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| Status |
Public on Jan 25, 2022 |
| Title |
Bigelowiella_natans_ATAC_rep1 |
| Sample type |
SRA |
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| Source name |
Bigelowiella_natans_ATAC_rep1
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| Organism |
Bigelowiella natans |
| Characteristics |
strain: CCMP2755
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| Growth protocol |
Bigelowiella natans strain CCMP2755 starting cultures were obtained from NCMA (National Center for Marine Algae and Microbiota) and cultured in L1-Si media on a 12-h-light:12-h-dark cycle.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
ATAC-seq experiments were performed following the omniATAC protocol. Briefly, ~1M B. natans cells were centrifuged at 1,000 g, then resuspended in 500 uL 1x PBS and centrifuged again. Cells were then resuspended in 50 uL 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 4C. Transposition was carried out by resuspending nuclei in a mix of 25 uL 2x TD buffer (20 mM Tris-HCl pH 7.6, 10 mM MgCl2, 20% Dimethyl Formamide), 2.5 uL transposase (custom produced) and 22.5 uL nuclease-free H2O, and incubating at 37C 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 |
Bigelowiella_natans_ATAC_rep1
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| Data processing |
read alignment, ATAC-seq and KAS-seq data: Bowtie 1.0.1
bigWig file generation: custom code
read alignment, Hi-C data: Juicer tools 1.8.9
Genome_build: Bigelowiella_natans_CCMP2755_v1.0 GCA_000320545.1
Supplementary_files_format_and_content: bedGraph of read coverage, normalized to RPM for bigWig files, .hic file for Hi-C
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| Submission date |
Aug 10, 2021 |
| Last update date |
Jan 25, 2022 |
| 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) |
| GSE181751 |
The chromatin organization of a chlorarachniophyte nucleomorph genome |
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| Relations |
| BioSample |
SAMN20692997 |
| SRA |
SRX11704348 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5510379_L1324-Bigelowiella_natans_500.2x36mers.unique.noNM-chrC-chrM.dedup.bigWig |
120.3 Mb |
(ftp)(http) |
BIGWIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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