|
| Status |
Public on Mar 01, 2019 |
| Title |
BRG1_KO-2.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 |
| 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 |
GPL21493 |
| Series (2) |
| GSE112128 |
Function of BRG1 in colitis and colitis-associated-cancer |
| GSE121206 |
Function of Epithelium BRG1 in colitis and CAC II |
|
| Relations |
| BioSample |
SAMN10238060 |
| SRA |
SRX4881810 |
