|
| Status |
Public on Oct 19, 2023 |
| Title |
L1604-DVNP_GM06_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
L1604-DVNP_GM06_rep1
|
| Organisms |
Saccharomyces cerevisiae; Candida albicans |
| Characteristics |
tissue: whole yeast
sample type: yeast expressing Hematodinium sp. DVNP.12 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.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
L1604-DVNP_GM06_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 |
SAMN37205242 |
| SRA |
SRX21542017 |
