|
| Status |
Public on Apr 11, 2018 |
| Title |
4BCBneg_1_S17 |
| Sample type |
SRA |
| |
|
| Source name |
metaphase II oocyte
|
| Organism |
Sus scrofa |
| Characteristics |
breed: commercial hybrid (Large White, Duroc and Berkshire)
cell type: metaphase II oocyte
developmental stage: mature oocyte
mtdna state: deficient
sample type: single cell
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA samples which are labelled with the word "SPIA" were extracted using Arcturus Picopure RNA extraction kit; RNA samples from single cells were prepared from in-tube extraction.
SPIA libraries were prepared using Nugen Ovation RNA-seq system V2 and Ovation Ultralow system V2; SoLo libraries were prepared using Nugen SoLo kit with Sus scrofa InDA-C primer mix.
RNA sequencing 100 bp paired end reads on Illumina HiSeq 3000.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
processed data file: gene_counts1.txt
|
| Data processing |
Data QC using fastqc and trimgalore.
Alignment of the reads with pig genome using tophat2 v2.0.14.
Differential expression analysis was done using RUVseq (RUVr) and edgeR.
Genome_build: GCF_000003025.5_Sscrofa10.2
Supplementary_files_format_and_content: gene_counts1.txt: Tab-delimited text table of geneX raw counts in single cell samples.
Supplementary_files_format_and_content: gene_counts2.txt: Tab-delimited text table of geneX raw counts in pooled samples.
|
| |
|
| Submission date |
Jan 08, 2018 |
| Last update date |
Apr 11, 2018 |
| Contact name |
Tesha Tsai |
| E-mail(s) |
tesha.tsai@gmail.com
|
| Phone |
+61422912625
|
| Organization name |
Hudson Institute of Medical Research
|
| Street address |
27-31 Wright Street, Clayton
|
| City |
Melbourne |
| State/province |
Vic |
| ZIP/Postal code |
3168 |
| Country |
Australia |
| |
|
| Platform ID |
GPL24486 |
| Series (1) |
| GSE108900 |
The molecular characterisation of mitochondrial DNA deficient oocytes using a pig model |
|
| Relations |
| BioSample |
SAMN08328476 |
| SRA |
SRX3541954 |
