|
| Status |
Public on Mar 07, 2024 |
| Title |
Chlamydomonas, Control 24 hours, rep3 |
| Sample type |
SRA |
| |
|
| Source name |
Vegetative, haploid, Cells
|
| Organism |
Chlamydomonas reinhardtii |
| Characteristics |
tissue: Vegetative, haploid, Cells
cell line: (CC-4533)
genotype: Wild-type
treatment: Control 24 hours
time point: rep3
|
| Treatment protocol |
Once cultures reached early-mid exponential phase (~2E+06 cells/ml) different osmolyte concentrations were inoculated, 100 mM NaCl (Sigma) and 300 mM mannitol using 1 liter Erlenmeyer flasks and grown with mild agitation (~150 rpm), 22 ºC and low continuous light
|
| Growth protocol |
RNA-seq samples: prior to sample collection wild-type strains (CMJ030/CC-4533) were refreshed in solid media and inoculated in liquid media, Tris-Acetate-Phosphate (TAP) with modified trace elements 95 at 22 ºC in low continuous light (100 μmol photons m-2 s-1). After 2 passages in liquid media (~6 doublings/passage), cells growing in early-mid exponential phase (~2E+06 cells/ml) were used for inoculation. Once cultures reached early-mid exponential phase (~2E+06 cells/ml) different osmolyte concentrations were inoculated, 100 mM NaCl (Sigma) and 300 mM mannitol using 1 liter Erlenmeyer flasks and grown with mild agitation (~150 rpm), 22 ºC and low continuous light
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction was performed using Direct-zol RNA miniprep kit (R2050) following manufacturer's instructions including in-column DNase I treatment prior RNA washing and elution steps
RNA-seq libraries were made using the Kapa mRNA HyperPrep kit (Roche, KK8540) following manufacturer’s protocols. Libraries were pooled based on fragment analyzer concentration
Libraries were pooled based on fragment analyzer concentrations
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
| |
|
| Description |
JV-46
|
| Data processing |
RNA-seq reads were aligned using BWA to the Chlamydomonas reference genome 5.6
DESeq2 package was used to call transcripts as differentially expressed at a false-discovery-rate (Benjamini-Hochberg method) FC > 2, (FDR < 0.01)
Assembly: Chlamydomonas reference genome 5.6
Supplementary files format and content: tab-limited text files, including raw counts fr each gene
|
| |
|
| Submission date |
Mar 04, 2024 |
| Last update date |
Mar 07, 2024 |
| Contact name |
Josep Vilarrasa Blasi |
| E-mail(s) |
pituvilarnadal@gmail.com
|
| Phone |
6506563386
|
| Organization name |
Aetna
|
| Street address |
787 corto street
|
| City |
Mountain View |
| State/province |
CA |
| ZIP/Postal code |
94043 |
| Country |
USA |
| |
|
| Platform ID |
GPL34271 |
| Series (1) |
| GSE260814 |
Multi-omics analysis of green lineage osmotic stress pathways unveils crucial roles of different cellular compartments |
|
| Relations |
| BioSample |
SAMN40254567 |
| SRA |
SRX23829969 |
