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| Status |
Public on Jun 04, 2021 |
| Title |
BSPCR_lib2_ZF108-SLN_T2-12-44_neg |
| Sample type |
SRA |
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| Source name |
rosette leaf
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| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: rosette leaf
ecotype: Col-0
genetic background: fwa
generation: T2
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| Growth protocol |
Plants were grown on soil in a greenhouse under long-day conditions (16h light / 8h dark).
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted with the CTAB protocol
The DNA was bisulfite treated using the Epitect Bisulfite Conversion kit (QIAGEN). The conversion reaction in the thermocycler was performed twice to increase the efficiency. The converted DNA was amplified with the primers indicated in the manuscript of this study, using the Pfu Turbo Cx DNA polymerase (Agilent). Different PCR products for the same sample were pooled and purified with AMPure beads (Beckman Coulter). Libraries were generated using the Kapa HyperPrep DNA kit (KR0961) and the TruSeq DNA UD adapters (IDT for Illumina).
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina iSeq 100 |
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| Description |
PCR products from genomic DNA
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| Data processing |
Library strategy: BS-PCR
For BS-PCR samples, reads were pre-processed by a custom script to keep only reads flanked by correct primer sequence and to truncate the primer sequences from each read. Pre-processed reads were mapped to TAIR10 using BSMAP and processed into per-position methylation data.
For BS-seq and EM-seq samples, reads were aligned to TAIR10 using Bismark.
For ChIP-seq and DAP-seq, reads were filtered based on quality score and trimmed using Trim Galore. Filtered reads were mapped with Bowtie2 with default parameters. PCR duplicates were removed using MarkDuplicates.jar from the Picard tools suite. Genome browser tracks were generated using deeptools (v 3.0.2) bamCoverage.
For RNA-seq samples, reads were filtered and trimmed using trim_galore to remove adapters, aligned to TAIR10 using STAR. Reads over genes were counted using htseq-count using default parameters. Sequencing depth tracks (bigWig) were obtained using bamCoverage (deepTools, options --binSize 10 --normalizeUsing RPKM).
Genome_build: TAIR10
Supplementary_files_format_and_content: For ChIP-seq, DAP-seq and RNA-seq, processed data files are sequencing depth tracks (bigWig) obtained using bamCoverage (deepTools). For BS-seq, processed data files are bigWig files of per position methylation ratio. For EM-seq , processed files are BED-like files containing per-position DNA methylation data (one file each for cytosines in the CG, CHG and CHH context). These files are in BED-like format and have 6 fields: chromosome, position of cytosine (0-based index), position+1, number of unmethylated reads, number of methylated reads, and percent methylated reads. For BS-PCR, the processed files are per-position DNA methylation ratios for each region of the FWA promoter.
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| Submission date |
Jan 19, 2021 |
| Last update date |
Jun 04, 2021 |
| Contact name |
Lucia Ichino |
| E-mail(s) |
lucia.ichino@gmail.com
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| Organization name |
University of California, Los Angeles
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| Department |
MCDB
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| Lab |
Jacobsen
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| Street address |
610 Charles E Young Dr East
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| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095 |
| Country |
USA |
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| Platform ID |
GPL29156 |
| Series (1) |
| GSE165095 |
MBD5 and MBD6 couple DNA methylation to gene silencing through the J-domain protein SILENZIO |
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| Relations |
| BioSample |
SAMN17383155 |
| SRA |
SRX9895739 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5026072_ZF108_DNAJ4_T2_12_44_neg_steve_methratio_type.txt_region1.txt.gz |
285 b |
(ftp)(http) |
TXT |
| GSM5026072_ZF108_DNAJ4_T2_12_44_neg_steve_methratio_type.txt_region2.txt.gz |
379 b |
(ftp)(http) |
TXT |
| GSM5026072_ZF108_DNAJ4_T2_12_44_neg_steve_methratio_type.txt_region3.txt.gz |
330 b |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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