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Sample GSM2534812 Query DataSets for GSM2534812
Status Public on Mar 14, 2017
Title primary HSCs infected with shRNA-control, biological rep2
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 2#
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
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
BioSample SAMN06563712
SRA SRX2635293

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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