GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE200776 Query DataSets for GSE200776
Status Public on Apr 14, 2022
Title Testing different rRNA removal methods in 4 species of model halophilic archaea
Organisms Halobacterium salinarum; Haloferax volcanii; Haloferax mediterranei; Haloarcula hispanica
Experiment type Expression profiling by high throughput sequencing
Summary We tested a number of rRNA removal methods (Illumina RiboZero Plus, NEBNext, NEB Core Depletion Set with custom probes, siTools Panarchaea, siTools RiboPool) on 4 model halophile species: Halobacterium salinarum, Haloferax volcanii, Haloferax meditteranei, Haloarcula hispanica). It was found that methods using custom probes (NEB Core Depletion set with HVO probes, siTools RiboPool with HVO probes) efficiently remove rRNA in species they are targeted to, and that Panarchaea efficiently removes rRNA in all 4 tested species.
Overall design Cells were grown to mid-exponential phase and cell pellets were extracted and immediately frozen in liquid N2. After 1-7 days at -80C, total RNA was extracted from frozen cell pellets using the Absolutely RNA Miniprep kit made by Agilent, with additional DNase treatment as necessary. 1-10ng of total RNA was used as input for rRNA removal methods, for which we followed manufacturer's protocols (with the exception of longer RNase digestion of 120 minutes instead of 30 minutes, for some samples of HBT treated with NEB Core Depletion set, labeled NEB_HVO_120). dsDNA libraries were created using NEBMultiplex Oligos (part of the NEBNext protocol for the relevant samples). They were quantified and quality-checked using DNA High Sensitivity Chip for the Agilent Bioanalyzer and were sent for sequencing to the Duke Center for Genomic and Computational Biology, where they were sequenced on Illumina NovaSeq 6000.
Contributor(s) Schmid A, Martinez-Pastor M, Sakrikar S
Citation(s) 35625610
Submission date Apr 13, 2022
Last update date Jun 01, 2022
Contact name Amy K Schmid
Organization name Duke University
Department Biology
Lab Schmid
Street address 125 Science Dr.
City Durham
State/province NC
ZIP/Postal code 27707
Country USA
Platforms (4)
GPL32164 Illumina NovaSeq 6000 (Halobacterium salinarum)
GPL32165 Illumina NovaSeq 6000 (Haloferax volcanii)
GPL32166 Illumina NovaSeq 6000 (Haloarcula hispanica)
Samples (39)
GSM6043539 Hbt sal: RiboZero Plus - rep 1
GSM6043540 Hbt sal: RiboZero Plus - rep 2
GSM6043541 Hbt sal: RiboZero Plus - rep 3
BioProject PRJNA826532

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE200776_RAW.tar 630.0 Kb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap