|
| Status |
Public on Aug 19, 2022 |
| Title |
Nopp1-2 |
| Sample type |
SRA |
| |
|
| Source name |
Ileum
|
| Organism |
Sus scrofa |
| Characteristics |
tissue: Ileum
tissue dissection: Ileum without Peyer's patches
breed: Mixed-breed
age: Seven weeks
gender: Female
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
10X Chromium Single Cell Gene Expression assay with v2 chemistry was used to constuct single-cell cDNA libraries
Libraries were prepared for 2x100 paired end sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
NoPP1
|
| Data processing |
R2 Illumina reads were corrected using R-corrector
3’ polyA tails longer than 10 bases were trimmed using custom Perl scripts
R2 longer than 25 bases were re-paired using BBMap
Read were aligned using CellRanger v4.0.6
Genome_build: Sus Scrofa 11.1
Genome_build: Annotation build: Sus Scrofa 11.1.97
Supplementary_files_format_and_content: Raw count matrix (matrix.mtx), cell barcodes (barcode.tsv) & gene feature table (feature.tsv) files in gun zipped format
|
| |
|
| Submission date |
Feb 08, 2022 |
| Last update date |
Aug 19, 2022 |
| Contact name |
Sathesh K Sivasankaran |
| E-mail(s) |
sathesh@iastate.edu
|
| Organization name |
University of Missouri
|
| Lab |
Bioinformatics and Analytics Core
|
| Street address |
Bond Life Sciences Center Suite 106, 1201 Rollins Street
|
| City |
Columbia |
| State/province |
MO |
| ZIP/Postal code |
65211 |
| Country |
USA |
| |
|
| Platform ID |
GPL24486 |
| Series (1) |
| GSE196388 |
Porcine intestinal innate lymphoid cells and lymphocyte spatial context revealed through single-cell RNA sequencing |
|
| Relations |
| SRA |
SRX14034153 |
| BioSample |
SAMN25558060 |
