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ENCSR398HXV

ENCSR ENCODE
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shRNA knockdown against NONO in K562 cells followed by RNA-seq. (NONO_BGKLV19)

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

Summary

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

Overall Design

shRNA knockdown against NONO in K562 cells followed by RNA-seq. (NONO_BGKLV19)

Analysis

View Data Processing
Analysis page is available for ENCSR398HXV.

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: 86.0 GB
Assay: shRNA RNA-seq
Target: NONO
Biosample: Homo sapiens K562 expressing RNAi targeting H. sapiens NONO
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
ENCFF351XXC ENCFF351XXC.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 4.2 GB link
ENCFF380OYY ENCFF380OYY.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 3.8 GB link
ENCFF540UIX ENCFF540UIX.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 3.2 GB link
ENCFF600XRK ENCFF600XRK.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 3.5 GB link
ENCFF250ZAN ENCFF250ZAN.bam bam (alignments); assembly: GRCh38; genome annotation: V29 alignments GRCh38 3.8 GB link
ENCFF367KMV ENCFF367KMV.bam bam (alignments); assembly: GRCh38; genome annotation: V29 alignments GRCh38 4.2 GB link
ENCFF458YTV ENCFF458YTV.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 3.1 GB link
ENCFF467RJQ ENCFF467RJQ.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 3.4 GB link
ENCFF473LQQ ENCFF473LQQ.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 3.4 GB link
ENCFF687USH ENCFF687USH.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 4.1 GB link
ENCFF802XVR ENCFF802XVR.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 3.7 GB link
ENCFF979TLK ENCFF979TLK.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 3.1 GB link
ENCFF332FTS ENCFF332FTS.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V24 transcriptome alignments GRCh38 5.0 GB link
ENCFF800RGS ENCFF800RGS.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V24 transcriptome alignments GRCh38 4.8 GB link
ENCFF859ILH ENCFF859ILH.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V29 transcriptome alignments GRCh38 5.7 GB link
ENCFF995KRO ENCFF995KRO.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V29 transcriptome alignments GRCh38 5.4 GB link
ENCFF542JNI ENCFF542JNI.bam bam (transcriptome alignments); assembly: hg19; genome annotation: V19 transcriptome alignments hg19 5.0 GB link
ENCFF764PPW ENCFF764PPW.bam bam (transcriptome alignments); assembly: hg19; genome annotation: V19 transcriptome alignments hg19 4.8 GB link
ENCFF165HBY ENCFF165HBY.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 78.3 MB link
ENCFF507KCS ENCFF507KCS.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 60.9 MB link
ENCFF948JDA ENCFF948JDA.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 67.0 MB link
ENCFF966HUH ENCFF966HUH.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 70.2 MB link
ENCFF441HSA ENCFF441HSA.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V29 minus strand signal of all reads GRCh38 78.2 MB link
ENCFF494SJA ENCFF494SJA.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V29 minus strand signal of all reads GRCh38 67.1 MB link
ENCFF128VUP ENCFF128VUP.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 61.8 MB link
ENCFF214OJP ENCFF214OJP.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 68.4 MB link
ENCFF248MZR ENCFF248MZR.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 76.8 MB link
ENCFF324CAX ENCFF324CAX.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 60.7 MB link
ENCFF475CBJ ENCFF475CBJ.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 70.5 MB link
ENCFF934FSJ ENCFF934FSJ.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 66.5 MB link
ENCFF591QVO ENCFF591QVO.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 64.9 MB link
ENCFF592KYD ENCFF592KYD.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 59.7 MB link
ENCFF662LDE ENCFF662LDE.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 69.2 MB link
ENCFF830NTB ENCFF830NTB.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 56.5 MB link
ENCFF280NQA ENCFF280NQA.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 minus strand signal of unique reads GRCh38 60.1 MB link
ENCFF526VVJ ENCFF526VVJ.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 minus strand signal of unique reads GRCh38 68.1 MB link
ENCFF039XUH ENCFF039XUH.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 68.3 MB link
ENCFF066BTT ENCFF066BTT.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 64.7 MB link
ENCFF202WDU ENCFF202WDU.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 57.1 MB link
ENCFF357DDV ENCFF357DDV.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 55.7 MB link
ENCFF671UWT ENCFF671UWT.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 62.3 MB link
ENCFF698XHG ENCFF698XHG.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 59.3 MB link
ENCFF028WZP ENCFF028WZP.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 67.9 MB link
ENCFF338GSN ENCFF338GSN.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 61.8 MB link
ENCFF695LVY ENCFF695LVY.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 79.3 MB link
ENCFF805TCI ENCFF805TCI.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 71.1 MB link
ENCFF250XAW ENCFF250XAW.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V29 plus strand signal of all reads GRCh38 79.2 MB link
ENCFF892WSA ENCFF892WSA.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V29 plus strand signal of all reads GRCh38 68.0 MB link
ENCFF003JYS ENCFF003JYS.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 69.7 MB link
ENCFF228ZJZ ENCFF228ZJZ.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 71.8 MB link
ENCFF407GGR ENCFF407GGR.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 61.8 MB link
ENCFF831GJM ENCFF831GJM.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 67.4 MB link
ENCFF965WBP ENCFF965WBP.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 77.8 MB link
ENCFF966ECH ENCFF966ECH.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 62.8 MB link
ENCFF165KBZ ENCFF165KBZ.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 66.3 MB link
ENCFF198CMJ ENCFF198CMJ.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 70.7 MB link
ENCFF583LQJ ENCFF583LQJ.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 61.0 MB link
ENCFF704YKQ ENCFF704YKQ.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 57.7 MB link
ENCFF711KMS ENCFF711KMS.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 plus strand signal of unique reads GRCh38 69.6 MB link
ENCFF808RHY ENCFF808RHY.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 plus strand signal of unique reads GRCh38 61.4 MB link
ENCFF414XFA ENCFF414XFA.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 60.7 MB link
ENCFF527UBL ENCFF527UBL.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 58.5 MB link
ENCFF590UWC ENCFF590UWC.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 57.1 MB link
ENCFF646VRQ ENCFF646VRQ.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 64.1 MB link
ENCFF740AZT ENCFF740AZT.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 66.3 MB link
ENCFF907DGY ENCFF907DGY.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 69.9 MB link
ENCFF267KXL ENCFF267KXL.fastq fastq (reads) reads 2.3 GB link
ENCFF725RTN ENCFF725RTN.fastq fastq (reads) reads 2.0 GB link
ENCFF844AFL ENCFF844AFL.fastq fastq (reads) reads 2.1 GB link
ENCFF903AKL ENCFF903AKL.fastq fastq (reads) reads 2.1 GB link
ENCFF224UEU ENCFF224UEU.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 3.4 MB link
ENCFF733OPY ENCFF733OPY.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 14.8 MB link
ENCFF922VKT ENCFF922VKT.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 3.9 MB link
ENCFF122SOI ENCFF122SOI.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 1.9 MB link
ENCFF157RAI ENCFF157RAI.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 2.9 MB link
ENCFF229FIW ENCFF229FIW.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 1.7 MB link
ENCFF771CKJ ENCFF771CKJ.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 5.5 MB link
ENCFF820UHX ENCFF820UHX.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 4.2 MB link
ENCFF115WLK ENCFF115WLK.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V24 gene quantifications GRCh38 9.4 MB link
ENCFF118QUJ ENCFF118QUJ.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V24 gene quantifications GRCh38 9.4 MB link
ENCFF058NKA ENCFF058NKA.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V29 gene quantifications GRCh38 10.4 MB link
ENCFF683ORS ENCFF683ORS.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V29 gene quantifications GRCh38 10.4 MB link
ENCFF190LAA ENCFF190LAA.tsv tsv (gene quantifications); assembly: hg19; genome annotation: V19 gene quantifications hg19 9.1 MB link
ENCFF329GND ENCFF329GND.tsv tsv (gene quantifications); assembly: hg19; genome annotation: V19 gene quantifications hg19 9.1 MB link
ENCFF015GWF ENCFF015GWF.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V24 transcript quantifications GRCh38 25.3 MB link
ENCFF597PKQ ENCFF597PKQ.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V24 transcript quantifications GRCh38 25.3 MB link
ENCFF045YYP ENCFF045YYP.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 27.3 MB link
ENCFF052JOU ENCFF052JOU.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 29.8 MB link
ENCFF099HJZ ENCFF099HJZ.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 27.3 MB link
ENCFF574PFZ ENCFF574PFZ.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 29.8 MB link
ENCFF451IYU ENCFF451IYU.tsv tsv (transcript quantifications); assembly: hg19; genome annotation: V19 transcript quantifications hg19 24.9 MB link
ENCFF558IXW ENCFF558IXW.tsv tsv (transcript quantifications); assembly: hg19; genome annotation: V19 transcript quantifications hg19 24.9 MB link