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| Status |
Public on May 28, 2020 |
| Title |
Biofilm_3 |
| Sample type |
SRA |
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| Source name |
Biofilm
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| Organism |
Vibrio cholerae |
| Characteristics |
strain: A1552 smooth variant
growth: biofilm
molecule subtype: rRNA-depleted RNA
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| Growth protocol |
Planktonic cultures were grown in 5 ml Lysogeny-Broth (LB) broth (1% tryptone, 0.5% yeast extract, 1% NaCl [pH 7.5]) at 30C for 16 hr 200 rpm. Biofilms cells were grown in 15cm silicon tube (ID 0.125/OD 0.250) with 2% LB (0.02% tryptone, 0.01% yeast extract, 1% NaCl [pH 7.5]), and grown at RT for 48 hr with a flow rate of 0.75 rpm
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| Extracted molecule |
total RNA |
| Extraction protocol |
V. cholerae wild-type cells were grown in planktonic or biofilm mode as described. Cells were collected and supernatant removed after centrifugation. Pellets were immediately resuspended in 2 ml of TRIzol (Invitrogen, Carlsbad, CA) and stored at -80 C. Total RNA was isolated according to the manufacturer’s instructions. To remove contaminating DNA, total RNA was incubated with RNase-free DNase I (Ambion, Grand Island, NY), and an RNeasy mini kit (Qiagen, Valencia, CA) and ethanol precipitation was used to clean up RNA after DNase digestion. RNA concentration was calculated in a nanodrop and the quality was evaluated in a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). Three biological replicates were generated for each condition.
Five micrograms of total RNA was treated with a MICROBExpress Kit (Ambion, Grand Island, NY) to remove ribosomal RNA, and the efficiency was confirmed in a 2100 Bioanalyzer. Libraries for RNA-seq were prepared using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA). Twelve indexed samples were sequenced per single lane using the HiSeq4000 Illumina sequencing platform for 100 bp single reads (UC Davis Genome Center, UC Davis, CA).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
PL4_invitro_Lib6_03-2018_AG_S588_L007
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| Data processing |
Illumina data were analyzed by UC Davis sequencing core with the newest available RTA and CASAVA software.
rRNA reads were filtered using riboPicker version 2.4.3 (PMID:22155869).
non-rRNA reads were mapped to V. cholerae O1 biovar El Tor str. N16961 (assembly GCA_000006745.1) transcripts using CLC-NGS Cell version 4.4.2 (Qiagen).
Significantly regulated genes were determined using EdgeR (PMID:19910308), fold change greater than 2.0 and false discovery rate less than 1% was used as a cutoff.
Genome_build: V. cholerae O1 biovar El Tor str. N16961 (assembly GCA_000006745.1)
Supplementary_files_format_and_content: Tab-delimited text files include raw counts for each sample.
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| Submission date |
Aug 15, 2019 |
| Last update date |
May 28, 2020 |
| Contact name |
Sinem Beyhan |
| E-mail(s) |
[email protected]
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| Organization name |
University of California, Santa Cruz
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| Department |
Microbiology and Environmental Toxicology
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| Lab |
Yildiz Lab
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| Street address |
1156 High Street
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| City |
Santa Cruz |
| State/province |
CA |
| ZIP/Postal code |
95064 |
| Country |
USA |
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| Platform ID |
GPL27062 |
| Series (1) |
| GSE135887 |
Vibrio cholerae biofilm and planktonic growth RNAseq analysis |
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| Relations |
| BioSample |
SAMN12586064 |
| SRA |
SRX6722495 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4037206_PL4_invitro_Lib6_03-2018_AG_S588_L007_R1_001.txt.gz |
17.3 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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