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| Status |
Public on May 19, 2021 |
| Title |
dMQ1 T1-R1 BSPCR [P3_T1_R1] |
| Sample type |
SRA |
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| Source name |
dMQ1 T1-R1 BSPCR
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| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype background: Col-0
genetic background: fwa drm1 drm2
transgene present: yes (dMQ1)
generation: T1
developmental stage: rosette stage
tissue: rosette leaf
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| Growth protocol |
Plants were grown under long-day conditions (16h light/8h dark) at 23°C in controlled growth chambers.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
CTAB-based method was used to extract DNA
Qiagen EpiTect bisulfite kit was used to treat DNA per manufacturer’s instruction. Libraries were made from purified PCR products amplified by using previously described primers (Gallego-Bartolomé et al. 2019) using an Ovation Ultralow V2 kit (NuGEN).
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
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 Bismark and processed into per-position methylation data.
For BS-seq samples, reads were filtered and trimmed using trim_galore to remove adapters, aligned to TAIR10 using Bismark, and PCR duplicates were removed using a custom Bismark script. A bismark function was used to process alignments into per-position methylation data.
For RNA-seq samples, reads were filtered and trimmed using trim_galore to remove adapters, aligned to TAIR10 using STAR, and only uniquely mapped reads were kept. Presumed PCR duplicates were removed using MarkDuplicates from the Picard tools suite. Reads over genes were counted using htseq-count using default parameters. Sequencing depth tracks (bigWig) were obtained using bamCoverage (deepTools, options --binSize 1 --normalizeUsing CPM).
Genome_build: TAIR10
Supplementary_files_format_and_content: For BS-seq and BSPCR, processed files are BED-like files containing per-position DNA methylation data over the primer-amplified regions (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 RNA-seq, count files are text files listing gene IDs and the number of overlapping reads (by htseq-count) in the first and second column, respectively. Coverage tracks are bigWig files and contain per-position sequencing coverage data for each RNA-seq library.
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| Submission date |
May 04, 2020 |
| Last update date |
May 20, 2021 |
| Contact name |
Colette L Picard |
| E-mail(s) |
clpicard@ucla.edu
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| Organization name |
University of California - Los Angeles
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| Department |
Molecular, Cell and Developmental Biology
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| Lab |
Colette L Picard
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| Street address |
610 Charles E Young Dr East, Room 4045
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| City |
Los Angeles |
| State/province |
California |
| ZIP/Postal code |
90095 |
| Country |
USA |
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| Platform ID |
GPL26208 |
| Series (1) |
| GSE149840 |
CRISPR-based targeting of DNA methylation in Arabidopsis thaliana by a bacterial CG specific DNA methyltransferase. |
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| Relations |
| BioSample |
SAMN14829387 |
| SRA |
SRX8246007 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4514081_P3_T1_R1_CHG.bed.gz |
161 b |
(ftp)(http) |
BED |
| GSM4514081_P3_T1_R1_CHH.bed.gz |
1.0 Kb |
(ftp)(http) |
BED |
| GSM4514081_P3_T1_R1_CpG.bed.gz |
342 b |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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