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Sample GSM3562679 Query DataSets for GSM3562679
Status Public on Jul 01, 2019
Title CCL4_CD24 rep2
Sample type SRA
 
Source name CCL4_CD24+ liver progenitor cells
Organism Mus musculus
Characteristics strain: C57BL/6
age: 6-8 weeks
cell type: hepatocytes
cell subtype: MACS-sorted CD24+ cells
treatment: carbon tetrachloride (CCL4)
Treatment protocol 8-week-old mice were i.p. injected with CCL4 (2 ml/kg, Sigma-Aldrich) dissolved in olive oil at a ratio of 1:4 twice a week for 6 weeks.HACY treatment groups were intraperitoneally injected three times a week for 6 weeks.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using RNeasy mini kit (Qiagen, Germany). Total RNA was quantified using a NanoDrop ND-2000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA)
The paired-end libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description CCL4_CD24_2
Data processing Raw data (raw reads) were processed using Trimmomatic. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads.
Then the clean reads were mapped to reference genome using hisat2.
FPKM value of each gene was calculated using cufflinks.
and the read counts of each gene were obtained by htseq-count.
DEGs were identified using the DESeq (2012) R package functions estimate Size Factors and nbinomTest.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized FPKM values and raw fragment counts for each Sample
 
Submission date Jan 15, 2019
Last update date Jul 02, 2019
Contact name yan hexin
E-mail(s) hexinyw@163.com
Organization name Renji Hospital Affiliated to Shanghai Jiaotong University School of Medicine
Street address No. 1630 East Road
City shanghai
ZIP/Postal code 200120
Country China
 
Platform ID GPL17021
Series (1)
GSE125095 Chemically Induced CD24+ hepatocyte-derived liver progenitor-like cells revert chronic hepatic dysfunction
Relations
BioSample SAMN10744212
SRA SRX5250612

Supplementary file Size Download File type/resource
GSM3562679_CCL4_CD24_2.txt.gz 157.6 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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