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| Status |
Public on Sep 27, 2016 |
| Title |
Paw-26 (2171)-2 |
| Sample type |
SRA |
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| Source name |
leaf
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| Organism |
Arabidopsis thaliana |
| Characteristics |
cultivar: Paw-26
ecotype id: 2171
tissue: leaf
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted using the DNeasy Plant Kit (Qiagen, Valencia, CA) from ground, frozen 10 rosette leaves, harvested just before bolting.
Two µg of genomic DNA was fragmented with a Covaris S2 (Covaris, Woburn, MA) to 200 bp, followed by end repair (End-It, Epicenter) and addition of a 3’ A base (Klenow (3'->5' exo-), dA-tailing buffer (NEB)). Cytosine-methylated adapters provided by Bio
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Map Bisulfite-seq reads to converted Arabidopsis genome by using bowtie 2.0.
Remove clonal reads and Call un-converted C position
Genome_build: TAIR 10 conversion (C-T,G-A)
Supplementary_files_format_and_content: tab delimited file with chromosome, position, strain, mC, h, and sum
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| Submission date |
Sep 26, 2016 |
| Last update date |
May 29, 2019 |
| Contact name |
Joseph R Ecker |
| E-mail(s) |
ecker@salk.edu
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| Phone |
8584534100
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| Organization name |
HHMI-Salk-Institute
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| Department |
Genomic Analysis Laboratory
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| Lab |
Ecker lab
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| Street address |
10010 North Torrey Pines Road
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| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92037 |
| Country |
USA |
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| Platform ID |
GPL17639 |
| Series (1) |
| GSE43857 |
Patterns of Population Epigenomic Diversity in Arabidopsis thaliana (Methyl-Seq) |
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| Relations |
| BioSample |
SAMN05826332 |
| SRA |
SRX2190724 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2328547_allc_2171.tsv.gz |
109.2 Mb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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