|
Status |
Public on Jul 06, 2022 |
Title |
ss11_211131, scRNAseq |
Sample type |
SRA |
|
|
Source name |
Pax2+ cells
|
Organism |
Gallus gallus |
Characteristics |
cell type: Pax2+ cells Stage: ss11
|
Treatment protocol |
Chick embryos were electroporated at head fold stage with pTK-Pax2E1-EGFP plasmids.
|
Growth protocol |
Chick embryos were electroporated and grown at 38°C until reaching the desired stage.
|
Extracted molecule |
total RNA |
Extraction protocol |
EGFP+ single cells were individually collected by FACS into 96 well plates. Libraries were prepared following SmartSeq2 NexteraXT indications. single cell RNA seq
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 4000 |
|
|
Data processing |
All data was processed using a custom Nextflow pipeline available at https://github.com/alexthiery/otic-reprogramming. All packages and versions are containerised in Docker images called by the pipeline. Full documentation of pipeline parameters and how to reproduce the analysis is available at https://alexthiery.github.io/otic-reprogramming/ Adaptor sequences were trimmed using cutadapt v2.10, aligned using hisat2 v2.2.1, sorted using samtools v1.10, and read counts obtained using htseq v0.12.4. RNA velocity counts were obtained using Velocyto v0.17.17. Genome_build: galgal6 Supplementary_files_format_and_content: assayData.csv (raw counts) phenoData.csv (sample metadata) gfpData.csv (raw gfp counts) onefilepercell_ss8-TSS_P2_C10_75_and_others_TVIUH.loom (raw velocyto counts)
|
|
|
Submission date |
Mar 02, 2021 |
Last update date |
Jul 06, 2022 |
Contact name |
Andrea Streit |
Organization name |
Kings College London
|
Department |
Centre for Craniofacial & Regenerative Biology
|
Street address |
Guys Hospital, Great Maze Pond
|
City |
London |
ZIP/Postal code |
SE1 9RT |
Country |
United Kingdom |
|
|
Platform ID |
GPL23499 |
Series (2) |
GSE168088 |
Sox8 reprogram ectoderm into ear vesicles and auditory neurons [smartseq2] |
GSE168089 |
Sox8 reprogram ectoderm into ear vesicles and auditory neurons |
|
Relations |
BioSample |
SAMN18110580 |
SRA |
SRX10208057 |