|
| Status |
Public on Nov 01, 2019 |
| Title |
EAE107 Co dist B2-0 |
| Sample type |
SRA |
| |
|
| Source name |
distal colon tissue
|
| Organism |
Mus musculus |
| Characteristics |
tissue: distal colon tissue
condition: Trp-def
strain: C57BL/6
gender: female
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from frozen colon whole tissues of the mice using the RNeasy mini kit from Qiagen using standard protocol. The frozen tissue samples were homogenized using Tissue Lyser II for the RNA extraction.
Individual strand-specific single-end sequencing libraries were constructed from the total RNA isolated from the samples using TruSeq Stranded mRNA kit (Illumina Inc.). Sequencing was performed on the Illumina HiSeq3000 (1 x 50 bp) using standard protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
colonic tissue from mouse under Tryptophan-deficient diet
H01577
|
| Data processing |
Sequence reads from were trimmed for adapters using the software Trimgalore (version 0.4.4)
All filtered reads were mapped to the GRCm38 reference using the software STAR (version 2.5.2b)
Expression counts of genes were estimated using featureCounts (version 1.5.2)
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files with expression counts for each sample
|
| |
|
| Submission date |
Feb 26, 2019 |
| Last update date |
Nov 02, 2019 |
| Contact name |
Neha Mishra |
| E-mail(s) |
n.mishra@ikmb.uni-kiel.de
|
| Organization name |
Institute of Clinical Molecular Biology
|
| Lab |
Cell biology Lab
|
| Street address |
Rosalind-Franklin-Str. 12
|
| City |
Kiel |
| ZIP/Postal code |
24105 |
| Country |
Germany |
| |
|
| Platform ID |
GPL21493 |
| Series (1) |
| GSE127190 |
RNA-sequencing analysis of colon tissue in a murine EAE model after dietary tryptophan deprivation. |
|
| Relations |
| BioSample |
SAMN11022252 |
| SRA |
SRX5431570 |
