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ENCSR542ESY

ENCSR ENCODE
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RNA-seq on HepG2 cells treated with an shRNA knockdown against KRR1. (KRR1_BGHLV27)

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

Summary

shRNA RNA-seq of KRR1 in Homo sapiens HepG2 expressing RNAi targeting H. sapiens KRR1

Overall Design

RNA-seq on HepG2 cells treated with an shRNA knockdown against KRR1. (KRR1_BGHLV27)

Analysis

View Data Processing
Analysis page is available for ENCSR542ESY.

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: 120.1 GB
Assay: shRNA RNA-seq
Target: KRR1
Biosample: Homo sapiens HepG2 expressing RNAi targeting H. sapiens KRR1
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
ENCFF318TSH ENCFF318TSH.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 5.0 GB link
ENCFF521BXO ENCFF521BXO.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 6.2 GB link
ENCFF670KST ENCFF670KST.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 3.8 GB link
ENCFF887KLE ENCFF887KLE.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 4.7 GB link
ENCFF025NBT ENCFF025NBT.bam bam (alignments); assembly: GRCh38; genome annotation: V29 alignments GRCh38 6.2 GB link
ENCFF829EHH ENCFF829EHH.bam bam (alignments); assembly: GRCh38; genome annotation: V29 alignments GRCh38 4.7 GB link
ENCFF151QED ENCFF151QED.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 3.7 GB link
ENCFF417WJR ENCFF417WJR.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 4.9 GB link
ENCFF497UDR ENCFF497UDR.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 4.5 GB link
ENCFF556XEJ ENCFF556XEJ.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 4.9 GB link
ENCFF576VLK ENCFF576VLK.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 6.0 GB link
ENCFF894DCG ENCFF894DCG.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 3.7 GB link
ENCFF183OWW ENCFF183OWW.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V24 transcriptome alignments GRCh38 6.1 GB link
ENCFF214WHR ENCFF214WHR.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V24 transcriptome alignments GRCh38 8.1 GB link
ENCFF594WTR ENCFF594WTR.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V29 transcriptome alignments GRCh38 9.3 GB link
ENCFF864UJH ENCFF864UJH.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V29 transcriptome alignments GRCh38 6.9 GB link
ENCFF165ZQY ENCFF165ZQY.bam bam (transcriptome alignments); assembly: hg19; genome annotation: V19 transcriptome alignments hg19 6.1 GB link
ENCFF516BIU ENCFF516BIU.bam bam (transcriptome alignments); assembly: hg19; genome annotation: V19 transcriptome alignments hg19 8.1 GB link
ENCFF211VUF ENCFF211VUF.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 95.7 MB link
ENCFF247FBE ENCFF247FBE.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 87.8 MB link
ENCFF603HCO ENCFF603HCO.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 101.0 MB link
ENCFF676XKU ENCFF676XKU.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 111.6 MB link
ENCFF363HPL ENCFF363HPL.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V29 minus strand signal of all reads GRCh38 95.8 MB link
ENCFF813DDX ENCFF813DDX.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V29 minus strand signal of all reads GRCh38 111.6 MB link
ENCFF053CDN ENCFF053CDN.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 97.8 MB link
ENCFF095UTZ ENCFF095UTZ.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 88.5 MB link
ENCFF305YCS ENCFF305YCS.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 95.9 MB link
ENCFF444OPE ENCFF444OPE.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 103.0 MB link
ENCFF489KGT ENCFF489KGT.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 109.7 MB link
ENCFF559RLO ENCFF559RLO.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 83.8 MB link
ENCFF080VZP ENCFF080VZP.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 99.6 MB link
ENCFF159RUM ENCFF159RUM.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 82.3 MB link
ENCFF257CRM ENCFF257CRM.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 94.6 MB link
ENCFF637LXI ENCFF637LXI.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 86.6 MB link
ENCFF450CBU ENCFF450CBU.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 minus strand signal of unique reads GRCh38 99.6 MB link
ENCFF653JNG ENCFF653JNG.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 minus strand signal of unique reads GRCh38 86.6 MB link
ENCFF180CIS ENCFF180CIS.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 98.7 MB link
ENCFF180ZQV ENCFF180ZQV.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 82.9 MB link
ENCFF388NRG ENCFF388NRG.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 86.6 MB link
ENCFF663KGH ENCFF663KGH.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 90.7 MB link
ENCFF686LXA ENCFF686LXA.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 78.0 MB link
ENCFF897MSG ENCFF897MSG.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 95.3 MB link
ENCFF170SDI ENCFF170SDI.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 89.0 MB link
ENCFF196VVE ENCFF196VVE.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 113.0 MB link
ENCFF238SRC ENCFF238SRC.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 102.3 MB link
ENCFF320HKG ENCFF320HKG.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 96.9 MB link
ENCFF340JVW ENCFF340JVW.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V29 plus strand signal of all reads GRCh38 97.0 MB link
ENCFF998HLO ENCFF998HLO.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V29 plus strand signal of all reads GRCh38 113.0 MB link
ENCFF019KEN ENCFF019KEN.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 99.2 MB link
ENCFF025FCD ENCFF025FCD.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 97.0 MB link
ENCFF052SJV ENCFF052SJV.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 104.6 MB link
ENCFF261AFL ENCFF261AFL.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 110.9 MB link
ENCFF604MXK ENCFF604MXK.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 85.2 MB link
ENCFF922TRN ENCFF922TRN.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 89.9 MB link
ENCFF349KSU ENCFF349KSU.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 88.5 MB link
ENCFF473KIU ENCFF473KIU.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 96.5 MB link
ENCFF883TCS ENCFF883TCS.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 83.9 MB link
ENCFF936MSA ENCFF936MSA.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 101.7 MB link
ENCFF709UXZ ENCFF709UXZ.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 plus strand signal of unique reads GRCh38 101.7 MB link
ENCFF852PSO ENCFF852PSO.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 plus strand signal of unique reads GRCh38 88.5 MB link
ENCFF133JII ENCFF133JII.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 84.7 MB link
ENCFF152WLD ENCFF152WLD.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 92.8 MB link
ENCFF470JFB ENCFF470JFB.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 97.4 MB link
ENCFF823GVO ENCFF823GVO.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 100.8 MB link
ENCFF937YMO ENCFF937YMO.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 88.5 MB link
ENCFF995CNO ENCFF995CNO.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 79.9 MB link
ENCFF058AVY ENCFF058AVY.fastq fastq (reads) reads 3.6 GB link
ENCFF260BAM ENCFF260BAM.fastq fastq (reads) reads 2.7 GB link
ENCFF269JTR ENCFF269JTR.fastq fastq (reads) reads 3.6 GB link
ENCFF319AYU ENCFF319AYU.fastq fastq (reads) reads 2.7 GB link
ENCFF463FSB ENCFF463FSB.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 4.3 MB link
ENCFF548MLC ENCFF548MLC.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 3.6 MB link
ENCFF723SFE ENCFF723SFE.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 16.6 MB link
ENCFF067VNJ ENCFF067VNJ.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 2.9 MB link
ENCFF084GVQ ENCFF084GVQ.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 5.6 MB link
ENCFF169CKN ENCFF169CKN.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 1.9 MB link
ENCFF565RIX ENCFF565RIX.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 4.3 MB link
ENCFF809DOT ENCFF809DOT.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 1.8 MB link
ENCFF732YKN ENCFF732YKN.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V24 gene quantifications GRCh38 9.5 MB link
ENCFF818YYR ENCFF818YYR.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V24 gene quantifications GRCh38 9.5 MB link
ENCFF489HZX ENCFF489HZX.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V29 gene quantifications GRCh38 10.4 MB link
ENCFF730EQK ENCFF730EQK.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V29 gene quantifications GRCh38 10.4 MB link
ENCFF764EQR ENCFF764EQR.tsv tsv (gene quantifications); assembly: hg19; genome annotation: V19 gene quantifications hg19 9.1 MB link
ENCFF973GFG ENCFF973GFG.tsv tsv (gene quantifications); assembly: hg19; genome annotation: V19 gene quantifications hg19 9.1 MB link
ENCFF616EOI ENCFF616EOI.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V24 transcript quantifications GRCh38 25.3 MB link
ENCFF943YXV ENCFF943YXV.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V24 transcript quantifications GRCh38 25.4 MB link
ENCFF142UYN ENCFF142UYN.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 27.3 MB link
ENCFF392KVJ ENCFF392KVJ.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 27.4 MB link
ENCFF472TZC ENCFF472TZC.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 29.9 MB link
ENCFF967JDE ENCFF967JDE.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 29.8 MB link
ENCFF008QZU ENCFF008QZU.tsv tsv (transcript quantifications); assembly: hg19; genome annotation: V19 transcript quantifications hg19 24.9 MB link
ENCFF961TMT ENCFF961TMT.tsv tsv (transcript quantifications); assembly: hg19; genome annotation: V19 transcript quantifications hg19 25.0 MB link