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ENCSR355OQC

ENCSR ENCODE
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RNA-seq on HepG2 cells treated with an shRNA knockdown against NAA15. (NAA15_BGHLV30)

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

Summary

shRNA RNA-seq of NAA15 in Homo sapiens HepG2 expressing RNAi targeting H. sapiens NAA15

Overall Design

RNA-seq on HepG2 cells treated with an shRNA knockdown against NAA15. (NAA15_BGHLV30)

Analysis

View Data Processing
Analysis page is available for ENCSR355OQC.

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: 91.8 GB
Assay: shRNA RNA-seq
Target: NAA15
Biosample: Homo sapiens HepG2 expressing RNAi targeting H. sapiens NAA15
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
ENCFF148IZQ ENCFF148IZQ.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 4.4 GB link
ENCFF332APE ENCFF332APE.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 3.8 GB link
ENCFF643NQB ENCFF643NQB.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 3.1 GB link
ENCFF928IPZ ENCFF928IPZ.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 3.5 GB link
ENCFF331BRW ENCFF331BRW.bam bam (alignments); assembly: GRCh38; genome annotation: V29 alignments GRCh38 4.4 GB link
ENCFF421ECC ENCFF421ECC.bam bam (alignments); assembly: GRCh38; genome annotation: V29 alignments GRCh38 3.8 GB link
ENCFF182PZY ENCFF182PZY.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 4.2 GB link
ENCFF393BWX ENCFF393BWX.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 3.5 GB link
ENCFF479PPT ENCFF479PPT.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 3.1 GB link
ENCFF515TAC ENCFF515TAC.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 3.1 GB link
ENCFF594GKW ENCFF594GKW.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 3.7 GB link
ENCFF880YEJ ENCFF880YEJ.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 3.5 GB link
ENCFF009VBR ENCFF009VBR.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V24 transcriptome alignments GRCh38 5.0 GB link
ENCFF370SKC ENCFF370SKC.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V24 transcriptome alignments GRCh38 6.0 GB link
ENCFF058QYI ENCFF058QYI.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V29 transcriptome alignments GRCh38 6.8 GB link
ENCFF423QQF ENCFF423QQF.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V29 transcriptome alignments GRCh38 5.7 GB link
ENCFF209YXR ENCFF209YXR.bam bam (transcriptome alignments); assembly: hg19; genome annotation: V19 transcriptome alignments hg19 5.9 GB link
ENCFF676MIZ ENCFF676MIZ.bam bam (transcriptome alignments); assembly: hg19; genome annotation: V19 transcriptome alignments hg19 5.0 GB link
ENCFF346DVJ ENCFF346DVJ.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 71.5 MB link
ENCFF820TPK ENCFF820TPK.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 68.9 MB link
ENCFF890SNA ENCFF890SNA.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 78.9 MB link
ENCFF993KZI ENCFF993KZI.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 76.8 MB link
ENCFF126BCD ENCFF126BCD.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V29 minus strand signal of all reads GRCh38 76.8 MB link
ENCFF376RBG ENCFF376RBG.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V29 minus strand signal of all reads GRCh38 78.9 MB link
ENCFF008OAC ENCFF008OAC.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 70.1 MB link
ENCFF370PCV ENCFF370PCV.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 66.3 MB link
ENCFF403DTR ENCFF403DTR.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 73.5 MB link
ENCFF528ABF ENCFF528ABF.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 79.0 MB link
ENCFF615UIM ENCFF615UIM.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 70.4 MB link
ENCFF922UKU ENCFF922UKU.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 76.2 MB link
ENCFF139ZUD ENCFF139ZUD.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 70.5 MB link
ENCFF399RGJ ENCFF399RGJ.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 67.6 MB link
ENCFF400VJT ENCFF400VJT.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 64.0 MB link
ENCFF412UNL ENCFF412UNL.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 68.7 MB link
ENCFF114RHZ ENCFF114RHZ.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 minus strand signal of unique reads GRCh38 70.8 MB link
ENCFF712XEV ENCFF712XEV.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 minus strand signal of unique reads GRCh38 68.6 MB link
ENCFF049TRY ENCFF049TRY.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 65.3 MB link
ENCFF058SSS ENCFF058SSS.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 67.9 MB link
ENCFF162EXO ENCFF162EXO.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 63.9 MB link
ENCFF176OUS ENCFF176OUS.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 67.9 MB link
ENCFF249XGC ENCFF249XGC.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 70.9 MB link
ENCFF780HNV ENCFF780HNV.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 61.5 MB link
ENCFF199BUV ENCFF199BUV.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 70.0 MB link
ENCFF500NFQ ENCFF500NFQ.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 78.1 MB link
ENCFF556NMZ ENCFF556NMZ.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 72.7 MB link
ENCFF708LLR ENCFF708LLR.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 80.4 MB link
ENCFF196VVK ENCFF196VVK.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V29 plus strand signal of all reads GRCh38 78.1 MB link
ENCFF512TNJ ENCFF512TNJ.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V29 plus strand signal of all reads GRCh38 80.4 MB link
ENCFF145POL ENCFF145POL.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 80.3 MB link
ENCFF196QFA ENCFF196QFA.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 77.3 MB link
ENCFF390HZK ENCFF390HZK.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 67.6 MB link
ENCFF550COA ENCFF550COA.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 71.4 MB link
ENCFF902APN ENCFF902APN.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 75.0 MB link
ENCFF927UAX ENCFF927UAX.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 71.9 MB link
ENCFF014CMG ENCFF014CMG.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 70.5 MB link
ENCFF172DLN ENCFF172DLN.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 69.3 MB link
ENCFF199YRY ENCFF199YRY.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 65.6 MB link
ENCFF509NOK ENCFF509NOK.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 72.4 MB link
ENCFF451AIC ENCFF451AIC.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 plus strand signal of unique reads GRCh38 70.4 MB link
ENCFF490ZTO ENCFF490ZTO.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 plus strand signal of unique reads GRCh38 72.7 MB link
ENCFF010CYB ENCFF010CYB.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 69.7 MB link
ENCFF108YHF ENCFF108YHF.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 72.9 MB link
ENCFF277YXF ENCFF277YXF.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 63.2 MB link
ENCFF285OAK ENCFF285OAK.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 69.8 MB link
ENCFF295VBU ENCFF295VBU.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 67.0 MB link
ENCFF635IVP ENCFF635IVP.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 65.8 MB link
ENCFF139NPY ENCFF139NPY.fastq fastq (reads) reads 2.2 GB link
ENCFF824VKD ENCFF824VKD.fastq fastq (reads) reads 2.6 GB link
ENCFF943RCH ENCFF943RCH.fastq fastq (reads) reads 2.2 GB link
ENCFF964IEU ENCFF964IEU.fastq fastq (reads) reads 2.6 GB link
ENCFF140LSH ENCFF140LSH.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 3.5 MB link
ENCFF349VUE ENCFF349VUE.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 15.1 MB link
ENCFF994DPX ENCFF994DPX.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 2.9 MB link
ENCFF122OZQ ENCFF122OZQ.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 4.2 MB link
ENCFF436OTQ ENCFF436OTQ.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 1.8 MB link
ENCFF562EVO ENCFF562EVO.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 2.8 MB link
ENCFF716LAU ENCFF716LAU.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 5.6 MB link
ENCFF795NGT ENCFF795NGT.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 1.9 MB link
ENCFF227BYW ENCFF227BYW.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V24 gene quantifications GRCh38 9.5 MB link
ENCFF782NJD ENCFF782NJD.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V24 gene quantifications GRCh38 9.5 MB link
ENCFF123MDC ENCFF123MDC.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V29 gene quantifications GRCh38 10.4 MB link
ENCFF449OGA ENCFF449OGA.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V29 gene quantifications GRCh38 10.4 MB link
ENCFF085DNF ENCFF085DNF.tsv tsv (gene quantifications); assembly: hg19; genome annotation: V19 gene quantifications hg19 9.1 MB link
ENCFF181FMH ENCFF181FMH.tsv tsv (gene quantifications); assembly: hg19; genome annotation: V19 gene quantifications hg19 9.1 MB link
ENCFF355FNO ENCFF355FNO.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V24 transcript quantifications GRCh38 25.4 MB link
ENCFF751OFV ENCFF751OFV.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V24 transcript quantifications GRCh38 25.3 MB link
ENCFF117SJN ENCFF117SJN.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 27.3 MB link
ENCFF190FMJ ENCFF190FMJ.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 27.3 MB link
ENCFF598CJA ENCFF598CJA.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 29.9 MB link
ENCFF980PVL ENCFF980PVL.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 29.8 MB link
ENCFF353TBY ENCFF353TBY.tsv tsv (transcript quantifications); assembly: hg19; genome annotation: V19 transcript quantifications hg19 24.9 MB link
ENCFF550QCV ENCFF550QCV.tsv tsv (transcript quantifications); assembly: hg19; genome annotation: V19 transcript quantifications hg19 25.0 MB link