|
Status |
Public on Jan 27, 2021 |
Title |
Stage47_Rep3 |
Sample type |
SRA |
|
|
Source name |
Brain
|
Organism |
Xenopus tropicalis |
Characteristics |
genotype: wildtype developmetal stage: Stage 47 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 |
SAMN15702346 |
SRA |
SRX8867459 |