|
| Status |
Public on Jul 06, 2022 |
| Title |
Sox3U3_rep4, RNAseq |
| Sample type |
SRA |
| |
|
| Source name |
Sox3U3 tagged epibranchial cells
|
| Organism |
Gallus gallus |
| Characteristics |
cell type: Epibranchial placode cells
Stage: ss18-21
treatment: Sox3U3 tagged
|
| Treatment protocol |
Chick embryos were electroporated in ovo at ss3-5 with either Lmx1aE1-EGFP or SoxU3-EGFP plasmids. Cells were dissociated and collected by FACS.
|
| Growth protocol |
Chick embryos were electroporated in ovo and grown at 38°C until reaching the desired stage (ss18-21).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Lmx1aE1-EGFP and Sox3U3-EGFP positive cells were collected into 20ul of lysis buffer.
Libraries were prepared following Nextera Sample low input kit (Illumina, 15028212).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Data was processed and aligned using the NF-core RNAseq v2.0 pipeline (doi: 10.5281/zenodo.1400710).
Reads were trimmed using Trim Galore! Reads were aligned using Star. Read counts were obtained using featureCounts.
Genome_build: galgal6
Supplementary_files_format_and_content: featurecounts.merged.counts.tsv (raw 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) |
| GSE168084 |
Sox8 reprograms ectoderm into ear vesicles and associated neurons [Lmx1aE1_rnaseq] |
| GSE168089 |
Sox8 reprogram ectoderm into ear vesicles and auditory neurons |
|
| Relations |
| BioSample |
SAMN18108866 |
| SRA |
SRX10207149 |
