|
| Status |
Public on Apr 04, 2024 |
| Title |
C.reinhardtii, short Fe timecourse, 240 min, rep 1 |
| Sample type |
SRA |
| |
|
| Source name |
cultured cells
|
| Organism |
Chlamydomonas reinhardtii |
| Characteristics |
strain: CC-4532
cell type: cultured cells
time point: 240 min
treatment: iron deprevation
cultured in: TAP medium without Fe-EDTA 240 min
|
| Treatment protocol |
Cells were grown to mid-logarithmic phase (approximately 4 x 10e6 cells mL-1), collected by centrifugation (2,500 xg for 5 min at room temperature), washed twice in TAP medium lacking Fe-EDTA and inoculated into fresh TAP medium lacking Fe-EDTA and sampled at the indicated times.
|
| Growth protocol |
Cells were cultured under continuous light of ~90 μmol photon m-2s-1 at 24C in liquid and on solid Tris-Acetate-Phosphate (TAP) medium.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Nucleic acids were isolated and analyzed according to standard procedures by hybridization or on an Agilent 2100 Bioanalyzer. For quantitative transcriptomes, RNAs were sequenced at Illumina HiSeq 2000 platform (UCLA).
RNA-Seq libraries compatible with the Illumina HiSeq platform were constructed using standard kits and protocols from Illumina.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
SMEU37F240TS_b1
|
| Data processing |
Reads were mapped to the C.reinhardtii reference assembly with STAR (v2.4.1.d) using STAR --outFilterMismatchNoverLmax 0.04 --alignIntronMax 10000 --readFilesCommand zcat --outFilterType BySJout
Normalized expression estimates were calculated with cuffdiff (v2.0.2) with cuffdiff --multi-read-correct --max-bundle-frags 1000000000
Assembly: The Chlamydomonas reinhardtii reference genome assembly and annotations (v5.6) available from Phytozome at (https://phytozome-next.jgi.doe.gov/)
Supplementary files format and content: The processed data file, Fe_timecourses.FPKMs.tsv, includes normalized expression estimates in terms of fragments per kb of gene per million mapped reads (FPKMs) for all C.reinhardtii nuclear genes in all samples. The mean of two biologicial replicates is presented.
|
| |
|
| Submission date |
Apr 04, 2024 |
| Last update date |
Apr 04, 2024 |
| Contact name |
Sean D. Gallaher |
| Organization name |
UC Berkeley
|
| Department |
California Institute for Quantitative Biosciences
|
| Lab |
Sabeeha Merchant
|
| Street address |
176 Stanley Hall, room 408
|
| City |
Berkeley |
| State/province |
California |
| ZIP/Postal code |
94720 |
| Country |
USA |
| |
|
| Platform ID |
GPL15922 |
| Series (1) |
| GSE263199 |
Chlamydomonas cells transition through distinct Fe nutrition stages within 48 h of transfer to Fe-free medium |
|
| Relations |
| BioSample |
SAMN40749211 |
| SRA |
SRX24153782 |
