|
| Status |
Public on Jun 12, 2017 |
| Title |
WT-mycelium-Light-R3 |
| Sample type |
SRA |
| |
|
| Source name |
WT strain exposed to light
|
| Organism |
Phycomyces blakesleeanus |
| Characteristics |
cell type: mycelium (Vegetative growth)
|
| Treatment protocol |
P. blakesleeanus dark-grown mycelia were exposed to blue light (2782.10 J/m2) at the age of 48 h for 30 min. After light exposure mycelia were collected and frozen in liquid nitrogen.
|
| Growth protocol |
104 activated spores (48 °C, 15 min) of each P. blakesleeanus strain were grown at 22 °C in minimal medium.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Mycelia were disrupted by two 0.5-min pulses in a cell homogenizer (FastPrep-24, MP Biomedicals) with 1.5 g of zirconium beads (0.5 mm diameter) using the RNeasy Plant Mini Kit (Qiagen) following the manufacturer procedure.
Libraries for RNAseq were prepared with RNA from mycelia of the wild type and the madC mutant strains using the TruSeq kit protocol (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
WT_L_vs_WT_D.txt
|
| Data processing |
100-base-pair-long reads were obtained and mapped to the P. blakesleeanus genome V2 using bowtie
We performed the mapping of the readings resulting from the RNAseq
experiment using the fasta file of the genome deposited at
http://genome.jgi.doe.gov/pages/dynamicOrganismDownload.jsf?organism=Phybl2
Identifying the file as Phycomyces blakesleeanus NRRL1555 v2.0: Project:
401760, Phycomyces_blakesleeanus_v2_filtered_transcripts.fasta.gz 5 MB; Wed Mar 07 16:56:13 PST 2012.
The identifiers used are those appearing in the Phycomyces blakesleeanus
NRRL1555 v2.0 genome file and can be accessed individually at
http://genome.jgi.doe.gov/pages/search-for-genes.jsf?organism=Phybl2.
Alignment results were recorded in BAM format for further downstream analysis. Read counts per gene were calculated for each library using a shell script and collapsed into a table.
Differential expression analysis of gene expression in the wild type and madC strains in response to light was performed using the edgeR package
Enrichment analysis was performed on the differential genes using GOseq
Supplementary_files_format_and_content: read counts, differential expression
|
| |
|
| Submission date |
Jan 03, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Alfredo Herrera-Estrella |
| E-mail(s) |
alfredo.herrera@cinvestav.mx
|
| Organization name |
LANGEBIO
|
| Department |
LANGEBIO
|
| Lab |
Lab 7
|
| Street address |
Libramiento Norte Carretera Leon Km 9.6
|
| City |
Irapuato |
| State/province |
Guanajuato |
| ZIP/Postal code |
36821 |
| Country |
Mexico |
| |
|
| Platform ID |
GPL22874 |
| Series (1) |
| GSE93056 |
A Ras GTPase associated protein is involved in the phototropic and circadian photobiology responses in fungi |
|
| Relations |
| BioSample |
SAMN06200037 |
| SRA |
SRX2459898 |
