|
| Status |
Public on Jul 17, 2019 |
| Title |
NA-03-3-SAL-HYP_S3 |
| Sample type |
SRA |
| |
|
| Source name |
Hypothalamus/Saline
|
| Organism |
Taeniopygia guttata |
| Characteristics |
agent: 0.9 percent saline
time point: 2 hours post-injection
tissue: hypothalamus
|
| Treatment protocol |
For hypothalamus and spleen samples, four birds from the from the captive colony at Western Kentucky University were injected i.p. with bacterial lipopolysaccharide (Escherichia coli) at a dose of 2 mg/kg BW. An additional four birds served as controls, and were injected with vehicle (0.9% saline). For red blood cell samples, six male zebra finch from the captive colony were injected i.p. with bacterial lipopolysaccharide (Escherichia coli) at a dose of 2mg/kg BW (dissolved in 0.9% saline). An additional six males served as controls injected with vehicle (0.9% saline).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Birds were euthanized at 2 h post-injection and tissue samples collected. Red blood cells were extracted from the trunk.The density gradient media Polymorphprep (Axis-Shield) was used to separate whole blood into the components of plasma, mononuclear white blood cells, polymorphonuclear white blood cells, and red blood cells. This media allowed the removal of polymorphonuclear white blood cells that would remain within the red blood cell layer by other separation methods. Total RNA was isolated using an RNeasy Kit (Qiagen) with a modified protocol involving Trizol (Life Technologies).
Libraries were prepared using the SMART-Seq v4 Ultra Low Input RNA Kit; Clonetech Catalog# 634889 and Nextera XT DNA; Illumina Catalog# FC-131-1024
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Illumina BaseSpace FastQ v1.0.0 used for basecalling
Raw sequences were checked for quality values using fastQC v0.10.1. Quality trimming was not deemed necessary.
Raw sequences were mapped to the Taeniopygia guttata genome assembly (Tg.fa) using tophat2 v2.0.13 generating alignments in bam format, using an Ensembl gene and transcript gtf as a guide.
Mapped reads were assembled according to the Ensembl taeGut3.2.4.84.gtf file using cufflinks v2.2.1.
The resulting mapped files from cufflinks were normalized and concatenated into a single tab-delimited gene matrix file using cuffnorm.
Differentially expressed genes were identified using cuffdiff v2.2.1.
Genome_build: taeGut3
Supplementary_files_format_and_content: FPKM
|
| |
|
| Submission date |
Oct 16, 2018 |
| Last update date |
Jul 17, 2019 |
| Contact name |
Eric Christian Rouchka |
| E-mail(s) |
eric.rouchka@louisville.edu
|
| Organization name |
University of Louisville
|
| Department |
Biochemistry and Molecular Genetics
|
| Lab |
KY INBRE Bioinformatics Core
|
| Street address |
522 East Gray Street
|
| City |
Louisville |
| State/province |
Kentucky |
| ZIP/Postal code |
40292 |
| Country |
USA |
| |
|
| Platform ID |
GPL22780 |
| Series (1) |
| GSE121348 |
Transcriptomics of the Avian Immune Response in Hypothalamus, Spleen, and Red Blood Cells using RNA-seq |
|
| Relations |
| BioSample |
SAMN10247611 |
| SRA |
SRX4893353 |
