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Sample GSM2787929 Query DataSets for GSM2787929
Status Public on Sep 30, 2019
Title HITS-CLIP_Cortex3
Sample type SRA
Source name cortex
Organism Mus musculus
Characteristics tissue: brain
degenerate linker: 25nt: begins with GCAT or CATG, ends with G
Growth protocol Cells were grown under standard conditions.
Extracted molecule total RNA
Extraction protocol Brain tissue and cell lines were UV irradiated and subjected to Elavl HITS-CLIP (detailed description in accompanying paper)
partial RNAse digestion, RNA linker ligation and PCR amplificiation
Elavl bound fragments were ligated to a degenerate 5'linker and a 3'linker
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina MiSeq
Description Elavl-CLIP
Data processing Library strategy: HITS-CLIP
filtering (min:0-4:20,mean:5-29:20)
collapsing of exact sequences
stripping of 5'degenerate linker (7 or 25nt)
removal of 3'adaptor (GTGTCAGTCACTTCCAGCGG)
alignment with novoalign (unambigous mapping)
collapsing of PCR duplicates
Genome_build: hg19
Supplementary_files_format_and_content: bed file containing genomic coordinates of 50bp region of CLIP peaks
Submission date Sep 19, 2017
Last update date Sep 30, 2019
Contact name Robert Darnell
Organization name Rockefeller University
Street address 1230 York Ave
City New York
State/province New York
ZIP/Postal code 10065
Country USA
Platform ID GPL16417
Series (1)
GSE104025 Elavl HITS-CLIP
BioSample SAMN07672115
SRA SRX3198632

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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