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Sample GSM3074712

Query DataSets for GSM3074712

Status

Public on Feb 18, 2019

Title

Podospora anserina, WGBS

Sample type

SRA

Source name

Whole organism

Organism

Podospora anserina

Characteristics

tissue: Whole organism
strain: NA
genotype: Lab colony

Extracted molecule

genomic DNA

Extraction protocol

Candida albicans, Candida auris, and Clavispora lusitianiae. MasturePure yeast DNA purification kit (Epicentre) following the manufacturer's instructions. Microbotryum lychnidis. Qiagen Kit 10243 (Courtaboeuf, France) following the manufacturer's instructions and using a Carver hydraulic press (reference 3968, Wabash, IN) for breaking cell walls. Lobosporangium transversale, Syncephalis fuscata, Spinellus fusiger, Parasitella parasitica, Kirkomyces cordense, Radiomyces spectabilis, and Sporobolomyces roseus. CTAB/Chloroform protocol (http://1000.fungalgenomes.org/home/protocols/high-quality-genomic-dna-extraction/). Aureobasidium pullulans, Coemansia reversa, Coemansia spiralis, Coprinopsis cinerea, Heterobasidion irregulare, Mixia osumundae, Phanerochaete chrysosporium, Pleurotus ostreatus, Pseudogymnoascus destructans, Tilletiopsis washingtonensis, and Wolfiporia cocos. A modified CTAB/Chloroform protocol (James et al. 2008; doi: 10.1111/j.1558-5646.2008.00462.x). Pholiota alnicola. EZNA Fungal DNA Mini Kit (Omega Bio-tek, Norcross, GA) following the manufacturer's instructions.
MethylC-seq libraries were prepared using the protocol described in Urich et al. (2015; doi:10.1038/nprot.2014.114). Lambda phage DNA was used as a control for the sodium bisulfite non-conversion rate.

Library strategy

Bisulfite-Seq

Library source

genomic

Library selection

RANDOM

Instrument model

Illumina NextSeq 500

Data processing

Reads generated from MethylC-seq were aligned to each species respective genome assembly using the latest version of methylpy (Schultz et al. 2015; doi: 10.1038/nature14465; https://bitbucket.org/schultzmattd/methylpy/wiki/Home). MethylC-seq analysis was performed as described in Schmitz et al. (2013; doi: 10.1101/gr.152538.112).
Genome_build: Agaricus bisporus. http://genome.jgi.doe.gov/Agabi_varbisH97_2/Agabi_varbisH97_2.home.html. Aspergillus flavus. http://genome.jgi.doe.gov/Aspfl1/Aspfl1.home.html. Aureobasidium pullulans. http://genome.jgi.doe.gov/Aurpu_var_pul1/Aurpu_var_pul1.home.html. Botrytis cinerea. http://genome.jgi.doe.gov/Botci1/Botci1.home.html. Candida albicans. http://genome.jgi.doe.gov/Canalb1/Canalb1.home.html. Candida auris. https://www.ncbi.nlm.nih.gov/genome/?term=Candida+auris%5Borgn%5D. Clavispora lusitianiae. https://www.ncbi.nlm.nih.gov/genome/286. Coemansia reversa. http://genome.jgi.doe.gov/Coere1/Coere1.home.html. Coemansia spiralis. http://genome.jgi.doe.gov/Coespi1/Coespi1.home.html. Coprinopsis cinerea. http://genome.jgi.doe.gov/Copci1/Copci1.home.html. Cordyceps militaris. http://genome.jgi.doe.gov/Cormi1/Cormi1.home.html. Cryptococcus neoformans. http://genome.jgi.doe.gov/Cryne_H99_1/Cryne_H99_1.home.html. Fusarium fujikuroi. http://genome.jgi.doe.gov/Fusfu1/Fusfu1.home.html. Hesseltinella vesiculosa. http://genome.jgi.doe.gov/Hesve2finisherSC/Hesve2finisherSC.home.html. Heterobasidion irregulare. http://genome.jgi.doe.gov/Hetan2/Hetan2.home.html. Kirkomyces cordense. http://genome.jgi.doe.gov/Kircor1/Kircor1.home.html. Laccaria bicolor. http://genome.jgi.doe.gov/Lacbi2/Lacbi2.home.html. Leptosphaeria maculans. http://genome.jgi.doe.gov/Lepmu1/Lepmu1.home.html. Lobosporangium transversale. http://genome.jgi.doe.gov/Lobtra1/Lobtra1.home.html. Magnaporthe oryzae. http://genome.jgi.doe.gov/Maggr1/Maggr1.home.html. Metarhizium robertsii. http://genome.jgi.doe.gov/Metro1/Metro1.home.html. Microbotryum lychnidis. http://genome.jgi.doe.gov/Micld1/Micld1.home.html. Mixia osmundae. http://genome.jgi.doe.gov/Mixos1/Mixos1.home.html. Neurospora crassa. http://genome.jgi.doe.gov/Neucr2/Neucr2.home.html. Parasitella parasitica. http://genome.jgi.doe.gov/Parpar1/Parpar1.home.html. Phanerochaete chrysosporium. http://genome.jgi.doe.gov/Phchr2/Phchr2.home.html. Pholiota alnicola. http://genome.jgi.doe.gov/Phoaln1/Phoaln1.home.html. Phycomyces blakesleeanus. http://genome.jgi.doe.gov/Phybl2/Phybl2.home.html. Pleurotus ostreatus. http://genome.jgi.doe.gov/PleosPC15_2/PleosPC15_2.home.html. Podospora anserina. http://genome.jgi.doe.gov/Podan2/Podan2.home.html. Postia placenta. http://genome.jgi.doe.gov/Pospl1/Pospl1.home.html. Pseudogymnoascus destructans. http://fungi.ensembl.org/Pseudogymnoascus_destructans_20631_21/Info/Index. Radiomyces spectabilis. http://genome.jgi.doe.gov/Radspe1/Radspe1.home.html. Saccharomyces cerevisiae. http://genome.jgi.doe.gov/Sacce1/Sacce1.home.html. Spinellus fusiger. http://genome.jgi.doe.gov/Spifus1/Spifus1.home.html. Sporobolomyces roseus. http://genome.jgi.doe.gov/Sporo1/Sporo1.home.html. Syncephalis fuscata. http://genome.jgi.doe.gov/Synfus1/Synfus1.home.html. Tilletiopsis washingtonensis. http://genome.jgi.doe.gov/Tilwa1/Tilwa1.home.html. Uncinocarpus reesii. http://genome.jgi.doe.gov/Uncre1/Uncre1.home.html. Wolfiporia cocos. http://genome.jgi.doe.gov/Wolco1/Wolco1.home.html.
Supplementary_files_format_and_content: Tab delimited; please see metadata.txt file (on series record) for column headers.

Submission date

Apr 03, 2018

Last update date

Feb 18, 2019

Contact name

Robert J Schmitz

E-mail(s)

schmitz@uga.edu

Organization name

University of Georgia

Department

Genetics

Street address

B416 Davison Life Sciences

City

Athens

State/province

GA

ZIP/Postal code

30602

Country

USA

Platform ID

Series (1)

Diversity of cytosine methylation across the fungi tree of life

Relations

BioSample

SRA

Supplementary file	Size	Download	File type/resource
GSM3074712_allc_Pod_ans.tsv.gz	78.7 Mb	(ftp)(http)	TSV
SRA Run Selector
Raw data are available in SRA
Processed data provided as supplementary file

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