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| Status |
Public on Feb 19, 2020 |
| Title |
M0D055233U_S_B2_TF_LG_NF_CCM |
| Sample type |
SRA |
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| Source name |
Tube feet
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| Organism |
Pisaster ochraceus |
| Characteristics |
batch: Batch_2
color: Brown
disease status: Symptomatic
feeding status: Not feeding
individual id: M0D055233U
site: McClures Beach (CCM)
size: large
tissue: Tube feet
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| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen RNeasy Mini Kit
Illumina TruSeq RNA Library Prep Kit v2
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
Trim Galore v. 0.4.4_dev was used to trim adapters, low quality bases (<Q20), and reads less than 20bp. Genestack v. 0.72.1 (https://genestack.com/) was used for analyses of trimmed sequences. Trimmed paired-end reads were subsampled to 5 million reads (smallest library size) and aligned to the Pisaster ochraceus nuclear genome using TopHat2 v. 2.0.13 (Kim et al., 2013) allowing 2 mismatches per read and yielding mean 2,599,568 mapped reads per library (range: 2,313,438–2,969,060). Raw coverage in genes was quantified using SAMtools v. 0.1.19 (Li et al., 2009). Differential gene expression was tested using EdgeR (McCarthy, Chen, & Smyth, 2012). Given the small sample sizes of individuals included in the asymptomatic (n = 2) compared to symptomatic (n = 2) analyses, a minimum criterion of CPM > 1 in a minimum of two libraries per asymptomatic and/or symptomatic categories was used. Gene enrichment analyses were performed in DAVID for the annotated differentially expressed genes (Huang, Sherman, & Lempicki, 2008, 2009) using the list of Pisaster ochraceus annotated genes as background.
genome annotation on DRYAD https://doi.org/10.6071/M3ND50
Genome_build: NCBI; BioProject PRJNA532896, SUB5448653; genome annotation on DRYAD https://doi.org/10.6071/M3ND50
Supplementary_files_format_and_content: compressed text file with raw counts per gene
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| Submission date |
Jan 28, 2020 |
| Last update date |
Feb 19, 2020 |
| Contact name |
Lauren Schiebelhut |
| E-mail(s) |
lschiebelhut@ucmerced.edu, lschiebelhut@gmail.com
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| Organization name |
University of California, Merced
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| Street address |
5200 N. Lake Rd.
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| City |
Merced |
| State/province |
CA |
| ZIP/Postal code |
95343 |
| Country |
USA |
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| Platform ID |
GPL28087 |
| Series (1) |
| GSE144422 |
An Initial Comparative Genomic Autopsy of Wasting Disease in Sea Stars |
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| Relations |
| BioSample |
SAMN13938419 |
| SRA |
SRX7644845 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4287922_M0D055233U_S_B2_TF_LG_NF_CCM_RawCounts.txt.gz |
64.2 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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