|
| Status |
Public on Jun 03, 2022 |
| Title |
ΔbapR, LCA, biological replicate 3 |
| Sample type |
SRA |
| |
|
| Source name |
Bacterial
|
| Organism |
Clostridioides difficile |
| Characteristics |
strain: 630deltaerm
cell type: Bacterial
genotype: deltabapR
treatment: 20 microM lithocholic acid
time: 1 hour
|
| Treatment protocol |
20 μM LCA or DMSO vehicle was added to log-phase cultures for 1 hour before harvesting RNA
|
| Growth protocol |
Cultured swirling anaerobically in BHIS broth
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were lysed using Lysing Matrix B (MP Bio); DNA was removed in two treatments with DNase I (NEB) and using an RNeasy kit (Qiagen)
mRNA libraries were made using Illumina Stranded Total RNA with Ribo Zero Plus kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
Geneious Prime 2022.1.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using BBDuk (parameters- Kmer length: 27; maximum substitutions: 1; minimum quality: 30; minimum length: 30)
Trimmed sequence reads were mapped to the C. difficile 630 genome using Geneious mapper (parameters- sensitivity: medium-low)
Expression levels were calculated using DEseq2
Assembly: NC_009089
Supplementary files format and content: csv files include raw counts, raw transcript, RPKM, and TPM for each gene
|
| |
|
| Submission date |
May 31, 2022 |
| Last update date |
Jun 06, 2022 |
| Contact name |
Aimee Shen |
| E-mail(s) |
aimee.shen@tufts.edu
|
| Organization name |
Tufts University
|
| Street address |
136 Harrison Ave
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02111 |
| Country |
USA |
| |
|
| Platform ID |
GPL32143 |
| Series (1) |
| GSE205226 |
Identification of a bile acid-binding transcription factor in Clostridioides difficile using chemical proteomics |
|
| Relations |
| BioSample |
SAMN28789772 |
| SRA |
SRX15528912 |
