|
| Status |
Public on Oct 16, 2023 |
| Title |
mxaF NdCl3 3 |
| Sample type |
SRA |
| |
|
| Source name |
strain
|
| Organism |
Methylorubrum extorquens AM1 |
| Characteristics |
tissue: strain
genotype: dmxaF
|
| Growth protocol |
Cells were grown in Half Hypho Medium with 50 mM methanol and 2 uM Nd at 30C and 250rpm. WT without Nd was used as a reference.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested at mid-exponential phase using Rneasy kit (Qiagen).
RNA libraries for RNA-seq were prepared using Illumina DNA prep kit according to manufacturer's protocol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
All processing occurred using Kbase
Reads aligned using HISTAT2
Aligned reads assemebeled using StringTie
Differential expression matrix generated using DeSeq2
Assembly: NC_012808.1
Supplementary files format and content: comma deliminated file includes raw gene counts for each sample
Supplementary files format and content: comma deliminated file includes FPKM values for each sample
|
| |
|
| Submission date |
Sep 26, 2023 |
| Last update date |
Oct 16, 2023 |
| Contact name |
Norma Cecilia Martinez-Gomez |
| E-mail(s) |
[email protected]
|
| Organization name |
University of California, Berkeley
|
| Department |
Plant and Microbial Biology
|
| Street address |
111 Koshland Hall
|
| City |
Berkeley |
| State/province |
CA |
| ZIP/Postal code |
94720 |
| Country |
USA |
| |
|
| Platform ID |
GPL33789 |
| Series (1) |
| GSE244060 |
Discovery and characterization of the first known biological lanthanide chelator |
|
| Relations |
| BioSample |
SAMN37546053 |
| SRA |
SRX21894976 |
