|
| Status |
Public on Oct 23, 2024 |
| Title |
hsf20-m1, imbibed embryo, biol rep 1 |
| 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: mu1085720
genotype: hsf20-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 |
E14_hsf20-m1_1
|
| 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 |
SAMN33370410 |
| SRA |
SRX19444838 |
