|
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
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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.
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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.
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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 |