|
Status |
Public on Oct 19, 2023 |
Title |
L1601-Control_MS47_rep2 |
Sample type |
SRA |
|
|
Source name |
L1601-Control_MS47_rep2
|
Organisms |
Saccharomyces cerevisiae; Candida albicans |
Characteristics |
tissue: whole yeast sample type: yeast control ATAC chip antibody: n/a
|
Growth protocol |
(B. minutum) The clonal axenic Symbiodinium/Breviolum minutum strain SSB01 was used. Stock cultures were grown in Daigo's IMK medium for marine microalgae (Wako Pure Chemicals) supplemented with casein hydrolysate (IMK+Cas) at 27C at a light intensity of 10 µmol photons m-2s-1 from Philips ALTO II 25-W bulbs on a 12-h-light:12-h-dark cycle. The medium was prepared in artificial seawater (ASW). (yeast) Standard yeast cell culture practices were followed. Cells were grown in YPD media at 30C until harvesting.
|
Extracted molecule |
genomic DNA |
Extraction protocol |
ATAC-seq was carried out on the nuclei isolated the same way as for SMF (before resuspension in Transposed DNA was isolated using the MinElute PCR Purification Kit (Qiagen Cat# 28004/28006), and PCR amplified for 10 cycles using the usual ATAC-seq settings. Libraries were purified using the MinElute kit, then sequenced on a Illumina NextSeq 550 instrument as 2x36mers.
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|
|
Library strategy |
ATAC-seq |
Library source |
genomic |
Library selection |
other |
Instrument model |
NextSeq 550 |
|
|
Description |
L1601-Control_MS47_rep2
|
Data processing |
(read alignment, ATAC-seq and MeDIP-seq data) Bowtie 1.0.1 (bigWig file generation) custom code (read alignment, SMF data) bwa-meth (read alignment, 5-hmU chemical conversion data) slamdunk Assembly: custom and GCA_000507305.1_ASM50730v1 for Breviolum minutum, hg38 for human, sacCer3 for S. cerevisiae; C_glabrata_CBS138 for Candida albicans Supplementary files format and content: bedGraph of read coverage, normalized to RPM for bigWig files for ATAC-seq and MeDIP-seq; slamdunk output for 5-hmU conversion datasets; MethylDacket bedGraph output for SMF datasets
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|
|
Submission date |
Aug 30, 2023 |
Last update date |
Oct 19, 2023 |
Contact name |
Georgi Kolev Marinov |
Organization name |
STANFORD UNIVERSITY
|
Department |
Genetics
|
Street address |
279 Campus Drive West, Beckman Center, B-257A/259
|
City |
Stanford |
State/province |
California |
ZIP/Postal code |
94305-5101 |
Country |
USA |
|
|
Platform ID |
GPL33723 |
Series (1) |
GSE241969 |
Genome-wide distribution of 5-hydroxymethyluracil and chromatin accessibility in the Breviolum minutum genome |
|
Relations |
BioSample |
SAMN37205245 |
SRA |
SRX21542015 |