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GSE72501

GSE GEO
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Ro60-knockout cells

Organism: Homo sapiens
Platform: GPL16791
Samples: 10
Experiment Types:
Expression profiling by high throughput sequencing
Submitted: Aug 28 2015
Last Updated: May 15 2019
Status: Public on Sep 16 2015
Contact: Tiffany,,hung (Genentech)

Relations

SubSeries of: GSE72420 BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA294174 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP062956

Summary

RNA-seq of Ro60-null GM12878 cell lines in order to determine the gene expression changes resulting from loss of Ro60.

Overall Design

3 separate clones of Ro60(Trove2)-null cells derived from zinc finger nuclease targeting of exon 2, two wildtype biological replicates, +/- IFNa for 6 hours.

Analysis (5 steps)

View Data Processing
Processing steps for GSE72501
  1. Illumina software used for basecalling.
  2. Sequenced reads were trimmed for adaptor sequence, filtered for rRNA contamination, filtered for low-complexity or low-quality sequence, then mapped to hg19 whole genome using GSNAP.
  3. Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
  4. In short, exons from all isoforms of a gene were merged to create one meta-transcript.
  5. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.

Supplementary Files (1)

GSE72501_GM12878submission_RPKMs.xls.gz Download
GEO Samples (10)
GSM1863315 GSM1863316 GSM1863317 GSM1863318 GSM1863319 GSM1863320 GSM1863321 GSM1863322 GSM1863323 GSM1863324

Dataset Citations (1)

The Ro60 autoantigen binds endogenous retroelements and regulates inflammatory gene expression.
PMID 26382853 · 2015 · Science (New York, N.Y.)
T Hung, G A Pratt, B Sundararaman, M J Townsend, C Chaivorapol, T Bhangale, R R Graham, W Ortmann, L A Criswell, G W Yeo, T W Behrens

SRA Experiments (10) and Runs (10)

Total: 10097 MB
SRX1167601 SRP062956 RNA-Seq SINGLE
GSM1863315: Wildtype I; Homo sapiens; RNA-Seq
Sample: SRS1047499
BioProject: PRJNA294174
BioSample: SAMN04017626
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Homo sapiens
Sample attributes
source_name: GM12878, wildtype, untreated
cell line: GM12878
cell type: ENCODE EBV-immortalized B cell line
genotype/variation: wildtype
treatment: none
replicate: I
Original files (1)
GM12878, wildtype, untreated
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR2192704 36694933 1834746650 1101.79 LIB23505_SAM19353354_R1.fastq.gz, SRR2192704, SRR2192704.sralite SRA
SRX1167602 SRP062956 RNA-Seq SINGLE
GSM1863316: Wildtype II; Homo sapiens; RNA-Seq
Sample: SRS1047498
BioProject: PRJNA294174
BioSample: SAMN04017627
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Homo sapiens
Sample attributes
source_name: GM12878, wildtype, untreated
cell line: GM12878
cell type: ENCODE EBV-immortalized B cell line
genotype/variation: wildtype
treatment: none
replicate: II
Original files (1)
GM12878, wildtype, untreated
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR2192705 34156345 1707817250 1026.65 LIB23506_SAM19353355_R1.fastq.gz, SRR2192705, SRR2192705.sralite SRA
SRX1167603 SRP062956 RNA-Seq SINGLE
GSM1863317: Wildtype I IFN; Homo sapiens; RNA-Seq
Sample: SRS1047497
BioProject: PRJNA294174
BioSample: SAMN04017628
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Homo sapiens
Sample attributes
source_name: GM12878, wildtype, IFNa
cell line: GM12878
cell type: ENCODE EBV-immortalized B cell line
genotype/variation: wildtype
treatment: IFNa
replicate: I
Original files (1)
GM12878, wildtype, IFNa
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR2192706 29384564 1469228200 968.58 LIB24545_SAM19590767_R1.fastq.gz, SRR2192706, SRR2192706.sralite SRA
SRX1167604 SRP062956 RNA-Seq SINGLE
GSM1863318: Wildtype II IFN; Homo sapiens; RNA-Seq
Sample: SRS1047496
BioProject: PRJNA294174
BioSample: SAMN04017629
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Homo sapiens
Sample attributes
source_name: GM12878, wildtype, IFNa
cell line: GM12878
cell type: ENCODE EBV-immortalized B cell line
genotype/variation: wildtype
treatment: IFNa
replicate: II
Original files (1)
GM12878, wildtype, IFNa
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR2192707 30459445 1522972250 1007.71 LIB24546_SAM19590768_R1.fastq.gz, SRR2192707, SRR2192707.sralite SRA
SRX1167605 SRP062956 RNA-Seq SINGLE
GSM1863319: Null 1; Homo sapiens; RNA-Seq
Sample: SRS1047495
BioProject: PRJNA294174
BioSample: SAMN04017630
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Homo sapiens
Sample attributes
source_name: GM12878, Ro60 null, untreated
cell line: GM12878
cell type: ENCODE EBV-immortalized B cell line
genotype/variation: Ro60 null
treatment: none
clone: 1
Original files (1)
GM12878, Ro60 null, untreated
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR2192708 35517923 1775896150 1068.57 LIB23499_SAM19353342_R1.fastq.gz, SRR2192708, SRR2192708.sralite SRA
SRX1167606 SRP062956 RNA-Seq SINGLE
GSM1863320: Null 1 IFN; Homo sapiens; RNA-Seq
Sample: SRS1047494
BioProject: PRJNA294174
BioSample: SAMN04017631
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Homo sapiens
Sample attributes
source_name: GM12878, Ro60 null, IFNa
cell line: GM12878
cell type: ENCODE EBV-immortalized B cell line
genotype/variation: Ro60 null
treatment: IFNa
clone: 1
Original files (1)
GM12878, Ro60 null, IFNa
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR2192709 31439151 1571957550 1033.4 LIB24542_SAM19590764_R1.fastq.gz, SRR2192709, SRR2192709.sralite SRA
SRX1167607 SRP062956 RNA-Seq SINGLE
GSM1863321: Null 2; Homo sapiens; RNA-Seq
Sample: SRS1047506
BioProject: PRJNA294174
BioSample: SAMN04017632
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Homo sapiens
Sample attributes
source_name: GM12878, Ro60 null, untreated
cell line: GM12878
cell type: ENCODE EBV-immortalized B cell line
genotype/variation: Ro60 null
treatment: none
clone: 2
Original files (1)
GM12878, Ro60 null, untreated
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR2192710 36159153 1807957650 1090.0 LIB23503_SAM19353350_R1.fastq.gz, SRR2192710, SRR2192710.sralite SRA
SRX1167608 SRP062956 RNA-Seq SINGLE
GSM1863322: Null 2 IFN; Homo sapiens; RNA-Seq
Sample: SRS1047505
BioProject: PRJNA294174
BioSample: SAMN04017633
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Homo sapiens
Sample attributes
source_name: GM12878, Ro60 null, IFNa
cell line: GM12878
cell type: ENCODE EBV-immortalized B cell line
genotype/variation: Ro60 null
treatment: IFNa
clone: 2
Original files (1)
GM12878, Ro60 null, IFNa
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR2192711 32804719 1640235950 1076.38 LIB24543_SAM19590765_R1.fastq.gz, SRR2192711, SRR2192711.sralite SRA
SRX1167609 SRP062956 RNA-Seq SINGLE
GSM1863323: Null 3; Homo sapiens; RNA-Seq
Sample: SRS1047504
BioProject: PRJNA294174
BioSample: SAMN04017634
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Homo sapiens
Sample attributes
source_name: GM12878, Ro60 null, untreated
cell line: GM12878
cell type: ENCODE EBV-immortalized B cell line
genotype/variation: Ro60 null
treatment: none
clone: 3
Original files (1)
GM12878, Ro60 null, untreated
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR2192712 28650327 1432516350 863.2 LIB23501_SAM19353346_R1.fastq.gz, SRR2192712, SRR2192712.sralite SRA
SRX1167610 SRP062956 RNA-Seq SINGLE
GSM1863324: Null 3 IFN; Homo sapiens; RNA-Seq
Sample: SRS1047502
BioProject: PRJNA294174
BioSample: SAMN04017635
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Homo sapiens
Sample attributes
source_name: GM12878, Ro60 null, IFNa
cell line: GM12878
cell type: ENCODE EBV-immortalized B cell line
genotype/variation: Ro60 null
treatment: IFNa
clone: 3
Original files (1)
GM12878, Ro60 null, IFNa
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR2192713 26046444 1302322200 860.24 LIB24544_SAM19590766_R1.fastq.gz, SRR2192713, SRR2192713.sralite SRA

Linked Publications (1)

The Ro60 autoantigen binds endogenous retroelements and regulates inflammatory gene expression.
Science (New York, N.Y.) · 2015

Data Files (10)

Accession File Name Stored Type Output Type Mapping Assembly Size Download
— LIB23499_SAM19353342_R1.fastq.gz RNA-Seq 1.0 GB link
— LIB23501_SAM19353346_R1.fastq.gz RNA-Seq 863.2 MB link
— LIB23503_SAM19353350_R1.fastq.gz RNA-Seq 1.1 GB link
— LIB23505_SAM19353354_R1.fastq.gz RNA-Seq 1.1 GB link
— LIB23506_SAM19353355_R1.fastq.gz RNA-Seq 1.0 GB link
— LIB24542_SAM19590764_R1.fastq.gz RNA-Seq 1.0 GB link
— LIB24543_SAM19590765_R1.fastq.gz RNA-Seq 1.1 GB link
— LIB24544_SAM19590766_R1.fastq.gz RNA-Seq 860.2 MB link
— LIB24545_SAM19590767_R1.fastq.gz RNA-Seq 968.6 MB link
— LIB24546_SAM19590768_R1.fastq.gz RNA-Seq 1007.7 MB link