|
| Status |
Public on May 23, 2019 |
| Title |
Dex-2 |
| Sample type |
SRA |
| |
|
| Source name |
CCS02 consolidator cells
|
| Organism |
Proteus mirabilis |
| Characteristics |
strain: BB2000:delta_ids:pidsBB-Dexchange
seq_date: 2016-06-14
genotype/variation: delta_ids complemented by a vector containing the ids operon, where the variable region of idsD was replaced with that of the variable region of P. mirabilis strain HI4320
|
| Growth protocol |
Samples were grown on CM55 swarming agar and harvested by scraping into RNA-Protect solution
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Lysates were prepared from RNA-protect cell suspension using RNEasy minikit. rRNA was digested with terminator 5' phosphate dependent exonuclease according to manufacturer's instructions.
Libraries were constructed using NEBNext Ultra library prep kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
processed mRNA
TippingGibbs2019.xlsx
|
| Data processing |
Basecalling done in Bauer core with Illumina CASAVA 1.8
Sequences were matched to BB2000 reference genome PMID: 24009111 using TopHat2, default arguments
mRNA abundance data were generated using Cufflinks 2.1.1, max-multiread-fraction 0.9, -multi-read-correct
Samples combined using cuffmerge, default arguments
Differential expression data were generated using Cuffdiff 2.1.1, total-hits-norm
Genome_build: PMID: 24009111
Supplementary_files_format_and_content: 1 xlsx file containing complete Cuffdiff output, including differential expression data
|
| |
|
| Submission date |
May 22, 2019 |
| Last update date |
May 23, 2019 |
| Contact name |
Murray Tipping |
| E-mail(s) |
[email protected]
|
| Organization name |
Harvard University
|
| Department |
MCB
|
| Street address |
16 Divinity Ave
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02138 |
| Country |
USA |
| |
|
| Platform ID |
GPL25281 |
| Series (1) |
| GSE131647 |
Peer pressure from a Proteus mirabilis self-recognition system controls participation in cooperative swarm motility |
|
| Relations |
| BioSample |
SAMN11831243 |
| SRA |
SRX5883504 |
