|
| Status |
Public on Jun 05, 2024 |
| Title |
Col(C24)xCol LCM CNS Embryo Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Embryo
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: Embryo
genotype: Col(C24)xCol
|
| Treatment protocol |
Plants were from controlled crosses, either reciprocal crosses of standrd C24 and Col-0, or from the CNS swpped versions
|
| Growth protocol |
Arabidopsis were grown under standard growth room lighting and temperature, with a 16/8 light/dark cycle
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from LCM-isolated tissue using the RNAqueous Micro Kit RNA isolation kit
Libraries were prepared using the NEB Ultra II RNA seq kit with poly-A selection module
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
H-em_S8
|
| Data processing |
Reads were first trimmed with trimmomatic
High-quality reads were mapped onto the TAIR10 genome using STAR
Reads overlapping each gene were counted using HTseq with the union and reverse stranded settings
Statistical analysis of differential expression was performed using EdgeR, using linear models to identify differentially expressed genes
Assembly: TAIR10
|
| |
|
| Submission date |
Dec 06, 2023 |
| Last update date |
Jun 05, 2024 |
| Contact name |
Z Jeffrey Jeffrey Chen |
| E-mail(s) |
zjchen@austin.utexas.edu
|
| Phone |
512-475-9327
|
| Organization name |
The University of Texas at Austin
|
| Department |
Molecular Biosciences
|
| Lab |
Polyploidy, Hybrid Vigor, and Epigenetics
|
| Street address |
2506 Speedway NMS 3.122 Stop A500
|
| City |
Austin |
| State/province |
TX |
| ZIP/Postal code |
78712-1597 |
| Country |
USA |
| |
|
| Platform ID |
GPL19580 |
| Series (1) |
| GSE249562 |
Imprinting but not cytonuclear interactions affects parent-of-origin effect on seed size in Arabidopsis hybrids |
|
| Relations |
| BioSample |
SAMN38699499 |
| SRA |
SRX22806432 |
