|
Status |
Public on Oct 08, 2022 |
Title |
F76 |
Sample type |
SRA |
|
|
Source name |
LPS F exposed to saline M
|
Organism |
Coturnix japonica |
Characteristics |
tissue: blood treatments: F_LPS female injection: LPS 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 |
SAMN19070859 |
SRA |
SRX10818058 |