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Sample GSM1228038 Query DataSets for GSM1228038
Status Public on Dec 19, 2013
Title GM12892_iCLIP_rep1
Sample type SRA
Source name GM12892
Organism Homo sapiens
Characteristics sample type: rRNA depleted
cell line: GM12892
Biomaterial provider Coriell;
Treatment protocol 2x10^7 GM cells (per biological replicate) were collected under log phase growth, washed in once in ice-cold 1xPBS, resuspended in 10x pellet volumes of ice-cold 1xPBS, plated out on 10cm tissue culture dishes. Cells were UV crosslinked at 254nm for 0.3J/cm^2, collected in ice-cold PBS and cell pellets were frozen on dry ice. Lysate preparation, RNaseA, and immunoprecipitation of AGO were performed as described by Chi et al. using the antiAGO antibody (clone 2A8, Millipore). To produce iCLIP libraries on-bead enzymatic steps and off-bead final library preparation was performed as described by Konig et al
Growth protocol GM12878, GM12891 and GM12892 cells were grown at 37˚C to ~0.6million cells/ml in RPMI media supplemented with 15% FBS, 2mM L-glutamine and 1% PenStep
Extracted molecule total RNA
Extraction protocol AGO iCLIP libraries were produced in biological duplicates for each individual (91, 92, and 78), barcoded, and pooled for sequencing. Samples were single-end sequenced for 75bp on an Illumina HiSeq2500 machine.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
Description AGO iCLIP in GM12892 cell replicate 1
Data processing Qaulity control using FASTX toolkit: low quality raw reads were removed; adapter sequence were trimmed off from the 3'end of raw reads; and PCR-duplicates' raw reads were then removed.
Reads pass through the quality control were mapped to hg19 genome using bowtie, and an extension of +/-10bp of the cross-linking position was performed to increase signal intensity.
Signals of each cell type was defined as the minimun signal of the replicates
Peaks were called by a 50bp sliding window and defined as the enrichment score of that window greater than 2
Genome_build: hg19
Supplementary_files_format_and_content: bed format with Transcript ID on the first column and peak start stop position relative to the first base of the transcript
Submission date Sep 10, 2013
Last update date May 15, 2019
Contact name Kun Qu
Organization name Stanford University
Department Dermatology
Lab Howard Chang
Street address 269 Campus Dr. CCSR 2150
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
Platform ID GPL16791
Series (1)
GSE50676 Landscape and variation of RNA secondary structure across the human transcriptome
BioSample SAMN02352772
SRA SRX347743

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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