|
| Status |
Public on Jan 18, 2024 |
| Title |
VA11 |
| Sample type |
SRA |
| |
|
| Source name |
skin
|
| Organism |
Taeniopygia guttata |
| Characteristics |
tissue: skin
age: hh28
genotype: wild type
location: ventral anterior
|
| Growth protocol |
Male and female individuals of Taeniopygia guttata were obtained from local suppliers (Oisellerie du Temple, Animotopia) and bred in the bird facility of the Collège de France for collection of fertilized eggs. Fertilized eggs were incubated at 37°C in Brinsea ova-easy 190 incubators.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Skin was dissected out on ice, kept in RNA later and stored at -80°C until RNA extraction was performed. Total RNA was extracted using the Rneasy micro kit (Qiagen) following the manufacturer's protocol.
10 ng of total RNA were amplified and converted to cDNA using SMART-Seq v4 Ultra Low Input RNA kit (Clontech). An average of 150 pg of amplified cDNA was used for library preparation following Nextera XT DNA kit (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Deseq2_normalized_gene_expression_with_annotations.txt
|
| Data processing |
Sequencing, data quality, reads repartition (e.g., for potential ribosomal contamination), and insert size estimation were performed using FastQC, Picard-Tools, Samtools and rseqc
Reads were mapped using STAR_2.4.0
Genome_build: taeGut1
Supplementary_files_format_and_content: Tab-delimited text file includes deseq2 normalized expression values for each gene and for each sample. Annotations from Zebrafinch FAST DB v2017_1 were also provide
|
| |
|
| Submission date |
Jan 19, 2021 |
| Last update date |
Jan 18, 2024 |
| Contact name |
Noémie Robil |
| E-mail(s) |
noemie.robil@genosplice.com
|
| Organization name |
GenoSplice technology
|
| Department |
Paris Biotech Santé
|
| Street address |
29, rue du Faubourg Saint-Jacques
|
| City |
Paris |
| ZIP/Postal code |
75014 |
| Country |
France |
| |
|
| Platform ID |
GPL19155 |
| Series (1) |
| GSE165119 |
A conserved paint box underlies color pattern diversity in Estrildid finches. |
|
| Relations |
| BioSample |
SAMN17384380 |
| SRA |
SRX9898281 |
