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| Status |
Public on Mar 08, 2019 |
| Title |
dnmt3a/dnmt3b |
| Sample type |
SRA |
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| Source name |
protonema
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| Organism |
Physcomitrium patens |
| Characteristics |
strain: Grandsen
age: 7 days
genotype/variation: dnmt3alpha/dnmt3beta
tissue/cell type: protonema
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| Growth protocol |
7 day protonemata on BCDAT medium
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was isolated from protonema, fragmented by sonication, end repaired, and ligated to custom synthesized methylated adaptors. Adaptor-ligated libraries were subjected to two successive treatments of sodium bisulfite conversion using the EpiTect Bisulfite kit (QIAGEN) as outlined in the manufacturer’s instructions. The bisulfite-converted libraries were then amplified by PCR and either gel purified (~300 bp band) or purified with the solid-phase reversible immobilization method using AM-Pure beads (Beckman Coulter) prior to quantification with a Bioanalyzer (Agilent).
DNA was extracted from approximately 500 mg tissue using NucleoSpin® Plant II Midi kit for Genomic DNA extraction from plant and fungi (Macherey-Nagel), according to recommended protocol
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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 |
Perl scripts were used to convert all the Cs in the ‘forward’ reads and reference sequence to Ts, and all the Gs in the ‘reverse’ reads and reference sequence to As
Reads were aligned to the reference genome using Bowtie1
Perl scripts were used to recover the original sequence information and, for each C (on either strand), to count the number of times it was sequenced as a C or a T.
For each sequence context (CG, CHG, CHH), the genomic averaged fractional methylation as well as fractional methylation within a 50 bp sliding window that were used in downstream analyses were calculated.
Genome_build: Ppatens v3.0
Supplementary_files_format_and_content: Separate gff files for each methylation context (CG, CHG and CHH), each entry represents one citosine. Scores represent methylation level for each position, column 9 contains numbers of times each cytosine was sequenced as either C or T, as well as total reads coverage of the given citosine.
Supplementary_files_format_and_content: Separate gff files for each methylation context (CG, CHG and CHH), each entry represents 50-bp window. Scores represent methylation level for each window, column 9 contains numbers of times cytosines within the given window were sequenced as either C or T, as well as total reads coverage of citosines within the window.
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| Submission date |
Aug 06, 2018 |
| Last update date |
Mar 13, 2019 |
| Contact name |
Katherine Domb |
| E-mail(s) |
katherined@mail.tau.ac.il
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| Organization name |
Tel Aviv University
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| Department |
School of Plant Sciences and Food Security
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| Lab |
Assaf Zemach
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| Street address |
Haim Levanon st.
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| City |
Tel-Aviv |
| ZIP/Postal code |
6997801 |
| Country |
Israel |
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| Platform ID |
GPL14798 |
| Series (1) |
| GSE118153 |
RdDM-independent de novo and heterochromatin DNA methylation by plant CMT and DNMT3 orthologs [Bisulfite-Seq] |
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| Relations |
| BioSample |
SAMN09768303 |
| SRA |
SRX4510569 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3319584_dnmt3ab.single-c-CG.gff.gz |
62.8 Mb |
(ftp)(http) |
GFF |
| GSM3319584_dnmt3ab.single-c-CHG.gff.gz |
72.3 Mb |
(ftp)(http) |
GFF |
| GSM3319584_dnmt3ab.single-c-CHH.gff.gz |
464.2 Mb |
(ftp)(http) |
GFF |
| GSM3319584_dnmt3ab.w50-CG.gff.gz |
28.1 Mb |
(ftp)(http) |
GFF |
| GSM3319584_dnmt3ab.w50-CHG.gff.gz |
32.7 Mb |
(ftp)(http) |
GFF |
| GSM3319584_dnmt3ab.w50-CHH.gff.gz |
72.9 Mb |
(ftp)(http) |
GFF |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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