|
| Status |
Public on Apr 09, 2024 |
| Title |
Synechococcus cells, labA-KO, replicate 3 |
| Sample type |
SRA |
| |
|
| Source name |
cyanobacteria
|
| Organism |
Synechococcus elongatus PCC 7942 = FACHB-805 |
| Characteristics |
cell type: cyanobacteria
time: collected after 12h in LL (with one 12h dark pulse before)
genotype: labA knock-out
|
| Treatment protocol |
Prior to collection, cells were grown for 3 days in constant light in plates of BG-11 media. Then, the 3 kaiA-Ex and the 3 kaiA-Ex/labA-KO samples were given 10µM ZnCl2 and transferred to dark for 12h, while the other 6 samples (3 of wild-type and 3 of labA-KO) were not given ZnCl2 and were instead just transferred to dark for 12h. After this dark pulse, the plates were put into constant light and collected for RNAseq extraction after 12h of being in constant light.
|
| Growth protocol |
Cells were maintained in plates of BG-11 and grown in constant light and constant 30ºC, under ~ 40µE of illumination with fluorescent lights.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from cells preserved in RNA Protect (Qiagen) and processed with the Rneasy Mini Kit (Qiagen). DNA contamination was removed with Dnase I (NEB).
Library preparation and rRNA depletion was performed using the NEBNext® rRNA Depletion Kit for Bacteria (New England BioLabs).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Tuxedo and DESeq
Sequence reads were trimmed for adaptors and low quality reads were removed using trim_galore v. 0.6.10, specifying that the sequences were paired-end
hisa2 v. 2.2.1 was used to build an index using assembly sequences available in NCBI (GenBank assembly accession: GCA_000012525.1) and to align our sequencing reads with the genome (parameters: -S, --dta, --no-spliced-alignment)
samtools v. 1.11.0 was used to convert the generated .sam files into .bam files
stringtie v. 2.1.7 was used to estimate transcript abundances, and the prepDE.py script provided with stringtie was used to generate a read counts matrix
the raw read counts were analyzed with DESeq2 v. 1.36.0 and p-values were calculated using a Wald test followed by multiple-comparisons correction using FDR. Log2FC cvalues were shrunk using adaptive shrinking to account for high levels of variation due to low counts or high dispersion values.
Assembly: GCA_000012525.1
Supplementary files format and content: comma-delimited csv file includes raw counts for the transcripts in each sample
|
| |
|
| Submission date |
Jul 20, 2023 |
| Last update date |
Apr 09, 2024 |
| Contact name |
Carl Hirschie Johnson |
| E-mail(s) |
carl.h.johnson@vanderbilt.edu
|
| Organization name |
Vanderbilt University
|
| Department |
Biological Sciences
|
| Street address |
465 21st Avenue South, U-8215 BSB/MRBIII
|
| City |
Nashville |
| State/province |
Tennessee |
| ZIP/Postal code |
37232 |
| Country |
USA |
| |
|
| Platform ID |
GPL32996 |
| Series (1) |
| GSE237858 |
Clocking Out and Letting Go to Engineer Circadian Gene Expression for Biotechnological Applications |
|
| Relations |
| BioSample |
SAMN36660212 |
| SRA |
SRX21113835 |
