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Status |
Public on Mar 28, 2024 |
Title |
Riftia_trophosome_sample_H2_N_HO_biological_replicate_3 |
Sample type |
SRA |
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Source name |
Symbiont-bearing trophosome tissue from R. pachyptila
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Organism |
Candidatus Endoriftia persephone |
Characteristics |
host: Riftia pachyptila tissue: Symbiont-bearing trophosome tissue from R. pachyptila treatment: H2_N_HO
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Treatment protocol |
Treatments varied by sulfide, oxygen, hydrogen and nitrate. For a list of treatments and their abbreviations, see README.txt
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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.
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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))
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
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Description |
Riftia pachyptila/Candidatus Endoriftia persephone 94j_RSEMbt2.genes.results (column names of processed data file Endoriftia_rsem_gene_count.matrix.txt)
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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
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Submission date |
Dec 05, 2023 |
Last update date |
Mar 28, 2024 |
Contact name |
Jessica Mitchell |
E-mail(s) |
jessicamitchell@fas.harvard.edu
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Organization name |
Harvard University
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Department |
Department of Organismic and Evolutionary Biology
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Lab |
Girguis Lab
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Street address |
16 Divinity St, Biolabs # 3102
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City |
Cambridge |
State/province |
Massachusetts |
ZIP/Postal code |
02138 |
Country |
USA |
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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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