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Sample GSM5128050 Query DataSets for GSM5128050
Status Public on Jul 06, 2022
Title ss8_P2A7, scRNAseq
Sample type SRA
 
Source name Pax2+ cells
Organism Gallus gallus
Characteristics cell type: Pax2+ cells
Stage: ss8
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 SAMN18110365
SRA SRX10207732

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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