|
| Status |
Public on Apr 23, 2019 |
| Title |
16Liver |
| Sample type |
SRA |
| |
|
| Source name |
Liver
|
| Organism |
Zonotrichia albicollis |
| Characteristics |
time: ZT6
migratory status: Migratory
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tissues were dissected and preserved in RNALater and stored at -20 until all samples collected. Total RNA extracted with Qiagen RNeasy Mini kit according to manufacturers protocol, with DNA digestion on columns.
Libraries prepared with Illumina TruSeq Total RNA Library Prep Kit with RiboZero Gold acording to manufacturers protocols and sequenced on an Illumina Hi Seq 2500 @ 100bp, single end reads
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Raw reads were trimmed for quality and adapter sequence using Trimmomatic
Trimmed reads were mapped to our de novo transcriptome using bowtie2
Finally, expression was quantified (both for counts and FPKM) using eXpress
Genome_build: sparrow_heart_transps.fasta & sparrow_liver_transps.fasta
Supplementary_files_format_and_content: tab delimited output for each sample from eXpress, including raw counts and FPKM by transcript
|
| |
|
| Submission date |
Jul 12, 2018 |
| Last update date |
Apr 23, 2019 |
| Contact name |
William J. Horton |
| E-mail(s) |
wjh23@psu.edu
|
| Organization name |
Pennsylvania State University
|
| Department |
Animal Science
|
| Street address |
324 Henning Bldg
|
| City |
University Park |
| State/province |
PA |
| ZIP/Postal code |
16802 |
| Country |
USA |
| |
|
| Platform ID |
GPL25324 |
| Series (1) |
| GSE116989 |
Transcriptome Analyses of Heart and Liver Reveal Novel Pathways for Regulating Songbird Migration |
|
| Relations |
| BioSample |
SAMN09650258 |
| SRA |
SRX4384351 |
