|
| Status |
Public on Jan 27, 2021 |
| Title |
Stage44_Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Brain
|
| Organism |
Xenopus tropicalis |
| Characteristics |
genotype: wildtype
developmetal stage: Stage 44
tissue: Brain
|
| Treatment protocol |
Treatment in drug at stage 30 onward. 5uM for cyclopamine, 10uM for beta-estradiol. No treatment for timecourse data.
|
| Growth protocol |
Standard X. tropicalis growth media
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol-based RNA extraction.
PolyA selection and stranded, low yield library preparation.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
xtrop_timecourse_rawcounts.csv
xtrop_timecourse_filtered_FQ_cpm.csv
|
| Data processing |
Reads were aligned to the XenBase X. tropicalis v9.1 reference genome using STAR v2.7.3 with default parameters and --quantmode GeneCounts to generate raw reads counts.
Read counts were converted to counts per million and filtered to keep only those with more than 1 cpm in at least 3 samples (replicate size).
Full quantile normalization was performed across samples within the two respective experiments (timecourse and small molecule treatments).
Please refer to XenBase JgiToXenbaseGenePage_9.1.txt file for the most up-to-date annotations for each gene ID.
Genome_build: XenBase X. tropicalis v9.1
Supplementary_files_format_and_content: rawcounts.csv, normcounts.csv, filtered_FQ_cpm.csv
|
| |
|
| Submission date |
Aug 03, 2020 |
| Last update date |
Jan 27, 2021 |
| Contact name |
Arthur Jeremy Willsey |
| E-mail(s) |
jeremy.willsey@ucsf.edu
|
| Phone |
4158023105
|
| Organization name |
UCSF
|
| Department |
Psychiatry
|
| Lab |
Willsey Lab
|
| Street address |
675 Nelson Rising Lane, Mail Code 0518
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94143 |
| Country |
USA |
| |
|
| Platform ID |
GPL23182 |
| Series (2) |
| GSE155553 |
Parallel in vivo analysis of large-effect autism genes implicates cortical neurogenesis and estrogen in risk and resilience [Xenopus] |
| GSE155554 |
Parallel in vivo analysis of large-effect autism genes implicates cortical neurogenesis and estrogen in risk and resilience |
|
| Relations |
| BioSample |
SAMN15702325 |
| SRA |
SRX8867449 |
