 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Nov 30, 2016 |
| Title |
CC Rice |
| Sample type |
SRA |
| |
|
| Source name |
central cell
|
| Organism |
Oryza sativa |
| Characteristics |
tissue: central cell
cultivar: Nipponbare
|
| Growth protocol |
Oryza sativa L. cv. Nipponbare was grown in environmental chambers (K30-7248, Koito Industries, Yokohama, Japan) at 26 °C in a 13/11h light/dark cycle.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Rice central cells were isolated according to (Uchiumi et al. 2006 Sex Plant Reprod 19:37-45) with a small modification. Central cells were collected from rice ovules with an incision in the peripheral region. Ovules were incubated in 650 mOsmol/kg H2O mannitol solution containing enzymes (Uchiumi et al. 2006 Sex Plant Reprod 19:37-45) for 30 min to 1 hr at room temperature until the central cell was released from the embryo sac. Central cells with visible polar nuclei and large vacuoles were collected. Rice egg cells were isolated according to (Abiko et al. 2013 J Exp Bot 64:1927-1940). Egg cells released from ovaries with an incision in the basal portion were collected and washed in 370 mOsmol/kg H2O mannitol solution without enzymes.
Bisulfite sequencing libraries were constructed as described in (Smallwood et al. 2014 Nat Methods 11:817-820). We followed the single-cell library preparation protocol using Klenow exo- from Enzymatics (Beverly, MA, USA). Library amplification was performed with 13 PCR cycles using the EPIK Amplification Kit (Bioline GmbH, Germany).
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Raw reads were trimmed using trim galore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore) with the --clip_R1 9 parameter
Trimmed reads were aligned to their respective reference genomes (TAIR10/MSU7 including mitochondira and chloroplast contigs) using Bismark (http://www.bioinformatics.babraham.ac.uk/projects/bismark/) with the --non_directional parameter
CG/CHG/CHH Methylation was extracted from the bismark BAM file using the bismark_methylation_extractor command using the following parameters; --comprehensive --cytosine_report --bedGraph --CX
Single_C: We used a Perl script to convert the extracted methylation from bismark_methylation_extrator into single-c files for each sequence context (CG, CHG, CHH)
50bp_window: We used a Perl script to calculate fractional methylation (#C/(#C+#T)) within a 50 bp sliding window for each sequence context (CG, CHG, CHH).
Genome_build: MSU7 (Oryza sativa)
Genome_build: TAIR10 (Arabidopsis thaliana)
Supplementary_files_format_and_content: All files are in GFF format. Files contain fractional methylation data either for individual cytosines (single-c) or in 50 bp windows.
|
| |
|
| Submission date |
Nov 13, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Xiaoqi Feng |
| E-mail(s) |
[email protected]
|
| Organization name |
John Innes Centre
|
| Department |
Cell and Developmental Biology
|
| Lab |
Xiaoqi Feng
|
| Street address |
Norwich Research Park
|
| City |
Norwich |
| State/province |
Norfolk |
| ZIP/Postal code |
NR4 7UH |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL21087 |
| Series (1) |
| GSE89789 |
DNA demethylation is initiated in the central cells of Arabidopsis and rice |
|
| Relations |
| BioSample |
SAMN06013835 |
| SRA |
SRX2343945 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2388872_CC_R1_rice.CG.w1.gff.gz |
123.0 Mb |
(ftp)(http) |
GFF |
| GSM2388872_CC_R1_rice.CG.w50.gff.gz |
41.6 Mb |
(ftp)(http) |
GFF |
| GSM2388872_CC_R1_rice.CHG.w1.gff.gz |
117.6 Mb |
(ftp)(http) |
GFF |
| GSM2388872_CC_R1_rice.CHG.w50.gff.gz |
45.9 Mb |
(ftp)(http) |
GFF |
| GSM2388872_CC_R1_rice.CHH.w1.gff.gz |
364.4 Mb |
(ftp)(http) |
GFF |
| GSM2388872_CC_R1_rice.CHH.w50.gff.gz |
63.7 Mb |
(ftp)(http) |
GFF |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
