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| Status |
Public on Aug 08, 2023 |
| Title |
WT_Light_1hr_biol_rep_2 |
| Sample type |
SRA |
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| Source name |
PCC 7942
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| Organism |
Synechococcus elongatus |
| Characteristics |
strain: PCC 7942
genotype: WT
treatment: Light 1hr
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| Growth protocol |
Cultures were grown in standard BG11, at 30°C, 150rpm. Three cultures for each genotype, WT and Δxpk, were harvested at 4 different time points (Light 1 h: 1 hour after switching to light; Light 12 h: 12-hour illumination; Dark 1 h: 1 hour after switching to dark; Dark 12 h: 12-hour darkness) for a total of 24 samples. Each sample consisted of 5 mL of culture with an OD730~1. The cells were pelleted by full-speed centrifugation for 10 seconds, frozen with liquid nitrogen, and stored at -80°C until all time points were harvested.
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| Extracted molecule |
total RNA |
| Extraction protocol |
For RNA extraction, the cell pellets were washed once with 300 µL of Qiagen RNAprotect® cell reagent, and the supernatant was removed after centrifugation. The cells were then once again frozen with liquid nitrogen and thawed by adding 350 µL of RLT solution from the Qiagen RNeasy kit. After 3 rounds of freeze-thaw-vortex steps, the samples were centrifuged at 15000g for 10 minutes. The supernatant was transferred to tubes and mixed with an equal volume of 100% ethanol before transferring to RNeasy mini-spin columns. The standard procedures of the Qiagen RNeasy kit were followed, and the Invitrogen TURBO DNA-free™ kit was used to remove DNA contamination.
For RNA-seq library preparation, RNA quality control was performed using the Agilent fragment analyzer 5200. Library preparation and rRNA depletion were performed using the Illumina Ribo-Zero Plus rRNA depletion kit. All sequencing was performed on Illumina Nextseq 2000 with P2 flowcell, 300 cycles, and pair-end 150 bp.
Standard Ribozero plus procedure
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
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| Description |
ST21-WN02
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| Data processing |
bcl2fastq 2.1.8for base-calling
CLC Genomics Workbench 22.0 for differential gene expression
Supplementary files format and content: Differential gene expression between WT and Δxpk across all conditions (across group, ANOVA-like), with TMM-normalized CPM values
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| Submission date |
Mar 15, 2023 |
| Last update date |
Aug 08, 2023 |
| Contact name |
James C. Liao |
| E-mail(s) |
liaoj@gate.sinica.edu.tw
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| Organization name |
Academia Sinica
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| Street address |
128 Academia Road, Section 2, Nankang, Taipei 11529, Taiwan
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| City |
Taipei |
| ZIP/Postal code |
11529 |
| Country |
Taiwan |
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| Platform ID |
GPL33256 |
| Series (1) |
| GSE227397 |
An ATP-sensitive phosphoketolase regulates carbon fixation in cyanobacteria |
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| Relations |
| BioSample |
SAMN33769458 |
| SRA |
SRX19681344 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7099963_WN02.txt.gz |
123.3 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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