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| Status |
Public on Feb 21, 2019 |
| Title |
WT-sperm |
| Sample type |
SRA |
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| Source name |
rice sperm
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| Organism |
Oryza sativa |
| Characteristics |
genotype/variation: WT
cultivar: Nipponbare
cell type: sperm
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Wild-type and ros1a/+ O. sativa cv. Nipponbare harboring a UBQ::H2B-GFP transgene were grown at 26 ºC in a 13/11 hr light/dark cycled chamber. Rice pollen was harvested from unopened flowers with elongated stamen. Pollen grains were burst open via osmotic pressure in 370 mOsmol/kg H2O mannitol solution for 5 minutes at room temperature. Sperm cells and vegetative cell nuclei were isolated using the differential interference contrast microscopy and GFP fluorescent microscopy, respectively, under a BX-71 inverted fluorescence microscope (Olympus, Tokyo, Japan). The sperm cells and vegetative cell nuclei were washed once in 370 mOsmol/kg H2O mannitol solution and stored at -80C.
Bisulfite sequencing libraries were constructed as described Smallwood et al., Nature Methods (2014)
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
wt_spm
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| Data processing |
Sequenced reads were trimmed using Trim Galore! With --clip_R1 9 parameter.
trimmed reads were mapped to msu7 rice reference genome using bismark --p 4 --non-directional parameters.
methylated cytosine / (methylated cytosine + unmethylated cytosine) was calculated for every cytosine.
methylated cytosine / (methylated cytosine + unmethylated cytosine) was calculated for every 50 base pair window.
Genome_build: MSU7
Supplementary_files_format_and_content: tab-delimited 50 bp window CG, CHG, and CHH methylation.
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| Submission date |
Feb 20, 2019 |
| Last update date |
Feb 21, 2019 |
| Contact name |
M. Yvonne Kim |
| E-mail(s) |
yvonne.kim@ucsf.edu
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| Organization name |
UC San Francisco
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| Street address |
3rd st.
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| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94143 |
| Country |
USA |
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| Platform ID |
GPL23013 |
| Series (1) |
| GSE126791 |
DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm |
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| Relations |
| BioSample |
SAMN10971016 |
| SRA |
SRX5394957 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3613362_wt_spm_RFYK16A.CGmap.CG.w50.gff.gz |
47.4 Mb |
(ftp)(http) |
GFF |
| GSM3613362_wt_spm_RFYK16A.CGmap.CHG.w50.gff.gz |
54.6 Mb |
(ftp)(http) |
GFF |
| GSM3613362_wt_spm_RFYK16A.CGmap.CHH.w50.gff.gz |
73.3 Mb |
(ftp)(http) |
GFF |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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