|
| Status |
Public on Sep 29, 2021 |
| Title |
F_0.5_ETOH_t_1.5hr |
| Sample type |
SRA |
| |
|
| Source name |
whole embryo
|
| Organism |
Xenopus laevis |
| Characteristics |
strain: wildtype
isolate: female F
dev_stage: st. 11
Sex: not determined
tissue: whole embryo
treatment: 0.5% ETOH t=1.5hr
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For each sample, 5-10 staged embryos were collected and stored at -80°C. RNA purification was performed using the Bio-Rad Aurum Total RNA Mini Kit (according to the manufacturer's instructions). RNA samples were used for cDNA synthesis using the Bio-Rad iScriptTM Reverse Transcription Supermix for RT-qPCR kit (according to the manufacturer's instructions).
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
0.5% ETOH for 2hrs; t=1.5hr after wash
The 0.5% ETOH treatment group was not included in downstream analysis
|
| Data processing |
Single cell scale RNA-seq libraries were sequenced using on an Illumina HiSeq 4000
Raw sequencing data (Illumina sequencer’s base call files (BCLs) was converted to fastq files using the Illumina bcl2fastq program
Reads were mapped to the genome using the Xenopus laevis 9.1 genome with STAR alignment and a modified BLAST and FASTQC in the NGS pipeline
Count data is rlog transformed (package DESeq2), batch corrected (COMBAT algorithm), expression filtered, quantile normalisation, filtered for significance and annotated with gene names.
The 0.5% ETOH treatments were not included in the downstream analysis
Genome_build: Xenopus laevis 9.1
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
|
| |
|
| Submission date |
Jul 14, 2020 |
| Last update date |
Sep 29, 2021 |
| Contact name |
Rajanikanth Vadigepalli |
| E-mail(s) |
rajanikanth.vadigepalli@jefferson.edu
|
| Organization name |
THOMAS JEFFERSON UNIVERSITY
|
| Street address |
1020 LOCUST ST RM 314
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19107 |
| Country |
USA |
| |
|
| Platform ID |
GPL22393 |
| Series (2) |
| GSE154399 |
Robustness of retinoic acid regulatory homeostasis during early development (RNA-seq) |
| GSE154408 |
Asymmetric robustness in the feedback control of the retinoic acid network response to environmental disturbances |
|
| Relations |
| BioSample |
SAMN12905938 |
| SRA |
SRX6943999 |
