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| Status |
Public on Jun 30, 2020 |
| Title |
10_GccF_2 |
| Sample type |
SRA |
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| Source name |
Bacterial cell
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| Organism |
Enterococcus faecalis |
| Characteristics |
strain: JH2-2
treatment: Cells treated with 250 nM GccF, harvested at 10 minutes
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| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were pelleted, and lysed by bead-milling with 0.1 mm diameter glass beads. RNA was isolated using Trizol with a Zymo Direct-zol RNA purification kit.
Library construction was carried out using Illumina TruSeq Stranded RNA Sample Preparation kit with RiboZero bacteria depletion.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Base calling done using Sanger / Illumina 1.9
Reads were trimmed using BBDuk, using the following parameters: kmer length of 23, hdist of 1, -tbo flag selected.
Trimmed reads were aligned to reference sequence using Bowtie2 version 2.2.9, using the default settings. Samples from strain JH2-2 were aligned to the reference genome for JH2-2, while samples from strain VI01 were aligned to the reference genome V583.
Aligned reads were processed using HTSeq version 0.6.0 to generate lists of counts for each gene.
Genome_build: GCA_000479105.1 (JH2-2), GCA_000007785.1 (V583)
Supplementary_files_format_and_content: Tab-delimited text files containing raw counts for each gene/ open reading frame
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| Submission date |
Oct 08, 2019 |
| Last update date |
Jul 01, 2020 |
| Contact name |
Sean William Bisset |
| E-mail(s) |
swbisset@live.com
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| Organization name |
Massey University
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| Department |
School of Fundamental Sciences
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| Lab |
Norris Lab
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| Street address |
Tennent Drive
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| City |
Palmerston North |
| State/province |
Manawatu |
| ZIP/Postal code |
4414 |
| Country |
New Zealand |
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| Platform ID |
GPL18799 |
| Series (1) |
| GSE138552 |
Transcriptional response of Enterococcus faecali to the glycosylated bacteriocin glycocin F |
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| Relations |
| BioSample |
SAMN12992913 |
| SRA |
SRX6962919 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4113627_10_GccF2.clean.counts.txt.gz |
12.2 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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