GSE72500
GSE GEORo60 iCLIP
Organism:
Homo sapiens
Platform:
GPL9115
Samples:
2
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/PRJNA294175
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP062952
Summary
Autoantibodies target the RNA-binding protein Ro60 in systemic lupus erythematosus (SLE) and Sjögren's syndrome. However, whether Ro60 and its associated RNAs contribute to disease pathogenesis is unclear. We catalogued the Ro60-associated RNAs in human cell lines.
Overall Design
iCLIP in 2 cell lines (GM12878, K562).
Analysis (3 steps)
View Data Processing
Processing steps for GSE72500
- Illumina software used for basecalling.
- Reads were mapped to human genome build hg19 using STAR (https://code.google.com/p/rna-star/) with the "outFilterMultimapNmax 20" option, then PCR duplicates were removed using unique nmers in the barcode sequence.
- Peak calling was performed using pyicoclip (http://regulatorygenomics.upf.edu/Software/Pyicoteo/pyicoclip.html) using RefSeq genes as the region file.
Supplementary Files (1)
GSE72500_RAW.tar
Download
GEO Samples (2)
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 (2) and Runs (2)
Total: 3647 MBGSM1863313: GM12878 Ro60 iCLIP; Homo sapiens; RIP-Seq
Sample: SRS1047392
BioProject: PRJNA294175
BioSample: SAMN04017616
Platform: ILLUMINA
Instrument: Illumina Genome Analyzer II
Organism: Homo sapiens
Sample attributes
source_name: GM12878, Ro60 iCLIP
cell line: GM12878
cell type: ENCODE cell line B lymphocyte
antibody: anti-Ro60 (AA-3) (Santa Cruz Biotech, sc-100844)
Original files (1)
GM12878, Ro60 iCLIP
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR2192577 | 76544546 | 3138326386 | 1948.51 | LIB19982_SAM18146099_R1_resequenced.R02.fastq.gz, SRR2192577, SRR2192… | SRA |
GSM1863314: K562 Ro60 iCLIP; Homo sapiens; RIP-Seq
Sample: SRS1047402
BioProject: PRJNA294175
BioSample: SAMN04017617
Platform: ILLUMINA
Instrument: Illumina Genome Analyzer II
Organism: Homo sapiens
Sample attributes
source_name: K562, Ro60 iCLIP
cell line: K562
cell type: ENCODE cell line lymphocyte
antibody: anti-Ro60 (AA-3) (Santa Cruz Biotech, sc-100844)
Original files (1)
K562, Ro60 iCLIP
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR2192578 | 64154234 | 2630323594 | 1698.1 | LIB19982_SAM18146099_R1_resequenced.R08.fastq.gz, SRR2192578, SRR2192… | SRA |
Linked Publications (1)
The Ro60 autoantigen binds endogenous retroelements and regulates inflammatory gene expression.
Science (New York, N.Y.) · 2015