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Sample GSM2157240 Query DataSets for GSM2157240
Status Public on Jun 01, 2017
Title STAT1-/- HSCs treated with IFNγ-2
Sample type SRA
 
Source name hematopoietic stem cells
Organism Mus musculus
Characteristics strain: (C57BL/6 X 129Sv) mixture
tissue: Bone marrow
age: 8-10 weeks
genotype: STAT1-/-
Extracted molecule total RNA
Extraction protocol After 5000 cultured HSCs were sorted, total RNA was extracted using ISOGEN reagent. First strand cDNA were synthesized using a SMARTer Pico cDNA amplification kit. Double-stranded cDNA was then amplified by 18 cycles of PCR.
RNA libraries were prepared for sequencing using standard Thermo Fisher Scientific protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Ion Torrent Proton
 
Description processed data: STAT1_KO_control-vs-IFNg.txt
Data processing Life Technologies Torrent Suite v3.6 software were used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using CLC genomic workbench v7.0.4.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read number and RPKM values for each Sample.
 
Submission date May 18, 2016
Last update date May 15, 2019
Contact name Terumasa Umemoto
Organization name Kumamoto University
Street address 2-2-1, Honjo, Chuo-Ku
City Kumamoto
ZIP/Postal code 862-0957
Country Japan
 
Platform ID GPL18635
Series (1)
GSE81559 mRNA profiles of hematopoieitc stme cells treated with interferon gamma and/or vitronectin
Relations
BioSample SAMN05007280
SRA SRX1771389

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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