← All datasets

ENCSR118KUN

ENCSR ENCODE
Export SRA CSV View on ENCODE

RNA-seq on HepG2 cells treated with an shRNA knockdown against DKC1. (DKC1_BGHLV31)

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

Summary

shRNA RNA-seq of DKC1 in Homo sapiens HepG2 expressing RNAi targeting H. sapiens DKC1

Overall Design

RNA-seq on HepG2 cells treated with an shRNA knockdown against DKC1. (DKC1_BGHLV31)

Analysis

View Data Processing
Analysis page is available for ENCSR118KUN.

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: 84.9 GB
Assay: shRNA RNA-seq
Target: DKC1
Biosample: Homo sapiens HepG2 expressing RNAi targeting H. sapiens DKC1
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
ENCFF275TGS ENCFF275TGS.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 3.8 GB link
ENCFF331YCN ENCFF331YCN.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 3.0 GB link
ENCFF368WCW ENCFF368WCW.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 3.7 GB link
ENCFF557DJT ENCFF557DJT.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 3.0 GB link
ENCFF238EAM ENCFF238EAM.bam bam (alignments); assembly: GRCh38; genome annotation: V29 alignments GRCh38 3.7 GB link
ENCFF538HEL ENCFF538HEL.bam bam (alignments); assembly: GRCh38; genome annotation: V29 alignments GRCh38 3.8 GB link
ENCFF006DCI ENCFF006DCI.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 2.9 GB link
ENCFF265NMT ENCFF265NMT.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 2.9 GB link
ENCFF454QYL ENCFF454QYL.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 3.6 GB link
ENCFF572VRD ENCFF572VRD.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 3.5 GB link
ENCFF688YAP ENCFF688YAP.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 2.9 GB link
ENCFF712RNK ENCFF712RNK.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 2.9 GB link
ENCFF121PKE ENCFF121PKE.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V24 transcriptome alignments GRCh38 5.4 GB link
ENCFF418BSD ENCFF418BSD.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V24 transcriptome alignments GRCh38 5.1 GB link
ENCFF331OLI ENCFF331OLI.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V29 transcriptome alignments GRCh38 6.1 GB link
ENCFF973PMG ENCFF973PMG.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V29 transcriptome alignments GRCh38 5.8 GB link
ENCFF956OVZ ENCFF956OVZ.bam bam (transcriptome alignments); assembly: hg19; genome annotation: V19 transcriptome alignments hg19 5.0 GB link
ENCFF988YNW ENCFF988YNW.bam bam (transcriptome alignments); assembly: hg19; genome annotation: V19 transcriptome alignments hg19 5.3 GB link
ENCFF232WWV ENCFF232WWV.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 80.2 MB link
ENCFF326TSG ENCFF326TSG.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 77.2 MB link
ENCFF536YNR ENCFF536YNR.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 69.9 MB link
ENCFF574GUO ENCFF574GUO.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 89.0 MB link
ENCFF499YUG ENCFF499YUG.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V29 minus strand signal of all reads GRCh38 77.3 MB link
ENCFF729RTQ ENCFF729RTQ.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V29 minus strand signal of all reads GRCh38 89.0 MB link
ENCFF051RWP ENCFF051RWP.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 76.3 MB link
ENCFF074UOC ENCFF074UOC.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 82.9 MB link
ENCFF261HZZ ENCFF261HZZ.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 79.2 MB link
ENCFF342FKU ENCFF342FKU.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 67.7 MB link
ENCFF490AKC ENCFF490AKC.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 88.7 MB link
ENCFF639TMJ ENCFF639TMJ.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 71.3 MB link
ENCFF201FNN ENCFF201FNN.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 76.1 MB link
ENCFF242SVU ENCFF242SVU.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 65.7 MB link
ENCFF408VTX ENCFF408VTX.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 69.5 MB link
ENCFF907PKS ENCFF907PKS.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 79.4 MB link
ENCFF322BTG ENCFF322BTG.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 minus strand signal of unique reads GRCh38 69.2 MB link
ENCFF454DDZ ENCFF454DDZ.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 minus strand signal of unique reads GRCh38 79.2 MB link
ENCFF081TVE ENCFF081TVE.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 68.6 MB link
ENCFF307UVH ENCFF307UVH.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 62.3 MB link
ENCFF633GCR ENCFF633GCR.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 76.5 MB link
ENCFF664QIX ENCFF664QIX.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 66.1 MB link
ENCFF865IUR ENCFF865IUR.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 72.8 MB link
ENCFF995LBP ENCFF995LBP.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 79.3 MB link
ENCFF316TWR ENCFF316TWR.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 71.6 MB link
ENCFF532VXO ENCFF532VXO.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 82.0 MB link
ENCFF562AVH ENCFF562AVH.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 79.0 MB link
ENCFF900FTE ENCFF900FTE.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 90.9 MB link
ENCFF010XMU ENCFF010XMU.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V29 plus strand signal of all reads GRCh38 79.1 MB link
ENCFF042IRV ENCFF042IRV.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V29 plus strand signal of all reads GRCh38 90.9 MB link
ENCFF535UYN ENCFF535UYN.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 84.8 MB link
ENCFF603AVZ ENCFF603AVZ.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 73.0 MB link
ENCFF680VCW ENCFF680VCW.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 81.1 MB link
ENCFF697BEM ENCFF697BEM.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 69.4 MB link
ENCFF736IUG ENCFF736IUG.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 77.7 MB link
ENCFF796UNZ ENCFF796UNZ.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 90.3 MB link
ENCFF104QSG ENCFF104QSG.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 78.3 MB link
ENCFF376BRV ENCFF376BRV.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 81.8 MB link
ENCFF469DLK ENCFF469DLK.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 67.6 MB link
ENCFF511YWA ENCFF511YWA.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 71.6 MB link
ENCFF943LNW ENCFF943LNW.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 plus strand signal of unique reads GRCh38 71.3 MB link
ENCFF956GKF ENCFF956GKF.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 plus strand signal of unique reads GRCh38 81.6 MB link
ENCFF338ITW ENCFF338ITW.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 81.8 MB link
ENCFF348QZY ENCFF348QZY.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 75.2 MB link
ENCFF401INB ENCFF401INB.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 78.9 MB link
ENCFF502LYA ENCFF502LYA.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 68.2 MB link
ENCFF634VJC ENCFF634VJC.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 64.4 MB link
ENCFF790AZV ENCFF790AZV.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 70.7 MB link
ENCFF079NDM ENCFF079NDM.fastq fastq (reads) reads 2.1 GB link
ENCFF424OZB ENCFF424OZB.fastq fastq (reads) reads 2.2 GB link
ENCFF475BKB ENCFF475BKB.fastq fastq (reads) reads 2.1 GB link
ENCFF975XQH ENCFF975XQH.fastq fastq (reads) reads 2.2 GB link
ENCFF514EXA ENCFF514EXA.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 16.7 MB link
ENCFF841XPZ ENCFF841XPZ.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 4.0 MB link
ENCFF953ELM ENCFF953ELM.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 3.3 MB link
ENCFF210PCK ENCFF210PCK.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 3.0 MB link
ENCFF353CHU ENCFF353CHU.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 1.7 MB link
ENCFF432CSP ENCFF432CSP.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 5.5 MB link
ENCFF432KPL ENCFF432KPL.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 4.4 MB link
ENCFF587VGK ENCFF587VGK.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 1.9 MB link
ENCFF389WUG ENCFF389WUG.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V24 gene quantifications GRCh38 9.5 MB link
ENCFF967HIG ENCFF967HIG.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V24 gene quantifications GRCh38 9.4 MB link
ENCFF097XMM ENCFF097XMM.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V29 gene quantifications GRCh38 10.4 MB link
ENCFF906PDZ ENCFF906PDZ.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V29 gene quantifications GRCh38 10.4 MB link
ENCFF447CYY ENCFF447CYY.tsv tsv (gene quantifications); assembly: hg19; genome annotation: V19 gene quantifications hg19 9.1 MB link
ENCFF997DOI ENCFF997DOI.tsv tsv (gene quantifications); assembly: hg19; genome annotation: V19 gene quantifications hg19 9.1 MB link
ENCFF445OKE ENCFF445OKE.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V24 transcript quantifications GRCh38 25.3 MB link
ENCFF578KNE ENCFF578KNE.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V24 transcript quantifications GRCh38 25.3 MB link
ENCFF431AYA ENCFF431AYA.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 27.3 MB link
ENCFF706MGC ENCFF706MGC.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 29.8 MB link
ENCFF919MIA ENCFF919MIA.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 29.8 MB link
ENCFF940PFC ENCFF940PFC.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 27.4 MB link
ENCFF127EOT ENCFF127EOT.tsv tsv (transcript quantifications); assembly: hg19; genome annotation: V19 transcript quantifications hg19 24.9 MB link
ENCFF467ENX ENCFF467ENX.tsv tsv (transcript quantifications); assembly: hg19; genome annotation: V19 transcript quantifications hg19 24.9 MB link