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ENCSR309PPC

ENCSR ENCODE
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shRNA knockdown against PA2G4 in K562 cells followed by RNA-seq. (PA2G4_BGKLV19)

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

Summary

shRNA RNA-seq of PA2G4 in Homo sapiens K562 expressing RNAi targeting H. sapiens PA2G4

Overall Design

shRNA knockdown against PA2G4 in K562 cells followed by RNA-seq. (PA2G4_BGKLV19)

Analysis

View Data Processing
Analysis page is available for ENCSR309PPC.

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: 96.2 GB
Assay: shRNA RNA-seq
Target: PA2G4
Biosample: Homo sapiens K562 expressing RNAi targeting H. sapiens PA2G4
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
ENCFF225TRZ ENCFF225TRZ.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 4.5 GB link
ENCFF309XON ENCFF309XON.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 3.7 GB link
ENCFF683PJT ENCFF683PJT.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 3.6 GB link
ENCFF989TMS ENCFF989TMS.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 4.4 GB link
ENCFF290NRN ENCFF290NRN.bam bam (alignments); assembly: GRCh38; genome annotation: V29 alignments GRCh38 4.5 GB link
ENCFF547ZAL ENCFF547ZAL.bam bam (alignments); assembly: GRCh38; genome annotation: V29 alignments GRCh38 4.4 GB link
ENCFF142UXQ ENCFF142UXQ.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 4.4 GB link
ENCFF355MHA ENCFF355MHA.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 3.6 GB link
ENCFF429TWH ENCFF429TWH.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 4.3 GB link
ENCFF503QON ENCFF503QON.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 3.7 GB link
ENCFF775PKF ENCFF775PKF.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 3.7 GB link
ENCFF909VJA ENCFF909VJA.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 3.6 GB link
ENCFF554YYL ENCFF554YYL.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V24 transcriptome alignments GRCh38 5.6 GB link
ENCFF935HPQ ENCFF935HPQ.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V24 transcriptome alignments GRCh38 5.5 GB link
ENCFF095ODS ENCFF095ODS.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V29 transcriptome alignments GRCh38 6.4 GB link
ENCFF182BIE ENCFF182BIE.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V29 transcriptome alignments GRCh38 6.2 GB link
ENCFF106YFD ENCFF106YFD.bam bam (transcriptome alignments); assembly: hg19; genome annotation: V19 transcriptome alignments hg19 5.5 GB link
ENCFF266LDQ ENCFF266LDQ.bam bam (transcriptome alignments); assembly: hg19; genome annotation: V19 transcriptome alignments hg19 5.6 GB link
ENCFF110VFE ENCFF110VFE.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 68.8 MB link
ENCFF315NKG ENCFF315NKG.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 71.6 MB link
ENCFF373QZA ENCFF373QZA.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 76.6 MB link
ENCFF414XHQ ENCFF414XHQ.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 79.1 MB link
ENCFF490WTR ENCFF490WTR.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V29 minus strand signal of all reads GRCh38 76.6 MB link
ENCFF877BTM ENCFF877BTM.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V29 minus strand signal of all reads GRCh38 79.0 MB link
ENCFF065MDT ENCFF065MDT.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 75.6 MB link
ENCFF254DML ENCFF254DML.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 78.5 MB link
ENCFF344SBZ ENCFF344SBZ.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 72.6 MB link
ENCFF528HMA ENCFF528HMA.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 68.2 MB link
ENCFF564LTO ENCFF564LTO.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 69.2 MB link
ENCFF578PFW ENCFF578PFW.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 70.8 MB link
ENCFF124ARP ENCFF124ARP.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 70.5 MB link
ENCFF341FPH ENCFF341FPH.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 64.3 MB link
ENCFF932HCJ ENCFF932HCJ.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 67.5 MB link
ENCFF979MVW ENCFF979MVW.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 66.1 MB link
ENCFF580KJV ENCFF580KJV.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 minus strand signal of unique reads GRCh38 70.5 MB link
ENCFF615MSB ENCFF615MSB.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 minus strand signal of unique reads GRCh38 67.8 MB link
ENCFF039UEF ENCFF039UEF.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 70.3 MB link
ENCFF123CJB ENCFF123CJB.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 64.9 MB link
ENCFF210SFV ENCFF210SFV.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 64.0 MB link
ENCFF263NEP ENCFF263NEP.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 67.0 MB link
ENCFF441WUR ENCFF441WUR.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 62.6 MB link
ENCFF898LWY ENCFF898LWY.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 67.7 MB link
ENCFF050DIX ENCFF050DIX.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 72.5 MB link
ENCFF180XCZ ENCFF180XCZ.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 77.5 MB link
ENCFF195PSM ENCFF195PSM.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 69.7 MB link
ENCFF270GES ENCFF270GES.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 80.1 MB link
ENCFF236JGN ENCFF236JGN.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V29 plus strand signal of all reads GRCh38 77.5 MB link
ENCFF502BQW ENCFF502BQW.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V29 plus strand signal of all reads GRCh38 80.1 MB link
ENCFF255DUW ENCFF255DUW.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 73.9 MB link
ENCFF271SSG ENCFF271SSG.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 76.5 MB link
ENCFF296YMS ENCFF296YMS.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 79.5 MB link
ENCFF495EWZ ENCFF495EWZ.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 70.4 MB link
ENCFF546DDS ENCFF546DDS.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 69.7 MB link
ENCFF923XVN ENCFF923XVN.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 72.1 MB link
ENCFF199PLX ENCFF199PLX.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 68.9 MB link
ENCFF265KTO ENCFF265KTO.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 65.5 MB link
ENCFF601GKI ENCFF601GKI.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 67.4 MB link
ENCFF907FDN ENCFF907FDN.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 72.0 MB link
ENCFF824JSK ENCFF824JSK.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 plus strand signal of unique reads GRCh38 69.2 MB link
ENCFF905ZRU ENCFF905ZRU.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 plus strand signal of unique reads GRCh38 72.0 MB link
ENCFF036OPB ENCFF036OPB.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 66.7 MB link
ENCFF085KUM ENCFF085KUM.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 69.3 MB link
ENCFF116BBK ENCFF116BBK.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 72.0 MB link
ENCFF160FJA ENCFF160FJA.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 65.5 MB link
ENCFF738JGJ ENCFF738JGJ.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 68.6 MB link
ENCFF786YAW ENCFF786YAW.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 64.2 MB link
ENCFF418DBS ENCFF418DBS.fastq fastq (reads) reads 2.3 GB link
ENCFF602TYI ENCFF602TYI.fastq fastq (reads) reads 2.5 GB link
ENCFF832JZQ ENCFF832JZQ.fastq fastq (reads) reads 2.4 GB link
ENCFF975IBI ENCFF975IBI.fastq fastq (reads) reads 2.3 GB link
ENCFF064XMH ENCFF064XMH.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 14.9 MB link
ENCFF253GVU ENCFF253GVU.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 3.9 MB link
ENCFF668UOE ENCFF668UOE.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 3.4 MB link
ENCFF055LYM ENCFF055LYM.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 5.5 MB link
ENCFF191UDE ENCFF191UDE.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 1.9 MB link
ENCFF489TPJ ENCFF489TPJ.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 4.1 MB link
ENCFF579XDD ENCFF579XDD.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 1.7 MB link
ENCFF698CLZ ENCFF698CLZ.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 2.8 MB link
ENCFF265BBJ ENCFF265BBJ.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V24 gene quantifications GRCh38 9.5 MB link
ENCFF542WGG ENCFF542WGG.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V24 gene quantifications GRCh38 9.5 MB link
ENCFF377KEV ENCFF377KEV.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V29 gene quantifications GRCh38 10.4 MB link
ENCFF563TKY ENCFF563TKY.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V29 gene quantifications GRCh38 10.4 MB link
ENCFF547KPJ ENCFF547KPJ.tsv tsv (gene quantifications); assembly: hg19; genome annotation: V19 gene quantifications hg19 9.1 MB link
ENCFF760FTG ENCFF760FTG.tsv tsv (gene quantifications); assembly: hg19; genome annotation: V19 gene quantifications hg19 9.1 MB link
ENCFF524ZGL ENCFF524ZGL.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V24 transcript quantifications GRCh38 25.3 MB link
ENCFF938NSK ENCFF938NSK.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V24 transcript quantifications GRCh38 25.3 MB link
ENCFF287PPC ENCFF287PPC.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 29.8 MB link
ENCFF323BKM ENCFF323BKM.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 27.3 MB link
ENCFF357ODZ ENCFF357ODZ.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 29.8 MB link
ENCFF667AGC ENCFF667AGC.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 27.3 MB link
ENCFF283XJX ENCFF283XJX.tsv tsv (transcript quantifications); assembly: hg19; genome annotation: V19 transcript quantifications hg19 24.9 MB link
ENCFF723DFE ENCFF723DFE.tsv tsv (transcript quantifications); assembly: hg19; genome annotation: V19 transcript quantifications hg19 24.9 MB link