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ENCSR082UWF

ENCSR ENCODE
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RNA-seq on K562 cells treated with an shRNA knockdown against STIP1. (STIP1_BGKLV24_B)

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

Summary

shRNA RNA-seq of STIP1 in Homo sapiens K562 expressing RNAi targeting H. sapiens STIP1

Overall Design

RNA-seq on K562 cells treated with an shRNA knockdown against STIP1. (STIP1_BGKLV24_B)

Analysis

View Data Processing
Analysis page is available for ENCSR082UWF.

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: 137.0 GB
Assay: shRNA RNA-seq
Target: STIP1
Biosample: Homo sapiens K562 expressing RNAi targeting H. sapiens STIP1
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
ENCFF396QZZ ENCFF396QZZ.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 6.2 GB link
ENCFF466BYB ENCFF466BYB.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 7.3 GB link
ENCFF677XLN ENCFF677XLN.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 6.0 GB link
ENCFF802SMN ENCFF802SMN.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 5.2 GB link
ENCFF249HNP ENCFF249HNP.bam bam (alignments); assembly: GRCh38; genome annotation: V29 alignments GRCh38 7.3 GB link
ENCFF712REF ENCFF712REF.bam bam (alignments); assembly: GRCh38; genome annotation: V29 alignments GRCh38 6.2 GB link
ENCFF142LOB ENCFF142LOB.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 6.1 GB link
ENCFF151YNB ENCFF151YNB.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 7.1 GB link
ENCFF543LNI ENCFF543LNI.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 5.1 GB link
ENCFF783EZE ENCFF783EZE.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 5.1 GB link
ENCFF804XHD ENCFF804XHD.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 5.9 GB link
ENCFF939VXA ENCFF939VXA.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 5.9 GB link
ENCFF287PZZ ENCFF287PZZ.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V24 transcriptome alignments GRCh38 6.6 GB link
ENCFF295ILB ENCFF295ILB.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V24 transcriptome alignments GRCh38 7.6 GB link
ENCFF672YJD ENCFF672YJD.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V29 transcriptome alignments GRCh38 7.4 GB link
ENCFF765MIB ENCFF765MIB.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V29 transcriptome alignments GRCh38 8.6 GB link
ENCFF256CBG ENCFF256CBG.bam bam (transcriptome alignments); assembly: hg19; genome annotation: V19 transcriptome alignments hg19 7.6 GB link
ENCFF911QYF ENCFF911QYF.bam bam (transcriptome alignments); assembly: hg19; genome annotation: V19 transcriptome alignments hg19 6.5 GB link
ENCFF014GXU ENCFF014GXU.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 85.5 MB link
ENCFF038HEI ENCFF038HEI.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 95.3 MB link
ENCFF398GBE ENCFF398GBE.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 111.2 MB link
ENCFF938GGC ENCFF938GGC.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 99.4 MB link
ENCFF120UMY ENCFF120UMY.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V29 minus strand signal of all reads GRCh38 111.2 MB link
ENCFF861XZX ENCFF861XZX.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V29 minus strand signal of all reads GRCh38 99.4 MB link
ENCFF012EYZ ENCFF012EYZ.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 110.1 MB link
ENCFF276IAT ENCFF276IAT.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 97.8 MB link
ENCFF284WNJ ENCFF284WNJ.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 97.7 MB link
ENCFF419OZO ENCFF419OZO.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 83.1 MB link
ENCFF566HFT ENCFF566HFT.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 92.3 MB link
ENCFF796ZZY ENCFF796ZZY.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 87.5 MB link
ENCFF359WKO ENCFF359WKO.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 89.1 MB link
ENCFF424YGI ENCFF424YGI.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 79.5 MB link
ENCFF493HBD ENCFF493HBD.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 87.0 MB link
ENCFF701SDU ENCFF701SDU.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 97.5 MB link
ENCFF136NGS ENCFF136NGS.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 minus strand signal of unique reads GRCh38 86.0 MB link
ENCFF398XKJ ENCFF398XKJ.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 minus strand signal of unique reads GRCh38 97.5 MB link
ENCFF062UIG ENCFF062UIG.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 79.9 MB link
ENCFF097LCD ENCFF097LCD.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 97.3 MB link
ENCFF539PZN ENCFF539PZN.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 75.5 MB link
ENCFF624LDA ENCFF624LDA.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 88.6 MB link
ENCFF696AJS ENCFF696AJS.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 85.3 MB link
ENCFF975NVW ENCFF975NVW.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 86.7 MB link
ENCFF317BRO ENCFF317BRO.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 86.5 MB link
ENCFF445GSX ENCFF445GSX.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 100.7 MB link
ENCFF461BQM ENCFF461BQM.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 112.6 MB link
ENCFF876TRQ ENCFF876TRQ.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 96.4 MB link
ENCFF354KOC ENCFF354KOC.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V29 plus strand signal of all reads GRCh38 100.7 MB link
ENCFF822KWP ENCFF822KWP.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V29 plus strand signal of all reads GRCh38 112.6 MB link
ENCFF447HTS ENCFF447HTS.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 99.4 MB link
ENCFF569RZS ENCFF569RZS.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 84.7 MB link
ENCFF907SDL ENCFF907SDL.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 93.9 MB link
ENCFF911XVW ENCFF911XVW.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 99.1 MB link
ENCFF922YML ENCFF922YML.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 89.1 MB link
ENCFF969AGE ENCFF969AGE.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 111.5 MB link
ENCFF028RML ENCFF028RML.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 81.2 MB link
ENCFF536UTW ENCFF536UTW.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 99.7 MB link
ENCFF908DEO ENCFF908DEO.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 90.8 MB link
ENCFF961ORE ENCFF961ORE.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 89.0 MB link
ENCFF231FXR ENCFF231FXR.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 plus strand signal of unique reads GRCh38 99.6 MB link
ENCFF610XKE ENCFF610XKE.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 plus strand signal of unique reads GRCh38 88.1 MB link
ENCFF040JUJ ENCFF040JUJ.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 89.0 MB link
ENCFF108EEW ENCFF108EEW.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 87.5 MB link
ENCFF356KOS ENCFF356KOS.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 90.8 MB link
ENCFF597ZWI ENCFF597ZWI.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 99.6 MB link
ENCFF801DMJ ENCFF801DMJ.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 77.6 MB link
ENCFF973PLS ENCFF973PLS.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 81.9 MB link
ENCFF289HLB ENCFF289HLB.fastq fastq (reads) reads 3.4 GB link
ENCFF489IZZ ENCFF489IZZ.fastq fastq (reads) reads 3.9 GB link
ENCFF533GLS ENCFF533GLS.fastq fastq (reads) reads 3.3 GB link
ENCFF702NXP ENCFF702NXP.fastq fastq (reads) reads 4.0 GB link
ENCFF066JOO ENCFF066JOO.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 3.7 MB link
ENCFF550GFC ENCFF550GFC.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 4.5 MB link
ENCFF636KGD ENCFF636KGD.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 16.1 MB link
ENCFF049ALV ENCFF049ALV.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 1.7 MB link
ENCFF230BFU ENCFF230BFU.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 4.3 MB link
ENCFF806FRX ENCFF806FRX.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 2.0 MB link
ENCFF913ZGU ENCFF913ZGU.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 2.7 MB link
ENCFF933ATM ENCFF933ATM.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 5.6 MB link
ENCFF259CCL ENCFF259CCL.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V24 gene quantifications GRCh38 9.5 MB link
ENCFF323BUZ ENCFF323BUZ.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V24 gene quantifications GRCh38 9.5 MB link
ENCFF518QPE ENCFF518QPE.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V29 gene quantifications GRCh38 10.4 MB link
ENCFF751CLQ ENCFF751CLQ.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V29 gene quantifications GRCh38 10.4 MB link
ENCFF429JJE ENCFF429JJE.tsv tsv (gene quantifications); assembly: hg19; genome annotation: V19 gene quantifications hg19 9.1 MB link
ENCFF964LLT ENCFF964LLT.tsv tsv (gene quantifications); assembly: hg19; genome annotation: V19 gene quantifications hg19 9.1 MB link
ENCFF662ELS ENCFF662ELS.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V24 transcript quantifications GRCh38 25.4 MB link
ENCFF790LUK ENCFF790LUK.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V24 transcript quantifications GRCh38 25.4 MB link
ENCFF443NTP ENCFF443NTP.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 29.9 MB link
ENCFF652NUY ENCFF652NUY.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 29.9 MB link
ENCFF803TIU ENCFF803TIU.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 27.4 MB link
ENCFF876YJQ ENCFF876YJQ.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 27.4 MB link
ENCFF371YBF ENCFF371YBF.tsv tsv (transcript quantifications); assembly: hg19; genome annotation: V19 transcript quantifications hg19 25.0 MB link
ENCFF989WPD ENCFF989WPD.tsv tsv (transcript quantifications); assembly: hg19; genome annotation: V19 transcript quantifications hg19 25.0 MB link