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| Status |
Public on Jun 06, 2022 |
| Title |
Experiment #2 Time 0 #6 |
| Sample type |
SRA |
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| Source name |
Cyanobacterial cell
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| Organism |
Synechococcus elongatus PCC 7942 = FACHB-805 |
| Characteristics |
cell type: Cyanobacterial cell
strain: PCC 7942
genotype: RB-TnSeq Library 2.0
growth vessel: flask
treatment: Fresh BG-11
fraction: Supernatant
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| Growth protocol |
The S. elongatus PCC 7942 RB-TnSeq library was revived from freeze stocks, grown in triplicate flasks, and then pooled. Aliquots of the pooled cultures were taken and frozen at -80°C to serve as Time 0 (T0) samples. The pooled libraries were used to inoculate bubbling tubes or flasks, in either fresh BG-11 media or Conditioned Media, for biofilm formation assays, depending upon the details of the experiment. After biofilm formation was visibly observed, planktonic cell samples were collected by decanting the supernatants of the cultures into sterile conical tubes. Each vessel was then gently washed once with water, which was decanted to a sterile conical tube to investigate settler cells. The remaining biofilms were resuspended in a water wash through physical scraping of the vessel and collected into a sterile conical tube. All samples were then centrifuged to generate cell pellets, which were frozen at -80°C prior to genomic DNA extraction.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Frozen cell pellets were thawed and genomic DNA was extracted using a phenol-chloroform and ethanol precipitation protocol, as previously described by Clerico, et al 2007.
Barcodes of transposon insertions in the pooled library were PCR amplified. Primers for this amplification contained adapters for Illumina sequencing, experiment-specific barcodes, and heterogenous spacers for enhanced length diversity, as described by Wetmore, et al. (2015). Amplicons were assessed by gel electrophoresis and purified using a PCR-purification kit (Zymo).
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
set9IT023
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| Data processing |
FASTQ files were analyzed using the scripts developed by Morgan Price and published as part of Wetmore, et al. (2015) to generate strain counts, gene counts, fitness scores, and T-values.
Assembly: A combined file of NC_007604.1 (chromosome), NC_007595.1 (large plasmid), and NC_004990.1 (small plasmid)
Supplementary files format and content: Raw Count Files: tab-delimited text files include raw barcode counts in each RB-TnSeq assessed gene for each sample
Library strategy: RB-TnSeq
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| Submission date |
Jun 03, 2022 |
| Last update date |
Jun 06, 2022 |
| Contact name |
Ryan Simkovsky |
| E-mail(s) |
rsimkovsky@ucsd.edu
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| Organization name |
University of California San Diego
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| Street address |
9500 Gilman Drive
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| City |
La Jolla |
| State/province |
California |
| ZIP/Postal code |
92093-0116 |
| Country |
USA |
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| Platform ID |
GPL32315 |
| Series (2) |
| GSE205443 |
Transcriptomic and phenomic investigations reveal elements in biofilm repression and formation in the cyanobacterium Synechococcus elongatus PCC 7942 [RB-TnSeq] |
| GSE205445 |
Transcriptomic and phenomic investigations reveal elements in biofilm repression and formation in the cyanobacterium Synechococcus elongatus PCC 7942 |
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| Relations |
| BioSample |
SAMN28860411 |
| SRA |
SRX15590246 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6212705_set9IT023_Counts.txt.gz |
8.7 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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