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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