|
| Status |
Public on Jun 09, 2015 |
| Title |
Late-maturation stage whole seed biological replicate 3 |
| Sample type |
SRA |
| |
|
| Source name |
Soybean seeds containing late-maturation (LM) stage embryos
|
| Organism |
Glycine max |
| Characteristics |
cultivar: Williams 82
developmental stage: late-maturation stage (LM)
|
| Growth protocol |
Soybean plants (Williams 82) were grown under standard greenhouse conditions (Le et al., PNAS 2010). Whole seeds containing globular (GLOB) stage, cotyledon (COT), early- (EM), mid- (B1), and late- (AA1) maturation stage embryos were collected. Whole dry (DRY) seeds containing dormant embryos were also collected. For seedlings, seeds were sown on soil and after six days after imbibition, the whole seedlings and the cotyledons of seedling were manually collected.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Harvested seeds were fixed in 3:1(v/v) ethanol:acetic acid and embedded in paraffin (Kerk et al., Plant Physiol.132. 27-35 (2003)). Seed compartment was captured from ten-micron sections using a Leica LMD6000. Genomic DNA was extracted using the QIAamp DNA FFPE Tissue Kit (Qiagen, Valencia, CA). Approximately 300 nanogram of genomic DNA was subjected to library preparation following the methods of Hsieh et al. (Hsieh T-F et al. 2009. Science 324:1451-1454) with modifications. We spiked-in ~ three nanogram of unmethylated lambda DNA (Promega) to serve as a control for complete bisulfite conversion. Adapter-ligated genomic DNA was subjected to two rounds of bisulfite (BS) treatment using the EpiTect kit (Qiagen, Valencia, CA). BS-treated DNA was purified using AMpure XP beads (Beckman) and PCR-amplified for 10 cycles using ExTaq (EpiCentre) DNA polymerase. PCR-amplified DNA fragments were size selected using the AMpure XP beads (Beckman). Phi-X174 DNA was spiked in to the library by the sequencing facility before cluster formation and sequencing.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Whole seeds 1.2 - 1.5 cm in length and have a fresh weight between 230 - 350 mg were collected. The entire embryo is yellow including the axis and cotyledons.
AA1
|
| Data processing |
Basecalls performed using RTA version 1.12.4.2
Original data file from the Illumina sequencing pipeline. Each lane of sequencing is attached as an individual compressed file. The sequence data are in the QSEQ format
We aligned the raw reads to a pre-processed reference genome using BS Seeker [Chen et al. BMC Bioinformatics (2010)] allowing for two mismatches. The pre-processed reference genome consisted of sequences from the soybean genome (Glyma version 1.0.1) [Schmutz et al. Nature (2010)] obtained from the Phytozome website (http://phytozome.net), soybean chloroplast genome (GenBank: DQ317523), lambda reference genome (GenBank: J02459), and Phi-X174 reference genome (GenBank: J02482).
Reads containing three consecutive methylation in the non-CG sites were removed, possibly representing non-converted cytosines (Cokus et al. Nature 2008). Clonal reads possibly arising during the PCR amplification step were collapsed into one read.
Methylation level of sampled cytosine was calculated as (methylated calls / (methylated calls + unmethylated calls)).
Genome_build: Glyma version 1.01
Supplementary_files_format_and_content: tab-delimited text file including methylation level of each sampled cytosine
|
| |
|
| Submission date |
Jun 09, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Bob Goldberg |
| E-mail(s) |
bobglab@mcdb.ucla.edu
|
| Phone |
310-825-3270
|
| Organization name |
University of California, Los Angeles
|
| Department |
Molecular, Cell and Developmental Biology
|
| Street address |
610 Charles E Young Drive East
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095 |
| Country |
USA |
| |
|
| Platform ID |
GPL15008 |
| Series (1) |
| GSE34637 |
Methylation Changes During Soybean Seed Development |
|
| Relations |
| BioSample |
SAMN03766011 |
| SRA |
SRX1054158 |
