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Status |
Public on Sep 01, 2017 |
Title |
Chlamydomonas reinhardtii, replicate 3 (4A+, log phase) |
Sample type |
SRA |
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|
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.
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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
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|
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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 |