|
| Status |
Public on Oct 29, 2019 |
| Title |
Pregnant stromal cells [PS39] |
| Sample type |
SRA |
| |
|
| Source name |
endometria
|
| Organism |
Sus scrofa |
| Characteristics |
tissue: stromal cells
group: pregnant pig on Day 14 of gestation
|
| Extracted molecule |
total RNA |
| Extraction protocol |
PicoPure RNA Isolation Kit
Ovation SoLo Single Cell RNA-Seq System
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
PS39
|
| Data processing |
The obtained sequence reads (Fastq files) were analyzed with a locally installed version of Galaxy
The adapter sequence was clipped (for shorter fragments where sequencing runs into the adapter) and 5 bp were removed from the start of the reads
Reads were filtered by CPM cutoff after removing the PCR duplicates with NUGEN nudup
The resulting read count table was used for statistical analysis in EdgeR to identify differentially expressed genes
note: R2 reads: UMI sequences to recognize PCR duplicates
Genome_build: Sscrofa 11.1
Supplementary_files_format_and_content: tabular.gz; Before cpm filter
Supplementary_files_format_and_content: _filter.tabular.gz; After cpm filter
|
| |
|
| Submission date |
Dec 03, 2018 |
| Last update date |
Oct 29, 2019 |
| Contact name |
Stefan Michael Bauersachs |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Zurich
|
| Department |
Department for Farm Animals
|
| Lab |
Genetics and Functional Genomics
|
| Street address |
Eschikon 27 EHB 23.1
|
| City |
Lindau |
| State/province |
Zurich |
| ZIP/Postal code |
8315 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL19176 |
| Series (1) |
| GSE123265 |
Spatial organization of endometrial gene expression at the onset of embryo attachment in pigs |
|
| Relations |
| BioSample |
SAMN10517139 |
| SRA |
SRX5088590 |
