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Sample GSM4338524 Query DataSets for GSM4338524
Status Public on Jul 23, 2020
Title Tkod_65deg_NaCNBH3_rep2
Sample type SRA
 
Source name archaeal cells
Organism Thermococcus kodakarensis
Characteristics genetic background: WT
treatment: NaCNBH3
growth condition: 65 degrees
Treatment protocol growth at various temperatures
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).
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
 
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina NovaSeq 6000
 
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.
 
Submission date Feb 25, 2020
Last update date Jul 23, 2020
Contact name Aldema Sas-Chen
E-mail(s) [email protected]
Organization name Tel Aviv University
Department Shmunis School of Biomedicine and Cancer Research
Lab Sas-Chen
Street address Tel Aviv University
City Tel Aviv
State/province Israel
ZIP/Postal code 69978
Country Israel
 
Platform ID GPL28196
Series (1)
GSE135826 Dynamic RNA acetylation revealed by quantitative cross-evolutionary mapping
Relations
BioSample SAMN14206225
SRA SRX7798989

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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