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Sample GSM3427840 Query DataSets for GSM3427840
Status Public on Mar 01, 2019
Title BRG1_KO-1.gene
Sample type SRA
Source name colon epithelial cells
Organism Mus musculus
Characteristics strain: C57BL/6
genotype/variation: KO
cell type: primary colon epithelial cells
Treatment protocol 1 weeks prior to isolatation of the colon epethelial cells BRG1F/F and Villin-CreERT2 BRG1F/Fmice 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 Total RNA was extracted from cell/tissues using the Trizol (invitrogen) according to the manufacturer’s protocol.
RNA libraries were prepared according to instructions of NEBNext® Ultra™ RNA Library Prep Kit for Illumina
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
Data processing Raw fastq sequences were treated with Trimmomatic tools(v 0.36) using the following options: : TRAILING:20, MINLEN:235 and CROP:235, to remove trailing sequences below a phred quality score of 20 and to achieve uniform sequence lengths for downstream clustering processes.
Sequencing read quality was inspected using the FastQC software. Adapter removal and read trimming were performed using Trimmomatic. Sequencing reads were trimmed from the end (base quality less than Q20) and filtered by length (less than 25).
Paired-end reads were aligned to the mouse reference genome mm10 with HISAT2. HTSeq v0. 6.0 was used to count the reads numbers mapped to each gene. The whole samples expression levels were presented as RPKM (expected number of Reads PerKilobase of transcript sequence per Million base pairs sequenced), which is the recommended and most common method to estimate the level of gene expression.
Genome_build: mm10
Submission date Oct 12, 2018
Last update date Mar 01, 2019
Contact name Yongfeng Liu
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 GPL21493
Series (2)
GSE112128 Function of BRG1 in colitis and colitis-associated-cancer
GSE121206 Function of Epithelium BRG1 in colitis and CAC II
BioSample SAMN10238057
SRA SRX4881809

Supplementary file Size Download File type/resource
GSM3427840_BRG1_KO-1.gene.FPKM.xlsx 1.1 Mb (ftp)(http) XLSX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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