|
| Status |
Public on Jun 03, 2020 |
| Title |
s5_E8_F |
| Sample type |
SRA |
| |
|
| Source name |
embryonic left gonad cells
|
| Organism |
Gallus gallus |
| Characteristics |
num individuals: 1
Sex: Female
developmental stage: E8.5
tissue: embryonic gonad (left)
|
| Growth protocol |
Fertile chicken eggs were incubated at 37.5°C such that different developmental stages were reached on the same day.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Chromium Single Cell 3' Library & Gel Bead Kit V2
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
5_E8-SF_S5
|
| Data processing |
Alignment - Reads aligned to chicken genome (protein-coding and lincRNA from ensembl v92 annotation) with cellRanger (v2.0.1, –force-cells) using STAR (v2.5.1b). The gene annotation was extended to include reads aligned just downstream, adding an extra 1000bp downstream of the last exon of each transcript. Samples aggregated without normalisation.
Gene quantification with featureCounts (subread v1.6.1, parameters: -s 1 -R BAM -O), and UMI-tools (v0.5.4)
Filtered to cells with at least 500 reads across 100 diffferent genes with no more than 30% of counts belonging to the 5 most abundant genes. Filtered to genes in at least 20 cells (in any sample). Using scran(v1.8.4) and Scater (v1.6.3).
Genome_build: galgal5
Supplementary_files_format_and_content: counts file
|
| |
|
| Submission date |
Jan 09, 2020 |
| Last update date |
Jun 03, 2020 |
| Contact name |
Craig Allen Smith |
| E-mail(s) |
Craig.Smith@monash.edu
|
| Phone |
61399050203
|
| Organization name |
Monash University
|
| Department |
Anatomy and Developmental Biology
|
| Lab |
Comparative Development
|
| Street address |
Wellington Road
|
| City |
Clayton |
| State/province |
Victoria |
| ZIP/Postal code |
3800 |
| Country |
Australia |
| |
|
| Platform ID |
GPL19787 |
| Series (1) |
| GSE143337 |
New insights into gonadal sex differentiation provided by single cell transcriptomics in the chicken embryo |
|
| Relations |
| BioSample |
SAMN13783749 |
| SRA |
SRX7526493 |
