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Sample GSM1684589 Query DataSets for GSM1684589
Status Public on Sep 01, 2017
Title Chlamydomonas reinhardtii, replicate 3 (4A+, log phase)
Sample type SRA
 
Source name Chlamydomonas reinhardtii, replicate (4A+, log phase) _Whole organism
Organism Chlamydomonas reinhardtii
Characteristics strain: 4A+
growth phase: log phase
Extracted molecule genomic DNA
Extraction protocol C. reinhardtii wild type strain 4a+ were cultured using Tris-acetate-phosphate (TAP) medium in Erlenmeyer flasks at 25 degrees Celsius with agitation at 180 rpm under light irradiation at 100 microE. Cells were harvested at mid-log phase (at approximately 2 x 106 cells/ml). Cells were lysed using lysis buffer (50mM Tris-HCl pH 8, 200mM NaCl, 2mM EDTA, 2% SDS and proteinase K) and genomic DNA was extracted using CTAB-based protocol39.
5ug of gDNA was sheared to 700bp using the focused-ultrasonicator S2 (Covaris) and spiked in with 50ng HaeIII digested lambda DNA for quality control. The fragments were treated with end-repair, A- tailing, and ligation of methylated Illumina adaptors (Illumina) using the DNA library preparation kit for Illumina (Kapa Biosystems). The adaptor ligated DNA was subjected to bisulfite treatment using EpiTect Bisulfite Kit (Qiagen). The bisulfite-treated DNA was amplified with 8 cycles of PCR with uracil-insensitive Taq polymerase (Pfu Turbo Cx Hotstart DNA polymerase; Stratagene). The PCR product was run on a 2% agarose gel followed by gel excision to select for fragments between 300 to 400bp. Purified library was sequenced on the Illumina Hiseq.
 
Library strategy Bisulfite-Seq
Library source genomic
Library selection RANDOM
Instrument model Illumina HiSeq 2500
 
Data processing Adaptors were trimmed, the paired reads were aligned to the reference genome by BSMAP.
Genome_build: C.Reinhardtii_236 (JGI Phytozome assembly V5.0)
Supplementary_files_format_and_content: bigWig file
 
Submission date May 13, 2015
Last update date May 15, 2019
Contact name Denis Tolkunov
Organization name DOE Joint Genome Institute
Street address 2800 Mitchell Dr
City Walnut Creek
State/province CA
ZIP/Postal code 94598
Country USA
 
Platform ID GPL18482
Series (1)
GSE68860 Genome-wide single-molecule sequencing of 6-methyladenine in eukaryotes
Relations
BioSample SAMN03657256
SRA SRX1026803

Supplementary file Size Download File type/resource
GSM1684589_cre5.IFFC.trimmed.n0.q30.primary.sorted.dedup.cov.bw 693.7 Mb (ftp)(http) BW
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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