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Status |
Public on Mar 03, 2021 |
Title |
Wt F. graminearum in NON preferred nutrient conditions for 24h rep1 |
Sample type |
SRA |
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Source name |
Fungal mycelia
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Organism |
Fusarium graminearum |
Characteristics |
strain: WT NRRL29169 environmental condition: NON Preferred Nutrient Growth timepoint: 24h sequencing: Illumina HiSeq4000 PE100 rRNA depleted mRNA Stranded Library
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Growth protocol |
6-well plate growth of fungal mycelia at 28C with shaking of 160RPM in the dark.
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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)
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 4000 |
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Description |
Wt F. graminearum in NON preferred nutrient conditions for 24h Each sample was performed in triplicate RNAseqAnalysis_ReadCounts_ProcessedFile_WT24hNP_Triplicate.xlsx RNAseqAnalysis_ComparisonTwoSampleGroups_ProcessedFile_24hNPWT vs_6hNPWT.xlsx RNAseqAnalysis_ComparisonTwoSampleGroups_ProcessedFile_24hNPWT vs_24hNPMutant.xlsx RNAseqAnalysis_ComparisonTwoSampleGroups_ProcessedFile_24hNPWT vs_24hPNWT.xlsx CDS_Extracted annotations.fa
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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).
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Submission date |
Nov 06, 2019 |
Last update date |
Mar 03, 2021 |
Contact name |
Christopher Thomas Bonner |
E-mail(s) |
chrisbonner19@gmail.com
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Phone |
6137597962
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Organization name |
Agriculture Canada
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Lab |
Subramaniam
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Street address |
960 Carling
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City |
Ottawa |
State/province |
Ontario |
ZIP/Postal code |
K1Y 4X2 |
Country |
Canada |
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Platform ID |
GPL24502 |
Series (1) |
GSE140030 |
Gene expression analysis by mRNAseq in Fusarium graminearum WT and a DNMT mutant |
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Relations |
BioSample |
SAMN13222347 |
SRA |
SRX7106929 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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