|
| Status |
Public on Feb 12, 2021 |
| Title |
Population SD - 7 ppt - replicate 2 [SD-7-2] |
| Sample type |
SRA |
| |
|
| Source name |
Population SD - 7 ppt_whole body
|
| Organism |
Tigriopus californicus |
| Characteristics |
population: San Diego (SD)
treatment: hypo-osmotic stress
tissue: Whole body
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Sigma-Aldrich's TRI Reagent Protocol
mRNA library preparations and Illumina HiSeq 2500 50x paired-end sequencing were done at University of North Carolina at Chapel Hill's High-Throughput Sequencing Facility
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
processed data file: read_counts_SD.xlsx
SD-7-2_TAGCTT_L002
|
| Data processing |
Quality control via FastQC (v.0.11.3)
Discarded reads with Quality Scores lower than 30 were done using CLC Genomics Workbench (v.8.0.3)
SD reads were aligned to the SD genome and AB reads were aligned to the AB genome, and annotated using the SD annotation in CLC Genomics Workbench (v.8.0.3). Exported BAM files from CLC Genomics Workbench.
BAM files imported into R and analyzed with package DESeq2 (v.1.10.1)
GO enrichment analysis done in Blast2GO Basic and Pro (v.5.2.5)
Genome_build: Reference for SD: TCALIF_genome_v3.fasta; reference for AB: AB_genome4_opt_15_merged.fa
Supplementary_files_format_and_content: Excel table of raw read counts per gene, population, treatment, and replicate.
|
| |
|
| Submission date |
Feb 11, 2021 |
| Last update date |
Feb 13, 2021 |
| Contact name |
Jeeyun Lee |
| Organization name |
University of North Carolina at Chapel Hill
|
| Department |
Biology
|
| Lab |
Willett Lab
|
| Street address |
Coker Hall, room 418
|
| City |
Chapel Hill |
| State/province |
NC |
| ZIP/Postal code |
27514 |
| Country |
USA |
| |
|
| Platform ID |
GPL21784 |
| Series (1) |
| GSE166634 |
Transcriptomic response of Tigriopus californicus populations to a fluctuation in salinity |
|
| Relations |
| BioSample |
SAMN17869515 |
| SRA |
SRX10079901 |
