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ENCSR210KJB

ENCSR ENCODE
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shRNA knockdown against RRP9 in K562 cells followed by RNA-seq. (RRP9_BGKLV19)

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

Summary

shRNA RNA-seq of RRP9 in Homo sapiens K562 expressing RNAi targeting H. sapiens RRP9

Overall Design

shRNA knockdown against RRP9 in K562 cells followed by RNA-seq. (RRP9_BGKLV19)

Analysis

View Data Processing
Analysis page is available for ENCSR210KJB.

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: 87.4 GB
Assay: shRNA RNA-seq
Target: RRP9
Biosample: Homo sapiens K562 expressing RNAi targeting H. sapiens RRP9
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
ENCFF370FDT ENCFF370FDT.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 4.1 GB link
ENCFF373FWY ENCFF373FWY.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 4.0 GB link
ENCFF526TMS ENCFF526TMS.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 3.2 GB link
ENCFF750ECA ENCFF750ECA.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 3.3 GB link
ENCFF357ADB ENCFF357ADB.bam bam (alignments); assembly: GRCh38; genome annotation: V29 alignments GRCh38 4.1 GB link
ENCFF718XKT ENCFF718XKT.bam bam (alignments); assembly: GRCh38; genome annotation: V29 alignments GRCh38 4.0 GB link
ENCFF306ATN ENCFF306ATN.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 3.8 GB link
ENCFF453RUA ENCFF453RUA.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 3.2 GB link
ENCFF708UCZ ENCFF708UCZ.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 3.2 GB link
ENCFF775CLV ENCFF775CLV.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 3.9 GB link
ENCFF852NOR ENCFF852NOR.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 3.2 GB link
ENCFF943DLA ENCFF943DLA.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 3.2 GB link
ENCFF402DPG ENCFF402DPG.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V24 transcriptome alignments GRCh38 5.0 GB link
ENCFF436BNF ENCFF436BNF.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V24 transcriptome alignments GRCh38 5.3 GB link
ENCFF336PUP ENCFF336PUP.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V29 transcriptome alignments GRCh38 5.7 GB link
ENCFF542YQH ENCFF542YQH.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V29 transcriptome alignments GRCh38 6.0 GB link
ENCFF084ITS ENCFF084ITS.bam bam (transcriptome alignments); assembly: hg19; genome annotation: V19 transcriptome alignments hg19 5.2 GB link
ENCFF884XIE ENCFF884XIE.bam bam (transcriptome alignments); assembly: hg19; genome annotation: V19 transcriptome alignments hg19 5.0 GB link
ENCFF056KOZ ENCFF056KOZ.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 69.0 MB link
ENCFF272JZW ENCFF272JZW.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 62.6 MB link
ENCFF595HHW ENCFF595HHW.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 71.1 MB link
ENCFF969FIV ENCFF969FIV.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 64.4 MB link
ENCFF487QCV ENCFF487QCV.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V29 minus strand signal of all reads GRCh38 69.0 MB link
ENCFF717ZSO ENCFF717ZSO.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V29 minus strand signal of all reads GRCh38 71.0 MB link
ENCFF072LRO ENCFF072LRO.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 63.9 MB link
ENCFF119KNQ ENCFF119KNQ.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 62.4 MB link
ENCFF170ZMY ENCFF170ZMY.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 70.2 MB link
ENCFF578YOF ENCFF578YOF.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 65.4 MB link
ENCFF623HEL ENCFF623HEL.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 68.8 MB link
ENCFF705SXO ENCFF705SXO.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 63.4 MB link
ENCFF070AFP ENCFF070AFP.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 58.5 MB link
ENCFF345JOD ENCFF345JOD.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 63.5 MB link
ENCFF366SJK ENCFF366SJK.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 61.4 MB link
ENCFF594SPZ ENCFF594SPZ.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 60.2 MB link
ENCFF019EYX ENCFF019EYX.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 minus strand signal of unique reads GRCh38 63.0 MB link
ENCFF625YDA ENCFF625YDA.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 minus strand signal of unique reads GRCh38 61.9 MB link
ENCFF050RNX ENCFF050RNX.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 60.4 MB link
ENCFF098HBF ENCFF098HBF.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 61.9 MB link
ENCFF343LQR ENCFF343LQR.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 58.0 MB link
ENCFF463OEH ENCFF463OEH.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 63.3 MB link
ENCFF806CKX ENCFF806CKX.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 58.4 MB link
ENCFF928NNX ENCFF928NNX.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 59.2 MB link
ENCFF009SKB ENCFF009SKB.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 70.1 MB link
ENCFF508ORM ENCFF508ORM.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 63.5 MB link
ENCFF716AMC ENCFF716AMC.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 65.4 MB link
ENCFF936NIH ENCFF936NIH.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 72.2 MB link
ENCFF044OJM ENCFF044OJM.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V29 plus strand signal of all reads GRCh38 72.1 MB link
ENCFF121CAE ENCFF121CAE.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V29 plus strand signal of all reads GRCh38 70.1 MB link
ENCFF010CMZ ENCFF010CMZ.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 69.8 MB link
ENCFF052YJZ ENCFF052YJZ.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 71.3 MB link
ENCFF260VUH ENCFF260VUH.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 63.8 MB link
ENCFF670GWE ENCFF670GWE.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 64.8 MB link
ENCFF940BIE ENCFF940BIE.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 66.7 MB link
ENCFF950KTW ENCFF950KTW.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 65.2 MB link
ENCFF467ALM ENCFF467ALM.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 61.6 MB link
ENCFF758FII ENCFF758FII.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 62.8 MB link
ENCFF842IKN ENCFF842IKN.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 59.9 MB link
ENCFF932PRH ENCFF932PRH.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 65.0 MB link
ENCFF189UAR ENCFF189UAR.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 plus strand signal of unique reads GRCh38 63.3 MB link
ENCFF261MUU ENCFF261MUU.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 plus strand signal of unique reads GRCh38 64.6 MB link
ENCFF197OQZ ENCFF197OQZ.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 59.8 MB link
ENCFF281XFJ ENCFF281XFJ.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 60.2 MB link
ENCFF300YGP ENCFF300YGP.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 65.0 MB link
ENCFF336YGK ENCFF336YGK.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 63.5 MB link
ENCFF485BWN ENCFF485BWN.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 60.8 MB link
ENCFF829IXC ENCFF829IXC.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 62.0 MB link
ENCFF044DKC ENCFF044DKC.fastq fastq (reads) reads 2.1 GB link
ENCFF288GAY ENCFF288GAY.fastq fastq (reads) reads 2.2 GB link
ENCFF648ZMK ENCFF648ZMK.fastq fastq (reads) reads 2.2 GB link
ENCFF665XYO ENCFF665XYO.fastq fastq (reads) reads 2.1 GB link
ENCFF007FYS ENCFF007FYS.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 3.9 MB link
ENCFF197LGC ENCFF197LGC.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 14.6 MB link
ENCFF830OTU ENCFF830OTU.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 3.4 MB link
ENCFF078VJR ENCFF078VJR.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 2.9 MB link
ENCFF362VKN ENCFF362VKN.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 1.9 MB link
ENCFF593MYK ENCFF593MYK.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 4.2 MB link
ENCFF771GYV ENCFF771GYV.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 1.8 MB link
ENCFF855LGZ ENCFF855LGZ.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 5.5 MB link
ENCFF349DGX ENCFF349DGX.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V24 gene quantifications GRCh38 9.4 MB link
ENCFF439WJA ENCFF439WJA.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V24 gene quantifications GRCh38 9.4 MB link
ENCFF258TLZ ENCFF258TLZ.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V29 gene quantifications GRCh38 10.4 MB link
ENCFF412EBR ENCFF412EBR.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V29 gene quantifications GRCh38 10.4 MB link
ENCFF060VTF ENCFF060VTF.tsv tsv (gene quantifications); assembly: hg19; genome annotation: V19 gene quantifications hg19 9.1 MB link
ENCFF079UMS ENCFF079UMS.tsv tsv (gene quantifications); assembly: hg19; genome annotation: V19 gene quantifications hg19 9.1 MB link
ENCFF159ZNZ ENCFF159ZNZ.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V24 transcript quantifications GRCh38 25.3 MB link
ENCFF527VUT ENCFF527VUT.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V24 transcript quantifications GRCh38 25.3 MB link
ENCFF139QLC ENCFF139QLC.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 27.3 MB link
ENCFF539UFL ENCFF539UFL.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 29.8 MB link
ENCFF897NVL ENCFF897NVL.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 27.3 MB link
ENCFF999BYI ENCFF999BYI.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 29.8 MB link
ENCFF061FRJ ENCFF061FRJ.tsv tsv (transcript quantifications); assembly: hg19; genome annotation: V19 transcript quantifications hg19 24.9 MB link
ENCFF361CKX ENCFF361CKX.tsv tsv (transcript quantifications); assembly: hg19; genome annotation: V19 transcript quantifications hg19 24.9 MB link