GEO Accession viewer

NCBI > GEO > Accession Display

Not logged in | Login

GEO help: Mouse over screen elements for information.

Sample GSM2157222

Query DataSets for GSM2157222

Status

Public on Jun 01, 2017

Title

Wt HSCs treated with VN-4

Sample type

SRA

Source name

hematopoietic stem cells

Organism

Mus musculus

Characteristics

strain: C57BL/6
tissue: Bone marrow
age: 8-10 weeks
genotype: wild type

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: Wt_Control-vs-VN.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