|
| Status |
Public on Jan 14, 2020 |
| Title |
Pectin rep 3 |
| Sample type |
SRA |
| |
|
| Source name |
Soil
|
| Organism |
soil metagenome |
| Characteristics |
replicate: 3
enrichment type: pectin
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Microbial cultures of a liquid culture were pelleted, flash frozen using liquid N2, and RNA was harvested using Trizol reagent. Ambien Turbo DNase was used to remove DNA, and MicrobExpress kit was used to deplete rRNA species before sending the purified mRNA to GENEWIZ for sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Enrichment of Prosser, WA soil microbes in liquid culture of M9 + pectin, rep 3.
|
| Data processing |
Raw reads from all samples were aligned to a previously obtained soil metagenome using the Burrows Wheeler Aligner.
Resulting reads were converted to raw counts using HTSeq.
Only transcripts with at least 75 cumulative counts across the 15 samples, and with no more than 3 zero counts, were retained for downstream analysis.
The dataset was normalized using DESeq.
Statistical analyses were conducted using R.
Genome_build: Prosser soil metagenome, NCBI Bioproject PRJNA597444
Supplementary_files_format_and_content: tab-delimited text files include raw counts and variance-stabilized normalized counts for full dataset, as well as HTSeq output (raw counts) for each sample
|
| |
|
| Submission date |
Jan 13, 2020 |
| Last update date |
Jan 15, 2020 |
| Contact name |
Daniel Torres Naylor |
| E-mail(s) |
dtnaylor@berkeley.edu, dtnaylor@pnnl.gov
|
| Organization name |
Pacific Northwest National Laboratory
|
| Department |
Biological Systems Division
|
| Street address |
3300 Stevens Drive, MSIN. J4-18
|
| City |
Richland |
| State/province |
WA |
| ZIP/Postal code |
99354 |
| Country |
USA |
| |
|
| Platform ID |
GPL20780 |
| Series (1) |
| GSE143587 |
RNA-Seq Analysis to confirm Different Transcriptomic Profiles of Soil-Derived Functional Module Consortia. |
|
| Relations |
| BioSample |
SAMN13839576 |
| SRA |
SRX7551182 |
