|
| Status |
Public on Sep 03, 2021 |
| Title |
Time Course IBD.DAY12.SCI133_05_S5 |
| Sample type |
SRA |
| |
|
| Source name |
Colon
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Colon
treatment: DSS
time point: Day 12
|
| Treatment protocol |
For time course study, mice were treated with 1.5%DSS for 6 days (Day0 to Day6) then switched to drinking water until Day15. For treatment study, 6 shots of murine recombinant Serpina3n or PBS was intravenously injected (20 μg/kg per day) from Day0 to Day5.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA-seq library was constructed using modified Smart-seq2 method.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
processed data file: tc_ibd.count_table.tsv
processed data file: tc_ibd.metadata.tsv
|
| Data processing |
The barcoded sequence was corrected by an edit distance < 2.
The corrected reads were processed using Drop-seq_tools-1.12 (https://github.com/broadinstitute/Drop-seq).
The Drop-seq_tools’ DigitalExpression output was filtered using the numbers of reads, transcripts and genes as well as the percentage of mitochondrial genes for each cell.
The alignment was done with STAR (v2.5b).
Genome_build: ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE63nnn/GSE63472/suppl/GSE63472_mm10_reference_metadata.tar.gz
Supplementary_files_format_and_content: count_table.tsv contains digital gene expression for every sample.
Supplementary_files_format_and_content: metadata.tsv contains various annotation, e.g. sample names, time point, treatment, etc.
|
| |
|
| Submission date |
Apr 16, 2020 |
| Last update date |
Sep 03, 2021 |
| Contact name |
Takashi Shimbo |
| E-mail(s) |
shimbot@sts.med.osaka-u.ac.jp
|
| Organization name |
Osaka university
|
| Street address |
2-2 Yamadaoka
|
| City |
Suita |
| State/province |
Osaka |
| ZIP/Postal code |
5650871 |
| Country |
Japan |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE148794 |
Longitudinal single cell RNA-seq of the inflamed colon |
|
| Relations |
| BioSample |
SAMN14606393 |
| SRA |
SRX8125182 |
