|
| Status |
Public on Dec 05, 2019 |
| Title |
CA_fgfr1_2 |
| Sample type |
SRA |
| |
|
| Source name |
Dissected hindbrain and surrounding tissues
|
| Organism |
Danio rerio |
| Characteristics |
tissue: Dissected hindbrain and surrounding tissues
Stage: 24-25hpf
strain: Tg(hsp70:ca-fgfr1)
genotype: constitutively active fgfr1
growth: 28.5°C until 22hpf, 30min at 38.5°C, 2hr 28.5°C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Embryos were decorionated and deyolked in DMEM with high Glucose, no Glutamine, no Calcium (11530556, Gibco); hindbrains were micro-dissected using 0.33mm micro-fine sterile needles; RNA was isolated using Quick-RNA Microprep kit (Zymo Research).
Samples were prepared with the Clontech SMARTer kit (634926, TaKaRa) for cDNA amplification, followed by NexteraXT (Illumina) for library preparation.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Reads were and aligned against zebrafish genome GRCz10 and Ensembl release 86 transcript annotations using STAR v2.5.1b via the transcript quantification software RSEM v1.2.31
RSEM estimated gene level counts were rounded to integers
Genome_build: GRCz10
Supplementary_files_format_and_content: Tab-delimited counts matrix with row representing genes and columns representing samples.
|
| |
|
| Submission date |
Dec 04, 2019 |
| Last update date |
Dec 06, 2019 |
| Contact name |
David Wilkinson |
| E-mail(s) |
david.wilkinson@crick.ac.uk
|
| Phone |
+44 2037961638
|
| Organization name |
The Francis Crick Institute
|
| Street address |
1 Midland Road
|
| City |
London |
| ZIP/Postal code |
NW1 1AT |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL21741 |
| Series (2) |
| GSE141426 |
A single cell transcriptome atlas of the developing zebrafish hindbrain [fgfr1] |
| GSE141428 |
A single cell transcriptome atlas of the developing zebrafish hindbrain |
|
| Relations |
| BioSample |
SAMN13477447 |
| SRA |
SRX7267028 |
