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| Status |
Public on Apr 07, 2021 |
| Title |
JD-9 |
| Sample type |
SRA |
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| Source name |
telencephalon
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| Organism |
Taeniopygia guttata |
| Characteristics |
Sex: F
age (days post hatching): 20dph
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| Growth protocol |
For RNA-seq, zebra finches (Taeniopygia guttata) were bred and raised at the University of Liège in an aviary containing 20 nest boxes maintained in a 13:11h light:dark cycle. Birds were provided ad libitum with food, water, grit and cuttlebone, and additional millet branches and egg food. Sprouted sunflower seeds were provided twice and nesting material once per week. The experiment was performed according to the Belgian law on animal experimentation and approved by the Ethical Committee for Animal Experimentation at the University of Liège (protocol 1396).
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| Extracted molecule |
total RNA |
| Extraction protocol |
Brains from male and female juvenile and adult zebra finches (age: 1, 20, 65 (± 3 days) and adults (> 170) dph) were used, with birds from one nest randomly assigned to different age groups. Birds were rapidly decapitated, and the brain immediately removed and handled under ribonuclease-free conditions. The telencephalon was separated from the rest of the brain. The brain tissue was rapidly frozen on dry ice and stored at -80°C until further processing.
Telencephalon samples were lysed in QiazolTM lysis reagent (Qiagen 79306) using a TissueLyser instrument (Qiagen 85300). RNA was extracted using the RNeasy mini kit (Qiagen 74106), according to the manufacturer’s instructions.
Quality control and library preparation for RNA sequencing was performed by the NXTGNT sequencing facility of Ghent University (Ghent, Belgium). RNA samples were quantified, and quality controlled using the Quant-iTTM Ribogreen® RNA Assay (Invitrogen R11491) kit and Agilent RNA 6000 Nano (Agilent 5067-1511; on Agilent Bioanalyzer). Upon DNase treatment, library preparation (Truseq stranded mRNA, Illumina RS-122-2101 and RS-122-2102) was performed on 1µg of each sample. As recommended by Illumina, fragmentation was performed for 8 minutes at 94°C. Samples were pooled and subsequently multiplex identifiers were added to each pool. To increase uniformity of the protocol, library preparation was performed using the IP-star® Compact Automated System (Diagenode B03000002). Bioanalyzer QC after library preparation (Agilent, High Sensitivity DNA kit) demonstrated no relevant batch effects. Single-end 75 bp sequencing was performed three times for each of the pooled libraries on the Illumina NextSeq500 (over four lanes).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
FastQC (v0.10.1) was used to assess RNA-seq data quality, indicating no relevant problems. Therefore, no additional trimming was performed. STAR (v2.5.2b) was used to align and map reads to the reference genome [20]. Samtools (v0.1.18) and htseq-count (v0.6.0) (based on GTF file, Ensembl, assembly 3.2.4, release 87) were used for downstream analysis and data summary, respectively.
Genome_build: taeGut3.2.4
Supplementary_files_format_and_content: htseq-count
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| Submission date |
Apr 02, 2020 |
| Last update date |
Apr 07, 2021 |
| Contact name |
Jeroen Galle |
| Organization name |
Ghent University
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| Department |
Dept. Of Mathematical Modelling, Statistics and Bioinformatics
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| Lab |
Biobix, Lab of Bioinformatics and Computational Genomics
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| Street address |
Coupure Links 653
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| City |
Ghent |
| ZIP/Postal code |
9000 |
| Country |
Belgium |
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| Platform ID |
GPL22780 |
| Series (2) |
| GSE147972 |
DNA methylation regulates transcription factor specific neurodevelopmental but not sexually dimorphic gene expression dynamics in zebra finch telencephalon [RNA-Seq] |
| GSE147974 |
DNA methylation regulates transcription factor specific neurodevelopmental but not sexually dimorphic gene expression dynamics in zebra finch telencephalon |
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| Relations |
| BioSample |
SAMN14525584 |
| SRA |
SRX8047034 |
| 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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