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| Status |
Public on Jun 03, 2013 |
| Title |
dtf1_DNA |
| Sample type |
SRA |
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| Source name |
Whole seedling
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| Organism |
Arabidopsis thaliana |
| Characteristics |
age: 12-day-old
genotype/variation: dtf1
tissue: whole seedling
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| Treatment protocol |
N/A
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| Growth protocol |
Seedlings were grown on 1/2 MS plates supplemented with 0.65% agarose and 1% sucrose for 12 days before harvested
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted at BGI (Beijing Genomics Institute), Inc. Libraries were prepared for sequencing according to the manufacturer's (Illumina, Inc) instructions.
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
whole-genome DNA methylation profiling
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| Data processing |
For BS-seq, adapter,and low-quality sequences (q < 20) were trimmed and clean reads were mapped to Arabidopsis thaliana TAIR 10 genome using BSMAP allowing two mismatches. Only cytosines with a depth of at least four in all libraries were retained for further analysis.
For sRNA-seq, after adapter sequences were trimmed, clean reads of size 18 nt–30 nt were mapped to the TAIR 10 genome and annotated structural RNAs (rRNAs, tRNAs, snRNAs, and snoRNAs) using Bowtie. Only sRNAs that had at least one perfect match to the genome and did not match structural RNAs were used for downstream analysis. Read counts were normalized to Reads Per Ten Million (RPTM) according to total number of clean reads (excluding structural sRNAs) in the library and number of hits to the genome. Normalized expression levels of 24-nt sRNAs were summarized in non-overlapping 500-nt windows over the nuclear genome and were compared between each mutant and the wild type. To remove lowly expressed regions, only 500-nt regions that had at least 200 RPTM combined expression in the mutant and the wild type were considered. 500-nt regions that showed 5-fold lower expression in the mutant were selected as sRNA-depleted regions.
Genome_build: TAIR10
Supplementary_files_format_and_content: BS-seq WIG files represent methylation level (from 0 to 1) of each cytosine that are covered ≥4 times in all 4 samples.
Supplementary_files_format_and_content: sRNA WIG files represent normalized RPTM (reads per ten million) counts of 24-nt RNAs that are uniquely mapped to the TAIR10 genome.
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| Submission date |
Feb 11, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Heng Zhang |
| E-mail(s) |
hengzhang@gmail.com
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| Organization name |
Shanghai Center for Plant Stress Biology
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| Street address |
300 Fenglin Rd, Room 705
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| City |
Shanghai |
| State/province |
Shanghai |
| ZIP/Postal code |
200032 |
| Country |
China |
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| Platform ID |
GPL13222 |
| Series (1) |
| GSE44209 |
DTF1 is a core component of RNA-directed DNA methylation and may assist in the recruitment of Pol IV |
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| Relations |
| SRA |
SRX234883 |
| BioSample |
SAMN01919548 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1080804_dtf1.mC.wig.gz |
21.0 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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