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| Status |
Public on Jul 23, 2020 |
| Title |
Tkod_85deg_mock_rep4 |
| Sample type |
SRA |
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| Source name |
archaeal cells
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| Organism |
Thermococcus kodakarensis |
| Characteristics |
genetic background: WT
treatment: mock
growth condition: 85 degrees
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| Treatment protocol |
growth at various temperatures
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| Growth protocol |
T. kodakarensis and T. sp AM4 strains – TS559 can derivatives thereof – were grown as previously described (Santangelo et al. 2007; Hileman and Santangelo 2012; Gehring et al. 2017) in artificial sea water (ASW) medium supplemented with vitamins and trace minerals. Pyrococcus furiosus strain COM1 was cultured at 75-95˚C in an artificial sea water based medium supplemented with cellobiose, maltose, yeast extract, S˚, trace minerals, cysteine and sodium tungstate as previously described (Lipscomb et al, APPLIED AND ENVIRONMENTAL MICROBIOLOGY, Apr. 2011, p. 2232–2238).
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from T. kodakarensis using TRIZOL according to manufacturer’s protocol. For the indicated samples of T. kodakarensis ,rRNAs were depleted according to Morlan et al.(Morlan et al. 2012) using reagents provided in the NEBNext® rRNA Depletion Kit (NEB #E6310). For indicated samples purifications of T. kodakarensis ribosomes of the wild-type and TkNat10 knockout were conducted similar to previously documented procedures (Matzov et al. 2017).
Fragmentation, 3' adapter ligation, cDNA synthesis, second adapter ligation and enrichment
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Library strategy: ac4C-seq
alignment using STAR (V. 2.5.3a)
base-calling using JACUSA v2.0.0 under default parameters
calculation of misincorporation rates per base
Genome_build: ASM996v1 for Thermococcus kodakarensis, ASM27560v1 for Pyrococcus furiosus, ASM15120v2 was used for Thermococcus sp. AM4, ASM700v1 for Sulfolobus solfataricus and ASM9166v1 for Methanocaldococcus jannaschii. For human GRCh37/hg19 with UCSC Genes annotations. For Saccharomyces cerevisiae samples the sacCer3 assembly.
Supplementary_files_format_and_content: TableS2_SasChen.xlsx an excel file detailing ac4C sites identified in each organism including the level of modification of each site.
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| Submission date |
Feb 25, 2020 |
| Last update date |
Jul 23, 2020 |
| Contact name |
Aldema Sas-Chen |
| E-mail(s) |
aldema.sas@gmail.com
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| Organization name |
Tel Aviv University
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| Department |
Shmunis School of Biomedicine and Cancer Research
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| Lab |
Sas-Chen
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| Street address |
Tel Aviv University
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| City |
Tel Aviv |
| State/province |
Israel |
| ZIP/Postal code |
69978 |
| Country |
Israel |
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| Platform ID |
GPL28196 |
| Series (1) |
| GSE135826 |
Dynamic RNA acetylation revealed by quantitative cross-evolutionary mapping |
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| Relations |
| BioSample |
SAMN14206220 |
| SRA |
SRX7798994 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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