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Sample GSM3056990 Query DataSets for GSM3056990
Status Public on Mar 01, 2019
Title BRG1_WT.gene
Sample type SRA
 
Source name colon epithelial cells
Organism Mus musculus
Characteristics strain: C57BL/6
genotype/variation: BRG1_WT
cell type: primary colon epithelial cells
Treatment protocol 2 weeks prior to isolatation of the colon epethelial cells WT and Villin-CreERT2 mice are intraperitoneal injected with Tamoxifen and then colon epithelial cells are isolated by EDTA digestion
Growth protocol no treatment
Extracted molecule total RNA
Extraction protocol RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) 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 Illumina HiSeq 4000
 
Data processing Filtering steps are as follows:1) Remove reads with adaptors;2) Remove reads in which unknown bases are more than 10%;3) Remove low quality reads (the percentage of low quality bases is over 50% in a read, we define the low quality base to be the base whose sequencing quality is no more than 5).
Use Bowtie2 to map clean reads to reference gene and use BWA to reference genome.
FPKM method is used in calculated expression level
Genome_build: mm10
Supplementary_files_format_and_content: FPKM
 
Submission date Mar 20, 2018
Last update date Mar 01, 2019
Contact name Yongfeng Liu
E-mail(s) lyf3433@163.com
Organization name The Institute of Health Sciences, SIBS, CAS / SJTUSM
Street address 320 Yueyang Road, Shanghai, 200025 P.R. China
City shanghai
ZIP/Postal code 200025
Country China
 
Platform ID GPL21103
Series (2)
GSE112069 Function of Epithelium BRG1 in colitis and CAC
GSE112128 Function of BRG1 in colitis and colitis-associated-cancer
Relations
BioSample SAMN08742754
SRA SRX3823519

Supplementary file Size Download File type/resource
GSM3056990_BRG1_WT.gene.FPKM.txt.gz 236.5 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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