|
| Status |
Public on Sep 30, 2018 |
| Title |
DE442_S06 |
| Sample type |
SRA |
| |
|
| Source name |
early stationary growth phase cells
|
| Organism |
Rhodobacter capsulatus DE442 |
| Characteristics |
genotype/variation: GTA hyperproducer
|
| Growth protocol |
RCV medium under anaerobic, photoheterotrophic conditions at 30℃
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were harvested at early stationary growth phase. Total RNA was purified using the NucleoSpin RNA Kit (Macherey-Nagel) and DNAseI treated on column according to the manufacturer’s protocol.
RNA yield was quantified and quality checked using a Nanodrop spectrophotometer and Aglient bioanalyser. Ribosomal RNA was removed from 1 µg good quality total RNA using the Ribo-Zero rRNA Removal Kit (Bacteria; Illumina). Libraries were then prepared from rRNA-depleted samples using the NEBNext RNA Ultra II Directional Library preparation kit for Illumina, with single 6 bp indices, according the manufacturer's guidelines for insert sizes of approximately 200 - 350 bp. Libraries were pooled at equimolar ratios, and the pool was sent for 2 x 150 base paired end sequencing on a HiSeq 3000 at the University of Leeds Next Generation Sequencing Facility.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
sleuth_matrix_est_counts.txt
sleuth_test_results.txt
|
| Data processing |
Illumina HiSeq 3000 sequencing
Reads were trimmed using Cutadapt v.1.8.3
Reads were pseudo-aligned to Rhodobacter Capsulatus SB1003 transcriptome using Kallisto 0.43.1
Differential expression anlaysis was performed by fitting linear models in Sleuth 0.29.0
Genome_build: SB1003 reference transcriptome (GenBank CP001313.1) and plasmid pRCB133 (GenBank CP001312.1)
Supplementary_files_format_and_content: sleuth_matrix_est_counts.txt: tab-delimited text file containing estimated count values from Kallisto quantification step; sleuth_test_results.tx: tab-delimted text file containing output from Sleuth linear modelingl looking at the effect of strain - p-values, qvalues, B values, std error of B values
|
| |
|
| Submission date |
Aug 03, 2018 |
| Last update date |
Sep 30, 2018 |
| Contact name |
Katherine Newling |
| E-mail(s) |
[email protected]
|
| Phone |
+44 (01904) 328767
|
| Organization name |
University of York
|
| Department |
Biology
|
| Street address |
Wentworth Way
|
| City |
York |
| ZIP/Postal code |
YO10 5DD |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL25421 |
| Series (1) |
| GSE118116 |
Comparison of the expression profiles of wild-type Rhodobacter capsulatus and a GTA hyperproducer (DE442) by RNAseq. |
|
| Relations |
| BioSample |
SAMN09765565 |
| SRA |
SRX4507382 |
