|
| Status |
Public on Sep 01, 2022 |
| Title |
Gasterosteus_f32_dorsal_spine_2_4sp_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
dorsal spine 2
|
| Organism |
Gasterosteus aculeatus |
| Characteristics |
Stage: finfold stage (stage 31)
parental populations: LITC x High-spine
tissue: dorsal spine 2
|
| 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.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| 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.
|
| |
|
| 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 |
| |
|
| 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 |
|
| Relations |
| BioSample |
SAMN21874134 |
| SRA |
SRX12379930 |
