|
| Status |
Public on Aug 22, 2017 |
| Title |
WT-DSS RNASeq rep1 |
| Sample type |
SRA |
| |
|
| Source name |
DSS treated colon
|
| Organism |
Mus musculus |
| Characteristics |
cell typr: primary colon epithelial cell
tissue: colon
genotype: wild type
|
| Treatment protocol |
mice were treated with 2% DSS for 3 day and isolated the colon epethelial cell
|
| 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 |
| |
|
| Description |
control DSS-1
|
| 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: hg19
|
| |
|
| Submission date |
Jul 26, 2016 |
| Last update date |
May 15, 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 (1) |
| GSE84857 |
The Role of Epithelium EZH2 in Experimental Colitis |
|
| Relations |
| BioSample |
SAMN05441301 |
| SRA |
SRX1978040 |
