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| Status |
Public on Sep 20, 2020 |
| Title |
BS-11 |
| Sample type |
SRA |
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| Source name |
Col-0/Col-0
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| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype background: Columbia-0
developmental stage: bolting
genotype/variation: Col-0/Col-0
tissue: rosette leaves
replicate type: biological rep 2
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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. 3 plants from msh1 mutant and dcl2,3,4,msh1 quadruple mitant rootstocks 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 |
genomic DNA |
| Extraction protocol |
genomic DNA extraction using DNeasy Plant kit (Qiagen, Germany).
Genomic DNA Sonicated to 100-300 bp fragments and purified with MiniElute PCR Purification Kit (Qiagen, Germany), incubated at 20 ℃ after add End Repair Mix. Then purified and added a single ‘A’ nucleotide to the 3’ ends of the blunt fragments, purified again and add Methylated Adapter to the 5’ and 3’ ends of each fragment. Then fragments with 300bp-400bp size-range were purified with QIAquick Gel Extraction kit (Qiagen, Germany) and subjected to bisulfite treatment by using Methylation-Gold kit (ZYMO). Followed with PCR and gel purification (350bp-400bp range fragments were selected). Qualified libraries sequenced pair end on the HiSeq X-ten system.
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
HiSeq X Ten |
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| Data processing |
Illumina for basecalling
The sequences were trimmed using trim_galore 0.4.1 and cutadapt 1.15 with cutoff 20
The sequences were aligned using Bismark (version 0.19.0) with default options.The deduplicate_bismark function in Bismark with default parameters was used to remove duplicated reads, and reads with coverage greater than 500 were removed to control PCR bias.
tab-delimited file generated with bismark2bedGraph with options -CX --ample_memory
Genome_build: Arabidopsis TAIR 10
Supplementary_files_format_and_content: tab-delimited file, 1-based genomic coords with <chromosome> <position> <strand> <count methylated> <count unmethylated> <C-context> <trinucleotide context>fields
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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 |
GPL23157 |
| Series (2) |
| GSE152564 |
Bisulfite (methylome) sequencing of progenies of Col-0 grafted on msh1; Col-0 grafted on dcl2,3,4,msh1; Col-0 grafted on Col-0; msh1 mutant; dcl2,3,4,msh1 quadruple mutant in Arabidopsis [msh1_graft_BS-seq] |
| GSE152570 |
Heritable enhanced growth vigor through grafting is associated with the RdDM pathway in plants |
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| Relations |
| BioSample |
SAMN15248546 |
| SRA |
SRX8554558 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4618283_BS-11.CX_report.txt.gz |
180.8 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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