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Sample GSM8588687 Query DataSets for GSM8588687
Status Public on Oct 23, 2024
Title hsf6-m1, imbibed embryo, biol rep 3
Sample type SRA
 
Source name imbibed embryo
Organism Zea mays
Characteristics tissue: imbibed embryo
developmental stage: R6, ~60 days after pollination, harvested and dried seed
age: 140 days after sowing
uniformmu id: mu1048425
genotype: hsf6-m1
treatment: mutant
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using the Qiagen RNeasy Plant Mini Kit
Paired-end libraries were prepared from a minimum of 500 ng of total RNA using the standard Illumina TruSeq Stranded mRNA library protocol. Single-end libraries were prepared from 2 µg of total RNA using the Illumina TruSeq RNA Sample Prep Kit
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description E25_hsf6-m1_3
Data processing nf-core RNA-seq pipeline Nextflow v20.10.0 for initial QC and raw read counting
Reads were trimmed using Trim Galore! v0.6.5 and aligned to the W22 reference genome using Hisat2 v2.1.0 with default parameters (hisat2 -x $db $input -p 12 --met-stderr --new-summary). Uniquely aligned reads were counted per feature by featureCounts v2.0.1.
Raw read counts were normalized by library size and corrected for library composition bias using the TMM normalization approach in edgeR v3.28.0 to give CPM (Counts Per Million reads) for each gene in each sample. CPM values were normalized by W22 gene CDS lengths to give FPKM (Fragments Per Kilobase of exon per Million reads) values.
Genes were considered expressed if their CPM was ≥ 1 in at least one sample per tissue
Assembly: Zea mays W22
Supplementary files format and content: Tab-delimited text file includes raw read counts, TMM normalized CPM values, FPKM values for each W22 gene in every sample. The B73v4 gene ID is recorded for W22 genes with one-to-one gene models between W22 and B73v4. The expressed column indicates if the W22 gene was considered expressed in our experiment (TRUE or FALSE). The filtered_DE column indicates if the gene was filtered from the differential expression analysis (TRUE = filtered out, FALSE = included). See Materials and Methods: Identification of TF mutant allele DE genes for further description.
 
Submission date Oct 23, 2024
Last update date Oct 23, 2024
Contact name Nathan Springer
Organization name University of Minnesota
Department Plant and Microbial Biology
Lab 140 Gortner Laboratory
Street address 1479 Gortner Ave
City St Paul
State/province MN
ZIP/Postal code 55108
Country USA
 
Platform ID GPL25410
Series (1)
GSE280139 Transcriptome profiling of maize transcription factor mutants to probe gene regulatory network predictions
Relations
BioSample SAMN33370421
SRA SRX19444850

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA

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