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Sample GSM4151697

Query DataSets for GSM4151697

Status

Public on Mar 03, 2021

Title

DNMT Double Gene Deletion in F. graminearum in NON preferred nutrient conditions for 24h rep3

Sample type

SRA

Source name

Fungal mycelia

Organism

Fusarium graminearum

Characteristics

strain: DAOMC251487
environmental condition: NON Preferred Nutrient Growth
timepoint: 24h
sequencing: Illumina HiSeq4000 PE100 rRNA depleted mRNA Stranded Library

Growth protocol

6-well plate growth of fungal mycelia at 28C with shaking of 160RPM in the dark.

Extracted molecule

polyA RNA

Extraction protocol

liquid N2/Trizol extraction followed by RNA cleanup with Stratec RNA clean up kit
mRNA Stranded Illumina HiSeq2500 PE125 or rRNA Depleted Stranded HiSeq4000 PE100 (noted in the characteristics)

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 4000

Description

DNMT Double Gene Deletion in F. graminearum in NON preferred nutrient conditions for 24h
Each sample was performed in triplicate
RNAseqAnalysis_ReadCounts_ProcessedFile_DKO24hNP_Triplicate.xlsx RNAseqAnalysis_ComparisonTwoSampleGroups_ProcessedFile_24hNPMutant vs_6hNPMutant.xlsx RNAseqAnalysis_ComparisonTwoSampleGroups_ProcessedFile_24hNPMutant vs_24hPNMutant.xlsx RNAseqAnalysis_ComparisonTwoSampleGroups_ProcessedFile_24hNPWT vs_24hNPMutant.xlsx CDS_Extracted annotations.fa

Data processing

Raw read QC and trimming (CLC genomics workbench V12): reads were trimmed of adaptor sequences and for low quality (limit 0.05) bases, and ambiguous bases were trimmed. Reads were filtered based on read length, with minumum length of 15 bases. 5 bases were default trimmed off of both the 5' and 3' ends.
Trimmed reads were aligned to the reference (NRRL29169 CDS - processed files) using the RNAseq Analysis function in CLC genomics workbench V12). Read alignment settings were as follows: Mismatch cost 2, Indel cost 3, length fraction 0.8, similarity fraction 0.8, auto-detect paired distances, both strands and maximum 10 hits per read. RNAseq analysis normalized read counts as per the TMM (trimmed mean of M values) method.
Differential expression analysis was performed in CLC genomics workbench V12 as per the Differential Expression in Two Groups function, which uses multi-factorial statistics based on a negative binomial GLM.
Genome_build: The reference used was the CDS of genes predicted in SPRZ00000000 in the NCBI WGS. The CDS fasta is provided in the processed files.
Supplementary_files_format_and_content: Processed datafiles come in two formats. The first format is the direct RNAseq analysis between two sample groups (eg. WT vs mutant, or environmental condition vs environmental conditions). This data is presented as a table with gene name, location (all beginning at position 1), max group mean, log2 fold change, fold change, P-value, FDR p-value and Bonferroni correction columns. We are interested in the genes which had a Pvalue of less than 0.05 and a fold change of less than or greater than 2. The second format of data is also a table, with columns gene name, transcripts per million, Unique gene reads and total gene reads. This is the processed RNAseq read counts used in the RNAseq comparision (Datafile type 1).

Submission date

Nov 06, 2019

Last update date

Mar 03, 2021

Contact name

Christopher Thomas Bonner

E-mail(s)

chrisbonner19@gmail.com

Phone

6137597962

Organization name

Agriculture Canada