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Sample GSM3425821 Query DataSets for GSM3425821
Status Public on Jan 15, 2019
Title P310.ms3.
Sample type SRA
 
Source name brain
Organism Mus musculus
Characteristics strain: C57BL/6
developmental age: P308
Extracted molecule total RNA
Extraction protocol OPCs were isolated from wild-type mice using magnetic cell sorting (MACS, Miltenyi Biotec). OPCs were enriched using microbeads conjugated to monoclonal PDGFRα (#130-101-502, Miltenyi). After OPC enrichment RNA was extracted using RNeasy Micro Kit (Qiagen) according to manufacturer’s instructions.
RNA libraries were prepared for sequencing using the SMARTer® Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian kit, according to manufacturer's instructions.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description Myelin debris were removed from single-cell suspension by myelin removal beads (#130-096-733, Miltenyi) prior to OPC enrichment.
Data processing RNA-seq reads were pre-processed and quality-trimmed using Trim Galore ! https://www.bioinformatics.babraham.ac.uk/projects/trim_galore). Reads were aligned to the mouse reference genome GRCm38/mm10 using Tophat (version 2.1.1, https://ccb.jhu.edu/software/tophat/index.shtml) allowing for one mismatch and selecting uniquely mapping reads only. Read counts per ENSEMBL (version 92) were obtained by featureCounts (http://bioinf.wehi.edu.au/featureCounts).
Supplementary_files_format_and_content: Read counts per ENSEMBL transcript (version 92) obtained by featureCounts.
 
Submission date Oct 10, 2018
Last update date Jan 15, 2019
Contact name Sabine Dietmann
Organization name Washington University School of Medicine
Street address 4565 McKinley Avenue
City St Louis
State/province MO
ZIP/Postal code 63110
Country USA
 
Platform ID GPL13112
Series (1)
GSE121083 Oligodendrocyte progenitor cells become regionally diverse and heterogeneous with age
Relations
BioSample SAMN10228451
SRA SRX4824738

Supplementary file Size Download File type/resource
GSM3425821_old.ms3.counts.txt.gz 2.4 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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