NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM3397534 Query DataSets for GSM3397534
Status Public on Apr 01, 2020
Title F-CT1
Sample type SRA
 
Source name Sinusoidal endothelial cells
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: liver
age: 12-14 weeks
cell type: Sinusoidal endothelial cells
Treatment protocol For conditional deletion of endothelial RBPj, male mice of four to six-week-old were injected intraperitoneally once a day with tamoxifen (2mg/20g body weight) for totally seven days, and were allowed to rest for another week after the last injection. To establish liver fibrosis, mice were subjected to intraperitoneal injection of CCl4 (0.6ul/g body weight, diluted in olive oil to yield a final concentration of 15%) twice a week for total six weeks. After the last CCl4 injection, SECs were isolated and RNA samples were obtained.
Extracted molecule total RNA
Extraction protocol Control SECs and RBPj knock out SECs were isolated and total RNA was immediatly isolated from the cells using Trizol (Invitrogen) according to standard protocols.
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
 
Data processing Illumina Bcl2FastQ  software 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 Tophat2 v2.0.13 with parameters --read_mismatches 2 --read_gap_length 2 --read_edit_dist 2
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 RPKM values and counts for each Sample
 
Submission date Sep 21, 2018
Last update date Apr 01, 2020
Contact name Bai Ruan
E-mail(s) bairuan@fmmu.edu.cn
Organization name Fourth Military Medical University
Street address No.169, Changle Road
City Xi'an
State/province Shannxi
ZIP/Postal code 710032
Country China
 
Platform ID GPL21493
Series (2)
GSE120282 RNA-sequence data of liver sinusoidal endothelial cells from control and endothelial RBPj-deficent mice with liver fibrosis
GSE120283 RNA-sequence data of liver sinusoidal endothelial cells in quiescent versus fibrotic and wild-type versus endothelial RBPj-deficent mice
Relations
BioSample SAMN10101960
SRA SRX4725922

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap