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| Status |
Public on Jul 14, 2022 |
| Title |
50 DPH male RA 1 |
| Sample type |
SRA |
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| Source name |
brain
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| Organism |
Taeniopygia guttata |
| Characteristics |
Sex: Male
age: 50 days posthatch
brain id: 1164
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| Growth protocol |
Birds were sacrificed within 20 min of lights-on and no singing was observed in any individual.
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| 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
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| Submission date |
Dec 20, 2021 |
| Last update date |
Jul 14, 2022 |
| Contact name |
Claudio V Mello |
| E-mail(s) |
melloc@ohsu.edu
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| Organization name |
Oregon Health & Science University
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| Department |
Behavioral Neuroscience
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| Street address |
3181 SW Sam Jackson Park Rd, L470
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| City |
Portland |
| State/province |
OR |
| ZIP/Postal code |
97239 |
| Country |
USA |
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| Platform ID |
GPL27119 |
| Series (1) |
| GSE191296 |
Emergence of sex-specific transcriptomes in a sexually-dimorphic brain nucleus |
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| Relations |
| BioSample |
SAMN24250512 |
| SRA |
SRX13458498 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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