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ENCSR112YTD

ENCSR ENCODE
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RNA-seq on K562 cells treated with an shRNA knockdown against SLBP. (SLBP_BGKLV24)

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

Summary

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

Overall Design

RNA-seq on K562 cells treated with an shRNA knockdown against SLBP. (SLBP_BGKLV24)

Analysis

View Data Processing
Analysis page is available for ENCSR112YTD.

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: 71.5 GB
Assay: shRNA RNA-seq
Target: SLBP
Biosample: Homo sapiens K562 expressing RNAi targeting H. sapiens SLBP
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
ENCFF260JUT ENCFF260JUT.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 3.3 GB link
ENCFF390ZJF ENCFF390ZJF.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 2.7 GB link
ENCFF789RAG ENCFF789RAG.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 2.9 GB link
ENCFF840EFF ENCFF840EFF.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 3.5 GB link
ENCFF603BJD ENCFF603BJD.bam bam (alignments); assembly: GRCh38; genome annotation: V29 alignments GRCh38 3.5 GB link
ENCFF645SBL ENCFF645SBL.bam bam (alignments); assembly: GRCh38; genome annotation: V29 alignments GRCh38 3.3 GB link
ENCFF215RZE ENCFF215RZE.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 2.9 GB link
ENCFF371GND ENCFF371GND.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 2.7 GB link
ENCFF569ZVG ENCFF569ZVG.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 2.7 GB link
ENCFF579RKL ENCFF579RKL.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 3.2 GB link
ENCFF741VFO ENCFF741VFO.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 3.4 GB link
ENCFF802JXU ENCFF802JXU.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 2.9 GB link
ENCFF799MEY ENCFF799MEY.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V24 transcriptome alignments GRCh38 3.6 GB link
ENCFF906NYG ENCFF906NYG.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V24 transcriptome alignments GRCh38 4.0 GB link
ENCFF352DUB ENCFF352DUB.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V29 transcriptome alignments GRCh38 4.1 GB link
ENCFF865PBA ENCFF865PBA.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V29 transcriptome alignments GRCh38 4.5 GB link
ENCFF221OYO ENCFF221OYO.bam bam (transcriptome alignments); assembly: hg19; genome annotation: V19 transcriptome alignments hg19 3.6 GB link
ENCFF999KVU ENCFF999KVU.bam bam (transcriptome alignments); assembly: hg19; genome annotation: V19 transcriptome alignments hg19 3.9 GB link
ENCFF222LJD ENCFF222LJD.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 69.2 MB link
ENCFF516HXU ENCFF516HXU.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 78.5 MB link
ENCFF817LJY ENCFF817LJY.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 76.7 MB link
ENCFF888CAR ENCFF888CAR.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 70.1 MB link
ENCFF064ZZS ENCFF064ZZS.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V29 minus strand signal of all reads GRCh38 76.7 MB link
ENCFF878OYK ENCFF878OYK.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V29 minus strand signal of all reads GRCh38 78.4 MB link
ENCFF200UXN ENCFF200UXN.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 77.4 MB link
ENCFF212KXZ ENCFF212KXZ.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 75.2 MB link
ENCFF358FVA ENCFF358FVA.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 69.8 MB link
ENCFF358SKF ENCFF358SKF.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 65.2 MB link
ENCFF671QCH ENCFF671QCH.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 70.7 MB link
ENCFF710YMV ENCFF710YMV.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 66.2 MB link
ENCFF198BFB ENCFF198BFB.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 64.0 MB link
ENCFF309GOJ ENCFF309GOJ.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 67.9 MB link
ENCFF511VSI ENCFF511VSI.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 67.8 MB link
ENCFF664FAH ENCFF664FAH.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 64.9 MB link
ENCFF218MPA ENCFF218MPA.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 minus strand signal of unique reads GRCh38 66.8 MB link
ENCFF542EYF ENCFF542EYF.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 minus strand signal of unique reads GRCh38 68.8 MB link
ENCFF085DGD ENCFF085DGD.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 67.5 MB link
ENCFF313DGA ENCFF313DGA.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 60.2 MB link
ENCFF379DBT ENCFF379DBT.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 60.8 MB link
ENCFF513WDJ ENCFF513WDJ.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 64.4 MB link
ENCFF637WMS ENCFF637WMS.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 68.7 MB link
ENCFF674VJU ENCFF674VJU.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 65.2 MB link
ENCFF299VYN ENCFF299VYN.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 70.9 MB link
ENCFF541CKJ ENCFF541CKJ.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 70.1 MB link
ENCFF544CQI ENCFF544CQI.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 77.7 MB link
ENCFF916EVY ENCFF916EVY.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 79.4 MB link
ENCFF419TXS ENCFF419TXS.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V29 plus strand signal of all reads GRCh38 79.4 MB link
ENCFF492YNE ENCFF492YNE.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V29 plus strand signal of all reads GRCh38 77.7 MB link
ENCFF162PLA ENCFF162PLA.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 71.2 MB link
ENCFF243TRW ENCFF243TRW.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 71.9 MB link
ENCFF586MXV ENCFF586MXV.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 76.3 MB link
ENCFF953UEI ENCFF953UEI.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 78.4 MB link
ENCFF972QBV ENCFF972QBV.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 66.6 MB link
ENCFF984WAP ENCFF984WAP.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 67.4 MB link
ENCFF242MBJ ENCFF242MBJ.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 69.5 MB link
ENCFF445AYD ENCFF445AYD.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 66.2 MB link
ENCFF656DYW ENCFF656DYW.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 65.5 MB link
ENCFF860HSI ENCFF860HSI.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 69.6 MB link
ENCFF222UPB ENCFF222UPB.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 plus strand signal of unique reads GRCh38 70.4 MB link
ENCFF306ULN ENCFF306ULN.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 plus strand signal of unique reads GRCh38 68.5 MB link
ENCFF065GZV ENCFF065GZV.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 69.4 MB link
ENCFF181VEZ ENCFF181VEZ.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 70.4 MB link
ENCFF205NIL ENCFF205NIL.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 62.0 MB link
ENCFF458IHG ENCFF458IHG.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 66.9 MB link
ENCFF505ZBB ENCFF505ZBB.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 66.2 MB link
ENCFF973MDK ENCFF973MDK.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 62.5 MB link
ENCFF122UFL ENCFF122UFL.fastq fastq (reads) reads 1.8 GB link
ENCFF519RFX ENCFF519RFX.fastq fastq (reads) reads 1.8 GB link
ENCFF654RRJ ENCFF654RRJ.fastq fastq (reads) reads 1.7 GB link
ENCFF994PGX ENCFF994PGX.fastq fastq (reads) reads 1.9 GB link
ENCFF346XLY ENCFF346XLY.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 3.3 MB link
ENCFF643OCB ENCFF643OCB.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 3.1 MB link
ENCFF959EDR ENCFF959EDR.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 13.1 MB link
ENCFF075HYV ENCFF075HYV.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 5.5 MB link
ENCFF239RGX ENCFF239RGX.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 4.2 MB link
ENCFF614YWP ENCFF614YWP.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 2.9 MB link
ENCFF680SRB ENCFF680SRB.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 1.8 MB link
ENCFF746HQF ENCFF746HQF.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 1.9 MB link
ENCFF073FLU ENCFF073FLU.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V24 gene quantifications GRCh38 9.4 MB link
ENCFF613PLF ENCFF613PLF.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V24 gene quantifications GRCh38 9.4 MB link
ENCFF529LXV ENCFF529LXV.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V29 gene quantifications GRCh38 10.4 MB link
ENCFF746ZYT ENCFF746ZYT.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V29 gene quantifications GRCh38 10.4 MB link
ENCFF543LCZ ENCFF543LCZ.tsv tsv (gene quantifications); assembly: hg19; genome annotation: V19 gene quantifications hg19 9.1 MB link
ENCFF616DAQ ENCFF616DAQ.tsv tsv (gene quantifications); assembly: hg19; genome annotation: V19 gene quantifications hg19 9.1 MB link
ENCFF153JAE ENCFF153JAE.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V24 transcript quantifications GRCh38 25.3 MB link
ENCFF429SZM ENCFF429SZM.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V24 transcript quantifications GRCh38 25.3 MB link
ENCFF139IZU ENCFF139IZU.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 29.8 MB link
ENCFF348NXB ENCFF348NXB.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 29.8 MB link
ENCFF448HII ENCFF448HII.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 27.3 MB link
ENCFF754IOS ENCFF754IOS.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 27.3 MB link
ENCFF193ZVT ENCFF193ZVT.tsv tsv (transcript quantifications); assembly: hg19; genome annotation: V19 transcript quantifications hg19 24.9 MB link
ENCFF594BFW ENCFF594BFW.tsv tsv (transcript quantifications); assembly: hg19; genome annotation: V19 transcript quantifications hg19 24.9 MB link