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ENCSR269SJB

ENCSR ENCODE
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RNA-seq on HepG2 cells treated with an shRNA knockdown against CKAP4. (CKAP4_BGHLV31)

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

Summary

shRNA RNA-seq of CKAP4 in Homo sapiens HepG2 expressing RNAi targeting H. sapiens CKAP4

Overall Design

RNA-seq on HepG2 cells treated with an shRNA knockdown against CKAP4. (CKAP4_BGHLV31)

Analysis

View Data Processing
Analysis page is available for ENCSR269SJB.

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: 89.5 GB
Assay: shRNA RNA-seq
Target: CKAP4
Biosample: Homo sapiens HepG2 expressing RNAi targeting H. sapiens CKAP4
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
ENCFF215GNR ENCFF215GNR.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 4.1 GB link
ENCFF328LEZ ENCFF328LEZ.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 3.3 GB link
ENCFF367NCV ENCFF367NCV.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 4.0 GB link
ENCFF846OKE ENCFF846OKE.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 3.2 GB link
ENCFF678SFU ENCFF678SFU.bam bam (alignments); assembly: GRCh38; genome annotation: V29 alignments GRCh38 4.1 GB link
ENCFF927FUA ENCFF927FUA.bam bam (alignments); assembly: GRCh38; genome annotation: V29 alignments GRCh38 4.0 GB link
ENCFF166BWS ENCFF166BWS.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 3.2 GB link
ENCFF219MPL ENCFF219MPL.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 3.2 GB link
ENCFF348ABY ENCFF348ABY.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 3.9 GB link
ENCFF592OCH ENCFF592OCH.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 3.1 GB link
ENCFF855TVS ENCFF855TVS.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 3.9 GB link
ENCFF860SKR ENCFF860SKR.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 3.1 GB link
ENCFF650OOP ENCFF650OOP.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V24 transcriptome alignments GRCh38 5.3 GB link
ENCFF733SBA ENCFF733SBA.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V24 transcriptome alignments GRCh38 5.2 GB link
ENCFF621ETM ENCFF621ETM.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V29 transcriptome alignments GRCh38 6.0 GB link
ENCFF747CFJ ENCFF747CFJ.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V29 transcriptome alignments GRCh38 6.0 GB link
ENCFF078BJS ENCFF078BJS.bam bam (transcriptome alignments); assembly: hg19; genome annotation: V19 transcriptome alignments hg19 5.2 GB link
ENCFF294HIB ENCFF294HIB.bam bam (transcriptome alignments); assembly: hg19; genome annotation: V19 transcriptome alignments hg19 5.2 GB link
ENCFF419SDY ENCFF419SDY.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 89.0 MB link
ENCFF546RXP ENCFF546RXP.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 89.3 MB link
ENCFF765PYL ENCFF765PYL.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 97.8 MB link
ENCFF804ZDY ENCFF804ZDY.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 98.9 MB link
ENCFF195MXX ENCFF195MXX.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V29 minus strand signal of all reads GRCh38 99.0 MB link
ENCFF376VPP ENCFF376VPP.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V29 minus strand signal of all reads GRCh38 97.9 MB link
ENCFF025GOU ENCFF025GOU.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 91.1 MB link
ENCFF124VHP ENCFF124VHP.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 98.3 MB link
ENCFF245OPM ENCFF245OPM.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 91.7 MB link
ENCFF529KQP ENCFF529KQP.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 87.8 MB link
ENCFF803ILA ENCFF803ILA.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 87.5 MB link
ENCFF995WAT ENCFF995WAT.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 98.1 MB link
ENCFF235ZWS ENCFF235ZWS.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 88.2 MB link
ENCFF575NRN ENCFF575NRN.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 83.9 MB link
ENCFF820OEN ENCFF820OEN.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 83.5 MB link
ENCFF916DEX ENCFF916DEX.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 88.6 MB link
ENCFF021CPN ENCFF021CPN.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 minus strand signal of unique reads GRCh38 88.2 MB link
ENCFF391YOL ENCFF391YOL.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 minus strand signal of unique reads GRCh38 88.6 MB link
ENCFF216MUR ENCFF216MUR.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 87.6 MB link
ENCFF270OGR ENCFF270OGR.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 84.5 MB link
ENCFF478IBZ ENCFF478IBZ.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 80.6 MB link
ENCFF744MNB ENCFF744MNB.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 80.2 MB link
ENCFF879XIS ENCFF879XIS.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 83.8 MB link
ENCFF885IRZ ENCFF885IRZ.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 88.6 MB link
ENCFF540GPL ENCFF540GPL.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 91.0 MB link
ENCFF762AUY ENCFF762AUY.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 100.8 MB link
ENCFF880TUO ENCFF880TUO.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 99.5 MB link
ENCFF902FBI ENCFF902FBI.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 90.7 MB link
ENCFF705WTQ ENCFF705WTQ.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V29 plus strand signal of all reads GRCh38 100.8 MB link
ENCFF948MIQ ENCFF948MIQ.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V29 plus strand signal of all reads GRCh38 99.6 MB link
ENCFF043OEB ENCFF043OEB.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 93.6 MB link
ENCFF182ZRE ENCFF182ZRE.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 99.5 MB link
ENCFF237WLH ENCFF237WLH.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 92.8 MB link
ENCFF408TLV ENCFF408TLV.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 89.2 MB link
ENCFF491UDZ ENCFF491UDZ.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 99.9 MB link
ENCFF982PKH ENCFF982PKH.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 89.7 MB link
ENCFF044HJR ENCFF044HJR.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 90.5 MB link
ENCFF438XKF ENCFF438XKF.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 85.5 MB link
ENCFF634TLP ENCFF634TLP.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 91.0 MB link
ENCFF960DHG ENCFF960DHG.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 86.0 MB link
ENCFF642SNC ENCFF642SNC.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 plus strand signal of unique reads GRCh38 90.5 MB link
ENCFF930FDC ENCFF930FDC.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 plus strand signal of unique reads GRCh38 91.0 MB link
ENCFF125CTV ENCFF125CTV.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 91.0 MB link
ENCFF267PJY ENCFF267PJY.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 86.9 MB link
ENCFF431YDJ ENCFF431YDJ.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 86.0 MB link
ENCFF641TBZ ENCFF641TBZ.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 82.6 MB link
ENCFF895SQI ENCFF895SQI.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 90.0 MB link
ENCFF950SRK ENCFF950SRK.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 83.1 MB link
ENCFF043TEG ENCFF043TEG.fastq fastq (reads) reads 2.3 GB link
ENCFF200VYJ ENCFF200VYJ.fastq fastq (reads) reads 2.3 GB link
ENCFF274EDD ENCFF274EDD.fastq fastq (reads) reads 2.3 GB link
ENCFF915KRE ENCFF915KRE.fastq fastq (reads) reads 2.3 GB link
ENCFF032YHW ENCFF032YHW.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 4.6 MB link
ENCFF712IPB ENCFF712IPB.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 17.0 MB link
ENCFF911OQR ENCFF911OQR.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 3.7 MB link
ENCFF171LXH ENCFF171LXH.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 3.0 MB link
ENCFF322LIQ ENCFF322LIQ.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 2.0 MB link
ENCFF377JVY ENCFF377JVY.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 4.4 MB link
ENCFF472WZR ENCFF472WZR.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 5.6 MB link
ENCFF683QYN ENCFF683QYN.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 1.8 MB link
ENCFF757OJK ENCFF757OJK.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V24 gene quantifications GRCh38 9.4 MB link
ENCFF817NTM ENCFF817NTM.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V24 gene quantifications GRCh38 9.5 MB link
ENCFF257KPE ENCFF257KPE.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V29 gene quantifications GRCh38 10.4 MB link
ENCFF923LNM ENCFF923LNM.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V29 gene quantifications GRCh38 10.4 MB link
ENCFF140CVY ENCFF140CVY.tsv tsv (gene quantifications); assembly: hg19; genome annotation: V19 gene quantifications hg19 9.1 MB link
ENCFF474IBM ENCFF474IBM.tsv tsv (gene quantifications); assembly: hg19; genome annotation: V19 gene quantifications hg19 9.1 MB link
ENCFF733UQY ENCFF733UQY.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V24 transcript quantifications GRCh38 25.3 MB link
ENCFF982IQR ENCFF982IQR.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V24 transcript quantifications GRCh38 25.3 MB link
ENCFF052DDR ENCFF052DDR.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 27.4 MB link
ENCFF541UJB ENCFF541UJB.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 29.8 MB link
ENCFF738PZJ ENCFF738PZJ.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 27.4 MB link
ENCFF770GIB ENCFF770GIB.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 29.8 MB link
ENCFF286VCJ ENCFF286VCJ.tsv tsv (transcript quantifications); assembly: hg19; genome annotation: V19 transcript quantifications hg19 24.9 MB link
ENCFF816CUH ENCFF816CUH.tsv tsv (transcript quantifications); assembly: hg19; genome annotation: V19 transcript quantifications hg19 24.9 MB link