|
| Status |
Public on Oct 09, 2019 |
| Title |
scRNA |
| Sample type |
SRA |
| |
|
| Source name |
scRNA
|
| Organism |
Gallus gallus |
| Characteristics |
genotype/variation: Wild-type
development: Embryo
development: HH8-9
tissue: Neural crest (NC1+ cells)
isolation_method: Dissociation and FACS
treatment: NC1:citrine electroporation at HH4
amplification: 10X Chromium v2
assay: scRNA-seq
|
| Treatment protocol |
Dissected cranial regions from electroporated embryos were dissociated with dispase (1.5mg/ml in DMEM/10mM Hepes pH 7.5) at 37°C for 15min with intermittent pipetting to achieve a single cell suspension and 0.05% Trypsin at 37°C for a final 3min. The reaction was stopped and cells were resuspended in an excess of Hanks buffer. Cells were centrifuged at 500g for 10min and resuspended in Hanks buffer, passed through a 0.22mm filter and centrifuged at 750g for 10min, pelleted cells were resuspended in 500µl Hanks buffer. Fluorescent positive cells were sorted and collected using BD FACS-Aria Fusion.
|
| Growth protocol |
Fertilised wild-type chicken eggs were obtained from Henry Stewart & Co (Norfolk), staged according to Hamburger and Hamilton (1951) (24). All experiments were performed on chicken embryos younger than 12 days of development, and as such were not regulated by the Animals (Scientific Procedures) Act 1986.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Isolated cells were then loaded onto the 10X Chromium machine and libraries prepared as per manufacturer's protocol
As per manufacturer's protocol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Sequenced files were demultiplexed and features counted using CellRanger (v3.0.0)
Seurat (v3.0.1) R package was used for data processing for scRNA samples and the Loupe Cell Browser for the scATAC samples
Genome_build: galGal5. Custom genomes were build using CellRanger to allow proper mapping of reads/fragments.
|
| |
|
| Submission date |
May 23, 2019 |
| Last update date |
Oct 11, 2019 |
| Contact name |
Tatjana Sauka-Spengler |
| E-mail(s) |
tatjana.sauka-spengler@imm.ox.ac.uk
|
| Organization name |
MRC Weatherall Institute of Molecular Medicine
|
| Department |
University of Oxford
|
| Lab |
Sauka-Spengler lab
|
| Street address |
Radcliffe Department of Medicine
|
| City |
Oxford |
| State/province |
Oxfordshire |
| ZIP/Postal code |
OX3 9DS |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL19787 |
| Series (2) |
| GSE121527 |
Reconstruction of the global neural crest gene regulatory network in vivo |
| GSE131688 |
Reconstruction of the global neural crest gene regulatory network in vivo [single cell] |
|
| Relations |
| BioSample |
SAMN11836282 |
| SRA |
SRX5887595 |
