|
| Status |
Public on Mar 26, 2013 |
| Title |
WT |
| Sample type |
SRA |
| |
|
| Source name |
WT (ATCC 19061)
|
| Organism |
Xenorhabdus nematophila |
| Characteristics |
illumina protocol: small RNA
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 |
SRX252362 |
| BioSample |
SAMN01984735 |
