|
| Status |
Public on May 18, 2012 |
| Title |
Dictyostelium rblA disruptant vegetative |
| Sample type |
SRA |
| |
|
| Source name |
vegetative cells
|
| Organism |
Dictyostelium discoideum |
| Characteristics |
background/strain: Ax2
genotype: rblA disruptant clone3A6-12
developmental stage: vegetative
|
| Growth protocol |
Vegetative cells were grown in HL5 medium and harvested at a density of 2E6 cells/ml. For development, cells were dispersed on Whatman 50 filters overlaid on Millipore absorbent pads moistened with LPS. Aggregates were harvested in the early culminant stage. Cells were synchronized in the cell cycle using the cold shock protocol (Maeda (1986) J Gen Microbiol 132, 1189-1196).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Libraries were prepared according to Illumina's instructions accompanying the mRNA-Seq Sample Prep Kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
2-rblA KO veg
polyA RNA
|
| Data processing |
Reads from barcoded samples were split into separate files according to their barcode, and the barcode sequences were trimmed off. Reads were aligned with BowTie v0.12.7 to the Dictyostelium discoideum chromosomal DNA sequences downloaded from dictybase.org on August 12, 2010, augmented with splice junction sequences. Introns were first located by mapping the pooled reads to the genomic sequence with BLAT; reads that aligned with >95% identity and coverage, but with gaps, were examined for the presence of plausible introns in the gaps. Splice junction sequences were constructed by concatenating 41 bases of sequence from the two flanks of the introns thus identified. Read alignments to the splice junction sequences were translated into gapped alignments to the genome. Reads that mapped equally well to more than one location were randomly assigned to one of the locations with probability proportional to the local depth of coverage by uniquely-mapped reads.
|
| |
|
| Submission date |
Jul 01, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Kimchi Audrey Strasser |
| Organization name |
Concordia University
|
| Department |
Biology
|
| Lab |
Dr.- Tsang L-SP510
|
| Street address |
7141 Sherbrooke Street West
|
| City |
Montreal |
| State/province |
Quebec |
| ZIP/Postal code |
H4B 1R6 |
| Country |
Canada |
| |
|
| Platform ID |
GPL9379 |
| Series (1) |
| GSE30368 |
The retinoblastoma orthologue, rblA, is a major regulator of S-phase, mitotic, and developmental gene expression in Dictyostelium |
|
| Relations |
| SRA |
SRX081687 |
| BioSample |
SAMN00631949 |
