|
| Status |
Public on Nov 13, 2020 |
| Title |
Meninges_Colitis_3 |
| Sample type |
SRA |
| |
|
| Source name |
Colon
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57bl/6
treatment: DSS
|
| Treatment protocol |
Mice recived 2%DSS for the first 5 days in drinking water after which it was replaced with normal water. The mice were culled after 6 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Meninges were extracted into RNA later and stored at -80 until processing. RNA was extracted with RNEasy plus micro kit (Qiagen)
Libraries were produced with TruSeq stranded total RNA library prep kit (Illumina)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
9
|
| Data processing |
Files were demutiplexed using Casava
Reads were checked for quality with FastQC and trimmed using TrimGalore!
Trimed reads were alligned to the mm10 genome with Hisat2 and counted usign Feature Counts from Rseubread
Genome_build: mm10
|
| |
|
| Submission date |
Aug 12, 2019 |
| Last update date |
Nov 13, 2020 |
| Contact name |
John Robert Ferdinand |
| Organization name |
University of Cambridge
|
| Street address |
Department of Medicine
|
| City |
Cambridge |
| ZIP/Postal code |
CB2 0QH |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
|
| Relations |
| BioSample |
SAMN12561867 |
| SRA |
SRX6706717 |
