|
| Status |
Public on Nov 08, 2014 |
| Title |
LLAM1_C4toC2_T1080m_2013_BR1 |
| Sample type |
SRA |
| |
|
| Source name |
Methylobacterium extorquens AM1_T1080
|
| Organism |
Methylorubrum extorquens AM1 |
| Characteristics |
strain: AM1
timepoint: T1080
|
| Growth protocol |
Succinate-limited chemostat cultures of wild-type Methylobacterium extorquens AM1 were grown with a dilution rate of 0.163 h^-1. After reaching steady-state, chemostat flows were stopped and 20 uM ethylamine was added to the bioreactor.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted as reported in Okubo, 2007
Libraries were constructed according to Illumina's instructions and performed by UW High Throughput Genomics Center (HTGC)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Quality filtering of raw reads was performed using Illumina's CASAVA
Reads were aligned to M. extorquens AM1 genome (MAGE, March 2nd, 2012) using BWA v.0.7.4-r385 with default parameters
Alignments were post-processed into sorted BAM files with SAMTools version 0.1.19-44428cd
Reads were attributed to open reading frames (ORFs) using htseq-count from the 'Htseq' framework version 0.5.4p5 in the 'intersection-nonempty' mode
Final abundance was measured by RPKM
Genome_build: MAGE, March 2nd, 2012
Supplementary_files_format_and_content: text file with RPKM values
|
| |
|
| Submission date |
Nov 07, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Nathan M Good |
| E-mail(s) |
[email protected]
|
| Organization name |
Michigan State University
|
| Department |
Microbiology and Molecular Genetics
|
| Lab |
Martinez Gomez
|
| Street address |
567 Wilson Rd
|
| City |
East Lansing |
| State/province |
MI |
| ZIP/Postal code |
48824 |
| Country |
USA |
| |
|
| Platform ID |
GPL19397 |
| Series (1) |
| GSE63115 |
Ethylmalonyl-CoA mutase Operates as a Metabolic Control Point in Methylobacterium extorquens AM1 |
|
| Relations |
| BioSample |
SAMN03169224 |
| SRA |
SRX755601 |
