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Status |
Public on Sep 20, 2020 |
Title |
R-15 |
Sample type |
SRA |
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Source name |
Col-0/msh1
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Organism |
Arabidopsis thaliana |
Characteristics |
ecotype background: Columbia-0 developmental stage: bolting genotype/variation: Col-0/msh1 tissue: rosette leaves replicate type: biological rep 3
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Treatment protocol |
3 progenies plants from each Col-0 on msh1; Col-0 on dcl2,3,4,msh1; Col-0 on Col-0 grafts were sequenced. Leaves at bolting were flash freezed in liquid nitrogen. Tissues were ground by motor and pestle in liquid nitrogen.
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Growth protocol |
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)
|
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.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
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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
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Submission date |
Jun 16, 2020 |
Last update date |
Sep 20, 2020 |
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 (2) |
GSE152565 |
Total RNA sequencing of progenies of Col-0 grafted on msh1; Col-0 grafted on dcl2,3,4,msh1; Col-0 grafted on Col-0 in Arabidopsis [msh1_graft_leaf_RNA-seq] |
GSE152570 |
Heritable enhanced growth vigor through grafting is associated with the RdDM pathway in plants |
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Relations |
BioSample |
SAMN15248568 |
SRA |
SRX8554577 |