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ENCSR921KDS

ENCSR ENCODE
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RNA-seq on K562 cells treated with an shRNA knockdown against RCC2. (RCC2_BGKLV21)

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

Summary

shRNA RNA-seq of RCC2 in Homo sapiens K562 expressing RNAi targeting H. sapiens RCC2

Overall Design

RNA-seq on K562 cells treated with an shRNA knockdown against RCC2. (RCC2_BGKLV21)

Analysis

View Data Processing
Analysis page is available for ENCSR921KDS.

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: 63.5 GB
Assay: shRNA RNA-seq
Target: RCC2
Biosample: Homo sapiens K562 expressing RNAi targeting H. sapiens RCC2
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
ENCFF383DKD ENCFF383DKD.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 2.6 GB link
ENCFF463BJD ENCFF463BJD.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 2.2 GB link
ENCFF466CKO ENCFF466CKO.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 3.3 GB link
ENCFF675JCQ ENCFF675JCQ.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 2.8 GB link
ENCFF693HZQ ENCFF693HZQ.bam bam (alignments); assembly: GRCh38; genome annotation: V29 alignments GRCh38 3.3 GB link
ENCFF825NYR ENCFF825NYR.bam bam (alignments); assembly: GRCh38; genome annotation: V29 alignments GRCh38 2.6 GB link
ENCFF316DRD ENCFF316DRD.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 3.2 GB link
ENCFF441MQQ ENCFF441MQQ.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 2.8 GB link
ENCFF451UBP ENCFF451UBP.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 2.2 GB link
ENCFF481CXX ENCFF481CXX.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 2.2 GB link
ENCFF712JJA ENCFF712JJA.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 2.6 GB link
ENCFF975LRN ENCFF975LRN.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 2.8 GB link
ENCFF173OWR ENCFF173OWR.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V24 transcriptome alignments GRCh38 3.9 GB link
ENCFF394GDR ENCFF394GDR.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V24 transcriptome alignments GRCh38 3.1 GB link
ENCFF157GSK ENCFF157GSK.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V29 transcriptome alignments GRCh38 4.3 GB link
ENCFF540EUF ENCFF540EUF.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V29 transcriptome alignments GRCh38 3.5 GB link
ENCFF427ULR ENCFF427ULR.bam bam (transcriptome alignments); assembly: hg19; genome annotation: V19 transcriptome alignments hg19 3.1 GB link
ENCFF928SLV ENCFF928SLV.bam bam (transcriptome alignments); assembly: hg19; genome annotation: V19 transcriptome alignments hg19 3.9 GB link
ENCFF114GFM ENCFF114GFM.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 58.3 MB link
ENCFF125WXV ENCFF125WXV.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 64.7 MB link
ENCFF350ECV ENCFF350ECV.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 56.4 MB link
ENCFF803LCV ENCFF803LCV.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 50.9 MB link
ENCFF553RBA ENCFF553RBA.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V29 minus strand signal of all reads GRCh38 56.4 MB link
ENCFF755PWF ENCFF755PWF.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V29 minus strand signal of all reads GRCh38 64.7 MB link
ENCFF116ZJB ENCFF116ZJB.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 64.3 MB link
ENCFF541FZC ENCFF541FZC.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 55.6 MB link
ENCFF781LVG ENCFF781LVG.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 55.7 MB link
ENCFF885RMV ENCFF885RMV.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 48.4 MB link
ENCFF894TUZ ENCFF894TUZ.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 59.2 MB link
ENCFF914XCI ENCFF914XCI.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 51.0 MB link
ENCFF179VEL ENCFF179VEL.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 57.5 MB link
ENCFF421AMV ENCFF421AMV.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 50.2 MB link
ENCFF453KLN ENCFF453KLN.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 46.8 MB link
ENCFF635ULU ENCFF635ULU.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 54.3 MB link
ENCFF508WRA ENCFF508WRA.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 minus strand signal of unique reads GRCh38 49.7 MB link
ENCFF911BHJ ENCFF911BHJ.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 minus strand signal of unique reads GRCh38 56.9 MB link
ENCFF048AXC ENCFF048AXC.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 57.4 MB link
ENCFF394WDE ENCFF394WDE.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 47.4 MB link
ENCFF439UEO ENCFF439UEO.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 44.2 MB link
ENCFF451CDP ENCFF451CDP.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 51.2 MB link
ENCFF634JIN ENCFF634JIN.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 53.9 MB link
ENCFF978IKZ ENCFF978IKZ.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 50.1 MB link
ENCFF181QIS ENCFF181QIS.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 51.3 MB link
ENCFF226KHH ENCFF226KHH.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 56.9 MB link
ENCFF615AYD ENCFF615AYD.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 65.4 MB link
ENCFF648TVE ENCFF648TVE.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 58.8 MB link
ENCFF194GFB ENCFF194GFB.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V29 plus strand signal of all reads GRCh38 56.9 MB link
ENCFF675LAX ENCFF675LAX.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V29 plus strand signal of all reads GRCh38 65.4 MB link
ENCFF113HWX ENCFF113HWX.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 49.2 MB link
ENCFF218RSG ENCFF218RSG.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 56.6 MB link
ENCFF266NVL ENCFF266NVL.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 65.1 MB link
ENCFF506IAU ENCFF506IAU.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 60.1 MB link
ENCFF538KBU ENCFF538KBU.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 56.2 MB link
ENCFF612JAX ENCFF612JAX.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 51.9 MB link
ENCFF101LFF ENCFF101LFF.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 51.2 MB link
ENCFF493CRF ENCFF493CRF.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 58.6 MB link
ENCFF676VTT ENCFF676VTT.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 55.2 MB link
ENCFF863DXG ENCFF863DXG.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 47.6 MB link
ENCFF240DIX ENCFF240DIX.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 plus strand signal of unique reads GRCh38 50.6 MB link
ENCFF384QYR ENCFF384QYR.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 plus strand signal of unique reads GRCh38 58.0 MB link
ENCFF201TRE ENCFF201TRE.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 55.1 MB link
ENCFF296OEM ENCFF296OEM.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 48.5 MB link
ENCFF334PYN ENCFF334PYN.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 58.7 MB link
ENCFF414LAK ENCFF414LAK.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 52.6 MB link
ENCFF916JYT ENCFF916JYT.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 45.3 MB link
ENCFF956TCU ENCFF956TCU.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 51.2 MB link
ENCFF589YEV ENCFF589YEV.fastq fastq (reads) reads 1.7 GB link
ENCFF595QMT ENCFF595QMT.fastq fastq (reads) reads 1.5 GB link
ENCFF792GRH ENCFF792GRH.fastq fastq (reads) reads 1.3 GB link
ENCFF870LAT ENCFF870LAT.fastq fastq (reads) reads 1.9 GB link
ENCFF218YIW ENCFF218YIW.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 3.0 MB link
ENCFF883BIL ENCFF883BIL.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 13.7 MB link
ENCFF976XXO ENCFF976XXO.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 3.5 MB link
ENCFF116GDA ENCFF116GDA.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 1.6 MB link
ENCFF166WFY ENCFF166WFY.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 4.2 MB link
ENCFF274ETS ENCFF274ETS.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 5.5 MB link
ENCFF593NZI ENCFF593NZI.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 2.9 MB link
ENCFF840WYN ENCFF840WYN.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 1.9 MB link
ENCFF241EPD ENCFF241EPD.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V24 gene quantifications GRCh38 9.4 MB link
ENCFF508ZYN ENCFF508ZYN.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V24 gene quantifications GRCh38 9.4 MB link
ENCFF114IYN ENCFF114IYN.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V29 gene quantifications GRCh38 10.4 MB link
ENCFF722NQY ENCFF722NQY.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V29 gene quantifications GRCh38 10.4 MB link
ENCFF406JGH ENCFF406JGH.tsv tsv (gene quantifications); assembly: hg19; genome annotation: V19 gene quantifications hg19 9.1 MB link
ENCFF624VPE ENCFF624VPE.tsv tsv (gene quantifications); assembly: hg19; genome annotation: V19 gene quantifications hg19 9.1 MB link
ENCFF289GVU ENCFF289GVU.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V24 transcript quantifications GRCh38 25.3 MB link
ENCFF603PCA ENCFF603PCA.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V24 transcript quantifications GRCh38 25.3 MB link
ENCFF123KHW ENCFF123KHW.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 27.2 MB link
ENCFF230OOR ENCFF230OOR.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 29.8 MB link
ENCFF354QUG ENCFF354QUG.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 27.2 MB link
ENCFF634OTB ENCFF634OTB.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 29.8 MB link
ENCFF145TLM ENCFF145TLM.tsv tsv (transcript quantifications); assembly: hg19; genome annotation: V19 transcript quantifications hg19 24.9 MB link
ENCFF377AGN ENCFF377AGN.tsv tsv (transcript quantifications); assembly: hg19; genome annotation: V19 transcript quantifications hg19 24.9 MB link