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Sample GSM2758970 Query DataSets for GSM2758970
Status Public on Dec 08, 2017
Title Qki5_CLIP1-3
Sample type SRA
Source name mouse embryonic brain
Organism Mus musculus
Characteristics strain/background: CD1
genotype/variation: wild-type
tissue: brain
developmental stage: E14.5
Treatment protocol Brain tissue was UV irradiated and subjected to Qki5-CLIP.
Partial RNase digestion, RNA linker ligation and PCR amplification.
Extracted molecule total RNA
Extraction protocol Qki5 bound fragments were ligated to a degenerate 3' linker to discriminate derivative tags from 3 different brains.
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina MiSeq
Description Qki5_CLIP1, Qki5_CLIP2, Qki5_CLIP3
Data processing Library strategy: HITS-CLIP
Collapsing of exact sequences.
Stripping of degenerate linker (barcode:First 5nt; ends with a C and next 9nt degenerate linker ends with a C) .
Alignment with Bowtie
to have Bed and wiggle file.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: Bed file, bedGraph file
Submission date Aug 29, 2017
Last update date May 15, 2019
Contact name Masato Yano
Organization name Niigata University
Department Division of Neurobiology and Anatomy
Street address 757, Ichibancho, Asahimachidori, Chuo-ku, Niigata-shi,
City Niigata
ZIP/Postal code 950-0907
Country Japan
Platform ID GPL16417
Series (2)
GSE103247 Qki5 CLIP in E14.5 mouse brain
GSE103248 RNAseq in control and shQk KD mouse neural stem cells, and Qki5 CLIP in E14.5 mouse brain
BioSample SAMN07571968
SRA SRX3144865

Supplementary file Size Download File type/resource
GSM2758970_Qki5_CLIP1-3.bed.gz 7.9 Mb (ftp)(http) BED
GSM2758970_Qki5_CLIP1-3.bedGraph.gz 2.0 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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