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ENCSR639LKS

ENCSR ENCODE
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shRNA knockdown against FKBP4 in HepG2 cells followed by RNA-seq. (FKBP4_BGHLV17)

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

Summary

shRNA RNA-seq of FKBP4 in Homo sapiens HepG2 expressing RNAi targeting H. sapiens FKBP4

Overall Design

shRNA knockdown against FKBP4 in HepG2 cells followed by RNA-seq. (FKBP4_BGHLV17)

Analysis

View Data Processing
Analysis page is available for ENCSR639LKS.

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: 97.0 GB
Assay: shRNA RNA-seq
Target: FKBP4
Biosample: Homo sapiens HepG2 expressing RNAi targeting H. sapiens FKBP4
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
ENCFF349HFT ENCFF349HFT.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 6.0 GB link
ENCFF764KJW ENCFF764KJW.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 3.1 GB link
ENCFF801LOD ENCFF801LOD.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 2.6 GB link
ENCFF819IHE ENCFF819IHE.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 5.1 GB link
ENCFF043BHT ENCFF043BHT.bam bam (alignments); assembly: GRCh38; genome annotation: V29 alignments GRCh38 3.1 GB link
ENCFF898HLC ENCFF898HLC.bam bam (alignments); assembly: GRCh38; genome annotation: V29 alignments GRCh38 6.0 GB link
ENCFF257YRE ENCFF257YRE.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 5.8 GB link
ENCFF377GZT ENCFF377GZT.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 5.0 GB link
ENCFF635BOE ENCFF635BOE.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 2.6 GB link
ENCFF655OGA ENCFF655OGA.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 2.6 GB link
ENCFF796LUO ENCFF796LUO.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 5.0 GB link
ENCFF982ALW ENCFF982ALW.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 3.0 GB link
ENCFF314ETQ ENCFF314ETQ.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V24 transcriptome alignments GRCh38 3.6 GB link
ENCFF727DAM ENCFF727DAM.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V24 transcriptome alignments GRCh38 7.3 GB link
ENCFF300XTR ENCFF300XTR.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V29 transcriptome alignments GRCh38 4.1 GB link
ENCFF495DZW ENCFF495DZW.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V29 transcriptome alignments GRCh38 8.1 GB link
ENCFF543ZKR ENCFF543ZKR.bam bam (transcriptome alignments); assembly: hg19; genome annotation: V19 transcriptome alignments hg19 3.6 GB link
ENCFF886PXP ENCFF886PXP.bam bam (transcriptome alignments); assembly: hg19; genome annotation: V19 transcriptome alignments hg19 7.2 GB link
ENCFF212DSP ENCFF212DSP.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 83.3 MB link
ENCFF301MLF ENCFF301MLF.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 61.9 MB link
ENCFF468CWO ENCFF468CWO.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 92.2 MB link
ENCFF846LVD ENCFF846LVD.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 55.9 MB link
ENCFF698KSC ENCFF698KSC.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V29 minus strand signal of all reads GRCh38 61.9 MB link
ENCFF820ZFG ENCFF820ZFG.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V29 minus strand signal of all reads GRCh38 92.2 MB link
ENCFF004PMF ENCFF004PMF.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 92.2 MB link
ENCFF113BCS ENCFF113BCS.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 53.7 MB link
ENCFF446FQD ENCFF446FQD.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 56.3 MB link
ENCFF761ZSI ENCFF761ZSI.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 61.2 MB link
ENCFF778TSO ENCFF778TSO.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 84.5 MB link
ENCFF811YVN ENCFF811YVN.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 81.1 MB link
ENCFF197FBR ENCFF197FBR.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 77.8 MB link
ENCFF482ABW ENCFF482ABW.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 52.7 MB link
ENCFF791HCK ENCFF791HCK.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 83.8 MB link
ENCFF815ZSZ ENCFF815ZSZ.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 56.2 MB link
ENCFF482EXB ENCFF482EXB.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 minus strand signal of unique reads GRCh38 56.2 MB link
ENCFF994ZIZ ENCFF994ZIZ.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 minus strand signal of unique reads GRCh38 83.8 MB link
ENCFF028VGL ENCFF028VGL.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 76.4 MB link
ENCFF293JCJ ENCFF293JCJ.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 79.0 MB link
ENCFF342NSA ENCFF342NSA.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 83.5 MB link
ENCFF466OEE ENCFF466OEE.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 52.5 MB link
ENCFF473JEF ENCFF473JEF.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 56.2 MB link
ENCFF710KYG ENCFF710KYG.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 49.7 MB link
ENCFF067HFG ENCFF067HFG.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 94.0 MB link
ENCFF193SLO ENCFF193SLO.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 85.1 MB link
ENCFF334AAT ENCFF334AAT.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 57.0 MB link
ENCFF943FVL ENCFF943FVL.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 63.2 MB link
ENCFF310JTF ENCFF310JTF.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V29 plus strand signal of all reads GRCh38 94.1 MB link
ENCFF840XZX ENCFF840XZX.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V29 plus strand signal of all reads GRCh38 63.2 MB link
ENCFF075KAE ENCFF075KAE.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 55.0 MB link
ENCFF117ZYM ENCFF117ZYM.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 62.2 MB link
ENCFF280PUO ENCFF280PUO.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 86.3 MB link
ENCFF568KHX ENCFF568KHX.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 57.5 MB link
ENCFF603WBK ENCFF603WBK.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 93.9 MB link
ENCFF741KMJ ENCFF741KMJ.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 82.9 MB link
ENCFF303AED ENCFF303AED.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 79.9 MB link
ENCFF480NVS ENCFF480NVS.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 57.7 MB link
ENCFF778UNC ENCFF778UNC.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 54.1 MB link
ENCFF844RJG ENCFF844RJG.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 86.2 MB link
ENCFF362HQF ENCFF362HQF.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 plus strand signal of unique reads GRCh38 86.3 MB link
ENCFF781GCC ENCFF781GCC.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 plus strand signal of unique reads GRCh38 57.7 MB link
ENCFF079VNE ENCFF079VNE.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 51.2 MB link
ENCFF460IKC ENCFF460IKC.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 54.0 MB link
ENCFF540QCM ENCFF540QCM.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 81.3 MB link
ENCFF656RLW ENCFF656RLW.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 57.8 MB link
ENCFF965OQP ENCFF965OQP.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 78.9 MB link
ENCFF976BBU ENCFF976BBU.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 86.0 MB link
ENCFF071HGB ENCFF071HGB.fastq fastq (reads) reads 3.2 GB link
ENCFF107HUY ENCFF107HUY.fastq fastq (reads) reads 1.6 GB link
ENCFF663YGQ ENCFF663YGQ.fastq fastq (reads) reads 3.3 GB link
ENCFF796SHO ENCFF796SHO.fastq fastq (reads) reads 1.7 GB link
ENCFF114VFW ENCFF114VFW.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 3.0 MB link
ENCFF280RZT ENCFF280RZT.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 15.4 MB link
ENCFF658FPH ENCFF658FPH.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 3.6 MB link
ENCFF199XRZ ENCFF199XRZ.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 1.9 MB link
ENCFF355AAY ENCFF355AAY.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 5.6 MB link
ENCFF615BYF ENCFF615BYF.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 1.8 MB link
ENCFF762SBM ENCFF762SBM.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 2.8 MB link
ENCFF841RAK ENCFF841RAK.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 4.2 MB link
ENCFF761XGP ENCFF761XGP.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V24 gene quantifications GRCh38 9.4 MB link
ENCFF869JWN ENCFF869JWN.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V24 gene quantifications GRCh38 9.4 MB link
ENCFF234REI ENCFF234REI.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V29 gene quantifications GRCh38 10.4 MB link
ENCFF462DOK ENCFF462DOK.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V29 gene quantifications GRCh38 10.4 MB link
ENCFF333XHH ENCFF333XHH.tsv tsv (gene quantifications); assembly: hg19; genome annotation: V19 gene quantifications hg19 9.1 MB link
ENCFF590SVM ENCFF590SVM.tsv tsv (gene quantifications); assembly: hg19; genome annotation: V19 gene quantifications hg19 9.1 MB link
ENCFF232XAN ENCFF232XAN.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V24 transcript quantifications GRCh38 25.3 MB link
ENCFF624ADG ENCFF624ADG.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V24 transcript quantifications GRCh38 25.3 MB link
ENCFF022ZAZ ENCFF022ZAZ.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 29.8 MB link
ENCFF435EXU ENCFF435EXU.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 27.2 MB link
ENCFF959ZEM ENCFF959ZEM.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 27.4 MB link
ENCFF980XPR ENCFF980XPR.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 29.7 MB link
ENCFF552BYK ENCFF552BYK.tsv tsv (transcript quantifications); assembly: hg19; genome annotation: V19 transcript quantifications hg19 24.9 MB link
ENCFF632HXZ ENCFF632HXZ.tsv tsv (transcript quantifications); assembly: hg19; genome annotation: V19 transcript quantifications hg19 24.9 MB link