|
Status |
Public on Aug 06, 2019 |
Title |
W-1-1 |
Sample type |
SRA |
|
|
Source name |
Columbia-0
|
Organism |
Arabidopsis thaliana |
Characteristics |
replicate type: biological rep 1 tissue: rosette leaves
|
Treatment protocol |
Five memory plants, four non-memory plants, and four Col-0 wild-type plants were sequenced were used. Leaves at bolting were flash freezed in liquid nitrogen. Tissues were ground by motor and pestle in liquid nitrogen.
|
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 |
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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|
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Library strategy |
Bisulfite-Seq |
Library source |
genomic |
Library selection |
RANDOM |
Instrument model |
HiSeq X Ten |
|
|
Description |
Wild-type control
|
Data processing |
Illumina for basecalling The sequences were trimmed using trim_galore 0.4.1 and cutadapt 1.9.1 with cutoff 20 The sequences were aligned using Erne-meth 2.1.1 with default options and set the output as a bismark coverage file tab-delimited file generated with bismark2bedGraph with options -CX --ample_memory Genome_build: TAIR 10 Supplementary_files_format_and_content: tab-delimited file, 1-based genomic coords with <chromosome> <start position> <end position> <methylation percentage> <count methylated> <count non-methylated> fields
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|
|
Submission date |
Aug 21, 2018 |
Last update date |
Aug 07, 2019 |
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 |
GPL23157 |
Series (1) |
GSE118874 |
Bisulfite (methylome) sequencing of msh1 memory line and non-memory (normal looking) sibling plants with isogenic Col-0 wild-type control in Arabidopsis |
|
Relations |
BioSample |
SAMN09873030 |
SRA |
SRX4589932 |