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Sample GSM2534811 Query DataSets for GSM2534811
Status Public on Mar 14, 2017
Title primary HSCs infected with shRNA-control, biological rep1
Sample type SRA
 
Source name primary HSCs infected with shRNA-control
Organism Mus musculus
Characteristics strain: Balb/c
tissue: liver
cell type: primary HSCs
Stage: day 6
infection: shRNA-control
Treatment protocol primary HSCs infected with shRNA-control (n=2), lncRNA-shRNA1 (n=2) and lncRNA-shRNA3 (n=2)
Growth protocol primary HSCs were cultured in Dulbecco’s modified Eagle’s medium (Invitrogen, Carlsbad, CA) supplemented with 10% fetal bovine serum, penicillin (100 U/ml) and streptomycin (100 μg/ml)
Extracted molecule total RNA
Extraction protocol RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model HiSeq X Ten
 
Description shRNA-control 1#
Data processing Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
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: mm8
Supplementary_files_format_and_content: tab-delimited text files include raw and normalized counts for each Sample
 
Submission date Mar 13, 2017
Last update date May 15, 2019
Contact name Kun Zhang
E-mail(s) zhangkun@tmu.edu.cn
Phone 022-83336819
Organization name Tianjin medical university
Department Department of Histology and Embryology
Street address Qixiangtai Road NO.22
City Tianjin
ZIP/Postal code 300070
Country China
 
Platform ID GPL21273
Series (1)
GSE96526 Expression data that were specifically regulated by lncRNA-LFAR1 in mouse primary HSCs
Relations
BioSample SAMN06563713
SRA SRX2635292

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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