA ENCFF473KWA.bam bam (alignments); assembly: GRCh38; genome annotation: V29 alignments GRCh38 3.3 GB link
ENCFF620KRD ENCFF620KRD.bam bam (alignments); assembly: GRCh38; genome annotation: V29 alignments GRCh38 3.5 GB link
ENCFF180OAP ENCFF180OAP.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 2.9 GB link
ENCFF523DDR ENCFF523DDR.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 2.7 GB link
ENCFF576JMA ENCFF576JMA.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 2.7 GB link
ENCFF655CAA ENCFF655CAA.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 2.9 GB link
ENCFF902UDT ENCFF902UDT.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 3.2 GB link
ENCFF990PXY ENCFF990PXY.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 3.4 GB link
ENCFF173IPH ENCFF173IPH.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V24 transcriptome alignments GRCh38 4.1 GB link
ENCFF859STP ENCFF859STP.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V24 transcriptome alignments GRCh38 3.8 GB link
ENCFF017KUD ENCFF017KUD.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V29 transcriptome alignments GRCh38 4.6 GB link
ENCFF716GVM ENCFF716GVM.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V29 transcriptome alignments GRCh38 4.3 GB link
ENCFF479VAY ENCFF479VAY.bam bam (transcriptome alignments); assembly: hg19; genome annotation: V19 transcriptome alignments hg19 3.8 GB link
ENCFF544DSO ENCFF544DSO.bam bam (transcriptome alignments); assembly: hg19; genome annotation: V19 transcriptome alignments hg19 4.1 GB link
ENCFF093ZND ENCFF093ZND.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 71.2 MB link
ENCFF157IFR ENCFF157IFR.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 64.5 MB link
ENCFF218CKL ENCFF218CKL.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 71.9 MB link
ENCFF785HWV ENCFF785HWV.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 64.4 MB link
ENCFF413YNU ENCFF413YNU.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V29 minus strand signal of all reads GRCh38 72.0 MB link
ENCFF537EQV ENCFF537EQV.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V29 minus strand signal of all reads GRCh38 71.3 MB link
ENCFF052GNT ENCFF052GNT.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 71.4 MB link
ENCFF111USR ENCFF111USR.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 65.3 MB link
ENCFF121NVZ ENCFF121NVZ.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 65.9 MB link
ENCFF247VVE ENCFF247VVE.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 61.8 MB link
ENCFF481VRD ENCFF481VRD.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 69.6 MB link
ENCFF940RPV ENCFF940RPV.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 60.5 MB link
ENCFF271OIV ENCFF271OIV.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 59.7 MB link
ENCFF305AEC ENCFF305AEC.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 60.6 MB link
ENCFF575LJM ENCFF575LJM.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 62.5 MB link
ENCFF760MCT ENCFF760MCT.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 63.1 MB link
ENCFF569JBM ENCFF569JBM.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 minus strand signal of unique reads GRCh38 63.6 MB link
ENCFF959AWZ ENCFF959AWZ.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 minus strand signal of unique reads GRCh38 62.7 MB link
ENCFF097LQL ENCFF097LQL.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 60.1 MB link
ENCFF167YIK ENCFF167YIK.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 60.1 MB link
ENCFF388EIO ENCFF388EIO.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 63.2 MB link
ENCFF425NKK ENCFF425NKK.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 56.7 MB link
ENCFF843VTC ENCFF843VTC.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 55.8 MB link
ENCFF904AWA ENCFF904AWA.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 63.0 MB link
ENCFF104SOX ENCFF104SOX.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 72.0 MB link
ENCFF848IYQ ENCFF848IYQ.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 65.1 MB link
ENCFF974HAP ENCFF974HAP.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 65.3 MB link
ENCFF977UEX ENCFF977UEX.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 72.7 MB link
ENCFF109GGY ENCFF109GGY.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V29 plus strand signal of all reads GRCh38 72.8 MB link
ENCFF705EZQ ENCFF705EZQ.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V29 plus strand signal of all reads GRCh38 72.0 MB link
ENCFF019MNI ENCFF019MNI.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 66.3 MB link
ENCFF556YMA ENCFF556YMA.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 61.5 MB link
ENCFF721YGD ENCFF721YGD.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 72.2 MB link
ENCFF751MWU ENCFF751MWU.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 67.1 MB link
ENCFF781OZY ENCFF781OZY.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 62.9 MB link
ENCFF989FXI ENCFF989FXI.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 70.4 MB link
ENCFF220QHT ENCFF220QHT.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 63.9 MB link
ENCFF350XOW ENCFF350XOW.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 64.5 MB link
ENCFF472CDA ENCFF472CDA.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 61.9 MB link
ENCFF987XQH ENCFF987XQH.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 61.0 MB link
ENCFF132ENB ENCFF132ENB.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 plus strand signal of unique reads GRCh38 65.1 MB link
ENCFF328HFM ENCFF328HFM.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 plus strand signal of unique reads GRCh38 64.1 MB link
ENCFF226SUI ENCFF226SUI.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 61.6 MB link
ENCFF280EZU ENCFF280EZU.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 58.2 MB link
ENCFF310HXH ENCFF310HXH.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 57.4 MB link
ENCFF367NYE ENCFF367NYE.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 61.5 MB link
ENCFF465ACU ENCFF465ACU.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 64.8 MB link
ENCFF911ZQU ENCFF911ZQU.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 64.6 MB link
ENCFF300PDX ENCFF300PDX.fastq fastq (reads) reads 1.7 GB link
ENCFF392ENF ENCFF392ENF.fastq fastq (reads) reads 1.8 GB link
ENCFF446DSH ENCFF446DSH.fastq fastq (reads) reads 2.0 GB link
ENCFF862RGW ENCFF862RGW.fastq fastq (reads) reads 1.8 GB link
ENCFF014DFI ENCFF014DFI.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 3.1 MB link
ENCFF533NEA ENCFF533NEA.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 12.9 MB link
ENCFF900AVX ENCFF900AVX.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 3.3 MB link
ENCFF009VAX ENCFF009VAX.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 5.5 MB link
ENCFF354PTB ENCFF354PTB.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 2.7 MB link
ENCFF567OWB ENCFF567OWB.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 1.9 MB link
ENCFF706RKX ENCFF706RKX.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 1.8 MB link
ENCFF742HVI ENCFF742HVI.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 4.0 MB link
ENCFF328ILX ENCFF328ILX.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V24 gene quantifications GRCh38 9.4 MB link
ENCFF951RQF ENCFF951RQF.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V24 gene quantifications GRCh38 9.4 MB link
ENCFF426TCB ENCFF426TCB.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V29 gene quantifications GRCh38 10.4 MB link
ENCFF542CKA ENCFF542CKA.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V29 gene quantifications GRCh38 10.4 MB link
ENCFF713RIW ENCFF713RIW.tsv tsv (gene quantifications); assembly: hg19; genome annotation: V19 gene quantifications hg19 9.1 MB link
ENCFF923IYZ ENCFF923IYZ.tsv tsv (gene quantifications); assembly: hg19; genome annotation: V19 gene quantifications hg19 9.1 MB link
ENCFF010FVP ENCFF010FVP.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V24 transcript quantifications GRCh38 25.3 MB link
ENCFF127HCV ENCFF127HCV.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V24 transcript quantifications GRCh38 25.3 MB link
ENCFF577ZUA ENCFF577ZUA.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 29.8 MB link
ENCFF773WQZ ENCFF773WQZ.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 29.8 MB link
ENCFF870UVK ENCFF870UVK.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 27.3 MB link
ENCFF914CEG ENCFF914CEG.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 27.3 MB link
ENCFF657XCE ENCFF657XCE.tsv tsv (transcript quantifications); assembly: hg19; genome annotation: V19 transcript quantifications hg19 24.9 MB link
ENCFF913SGQ ENCFF913SGQ.tsv tsv (transcript quantifications); assembly: hg19; genome annotation: V19 transcript quantifications hg19 24.9 MB link