|
| Status |
Public on Jul 08, 2022 |
| Title |
epi_24_root_P2 |
| Sample type |
SRA |
| |
|
| Source name |
Columbia-0
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
replicate type: biological rep 2
tissue: root
developmental stage: 10 days old plant
|
| Treatment protocol |
3 progenies plants from each of the epi populations (epi8, epi24, epi10, epi19) and Col-0 WT were sequenced using either rosette leaves, root, or floral stem. Epi8 and epi 24 were derived from same cross while epi 10 and epi19 were from the same cross. Tissues were flash frozen in liquid nitrogen. Tissues were ground by motor and pestle in liquid nitrogen.
|
| Growth protocol |
For leaves and floral stem tissue, seeds were sown on peat mix in square pots in reach-in chambers at 12hrs daylenght (22 °C, 120-150 μmol/(m^2*s) light). For root tissue, plants were grown on 0.5 MS growth medium for 10 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from each sample was extracted by NucleoSpin RNA Plant kit (Macherey-Nagel, Germany) following manufacturer’s protocol, including genomic DNA removal.
RNA libraries were constructed as described in the TruSeq RNA Sample Preparation v2 Guide.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
epi_24_root
|
| Data processing |
Illumina for basecalling
Alignments were performed using STAR (version 2.7.3a) with –twopassMode = Basic and –outFilterMultimapNmax = 1 parameters (Grant et al., 2011)
The read count data were generated from the BAM files by using QoRTs software package (Hartley and Mullikin, 2015) --minMAPQ 25 --dropChrom Pt,Mt
edgeR (version 3.26.8) was used to calculate the differential expression.
Genome_build: Arabidopsis TAIR 10
Supplementary_files_format_and_content: Text file with GENEID and COUNTS to be used with edgeR
|
| |
|
| Submission date |
Dec 21, 2021 |
| Last update date |
Jul 08, 2022 |
| Contact name |
Hardik Kundariya |
| E-mail(s) |
hsk13@psu.edu
|
| Organization name |
The Pennsylvania State University
|
| Street address |
361 N. Frear
|
| City |
University Park |
| State/province |
PA |
| ZIP/Postal code |
16801 |
| Country |
USA |
| |
|
| Platform ID |
GPL26208 |
| Series (1) |
| GSE192429 |
MSH1 disruption in plants triggers RdDM-mediated reprogramming of phenotypic plasticity (RNA-Seq) |
|
| Relations |
| BioSample |
SAMN24289027 |
| SRA |
SRX13476202 |
