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Sample GSM2443089 Query DataSets for GSM2443089
Status Public on Jun 12, 2017
Title WT-mycelium-Light-R1
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
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
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
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
BioSample SAMN06200041
SRA SRX2459896

Supplementary data files not provided
SRA Run SelectorHelp
Processed data are available on Series record
Raw data are available in SRA

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