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Sample GSM5743104 Query DataSets for GSM5743104
Status Public on Jul 14, 2022
Title 50 DPH female RA 2
Sample type SRA
 
Source name brain
Organism Taeniopygia guttata
Characteristics Sex: Female
age: 50 days posthatch
brain id: 1197R
Growth protocol Birds were sacrificed within 20 min of lights-on and no singing was observed in any individual.
Extracted molecule total RNA
Extraction protocol Brains were removed, flash frozen in a slurry of dry ice and isopropanol, cryosectioned onto PEN membrane glass slides (Leica, No. 11505158), fixed in 100% cold ethanol, and stained using cresyl violet. Brain nucleus RA was extracted from PEN slides into RLT buffer (Qiagen) using laser capture microdissection (Leica LMD 6500). RNA was isolated using the RNeasy Micro Kit (Qiagen) with on-column DNase digestion.
Using the SmartSeq v4 PLUS Kit (Takara Bio USA), cDNAs were generated from 1 ng total RNA , then the resulting cDNA was bioanalyzed on a High Sensitivity DNA chip, and 5 ng was used as input for the libraries.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing Base calls were made by Illumina's RTA v3.4.4
Quality control and trimming were performed prior to genome alignment using trimmomatic (v0.36, parameters ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36), and no issues were detected from FastQC (v0.11.9) reports.
Splice-aware STAR (v2.6.1, parameters --sjdbOverhang 99 --quantMode GeneCounts) was used to align reads and generate read counts per gene based on the bTaeGut1_v1.p zebra finch assembly (GCF_003957565.1) and associated genome features from the NCBI Taeniopygia guttata Annotation Release 104.
Genome_build: GCF_003957565.1
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
 
Submission date Dec 20, 2021
Last update date Jul 14, 2022
Contact name Claudio V Mello
E-mail(s) melloc@ohsu.edu
Organization name Oregon Health & Science University
Department Behavioral Neuroscience
Street address 3181 SW Sam Jackson Park Rd, L470
City Portland
State/province OR
ZIP/Postal code 97239
Country USA
 
Platform ID GPL27119
Series (1)
GSE191296 Emergence of sex-specific transcriptomes in a sexually-dimorphic brain nucleus
Relations
BioSample SAMN24250499
SRA SRX13458511

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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