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| Status |
Public on Apr 30, 2021 |
| Title |
T3 T72 |
| Sample type |
SRA |
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| Source name |
Thiosulfate, T=72
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| Organism |
seawater metagenome |
| Characteristics |
depth: 2000 m
latitude: 50.86ºN
longitude: 331.14ºE
treatment: Thiosulfate
time: 72h
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| Treatment protocol |
Thiosulfate (1µM)
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| Growth protocol |
In the dark, in situ temperature (~3ºC)
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| Extracted molecule |
total RNA |
| Extraction protocol |
Water samples were filtered onto 0.2µm pore size polycarbonate filters, flash frozen in liquid nitrogen and preserved at -80ºC. RNA was extracted using the mirVana™ miRNA Isolation Kit, purified and concentrated with the RNeasy MinElute Cleanup Kit. cDNA libraries were generated using the Ovation RNA-Seq System V2 Kit. Sequencing libraries were constructed using Illumina’s Truseq RNA Sample Prep kit v2 according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1000 |
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| Data processing |
The sequencing single reads were trimmed for adaptor sequence, and filtered for low-complexity and low-quality sequence.
Reads shorter than 50 bp or with quality mean < 30 were removed using Prinseq-lite-0.20.3.
Full length ribosomal genes were reconstructed from short reads in each sample with Emirge with parameters -f ./silva/SSURef_111_candidate_db.fasta -b ./silva/SSURef_111_candidate_db_btindex --phred33 -j 0.97
Contigs were built out of short-read using the Velvet de novo assembler. The minimun contig length was 500 bp
Prokka 1.11 was used for the annotation of coding regions and RNA genes present on the contigs with parameters --kingdom Bacteria --usegenus --hmms /home/software/prokka-1.11/db/hmm/Pfam-A.hmm --metagenome --evalue 1e-08. Gene abundance was calculated based on the Prokka annotation
Genome_build: Prokka v. 1.11
Supplementary_files_format_and_content: .txt file reports abundance measurements
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| Submission date |
Sep 02, 2019 |
| Last update date |
Apr 30, 2021 |
| Contact name |
Juan A.L. Garcia |
| E-mail(s) |
jagarcia4@gmail.com
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| Organization name |
University of Vienna
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| Street address |
Althanstraße 14
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| City |
Vienna |
| ZIP/Postal code |
1220 |
| Country |
Austria |
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| Platform ID |
GPL27409 |
| Series (1) |
| GSE136729 |
Role of thiosulfate as a source of energy in the bathypelagic North Atlantic Ocean |
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| Relations |
| BioSample |
SAMN12672765 |
| SRA |
SRX6790166 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4056813_s5_prot_abundance.txt.gz |
386.8 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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