|
| Status |
Public on Jan 21, 2022 |
| Title |
wild-type rep A |
| Sample type |
SRA |
| |
|
| Source name |
bacterial culture
|
| Organism |
Bacteroides thetaiotaomicron |
| Characteristics |
strain: VPI-5482 delta-tdk
treatment: induction n/a
|
| Treatment protocol |
Bacteria with the iSPT background strain were induced with 100 ng/mL anhydrotetracycline
|
| Growth protocol |
15-hour anaerobic growth in Bacteroides minimal medium at 37 deg C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
QIAzol lysis reagent and miRNeasy Mini Kit (Qiagen)
rRNA was removed with the Bacterial RiboMinus Transcriptome Isolation Kit (Invitrogen) and the library prepared with the TruSeq Stranded Total RNA Library Kit (Illumina)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
Sequence reads were trimmed to remove adapter, quality assessed using FastQC, quality filtered with bbduk (quality cutoff = 20)
Reads were aligned to the Ensembl Bacteroides thetaiotaomicron VPI-5482 genome with bowtie 2
Aligned reads were assigned using htseq-count (alignment quality cutoff = 10)
Supplementary_files_format_and_content: tab-delimited text files include log2-counts per million for each sample
|
| |
|
| Submission date |
Jan 14, 2022 |
| Last update date |
Jan 21, 2022 |
| Contact name |
Stacey Heaver |
| Organization name |
Max Planck Institute for Biology Tuebingen
|
| Department |
Microbiome Science
|
| Street address |
Max-Planck-Ring 5
|
| City |
Tuebingen |
| ZIP/Postal code |
72076 |
| Country |
Germany |
| |
|
| Platform ID |
GPL31230 |
| Series (1) |
| GSE193734 |
Transcriptomic analysis of Bacteroides thetaiotaomicron inositol lipid knockout strains |
|
| Relations |
| BioSample |
SAMN25003317 |
| SRA |
SRX13790804 |
