|
| Status |
Public on Mar 28, 2024 |
| Title |
Riftia_trophosome_sample_HS_N_LO_biological_replicate_2 |
| Sample type |
SRA |
| |
|
| Source name |
Symbiont-bearing trophosome tissue from R. pachyptila
|
| Organism |
Candidatus Endoriftia persephone |
| Characteristics |
host: Riftia pachyptila
tissue: Symbiont-bearing trophosome tissue from R. pachyptila
treatment: HS_N_LO
|
| Treatment protocol |
Treatments varied by sulfide, oxygen, hydrogen and nitrate. For a list of treatments and their abbreviations, see README.txt
|
| Growth protocol |
Symbiont bearing trophosome sampled from Riftia pachyptila maintained at high pressures in flow through aquaria in seawater amended with sulfide (or hydrogen), oxygen, carbon dioxide and nitrate for ~2-3 days prior to sampling.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the Direct-Zol RNA MiniPrep (Zymo research Inc), following manufacturer's instructions and quality checked using an Agilent Bioanalyzer 2100
cDNA libraries were constructed from 0.5 to 1 µg of RNA using a modified RNAtag-seq protocol (Shishkin, A. A. et al. Simultaneous generation of many RNA-seq libraries in a single reaction. Nat Methods 12, 323–325 (2016))
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Riftia pachyptila/Candidatus Endoriftia persephone
115j_RSEMbt2.genes.results (column names of processed data file Endoriftia_rsem_gene_count.matrix.txt)
|
| Data processing |
raw, unfiltered sequencing reads was assessed using FastQC
adapter sequences were removed with TrimGalore!
overrepresented reads were removed (https://github.com/harvardinformatics/TranscriptomeAssemblyTools) and rRNA was filtered out using the silva rRNA database.
Assembly: transcript abundances were quantified with RSEM, using the Candidatus Endoriftia persephone genome (GCF_023733635.1) as a reference.
expression estimates were normalized using the TMM method in limma-voom
Using limma-voom, comparisons between pairs of conditions of interest were then performed by extracting linear contrasts for these comparisons. Differentially expressed genes were determined using a false discovery rate (FDR) cut-off of ≤ 0.05
Coexpression analysis was done using the Weighted Gene Co-Expression Network Analysis (WGCNA) package in R
Supplementary files format and content: A count .matrix file with transcript abundance estimates for each sample corresponding to genes in the Endoriftia genome (GCF_023733635.1)
Supplementary files format and content: A .csv file containing the results of the differential expression analysis for each pairwise comparison
Supplementary files format and content: A text file containg edge weights for each node (gene) in the coexpression network built with WGCNA in R, made to be imported into Cytoscape
Supplementary files format and content: A text file containg node information in the coexpression network built with WGCNA in R, made to be imported into Cytoscape
Supplementary files format and content: A .csv file conatining the module membership (MM) and gene significance (GS) for the conditions sulfide and oxygen, from the WGCNA analysis in R
|
| |
|
| Submission date |
Dec 05, 2023 |
| Last update date |
Mar 28, 2024 |
| Contact name |
Jessica Mitchell |
| E-mail(s) |
jessicamitchell@fas.harvard.edu
|
| Organization name |
Harvard University
|
| Department |
Department of Organismic and Evolutionary Biology
|
| Lab |
Girguis Lab
|
| Street address |
16 Divinity St, Biolabs # 3102
|
| City |
Cambridge |
| State/province |
Massachusetts |
| ZIP/Postal code |
02138 |
| Country |
USA |
| |
|
| Platform ID |
GPL33985 |
| Series (1) |
| GSE249345 |
Co-expression analysis reveals distinct alliances around two carbon fixation pathways in hydrothermal vent symbionts |
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