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| Status |
Public on Oct 19, 2023 |
| Title |
L505-34C-ATAC-rep1 |
| Sample type |
SRA |
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| Source name |
L505-34C-ATAC-rep1
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| Organism |
Bigelowiella natans |
| Characteristics |
tissue: whole flagellate
sample type: B. minutum 34C ATAC-seq
chip antibody: n/a
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| 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.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
ATAC-seq experiments were performed following the omniATAC protocol. Briefly, ∼100K B. minutum cells were centrifuged at 1,000 g, then resuspended in 500 µL 1× PBS and centrifuged again. Cells were then resuspended in 50 µL ATAC-RSB-Lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630, 0.1% Tween-20, 0.01% Digitonin) and incubated on ice for 3 minutes. Subsequently 1 mL ATAC-RSB-Wash buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 0.01% Digitonin) were added, the tubes were inverted several times, and nuclei were centrifuged at 500 g for 5 min at 4◦C. Transposition was carried out by resuspending nuclei in a mix of 25 µL 2× TD buffer (20 mM Tris-HCl pH 7.6, 10 mM MgCl2, 20% Dimethyl Formamide), 2.5 µL transposase (custom produced) and 22.5 µL nuclease-free H2O, and incubating at 37◦C for 30 min in a Thermomixer at 1000 RPM.
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 |
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| Description |
L505-34C-ATAC-rep1
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| 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
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| Department |
Genetics
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| Street address |
279 Campus Drive West, Beckman Center, B-257A/259
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| City |
Stanford |
| State/province |
California |
| ZIP/Postal code |
94305-5101 |
| Country |
USA |
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| Platform ID |
GPL30494 |
| Series (1) |
| GSE241969 |
Genome-wide distribution of 5-hydroxymethyluracil and chromatin accessibility in the Breviolum minutum genome |
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| Relations |
| BioSample |
SAMN37205259 |
| SRA |
SRX21542008 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7746901_L505-34C-rep1.2x36mers.unique.dedup.bigWig |
557.9 Mb |
(ftp)(http) |
BIGWIG |
SRA Run Selector |
| Raw data are available in SRA |
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