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| Status |
Public on Sep 20, 2020 |
| Title |
R-16 |
| Sample type |
SRA |
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| Source name |
Col-0/dcl2,3,4,msh1
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| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype background: Columbia-0
developmental stage: bolting
genotype/variation: Col-0/dcl2,3,4,msh1
tissue: rosette leaves
replicate type: biological rep 1
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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)
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| 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
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| Organization name |
The Pennsylvania State University
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| Street address |
361 N. Frear
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| City |
University Park |
| State/province |
PA |
| ZIP/Postal code |
16801 |
| Country |
USA |
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| 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 |
SAMN15248567 |
| SRA |
SRX8554578 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4618303_R-16.geneCounts.formatted.for.DESeq.txt.gz |
126.4 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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