|
| Status |
Public on Mar 11, 2021 |
| Title |
marR-MeOH-3 |
| Sample type |
SRA |
| |
|
| Source name |
ΔttmR mutant
|
| Organism |
Methylorubrum extorquens PA1 |
| Characteristics |
strain number: CM4732
genotype: <delta>ttmR
growth phase: early exponential
carbon source: 15 mM methanol
|
| Treatment protocol |
NA
|
| Growth protocol |
Cells were grown in liquid Methylobacterium PIPES (MP) medium supplemented with 15 mM methanol at 30 ℃ with shaking.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The total RNA was extracted with the RNeasy Plus Mini Kit (Qiagen); rRNA was depleted with the Ribo-Zero rRNA removal kit (Illumina); the quality of resulting RNA samples was determined with an Agilent 2100 BioAnalyzer and Qubit assay.
RNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapter was ligated to cDNA fragments, followed by index addition and library enrichment with limited cycle PCR.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
ΔttmR
mRNA
Bazurto_ttmR_raw_read_counts.xlsx
Bazurto_ttmR_final_full_dataset.xlsx
|
| Data processing |
FastQC was used to assess the quality of the sequencing data.
Trimmomatic was used to remove the low quality bases and adapter sequences.
HISAT2 was used to align the curated reads to the M. extorquens PA1 genome.
Cuffquant and Cufnorm from the Cufflinks package were used to generate FPKM expression values.
featureCounts from the Rsubread R package was used to generate raw read counts.
DESeq2 was used to convert raw count data to normalized counts.
All further statistical analyses were carried out in R.
Genome_build: GenBank accession: CP000908.1
Supplementary_files_format_and_content: Bazurto_ttmR_raw_read_counts.xlsx: Raw read counts in an Excel file.
Supplementary_files_format_and_content: Bazurto_ttmR_final_full_dataset.xlsx: Fully processed data set comparing wild-type to ΔttmR mutant (includes Log2FC values, p-values, q-values for all genes).
|
| |
|
| Submission date |
Oct 20, 2020 |
| Last update date |
Mar 11, 2021 |
| Contact name |
Jannell V. Bazurto |
| E-mail(s) |
jbazurto@umn.edu
|
| Phone |
9549806236
|
| Organization name |
University of Minnesota
|
| Department |
Plant and Microbial Biology
|
| Lab |
Bazurto
|
| Street address |
1500 Gortner Ave
|
| City |
Saint Paul |
| State/province |
MINNESOTA |
| ZIP/Postal code |
55108 |
| Country |
USA |
| |
|
| Platform ID |
GPL29261 |
| Series (1) |
| GSE159711 |
Formaldehyde-responsive proteins, TtmR and EfgA, reveal a tradeoff between formaldehyde resistance and efficient transition to methylotrophy in Methylorubrum extorquens |
|
| Relations |
| BioSample |
SAMN16490094 |
| SRA |
SRX9319247 |
