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Sample GSM6208847 Query DataSets for GSM6208847
Status Public on Jun 03, 2022
Title ΔbapR, LCA, biological replicate 2
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 SAMN28789773
SRA SRX15528911

Supplementary file Size Download File type/resource
GSM6208847_Sample_11_processed.csv.gz 77.3 Kb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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