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Sample GSM7746916 Query DataSets for GSM7746916
Status Public on Oct 19, 2023
Title L1602-DVNP_GM05_rep1
Sample type SRA
 
Source name L1602-DVNP_GM05_rep1
Organisms Saccharomyces cerevisiae; Candida albicans
Characteristics tissue: whole yeast
sample type: yeast expressing B. minutum DVNP symbB.v1.2.006931 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 ┬Ámol 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.
 
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model NextSeq 550
 
Description L1602-DVNP_GM05_rep1
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
 
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 SAMN37205244
SRA SRX21542016

Supplementary file Size Download File type/resource
GSM7746916_L1602-DVNP_GM05_rep1.2x36mers.sacCer3.a.nochrM.ERMTOC.fragment_sacCer.bigWig 5.6 Mb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Raw data are available in SRA

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