|
| Status |
Public on May 03, 2013 |
| Title |
Chlamydomonas reinhardtii 2137 - TAP supplemented with a revised trace element recipe |
| Sample type |
SRA |
| |
|
| Source name |
Chlamydomonas cultured cells
|
| Organism |
Chlamydomonas reinhardtii |
| Characteristics |
strain: 2137
treatment: Zn deprivation
|
| Treatment protocol |
Cells grown on TAP agar plates supplemented with Hutner's trace elements were grown to mid to late log phase (10e6-10e7 cells/ml) in TAP supplemented with a revised trace element recipe and diluted 1/100 into fresh medium.
|
| Growth protocol |
Cells were cultured under continuous light of ~50-90 μmol photon m-2s-1 at 23ºC in liquid and on solid Tris-Acetate-Phosphate (TAP) medium supplemented with a revised trace element recipe.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted by Cell lysis by SDS / proteinase K, Purification by phenol / chloroform extraction, and EtOH precipitation. 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 by whole transcriptome analysis.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
Illumina's RNA-Seq whole transcriptome analysis
|
| Data processing |
Illumina's proprietary software was used for basecalling.
The reads were aligned using bowtie in single-end mode and with a maximum tolerance of 3 mismatches to the Au10.2 transcripts sequences (http://www.phytozome.net/chlamy), corresponding to the version 4.0 assembly of the Chlamydomonas genome.
Expression estimates where obtained for each individual run in units of RPKMs (reads per kilobase of mappable transcript length per million mapped reads) after normalization by the number of aligned reads and transcript mappable length. Final expression estimates and fold changes where obtained from the average of both technical and biological replicates.
Genome_build: version 4.0 assembly of the Chlamydomonas genome
Supplementary_files_format_and_content: Processed files correpond to expression estimates per lane, in units of RPKMs, including those for the control samples (GEO record GSE25622)
|
| |
|
| Submission date |
Sep 24, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Sabeeha Merchant |
| E-mail(s) |
merchant@chem.ucla.edu
|
| Phone |
310-825-8300
|
| Organization name |
University of California Los Angeles
|
| Department |
Department of Chemistry and Biochemistry
|
| Street address |
607 Charles E. Young Drive East
|
| City |
Los Angeles |
| State/province |
California |
| ZIP/Postal code |
90095-1569 |
| Country |
USA |
| |
|
| Platform ID |
GPL9152 |
| Series (1) |
| GSE41096 |
Zinc deficiency impacts CO2 assimilation and disrupts copper homeostasis in Chlamydomonas reinhardtii |
|
| Relations |
| SRA |
SRX189183 |
| BioSample |
SAMN01728932 |
