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| Status |
Public on Dec 13, 2016 |
| Title |
c3_Sperm |
| Sample type |
SRA |
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| Source name |
isolated nuclei from pollen
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| Organism |
Arabidopsis thaliana |
| Characteristics |
genotype: cmt3
nuclei type: sperm
ecotype: Col-0
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| Growth protocol |
A. thaliana plants were grown under 16h light/ 8h dark in a growth chamber (21°C, 70% humidity)
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Sperm and vegetative nuclei were isolated by FACS as previously described (1). DNA was extracted with ChargeSwitch kit following the manufacturer’s instructions. Reference: 1. Ibarra CA, et al. (2012) Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes. Science 337:1360-1364.
Libraries were prepared with Ovation Ultralow Methyl Seq kit following the manufacturer’s instructions.
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Bisulfite-Seq: We used Perl scripts to convert all the Cs in the reads (and in the scaffolds) to Ts, and aligned the converted reads to the converted reference scaffold, allowing up to two mismatches per read. 76 base reads were divided into the first 45 and the last 31 bases, 100 base reads and 150 base reads were divided in half. Each half of the read was aligned independently using bowtie, allowing up to two mismatches. The coordinates of the two halves were subsequently correlated; the second half was discarded if it did not match the first.
Single_C: We used Perl scripts to recover the original sequence of each mapped read and, for each C (on either strand), count the number of times it was sequenced as a C or a T.
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: TAIR10
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.
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| Submission date |
Sep 21, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Xiaoqi Feng |
| E-mail(s) |
xiaoqi.feng@jic.ac.uk
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| Organization name |
John Innes Centre
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| Department |
Cell and Developmental Biology
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| Lab |
Xiaoqi Feng
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| Street address |
Norwich Research Park
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| City |
Norwich |
| State/province |
Norfolk |
| ZIP/Postal code |
NR4 7UH |
| Country |
United Kingdom |
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| Platform ID |
GPL19580 |
| Series (1) |
| GSE87170 |
DNA methylation inheritance across generations |
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| Relations |
| BioSample |
SAMN05792879 |
| SRA |
SRX2182200 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2323842_c3.spm.CG.tair10.gff.gz |
35.4 Mb |
(ftp)(http) |
GFF |
| GSM2323842_c3.spm.CG.tair10.w50.gff.gz |
12.8 Mb |
(ftp)(http) |
GFF |
| GSM2323842_c3.spm.CHG.tair10.gff.gz |
38.4 Mb |
(ftp)(http) |
GFF |
| GSM2323842_c3.spm.CHG.tair10.w50.gff.gz |
13.7 Mb |
(ftp)(http) |
GFF |
| GSM2323842_c3.spm.CHH.tair10.gff.gz |
180.6 Mb |
(ftp)(http) |
GFF |
| GSM2323842_c3.spm.CHH.tair10.w50.gff.gz |
21.0 Mb |
(ftp)(http) |
GFF |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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