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| Status |
Public on Nov 01, 2016 |
| Title |
C24_nrpd1_methyl-Seq |
| Sample type |
SRA |
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| Source name |
seedlings
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| Organism |
Arabidopsis thaliana |
| Characteristics |
background: C24
genotype/variation: nrpd1 mutant
tissue: seedlings
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
The genomic DNA was extracted from 1 gram of 14-day-old seedlings using the Plant DNeasy Maxi Kit from Qiagen. And 5 µg of gDNA was used for library construction using Illumina’s standard DNA methylation analyses protocol and the TruSeq DNA sample preparation kit. The samples were sequenced in the Genomics Core Facilities of the Shanghai Center for Plant Stress Biology, SIBS, CAS (Shanghai, China) with Illumina HiSeq 2500.
And 5 µg of gDNA was used for library construction using Illumina’s standard DNA methylation analyses protocol and the TruSeq DNA sample preparation kit. The samples were sequenced in the Genomics Core Facilities of the Shanghai Center for Plant Stress Biology, SIBS, CAS (Shanghai, China) with Illumina HiSeq 2500.
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
treated with bisulfite
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| Data processing |
Basecalling, trimming for low quality reads and adaptor sequence were done by BGI (Shenzhen, China)
A pseudo-C24 genome was generated through the replacement of SNPs in the Col-0 genome with C24 variants (http://1001genomes.org/data/ MPI/MPISchneeberger2011/releases/current//C24/Marker/C24.SNPs.TAIR9.txt)
Clean reads were mapped to the pseudo-C24 genome using BRAT-BW with parameters -m 2 -i 0 -a 1000
Copy-duplicates were remove using remove-dupl command of BRAT-BW
acgt-count command of BRAT-BW was used to count mapped Cs and Ts at each cytosine of forward and reverse strands of the reference
Genome_build: A pseudo-C24 genome was generated through the replacement of SNPs in the Col-0 genome (TAIR10) with C24 variants (http://1001genomes.org/data/ MPI/MPISchneeberger2011/releases/current//C24/Marker/C24.SNPs.TAIR9.txt)
Supplementary_files_format_and_content: The wig files give methylation level for all Cs(three contexts) with depth >= 4. Methylation level of each cytosine base was calculated according to number of converted and unconverted C mapped at that position (unconverted_C / ( converted_C+ unconverted_C ) ).
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| Submission date |
Jun 28, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Jian-Kang Zhu |
| E-mail(s) |
zhu132@purdue.edu
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| Organization name |
Purdue University
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| Department |
Department of Horticulture and Landscape Architecture
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| Street address |
625 Agriculture Mall Dr.
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| City |
West Lafayette |
| State/province |
IN |
| ZIP/Postal code |
47907 |
| Country |
USA |
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| Platform ID |
GPL17639 |
| Series (2) |
| GSE83801 |
Whole genome bisulfite sequencing of nrpd1 mutant in C24 background [methyl-seq] |
| GSE83802 |
The DNA demethylase ROS1 targets genomic regions with distinct chromatin modifications |
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| Relations |
| BioSample |
SAMN05300526 |
| SRA |
SRX1881711 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2218939_C24_nrpd1_NCBI_depth4_mCG.wig.gz |
12.4 Mb |
(ftp)(http) |
WIG |
| GSM2218939_C24_nrpd1_NCBI_depth4_mCHG.wig.gz |
13.2 Mb |
(ftp)(http) |
WIG |
| GSM2218939_C24_nrpd1_NCBI_depth4_mCHH.wig.gz |
57.1 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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