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Sample GSM2333660 Query DataSets for GSM2333660
Status Public on Dec 15, 2016
Title y53
Sample type SRA
 
Source name brain (hypothalamus + optic chiasma)
Organism Catharus ustulatus
Characteristics migration status: Non-migratory
ecotype: Coastal
Sex: Male
tissue: brain (hypothalamus + optic chiasma)
time of tissue collection (hours after lights on): 4.6
date of tissue collection: 2011-08-08
Treatment protocol Birds were kept in captivity under constant conditions except photoperiod, which was adjusted weekly to mimic natural daylength. Samples were collected 10 weeks apart-- half were collected during the non-migratory period (summer) and half were collected during the migratory period (fall).
Extracted molecule total RNA
Extraction protocol Brain tissue was flash frozen on dry ice. mRNA was extracted using the Trizol Plus RNA Purification Kit, with DNAse treatment with the Ambion RNAse-Free DNAse Set and column cleanup with the PureLink RNA Mini Kit (Invitrogen, Carlsbad, CA USA).
cDNA libraries were synthesized using the TruSeq RNA Sample Preparationv2 kit (Illumina) with TruSeq Indexes.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Data processing Reads were filtered with Trim Galore v.0.3.1 with the following parameters: --q 20 --l 25 --s 3
Reads were mapped to the Ficedula albicollis genome (Ensembl version 1.4.74, unmasked) using Tophat2. Tophat2 parameters were: read-mismatches 16, read-gap-length 10, read-edit-dist 28, splice-mismatches 1, max-insertion-length 12, max-deletion-length 12, max-multihits 5, b2-D 15, b2-N 1, b2-L 20, b2-i S,1,0.50.
The expression level of each gene was quantified using the union mode of the python script htseq-count (HTSeq).
Genes were filtered to only include protein-coding genes.
We used conditional quantile normalization (cqn package in R) to normalize for sequencing depth (TMM), GC-content, and gene length (averaged from the transcripts in the ficalb1.4.74 gtf file).
Genome_build: FicAlb_1.4
Supplementary_files_format_and_content: Tab-delimited text file containing gene transcript abundance measurements. The unit of measure is the log2 transformed read counts controlling for library size, GC content, and gene length, as produced by CQN (R package) and analagous to RPKM.
 
Submission date Oct 03, 2016
Last update date May 15, 2019
Contact name Rachel A Johnston
E-mail(s) racheljohnston7@gmail.com
Organization name Duke University
Department Evolutionary Anthropology
Lab Jenny Tung
Street address 130 Science Dr, Rm 108 Biological Sciences
City Durham
State/province NC
ZIP/Postal code 27708
Country USA
 
Platform ID GPL22518
Series (1)
GSE87549 Seasonal gene expression in a migratory songbird
Relations
BioSample SAMN05858772
SRA SRX2207634

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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