|
| Status |
Public on Nov 18, 2020 |
| Title |
bulk RNA-seq_WT H2O replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
Colon
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Colon
age: 16 Week
genotype: wild type
treatment: H2O
Sex: female
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The frozen tissues were disaggregated using a motorized homogenizer followed by RNA extraction using the RNeasy Mini Kit (QIAGEN)
RNA libraries were prepared for sequencing using TruSeq Stranded mRNA Library Prep Kit (Illumina)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
MEKK2 KO RNASeq.xlsx
|
| Data processing |
Illumina Bcl2fastq software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie2
HTSeq-count was used to enumerate transcripts associated with each gene
Genome_build: mm10
Supplementary_files_format_and_content:tab-delimited text files include CPM values for each Sample
|
| |
|
| Submission date |
Nov 17, 2020 |
| Last update date |
Nov 18, 2020 |
| Contact name |
Hongxiang Sun |
| E-mail(s) |
sun758426@sjtu.edu.cn
|
| Organization name |
Shanghai Jiaotong University
|
| Department |
Shanghai Institute of Immunology
|
| Lab |
Bing Su
|
| Street address |
280 South Chongqing Rd.
|
| City |
Shanghai |
| ZIP/Postal code |
200025 |
| Country |
China |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE156245 |
Map3k2-regulated intestinal stromal cells define a distinct intestine stem cell niche for tissue repair |
|
| Relations |
| BioSample |
SAMN13547454 |
| SRA |
SRX7352064 |
