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Status |
Public on Sep 01, 2022 |
Title |
Gasterosteus_f55_pterygiophore_3sp_rep12 |
Sample type |
SRA |
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Source name |
pterygiophore
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Organism |
Gasterosteus aculeatus |
Characteristics |
Stage: finfold stage (stage 31) parental populations: LITC x High-spine tissue: pterygiophore
|
Growth protocol |
Fry were generated by in vitro fertilization and raised in 10% seawater at 16 degrees C in a petri dish until they were 11-13mm in standard length.
|
Extracted molecule |
total RNA |
Extraction protocol |
Tissues were dissected from fish and flash frozen in liquid nitrogen and stored at -80 degrees. The tissues were homogenized in a MP FastPrep with Matrix M. RNA was extracted with Takara NucleoSpin RNA XS kit with an on-column DNase step. 20-100 ng of RNA was used to make sequencing libraries with Illumina Stranded mRNA Prep kit according to manufacturer's instructions. PCR cycle number was determined by qPCR.
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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 |
Sequencing: All RNA-Seq libraries were sequenced on an Illumina NovaSeq 6000 by Novogene. Trimming: All raw sequencing data were quality and adapter trimmed by using a wrapper script TrimGalore that combines Cutadapt (ver. 2.4) and FastQC (ver. 0.11.9) with adapter overlap stringency of 1 and Phred quality score cutoff of 20. Mapping: STAR 2-pass mapping (ver. 2.7.4). Data cleanup: The best practices as outlined by gatk for RNA-seq short variant discovery were followed using picard (ver. 2.23.4) to mark and sort duplicates, samtools (ver.1.10) to index, splitNCigarReads (ver. gatk4/4.1.4.1), and Base Recalibration (ver. gatk4/4.1.4.1). This produced the analysis ready .bam files for read counts. Variant Discovery: HaplotypeCaller (ver. gatk4/4.1.4.1) was used to identify variants in the dataset, and bcftools (ver 1.11) was used to identify only the biallelic SNPs for further downstream analysis. This produced a .vcf file that was used to generate the read counts. Read Counts: ASEReadCounter (ver. gatk4/4.1.4.1) was used to generate a table of allele counts at variants found in the populations (.vcf). Genome_build: gasAcu1-4 (https://datadryad.org/stash/dataset/doi:10.5061/dryad.547d7wm6t) Supplementary_files_format_and_content: *.tab: Tables of allele counts at SNPs present in the two populations.
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Submission date |
Sep 27, 2021 |
Last update date |
Sep 01, 2022 |
Contact name |
David M Kingsley |
E-mail(s) |
kingsley@stanford.edu
|
Organization name |
Stanford University
|
Department |
Developmental Biology
|
Street address |
279 Campus Drive
|
City |
Stanford |
State/province |
CA |
ZIP/Postal code |
94305 |
Country |
USA |
|
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Platform ID |
GPL30674 |
Series (2) |
GSE184885 |
Allele-specific gene expression in stickleback (Gasterosteus aculeatus) spine and fins |
GSE184888 |
Allele-specific gene expression in stickleback spine, fins, and embryos |
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Relations |
BioSample |
SAMN21874170 |
SRA |
SRX12380025 |