NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1101767 Query DataSets for GSM1101767
Status Public on Mar 26, 2013
Title WT protocol 1.5
Sample type SRA
 
Source name WT (ATCC 19061)
Organism Xenorhabdus nematophila
Characteristics illumina protocol: version 1.5
genotype: WT (ATCC 19061)
Treatment protocol To reduce potential interference from tRNAs and 5S rRNAs, a stable RNA depletion protocol was included.
Growth protocol LB broth. Late exponential phase.
Extracted molecule total RNA
Extraction protocol The mirVan miRNA Isolation Kit (Ambion) was used to isolate and enrich sRNAs, 3 mg of which were used for sRNA library construction.
Libraries of sRNAs ranging from 18-200 bp were constructed by using the Small RNA Sample Prep Kit (Illumina) following the standard manufacturer's protocol (Illumina Small RNA Sample Preparation Guide).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina Genome Analyzer II
 
Data processing Rockhopper version 1.20 (manuscript submitted) was used for alignment, normalization, and quantification. Rockhopper is available for download from http://cs.wellesley.edu/~btjaden/Rockhopper
Genome_build: Xenorhabdus nematophila ATCC 19061 (NC_014228.1)
Supplementary_files_format_and_content: Tab delimited text files containing transcription coordinates and abundance estimates.
 
Submission date Mar 19, 2013
Last update date May 15, 2019
Contact name Brian Tjaden
Organization name Wellesley College
Street address 106 Central Street
City Wellesley
State/province MA
ZIP/Postal code 02481
Country USA
 
Platform ID GPL16821
Series (1)
GSE45298 RNA-seq analysis of Xenorhabdus nematophila
Relations
SRA SRX252364
BioSample SAMN01984737

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

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