ENCSR494VSD
ENCSR ENCODEshRNA knockdown against CSDA in HepG2 cells followed by RNA-seq. (CSDA-30-BGHLV20)
Organism:
Homo sapiens
Experiment Types:
shRNA RNA-seq
Status:
released
Contact:
Brenton Graveley, UConn
Summary
shRNA RNA-seq of YBX3 in Homo sapiens HepG2 expressing RNAi targeting H. sapiens YBX3
Overall Design
shRNA knockdown against CSDA in HepG2 cells followed by RNA-seq. (CSDA-30-BGHLV20)
Analysis
View Data Processing
Analysis page is available for ENCSR494VSD.
Dataset Citations (3)
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: 89.1 GBAssay: shRNA RNA-seq
Target: YBX3
Biosample: Homo sapiens HepG2 expressing RNAi targeting H. sapiens YBX3
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)
Data Files (92)
| Accession | File Name | Stored Type | Output Type | Mapping Assembly | Size | Download | |
|---|---|---|---|---|---|---|---|
| ENCFF026RYV | ENCFF026RYV.bam | bam (alignments) | alignments | 3.7 GB | link | ||
| ENCFF036XRE | ENCFF036XRE.bam | bam (alignments) | alignments | 4.3 GB | link | ||
| ENCFF067OBC | ENCFF067OBC.bam | bam (alignments) | alignments | 3.3 GB | link | ||
| ENCFF118VJE | ENCFF118VJE.bam | bam (alignments) | alignments | 3.7 GB | link | ||
| ENCFF121VWZ | ENCFF121VWZ.bam | bam (alignments) | alignments | 3.2 GB | link | ||
| ENCFF296FTT | ENCFF296FTT.bam | bam (alignments) | alignments | 3.7 GB | link | ||
| ENCFF370KTD | ENCFF370KTD.bam | bam (alignments) | alignments | 3.8 GB | link | ||
| ENCFF611FYD | ENCFF611FYD.bam | bam (alignments) | alignments | 4.4 GB | link | ||
| ENCFF663DXL | ENCFF663DXL.bam | bam (alignments) | alignments | 3.2 GB | link | ||
| ENCFF671TGN | ENCFF671TGN.bam | bam (alignments) | alignments | 4.4 GB | link | ||
| ENCFF713TPG | ENCFF713TPG.bam | bam (alignments) | alignments | 3.8 GB | link | ||
| ENCFF830UUD | ENCFF830UUD.bam | bam (alignments) | alignments | 3.8 GB | link | ||
| ENCFF162HOF | ENCFF162HOF.bam | bam (transcriptome alignments) | transcriptome alignments | 4.6 GB | link | ||
| ENCFF543HDA | ENCFF543HDA.bam | bam (transcriptome alignments) | transcriptome alignments | 5.1 GB | link | ||
| ENCFF608KYP | ENCFF608KYP.bam | bam (transcriptome alignments) | transcriptome alignments | 5.5 GB | link | ||
| ENCFF644NAK | ENCFF644NAK.bam | bam (transcriptome alignments) | transcriptome alignments | 5.5 GB | link | ||
| ENCFF857VCX | ENCFF857VCX.bam | bam (transcriptome alignments) | transcriptome alignments | 4.6 GB | link | ||
| ENCFF974GPH | ENCFF974GPH.bam | bam (transcriptome alignments) | transcriptome alignments | 6.1 GB | link | ||
| ENCFF145UQU | ENCFF145UQU.bigWig | bigWig (minus strand signal of all reads) | minus strand signal of all reads | 65.4 MB | link | ||
| ENCFF403DZX | ENCFF403DZX.bigWig | bigWig (minus strand signal of all reads) | minus strand signal of all reads | 64.2 MB | link | ||
| ENCFF486WPP | ENCFF486WPP.bigWig | bigWig (minus strand signal of all reads) | minus strand signal of all reads | 64.0 MB | link | ||
| ENCFF491KLM | ENCFF491KLM.bigWig | bigWig (minus strand signal of all reads) | minus strand signal of all reads | 70.8 MB | link | ||
| ENCFF558EGN | ENCFF558EGN.bigWig | bigWig (minus strand signal of all reads) | minus strand signal of all reads | 71.0 MB | link | ||
| ENCFF571RGP | ENCFF571RGP.bigWig | bigWig (minus strand signal of all reads) | minus strand signal of all reads | 72.0 MB | link | ||
| ENCFF664FHG | ENCFF664FHG.bigWig | bigWig (minus strand signal of all reads) | minus strand signal of all reads | 63.6 MB | link | ||
| ENCFF733NYK | ENCFF733NYK.bigWig | bigWig (minus strand signal of all reads) | minus strand signal of all reads | 61.0 MB | link | ||
| ENCFF810AEB | ENCFF810AEB.bigWig | bigWig (minus strand signal of all reads) | minus strand signal of all reads | 70.3 MB | link | ||
| ENCFF864TWT | ENCFF864TWT.bigWig | bigWig (minus strand signal of all reads) | minus strand signal of all reads | 70.8 MB | link | ||
| ENCFF875JDU | ENCFF875JDU.bigWig | bigWig (minus strand signal of all reads) | minus strand signal of all reads | 71.9 MB | link | ||
| ENCFF922YJV | ENCFF922YJV.bigWig | bigWig (minus strand signal of all reads) | minus strand signal of all reads | 60.7 MB | link | ||
| ENCFF048OWP | ENCFF048OWP.bigWig | bigWig (minus strand signal of unique reads) | minus strand signal of unique reads | 59.9 MB | link | ||
| ENCFF161SRL | ENCFF161SRL.bigWig | bigWig (minus strand signal of unique reads) | minus strand signal of unique reads | 63.2 MB | link | ||
| ENCFF236FRO | ENCFF236FRO.bigWig | bigWig (minus strand signal of unique reads) | minus strand signal of unique reads | 60.6 MB | link | ||
| ENCFF309RRK | ENCFF309RRK.bigWig | bigWig (minus strand signal of unique reads) | minus strand signal of unique reads | 63.6 MB | link | ||
| ENCFF345IRH | ENCFF345IRH.bigWig | bigWig (minus strand signal of unique reads) | minus strand signal of unique reads | 59.8 MB | link | ||
| ENCFF370UIU | ENCFF370UIU.bigWig | bigWig (minus strand signal of unique reads) | minus strand signal of unique reads | 63.4 MB | link | ||
| ENCFF475BMM | ENCFF475BMM.bigWig | bigWig (minus strand signal of unique reads) | minus strand signal of unique reads | 64.3 MB | link | ||
| ENCFF497MAW | ENCFF497MAW.bigWig | bigWig (minus strand signal of unique reads) | minus strand signal of unique reads | 56.4 MB | link | ||
| ENCFF505QSH | ENCFF505QSH.bigWig | bigWig (minus strand signal of unique reads) | minus strand signal of unique reads | 60.3 MB | link | ||
| ENCFF558ZLL | ENCFF558ZLL.bigWig | bigWig (minus strand signal of unique reads) | minus strand signal of unique reads | 64.9 MB | link | ||
| ENCFF597UEG | ENCFF597UEG.bigWig | bigWig (minus strand signal of unique reads) | minus strand signal of unique reads | 56.2 MB | link | ||
| ENCFF908ZOJ | ENCFF908ZOJ.bigWig | bigWig (minus strand signal of unique reads) | minus strand signal of unique reads | 64.9 MB | link | ||
| ENCFF005CFT | ENCFF005CFT.bigWig | bigWig (plus strand signal of all reads) | plus strand signal of all reads | 73.4 MB | link | ||
| ENCFF078ZOW | ENCFF078ZOW.bigWig | bigWig (plus strand signal of all reads) | plus strand signal of all reads | 66.8 MB | link | ||
| ENCFF284OTQ | ENCFF284OTQ.bigWig | bigWig (plus strand signal of all reads) | plus strand signal of all reads | 72.3 MB | link | ||
| ENCFF293SVX | ENCFF293SVX.bigWig | bigWig (plus strand signal of all reads) | plus strand signal of all reads | 62.1 MB | link | ||
| ENCFF362PLE | ENCFF362PLE.bigWig | bigWig (plus strand signal of all reads) | plus strand signal of all reads | 64.9 MB | link | ||
| ENCFF395SCX | ENCFF395SCX.bigWig | bigWig (plus strand signal of all reads) | plus strand signal of all reads | 72.3 MB | link | ||
| ENCFF435BSQ | ENCFF435BSQ.bigWig | bigWig (plus strand signal of all reads) | plus strand signal of all reads | 62.4 MB | link | ||
| ENCFF575HPJ | ENCFF575HPJ.bigWig | bigWig (plus strand signal of all reads) | plus strand signal of all reads | 65.3 MB | link | ||
| ENCFF686UKP | ENCFF686UKP.bigWig | bigWig (plus strand signal of all reads) | plus strand signal of all reads | 65.5 MB | link | ||
| ENCFF764HLQ | ENCFF764HLQ.bigWig | bigWig (plus strand signal of all reads) | plus strand signal of all reads | 72.3 MB | link | ||
| ENCFF802HYU | ENCFF802HYU.bigWig | bigWig (plus strand signal of all reads) | plus strand signal of all reads | 71.6 MB | link | ||
| ENCFF812MHH | ENCFF812MHH.bigWig | bigWig (plus strand signal of all reads) | plus strand signal of all reads | 73.4 MB | link | ||
| ENCFF027GIK | ENCFF027GIK.bigWig | bigWig (plus strand signal of unique reads) | plus strand signal of unique reads | 66.8 MB | link | ||
| ENCFF176FRH | ENCFF176FRH.bigWig | bigWig (plus strand signal of unique reads) | plus strand signal of unique reads | 61.6 MB | link | ||
| ENCFF230HHM | ENCFF230HHM.bigWig | bigWig (plus strand signal of unique reads) | plus strand signal of unique reads | 66.2 MB | link | ||
| ENCFF257XPQ | ENCFF257XPQ.bigWig | bigWig (plus strand signal of unique reads) | plus strand signal of unique reads | 65.5 MB | link | ||
| ENCFF313CJK | ENCFF313CJK.bigWig | bigWig (plus strand signal of unique reads) | plus strand signal of unique reads | 58.2 MB | link | ||
| ENCFF400FHJ | ENCFF400FHJ.bigWig | bigWig (plus strand signal of unique reads) | plus strand signal of unique reads | 58.0 MB | link | ||
| ENCFF420RSN | ENCFF420RSN.bigWig | bigWig (plus strand signal of unique reads) | plus strand signal of unique reads | 61.9 MB | link | ||
| ENCFF488FWZ | ENCFF488FWZ.bigWig | bigWig (plus strand signal of unique reads) | plus strand signal of unique reads | 62.4 MB | link | ||
| ENCFF512EDN | ENCFF512EDN.bigWig | bigWig (plus strand signal of unique reads) | plus strand signal of unique reads | 65.1 MB | link | ||
| ENCFF563DRE | ENCFF563DRE.bigWig | bigWig (plus strand signal of unique reads) | plus strand signal of unique reads | 66.8 MB | link | ||
| ENCFF598CRO | ENCFF598CRO.bigWig | bigWig (plus strand signal of unique reads) | plus strand signal of unique reads | 61.6 MB | link | ||
| ENCFF920YJA | ENCFF920YJA.bigWig | bigWig (plus strand signal of unique reads) | plus strand signal of unique reads | 65.4 MB | link | ||
| ENCFF212RVY | ENCFF212RVY.fastq | fastq (reads) | reads | 2.1 GB | link | ||
| ENCFF438PPS | ENCFF438PPS.fastq | fastq (reads) | reads | 1.9 GB | link | ||
| ENCFF552XHQ | ENCFF552XHQ.fastq | fastq (reads) | reads | 2.3 GB | link | ||
| ENCFF715FJL | ENCFF715FJL.fastq | fastq (reads) | reads | 2.5 GB | link | ||
| ENCFF188RMG | ENCFF188RMG.tar | tar (differential splicing quantifications) | differential splicing quantifications | 3.3 MB | link | ||
| ENCFF211GMC | ENCFF211GMC.tar | tar (differential splicing quantifications) | differential splicing quantifications | 2.8 MB | link | ||
| ENCFF597SDA | ENCFF597SDA.tar | tar (differential splicing quantifications) | differential splicing quantifications | 14.9 MB | link | ||
| ENCFF034NMG | ENCFF034NMG.tsv | tsv (differential expression quantifications) | differential expression quantifications | 5.5 MB | link | ||
| ENCFF571NNW | ENCFF571NNW.tsv | tsv (differential expression quantifications) | differential expression quantifications | 1.9 MB | link | ||
| ENCFF608QFL | ENCFF608QFL.tsv | tsv (differential expression quantifications) | differential expression quantifications | 4.2 MB | link | ||
| ENCFF682EPA | ENCFF682EPA.tsv | tsv (differential expression quantifications) | differential expression quantifications | 2.8 MB | link | ||
| ENCFF764GOM | ENCFF764GOM.tsv | tsv (differential expression quantifications) | differential expression quantifications | 1.8 MB | link | ||
| ENCFF041OQG | ENCFF041OQG.tsv | tsv (gene quantifications) | gene quantifications | 9.4 MB | link | ||
| ENCFF369BJG | ENCFF369BJG.tsv | tsv (gene quantifications) | gene quantifications | 10.4 MB | link | ||
| ENCFF455HHH | ENCFF455HHH.tsv | tsv (gene quantifications) | gene quantifications | 9.4 MB | link | ||
| ENCFF837IIK | ENCFF837IIK.tsv | tsv (gene quantifications) | gene quantifications | 9.1 MB | link | ||
| ENCFF852VXW | ENCFF852VXW.tsv | tsv (gene quantifications) | gene quantifications | 9.1 MB | link | ||
| ENCFF930LRB | ENCFF930LRB.tsv | tsv (gene quantifications) | gene quantifications | 10.4 MB | link | ||
| ENCFF162DLM | ENCFF162DLM.tsv | tsv (transcript quantifications) | transcript quantifications | 25.3 MB | link | ||
| ENCFF264JQK | ENCFF264JQK.tsv | tsv (transcript quantifications) | transcript quantifications | 24.9 MB | link | ||
| ENCFF317FLH | ENCFF317FLH.tsv | tsv (transcript quantifications) | transcript quantifications | 27.2 MB | link | ||
| ENCFF333GZO | ENCFF333GZO.tsv | tsv (transcript quantifications) | transcript quantifications | 29.8 MB | link | ||
| ENCFF415YSJ | ENCFF415YSJ.tsv | tsv (transcript quantifications) | transcript quantifications | 27.3 MB | link | ||
| ENCFF531HNE | ENCFF531HNE.tsv | tsv (transcript quantifications) | transcript quantifications | 25.3 MB | link | ||
| ENCFF771ZAX | ENCFF771ZAX.tsv | tsv (transcript quantifications) | transcript quantifications | 24.9 MB | link | ||
| ENCFF880ABX | ENCFF880ABX.tsv | tsv (transcript quantifications) | transcript quantifications | 29.8 MB | link |