|
| Status |
Public on Aug 13, 2023 |
| Title |
IL-10 KO-1-18-100nt |
| Sample type |
SRA |
| |
|
| Source name |
Stool
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
profile: Stool
genotype: IL-10-/-
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from the fecal samples was prepared using TRIzol Reagent (Thermo Fisher Scientific). Solexa sequencing was used to identify differentially expressed sRNAs in IL-10 KO chronic colitis mice.
CDNA libraries (18-100 nt and 100-500 nt) were prepared with the TruSeq Small RNA Library Preparation Kit (Illumina, San Diego, CA, USA) and sequenced using an Illumina Genome Analyzer according to the manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
IL-10 KO-18-100nt-rpkm.txt
Control-VS-IL-10_KO-18-100nt.sRNADiffExp.txt
|
| Data processing |
The image files generated by the sequencer were then processed to produce digital data.
The subsequent procedures included summarizing the data produced, evaluating the sequencing quality and depth, and filtering the contaminated reads.
Then, the protein-coding ability of each transcript was predicted using Coding Potential Calculator (CPC) as previously described
The potential sRNAs of B. acidifaciens were predicted by comparison with its genome
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with raw sRNA counts for every sRNA and every sample
Supplementary_files_format_and_content: tab-delimited text file include FPKM values for each Sample ...
|
| |
|
| Submission date |
Jul 24, 2020 |
| Last update date |
Aug 13, 2023 |
| Contact name |
chen Wang |
| E-mail(s) |
[email protected]
|
| Organization name |
Nanjing University
|
| Street address |
xianlin street num 163
|
| City |
Nanjing |
| ZIP/Postal code |
210037 |
| Country |
China |
| |
|
| Platform ID |
GPL11002 |
| Series (2) |
| GSE155039 |
B. acidifaciens-derived small RNA promotes colitis development by targeting mucin 2 to impair the gut mucosal barrier function [IL-10 KO-sRNA-sequence] |
| GSE155041 |
B. acidifaciens-derived small RNA promotes colitis development by targeting mucin 2 to impair the gut mucosal barrier function |
|
| Relations |
| BioSample |
SAMN15638176 |
| SRA |
SRX8817811 |
