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| Status |
Public on Jun 04, 2013 |
| Title |
R-11272-MethylC-Seq |
| Sample type |
SRA |
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| Source name |
Trifoliolate leaves from three-week-old plants
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| Organism |
Glycine max |
| Characteristics |
ecotype: R-11272
tissue: Trifoliolate leaves
age: 3 weeks
genotype: RIL-11272
treatment: 190 mmol PAR m-2s-1, 23C, 60% R.H., and 16 h photoperiod
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| Growth protocol |
Seeds were surface sterilized [30% bleach, rinsed several times with sterile, double-distillated H2O (ddiH2O)], planted in soil-less medium (SogeMix “SM-2”-general purpose growing medium), and germinated in growth chambers (190 mmol PAR m-2s-1, 230C, 60% R.H., and 16 h photoperiod)
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA (gDNA) was purified from 0.5 g of leaves by using DNeasy Plant MiniKit (Qiagen, Valencia, CA), according to the manufacturer’s instructions. MethylC-Seq libraries were constructed according to Schmitz, R.J. et al. Transgenerational epigenetic instability is a source of novel methylation variants. Science 334, 369-73 (2011).
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Data were mapped to the Glycine max 1.0 reference genome
MethylC-Seq analysis were performed as described in Lister, R. et al. Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133, 523-36 (2008), PMID: 18423832.
RNA-Seq RPKM data were generated using Bowtie version 0.12.7 and Tophat version 1.3.3 (flags = -g 1, –F 0). Gene expression values were calculated using Cufflinks version 1.1.0 (flags = -F 0, -b, -N).
Genome_build: Gm1.0
Supplementary_files_format_and_content: mc*.txt file represents MethylC-Seq data.
Supplementary_files_format_and_content: RPKM file represents RNA-Seq data.
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| Submission date |
Oct 23, 2012 |
| Last update date |
May 15, 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 |
GPL15008 |
| Series (1) |
| GSE41753 |
Single-base resolution DNA methylomes of soybean recombinant inbred lines reveals heritability patterns of natural methylation variants |
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| Relations |
| SRA |
SRX200139 |
| BioSample |
SAMN01779512 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1024008_allc_11272.tsv.gz |
869.1 Mb |
(ftp)(http) |
TSV |
| GSM1024008_mc_11272.txt.gz |
162.8 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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