ENCSR064DXG
ENCSR ENCODEshRNA knockdown against PTBP1 in HepG2 cells followed by RNA-seq. (PTBP1-BGHLV12)
Organism:
Homo sapiens
Experiment Types:
shRNA RNA-seq
Status:
released
Contact:
Brenton Graveley, UConn
Summary
shRNA RNA-seq of PTBP1 in Homo sapiens HepG2 expressing RNAi targeting H. sapiens PTBP1
Overall Design
shRNA knockdown against PTBP1 in HepG2 cells followed by RNA-seq. (PTBP1-BGHLV12)
Analysis
View Data Processing
Analysis page is available for ENCSR064DXG.
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: 108.0 GBAssay: shRNA RNA-seq
Target: PTBP1
Biosample: Homo sapiens HepG2 expressing RNAi targeting H. sapiens PTBP1
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 | |
|---|---|---|---|---|---|---|---|
| ENCFF211UDA | ENCFF211UDA.bam | bam (alignments); assembly: GRCh38; genome annotation: V24 | alignments | GRCh38 | 3.8 GB | link | |
| ENCFF246XSM | ENCFF246XSM.bam | bam (alignments); assembly: GRCh38; genome annotation: V24 | alignments | GRCh38 | 3.2 GB | link | |
| ENCFF709DTV | ENCFF709DTV.bam | bam (alignments); assembly: GRCh38; genome annotation: V24 | alignments | GRCh38 | 5.2 GB | link | |
| ENCFF854PFR | ENCFF854PFR.bam | bam (alignments); assembly: GRCh38; genome annotation: V24 | alignments | GRCh38 | 6.2 GB | link | |
| ENCFF125RUG | ENCFF125RUG.bam | bam (alignments); assembly: GRCh38; genome annotation: V29 | alignments | GRCh38 | 6.2 GB | link | |
| ENCFF707AEZ | ENCFF707AEZ.bam | bam (alignments); assembly: GRCh38; genome annotation: V29 | alignments | GRCh38 | 3.8 GB | link | |
| ENCFF019ZBE | ENCFF019ZBE.bam | bam (alignments); assembly: hg19; genome annotation: V19 | alignments | hg19 | 3.2 GB | link | |
| ENCFF022QUQ | ENCFF022QUQ.bam | bam (alignments); assembly: hg19; genome annotation: V19 | alignments | hg19 | 5.1 GB | link | |
| ENCFF145TKU | ENCFF145TKU.bam | bam (alignments); assembly: hg19; genome annotation: V19 | alignments | hg19 | 3.7 GB | link | |
| ENCFF155FIK | ENCFF155FIK.bam | bam (alignments); assembly: hg19; genome annotation: V19 | alignments | hg19 | 5.1 GB | link | |
| ENCFF527FPF | ENCFF527FPF.bam | bam (alignments); assembly: hg19; genome annotation: V19 | alignments | hg19 | 3.2 GB | link | |
| ENCFF855TDM | ENCFF855TDM.bam | bam (alignments); assembly: hg19; genome annotation: V19 | alignments | hg19 | 6.0 GB | link | |
| ENCFF039GZQ | ENCFF039GZQ.bam | bam (transcriptome alignments); assembly: GRCh38; genome annotation: V24 | transcriptome alignments | GRCh38 | 7.7 GB | link | |
| ENCFF794VHJ | ENCFF794VHJ.bam | bam (transcriptome alignments); assembly: GRCh38; genome annotation: V24 | transcriptome alignments | GRCh38 | 4.6 GB | link | |
| ENCFF434LRA | ENCFF434LRA.bam | bam (transcriptome alignments); assembly: GRCh38; genome annotation: V29 | transcriptome alignments | GRCh38 | 5.2 GB | link | |
| ENCFF546YNH | ENCFF546YNH.bam | bam (transcriptome alignments); assembly: GRCh38; genome annotation: V29 | transcriptome alignments | GRCh38 | 8.6 GB | link | |
| ENCFF766ENP | ENCFF766ENP.bam | bam (transcriptome alignments); assembly: hg19; genome annotation: V19 | transcriptome alignments | hg19 | 7.6 GB | link | |
| ENCFF910GEM | ENCFF910GEM.bam | bam (transcriptome alignments); assembly: hg19; genome annotation: V19 | transcriptome alignments | hg19 | 4.6 GB | link | |
| ENCFF277MSH | ENCFF277MSH.bigWig | bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 | minus strand signal of all reads | GRCh38 | 94.3 MB | link | |
| ENCFF691LTL | ENCFF691LTL.bigWig | bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 | minus strand signal of all reads | GRCh38 | 103.6 MB | link | |
| ENCFF740PQI | ENCFF740PQI.bigWig | bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 | minus strand signal of all reads | GRCh38 | 78.2 MB | link | |
| ENCFF917JYP | ENCFF917JYP.bigWig | bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 | minus strand signal of all reads | GRCh38 | 70.5 MB | link | |
| ENCFF296AWP | ENCFF296AWP.bigWig | bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V29 | minus strand signal of all reads | GRCh38 | 103.7 MB | link | |
| ENCFF773RTF | ENCFF773RTF.bigWig | bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V29 | minus strand signal of all reads | GRCh38 | 78.2 MB | link | |
| ENCFF204CNP | ENCFF204CNP.bigWig | bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 | minus strand signal of all reads | hg19 | 92.6 MB | link | |
| ENCFF443YZO | ENCFF443YZO.bigWig | bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 | minus strand signal of all reads | hg19 | 103.2 MB | link | |
| ENCFF448JLC | ENCFF448JLC.bigWig | bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 | minus strand signal of all reads | hg19 | 71.2 MB | link | |
| ENCFF451TIO | ENCFF451TIO.bigWig | bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 | minus strand signal of all reads | hg19 | 77.0 MB | link | |
| ENCFF645NZT | ENCFF645NZT.bigWig | bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 | minus strand signal of all reads | hg19 | 68.2 MB | link | |
| ENCFF908UXW | ENCFF908UXW.bigWig | bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 | minus strand signal of all reads | hg19 | 95.8 MB | link | |
| ENCFF207ZEG | ENCFF207ZEG.bigWig | bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 | minus strand signal of unique reads | GRCh38 | 88.6 MB | link | |
| ENCFF235RFS | ENCFF235RFS.bigWig | bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 | minus strand signal of unique reads | GRCh38 | 93.4 MB | link | |
| ENCFF386JWH | ENCFF386JWH.bigWig | bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 | minus strand signal of unique reads | GRCh38 | 66.3 MB | link | |
| ENCFF836WHJ | ENCFF836WHJ.bigWig | bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 | minus strand signal of unique reads | GRCh38 | 70.4 MB | link | |
| ENCFF723SVB | ENCFF723SVB.bigWig | bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 | minus strand signal of unique reads | GRCh38 | 70.4 MB | link | |
| ENCFF921IZK | ENCFF921IZK.bigWig | bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 | minus strand signal of unique reads | GRCh38 | 93.1 MB | link | |
| ENCFF329GBF | ENCFF329GBF.bigWig | bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 | minus strand signal of unique reads | hg19 | 63.6 MB | link | |
| ENCFF354DYX | ENCFF354DYX.bigWig | bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 | minus strand signal of unique reads | hg19 | 93.4 MB | link | |
| ENCFF600AAY | ENCFF600AAY.bigWig | bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 | minus strand signal of unique reads | hg19 | 85.6 MB | link | |
| ENCFF601HBO | ENCFF601HBO.bigWig | bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 | minus strand signal of unique reads | hg19 | 65.9 MB | link | |
| ENCFF667CQV | ENCFF667CQV.bigWig | bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 | minus strand signal of unique reads | hg19 | 89.2 MB | link | |
| ENCFF741KIN | ENCFF741KIN.bigWig | bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 | minus strand signal of unique reads | hg19 | 70.0 MB | link | |
| ENCFF089PQW | ENCFF089PQW.bigWig | bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 | plus strand signal of all reads | GRCh38 | 79.7 MB | link | |
| ENCFF481INY | ENCFF481INY.bigWig | bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 | plus strand signal of all reads | GRCh38 | 96.1 MB | link | |
| ENCFF518UIR | ENCFF518UIR.bigWig | bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 | plus strand signal of all reads | GRCh38 | 105.6 MB | link | |
| ENCFF984XGQ | ENCFF984XGQ.bigWig | bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 | plus strand signal of all reads | GRCh38 | 71.9 MB | link | |
| ENCFF832CVZ | ENCFF832CVZ.bigWig | bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V29 | plus strand signal of all reads | GRCh38 | 105.6 MB | link | |
| ENCFF886SWZ | ENCFF886SWZ.bigWig | bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V29 | plus strand signal of all reads | GRCh38 | 79.7 MB | link | |
| ENCFF005WTR | ENCFF005WTR.bigWig | bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 | plus strand signal of all reads | hg19 | 72.7 MB | link | |
| ENCFF014RQD | ENCFF014RQD.bigWig | bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 | plus strand signal of all reads | hg19 | 98.0 MB | link | |
| ENCFF195XWA | ENCFF195XWA.bigWig | bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 | plus strand signal of all reads | hg19 | 78.3 MB | link | |
| ENCFF267OIE | ENCFF267OIE.bigWig | bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 | plus strand signal of all reads | hg19 | 94.7 MB | link | |
| ENCFF326JSI | ENCFF326JSI.bigWig | bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 | plus strand signal of all reads | hg19 | 105.0 MB | link | |
| ENCFF854OQK | ENCFF854OQK.bigWig | bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 | plus strand signal of all reads | hg19 | 69.7 MB | link | |
| ENCFF204GST | ENCFF204GST.bigWig | bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 | plus strand signal of unique reads | GRCh38 | 96.0 MB | link | |
| ENCFF511LWB | ENCFF511LWB.bigWig | bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 | plus strand signal of unique reads | GRCh38 | 72.3 MB | link | |
| ENCFF543WTI | ENCFF543WTI.bigWig | bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 | plus strand signal of unique reads | GRCh38 | 91.1 MB | link | |
| ENCFF776JVF | ENCFF776JVF.bigWig | bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 | plus strand signal of unique reads | GRCh38 | 68.1 MB | link | |
| ENCFF638IWS | ENCFF638IWS.bigWig | bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 | plus strand signal of unique reads | GRCh38 | 72.3 MB | link | |
| ENCFF881RDD | ENCFF881RDD.bigWig | bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 | plus strand signal of unique reads | GRCh38 | 95.8 MB | link | |
| ENCFF084MUD | ENCFF084MUD.bigWig | bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 | plus strand signal of unique reads | hg19 | 96.2 MB | link | |
| ENCFF394KKK | ENCFF394KKK.bigWig | bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 | plus strand signal of unique reads | hg19 | 88.1 MB | link | |
| ENCFF398BJQ | ENCFF398BJQ.bigWig | bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 | plus strand signal of unique reads | hg19 | 65.4 MB | link | |
| ENCFF497YCS | ENCFF497YCS.bigWig | bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 | plus strand signal of unique reads | hg19 | 67.8 MB | link | |
| ENCFF793USF | ENCFF793USF.bigWig | bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 | plus strand signal of unique reads | hg19 | 91.9 MB | link | |
| ENCFF879ENJ | ENCFF879ENJ.bigWig | bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 | plus strand signal of unique reads | hg19 | 72.0 MB | link | |
| ENCFF486ADH | ENCFF486ADH.fastq | fastq (reads) | reads | 2.0 GB | link | ||
| ENCFF555EDL | ENCFF555EDL.fastq | fastq (reads) | reads | 3.4 GB | link | ||
| ENCFF887GOE | ENCFF887GOE.fastq | fastq (reads) | reads | 2.0 GB | link | ||
| ENCFF983TGB | ENCFF983TGB.fastq | fastq (reads) | reads | 3.3 GB | link | ||
| ENCFF044JDS | ENCFF044JDS.tar | tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 | differential splicing quantifications | hg19 | 3.3 MB | link | |
| ENCFF081GDG | ENCFF081GDG.tar | tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 | differential splicing quantifications | hg19 | 4.1 MB | link | |
| ENCFF364DPS | ENCFF364DPS.tar | tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 | differential splicing quantifications | hg19 | 16.5 MB | link | |
| ENCFF044UQQ | ENCFF044UQQ.tsv | tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 | differential expression quantifications | hg19 | 2.0 MB | link | |
| ENCFF089VRS | ENCFF089VRS.tsv | tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 | differential expression quantifications | hg19 | 5.6 MB | link | |
| ENCFF207MJK | ENCFF207MJK.tsv | tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 | differential expression quantifications | hg19 | 2.9 MB | link | |
| ENCFF251MLR | ENCFF251MLR.tsv | tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 | differential expression quantifications | hg19 | 1.8 MB | link | |
| ENCFF903PZF | ENCFF903PZF.tsv | tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 | differential expression quantifications | hg19 | 4.4 MB | link | |
| ENCFF003BXW | ENCFF003BXW.tsv | tsv (gene quantifications); assembly: GRCh38; genome annotation: V24 | gene quantifications | GRCh38 | 9.5 MB | link | |
| ENCFF338PVO | ENCFF338PVO.tsv | tsv (gene quantifications); assembly: GRCh38; genome annotation: V24 | gene quantifications | GRCh38 | 9.4 MB | link | |
| ENCFF035CXU | ENCFF035CXU.tsv | tsv (gene quantifications); assembly: GRCh38; genome annotation: V29 | gene quantifications | GRCh38 | 10.4 MB | link | |
| ENCFF140JMY | ENCFF140JMY.tsv | tsv (gene quantifications); assembly: GRCh38; genome annotation: V29 | gene quantifications | GRCh38 | 10.4 MB | link | |
| ENCFF663OZT | ENCFF663OZT.tsv | tsv (gene quantifications); assembly: hg19; genome annotation: V19 | gene quantifications | hg19 | 9.1 MB | link | |
| ENCFF917GHN | ENCFF917GHN.tsv | tsv (gene quantifications); assembly: hg19; genome annotation: V19 | gene quantifications | hg19 | 9.1 MB | link | |
| ENCFF041ZQE | ENCFF041ZQE.tsv | tsv (transcript quantifications); assembly: GRCh38; genome annotation: V24 | transcript quantifications | GRCh38 | 25.2 MB | link | |
| ENCFF390KOO | ENCFF390KOO.tsv | tsv (transcript quantifications); assembly: GRCh38; genome annotation: V24 | transcript quantifications | GRCh38 | 25.3 MB | link | |
| ENCFF192HMF | ENCFF192HMF.tsv | tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 | transcript quantifications | GRCh38 | 27.3 MB | link | |
| ENCFF359DYS | ENCFF359DYS.tsv | tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 | transcript quantifications | GRCh38 | 29.7 MB | link | |
| ENCFF802ZMS | ENCFF802ZMS.tsv | tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 | transcript quantifications | GRCh38 | 29.8 MB | link | |
| ENCFF978OGD | ENCFF978OGD.tsv | tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 | transcript quantifications | GRCh38 | 27.4 MB | link | |
| ENCFF098FKT | ENCFF098FKT.tsv | tsv (transcript quantifications); assembly: hg19; genome annotation: V19 | transcript quantifications | hg19 | 24.8 MB | link | |
| ENCFF139AUJ | ENCFF139AUJ.tsv | tsv (transcript quantifications); assembly: hg19; genome annotation: V19 | transcript quantifications | hg19 | 24.9 MB | link |