|
| Status |
Public on Mar 01, 2019 |
| Title |
BRG1_KO.gene |
| Sample type |
SRA |
| |
|
| Source name |
colon epithelial cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
genotype/variation: BRG1_KO
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 |
SAMN08742755 |
| SRA |
SRX3823518 |
