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Sample GSM2741760 Query DataSets for GSM2741760
Status Public on Jul 11, 2018
Title anti-PanQk iCLIP 72h differentiated C2C12 myotubes (MiSeq + HiSeq)
Sample type SRA
 
Source name myotube
Organism Mus musculus
Characteristics cell type: myotube
cell line: C2C12
Treatment protocol crosslinking was performed by irradiating cells with UV light with 400 mJ in an Aglient Stratalinker
Growth protocol C2C12 cells were maintained in DMEM (high glucose) supplemented with 10% FBS; for myotube differentiation, C2C12 myoblasts were allowed to reach ~90% confluence then media were changed to DMEM (high glucose) supplemented with 2% horse serum and cultured an additional 72h with daily media change
Extracted molecule total RNA
Extraction protocol following immunoprecipitation and radiolabeling, protein:RNA complexes were separated by SDS-PAGE then transferred to nitrocellulose where they were extracted from a region corresponding to protein:RNA then extracted with phenol:chloroform:isoamyl alcohol after proteinase digestion
All libraries prepared according to Konig et al J Vis Exp. 2011 30;50 and Huppertz et al Methods. 2014 Feb; 65(3):274-87.
 
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina MiSeq
 
Description UUUCGGAUU bp 1 to 9 of read1 is UMI
c2c12_pqkd_ls055
Data processing Library strategy: iCLIP-Seq
iCLIP 1: based on random bases of internal barcode positions 1-9 of each read, the readIDs were divided into classes (for later use in duplicate removal). Note: positions 4-7 comprised fixed values for each sample
iCLIP 2: each read was searched for the presence of adaptor sequence AGATCGGA and trimmed from that point on. Reads shorter than 30bp after trimming (including internal barcode positions 1-9) were discarded.
iCLIP 3: internal barcode positions 1-9 were trimmed before mapping
iCLIP 4: reads mapping (by Bowtie2) to mouse repeatMasker elements were discarded
iCLIP 5: reads were mapped to mm9 by Tophat, aided by a gtf file based on UCSC Knowngenes, and with parameters --no-novel-juncs, --no-coverage-search
iCLIP 6: for each class of internal random barcode bases from step (1), duplicate read mappings of the same length and position were discarded
iCLIP 7: peaks were called on the dup-removed bam files from step (6) by Clipper (Yeo et al) using default parameters for mm9 and --premRNA.
Genome_build: mm9
Supplementary_files_format_and_content: SupplementalTable_QK_CLIPper_Data.xlsx is an Excel spreadsheet file with one worksheet contaiing peak calls for each sample analyzed by Clipper.
 
Submission date Aug 14, 2017
Last update date May 15, 2019
Contact name W. Samuel Fagg
E-mail(s) sam.fagg@gmail.com
Organization name University of Texas Medical Branch
Department Surgery/Biochemistry and Molecular Biology
Street address 301 University Blvd, Department of Surgery, MRB5.150, L21875
City Galveston
State/province TX
ZIP/Postal code 77551
Country USA
 
Platform ID GPL16417
Series (2)
GSE102614 Determination of direct binding targets of Quaking RNA binding proteins
GSE102615 Quaking isoform depletion in C2C12 myoblasts; direct binding targets of Quaking RNA binding proteins
Relations
BioSample SAMN07503564
SRA SRX3091900

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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