|
| Status |
Public on Nov 27, 2017 |
| Title |
media -Cu |
| Sample type |
SRA |
| |
|
| Source name |
liquid culture
|
| Organism |
Chlamydomonas reinhardtii |
| Characteristics |
strain: CC-124 x CC-4425
media: tris acetate phosphate medium -Cu
light regime: continuous light
library protocol: RiboZero
|
| Growth protocol |
Growth in media without Cu.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was purified from pelleted cells by freezing in SDS/proteinase K digestion buffer followed extraction with Trizol reagent.
~2 ug total RNA was used as starting material for either rRNA-depletion by RiboZero Plant Leaf kit or for enrichment of poly-A transcripts by binding oligo-T beads (indicated by "library protocol" above). The resulting RNA was then used to generate strand-specific Illumina libraries.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
processed data file: fpkms.copper.tsv
|
| Data processing |
Basecalling performed using Illumina RTA software.
Conversion of qseq to fastq format and demultiplexing by in-house scripts
Removal of contaminating rRNA reads by alignment to rRNA+snoRNA.fasta with RNA-STAR (STAR_2.4.0j). Unmapped reads selected for further analysis with "--outReadsUnmapped Fastx" option of STAR.
Alignment to C.reinhardtii nuclear genome (Phytozome v5.5) plus chloroplast genome (CPv4) plus mitochondrial genome (MTv4) by RNA-STAR (STAR_2.4.0j) with default parameters except --alignIntronMax 5000
SAM alignments sorted and converted to BAM format by samtools (v1.3).
Counts per gene and FPKMs calculated by cuffdiff (v2.0.2) with "--multi-read-correct --max-bundle-frags 1000000000 --library-type fr-firststrand"
Genome_build: Cre.nuc.v5.5.cp.v4.4.mt.v4.4
Supplementary_files_format_and_content: tab-delimited text files (.tsv) containing transcript abundance determinations calculated as FPKMs
|
| |
|
| Submission date |
Jul 27, 2017 |
| Last update date |
May 15, 2019 |
| 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) |
| GSE101944 |
Transcriptome analysis of Chlamydomonas reinhardtii chloroplast and mitochondria |
|
| Relations |
| BioSample |
SAMN07418739 |
| SRA |
SRX3041728 |
