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| Status |
Public on Sep 02, 2016 |
| Title |
L_japonicus |
| Sample type |
SRA |
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| Source name |
Lotus japonicus
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| Organism |
Lotus japonicus |
| Characteristics |
accession: Gifu
tissue: leaf
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Tissue was flash frozen in liquid nitrogen for all experiments including ChIP-seq, RNA-seq and MethylC-seq. DNA was isolated using a Qiagen Plant DNeasy kit (Qiagen, Valencia, CA) following the manufacturer’s recommendations. RNA was isolated using TRIzol (Thermo Scientific, Waltham, MA) following the manufacturer’s instructions
MethylC-seq libraries were constructed using the MethylC-seq protocol (Urich et al. 2015).
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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 Bisulphite Sequencing of L. japonicus
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| Data processing |
For MethylC-seq data: Reads were trimmed, aligned, and methylation called using the methylpy pipeline (Schultz et al. 2015). The genome is converted into a forward strand reference (all Cs to Ts) and a reverse strand reference (all Gs to As). Cutadapt (Martin et al. 2011) is used to trim adaptor sequences and then bowtie (Langmead et al. 2009) aligns reads to the two converted reference genomes. Only uniquely aligned reads are retained and the non-conversion rate calculated from unmethylated reads aligned to the chloroplast genome or spiked in unmethylated lambda DNA.
genome build: A. lyrata = v1.0; A. thaliana = TAIR10; A. trichopoda = v1.0; B. distachyon = v2.1; B. oleracea = TO1000 v1.0; B. rapa = FPsc v1.3; B. vulgaris = v1.1; C. clementina = v1.0; C. rubella = v1.0; C. sativa = canSat3; C. sativus = v1.0; E. grandis = v1.1; E. salsugineum = v1.0, F. vesca = v1.1; G. max = w82.a2.v1; G. raimondii = v2.1; L. japonicus = v2.5; M. domestica = v1.0; M. esculenta = v4.1; M. guttatus = v2.0; M. truncatula = Mt4.0v1; O. sativa = v7.0; P. hallii = v0.5; P. persica = v1.0; P trichocarpa = v3.0; P. virgatum = v1.1; P. vulgaris = v1.0; R. communis = v0.1; S. bicolor = v2.1; S. lycopersicum = iTAG2.3; S. viridis = unpublished; T. cacao = V1.1; V. vinifera = GENOSCOPE.12X; Z. mays = AGPv3.21 (6a)
processed data files format and content: MethylC-seq data (marked as “allc_total.tsv”) column 1 = chr = chromosome; column 2 = pos = coordinate for the cytosine position on the chromosome; column 3 = strand = + or - strand; column 4 = mc_class = context of the cytosine and the two following bases from the same strand; column 5 = mc_count = number of reads supporting a methylated cytosine; column 6 = total = total number of reads at that position; column 7 = methylated = cytosine is considered methylated if there is a 1 or unmethylated if there is a 0
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| Submission date |
Mar 23, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Robert J Schmitz |
| E-mail(s) |
schmitz@uga.edu
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| Organization name |
University of Georgia
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| Department |
Genetics
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| Street address |
B416 Davison Life Sciences
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| City |
Athens |
| State/province |
GA |
| ZIP/Postal code |
30602 |
| Country |
USA |
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| Platform ID |
GPL20925 |
| Series (1) |
| GSE79526 |
Widespread natural variation of DNA methylation within angiosperms |
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| Relations |
| BioSample |
SAMN04576087 |
| SRA |
SRX1656921 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2096965_L_japonicus_allc_total.tsv.gz |
363.8 Mb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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