|
| Status |
Public on Jul 30, 2018 |
| Title |
clnR control - repl 2 |
| Sample type |
SRA |
| |
|
| Source name |
bacterial culture
|
| Organism |
Clostridioides difficile |
| Characteristics |
strain: clnR
ll-37: none
|
| Treatment protocol |
Samples for RNA extraction were stored in 1:1 ethanol:acetone at -80˚C.
|
| Growth protocol |
Active cultures of bacteria were diluted to an OD600 of approximately 0.05 in BHIS medium in an anaerobic chamber at 37˚C with or without the addition of 2 µg/ml LL-37. Samples were harvested for RNA extraction at OD600 = 0.50 during mid-logarithmic growth.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the Qiagen RNeasy kit and treated with DNase I.
Ribosomal transcripts were depleted from 2 ug of total RNA, and libraries were generated following Illumina's Scripseq V2 Complete- Bacterial library prep kits. (Epicentre, Madison, WI, USA)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
410_McBride_E1_normcounts.txt
|
| Data processing |
Illumina bcl2fastq v2.17.1.14 was used for demultiplexing.
Reads were mapped to the Clostridium difficile Strain: 630Derm GCA_000953275.1 assembly genomic reference with the STAR aligner (v2.5.2b) with default alignment parameters.
Abundance estimation was performed with htseq-count (v 0.9.1)
Normalized expression (normalized read counts) was performed with DESeq2 (v1.10.1)
Genome_build: Clostridium difficile (Clostridioides difficile) Strain: 630Derm, (GCA_000953275.1_CD630DERM_genomic.fna, GCA_000953275.1_CD630DERM_genomic.gff)
Supplementary_files_format_and_content: tab delimited text file containing normalized read counts for each sample (in columns) and each annotated transcript (in rows).
|
| |
|
| Submission date |
Jun 11, 2018 |
| Last update date |
Jul 31, 2018 |
| Contact name |
Gregory K Tharp |
| E-mail(s) |
gktharp@emory.edu
|
| Phone |
404-727-7797
|
| Organization name |
Yerkes National Primate Research Center
|
| Department |
Developmental and Cognitive Neuroscience
|
| Lab |
Genomics Core
|
| Street address |
954 Gatewood Dr
|
| City |
Atlanta |
| State/province |
GA |
| ZIP/Postal code |
30329-4208 |
| Country |
USA |
| |
|
| Platform ID |
GPL25175 |
| Series (1) |
| GSE115638 |
The C. difficile clnRAB operon initiates adaptations to the host environment in response to LL-37 |
|
| Relations |
| BioSample |
SAMN09396551 |
| SRA |
SRX4195450 |
