|
| Status |
Public on Oct 08, 2022 |
| Title |
F74 |
| Sample type |
SRA |
| |
|
| Source name |
control F exposed to saline M
|
| Organism |
Coturnix japonica |
| Characteristics |
tissue: blood
treatments: M_SAL
female injection: SAL
male treatment: SAL
|
| Extracted molecule |
total RNA |
| Extraction protocol |
An aliquot of blood was placed in Qiazol lysis reagent and homogeneized; Total RNA was extracted from the aqueous layer formed after chloroform precipitation, using the RNA Clean & Concentrator Kit-5 (Zymo Research, item # R1013) following manufacturer’s instructions and including the DNase I in-column treatment step.
RNA libraries were prepared for sequencing using NEBNext® UltraTM RNA Library Prep Kit, following standard protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.8.2
Data filtering: reads containing adapters, reads containing N > 10% and low quality reads were filtered out
Mapping was done using HISAT2
Normalized abundance counts were generated using the DESeq2 R package
Genome_build: GCA_001577835.1 Coturnix_japonica_2.0
Supplementary_files_format_and_content: tab-delimited text file includes raw (not normalized) readcount values for each sample
|
| |
|
| Submission date |
May 07, 2021 |
| Last update date |
Oct 08, 2022 |
| Contact name |
Patricia C Lopes |
| E-mail(s) |
lopes@chapman.edu
|
| Organization name |
Chapman University
|
| Department |
Biological Sciences
|
| Street address |
450 N Center St
|
| City |
Orange |
| State/province |
CA |
| ZIP/Postal code |
92866 |
| Country |
USA |
| |
|
| Platform ID |
GPL29461 |
| Series (1) |
| GSE174094 |
Blood transcripts from female Japanese quail given LPS injection or saline |
|
| Relations |
| BioSample |
SAMN19070839 |
| SRA |
SRX10818057 |
