 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Dec 21, 2023 |
| Title |
anther, Mv 17-09 treated rep3 |
| Sample type |
SRA |
| |
|
| Source name |
anther
|
| Organism |
Triticum aestivum |
| Characteristics |
tissue: anther
cultivar: Mv 17-09
stress: treated
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Anther tissue was ground using a mortar and pestle in liquid nitrogen. Total RNA was extracted using Direct-zol™ RNA MiniPrep Kit, following the manufacturer’s protocol (Zymo Research, Irvine, CA, USA).
The libraries for RNA-seq were prepared with the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB, Ipswitch, MA, USA). Briefly, ribosomal RNA was depleted from 400 ng of total RNA using the QIAseq FastSelect rRNA Plant Kit (Qiagen, Hilden, Germany). The depleted RNA was fragmented, end-prepped, adapter ligated, and the libraries were amplified according to the manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Sequencing results were analyzed by FASTQC v0.11.8 (Babraham Bioinformatics, https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) to assess the read quality.
Trimming and adapter removal were performed using CLC Genomics Workbench v23.3 (Qiagen).
The trimmed short reads were mapped to the IWGSC RefSeq v2.1 reference genome assembly (https://wheat-urgi.versailles.inra.fr/Seq-Repository/Assemblies) by CLC Genomics Workbench v23.3.
Expression values were normalized by the TMM method using CLC Genomics Workbench v23.3.
Assembly: IWGSC RefSeq v2.1
Supplementary files format and content: tab-delimited text file includes RPKM values for each sample
|
| |
|
| Submission date |
Oct 06, 2023 |
| Last update date |
Dec 21, 2023 |
| Contact name |
Attila Fábián |
| Organization name |
Centre for Agricultural Research
|
| Street address |
Brunszvik 2
|
| City |
Martonvásár |
| ZIP/Postal code |
2462 |
| Country |
Hungary |
| |
|
| Platform ID |
GPL25409 |
| Series (1) |
| GSE244819 |
Heat stress during male meiosis impairs cytoskeletal organization, spindle assembly and tapetum degeneration in wheat |
|
| Relations |
| BioSample |
SAMN37706893 |
| SRA |
SRX22012692 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7830292_Mv_HS_A2_12.txt.gz |
943.3 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
|
|
|
|
 |
