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| Status |
Public on Jul 08, 2020 |
| Title |
L1242-SSB01-a_amanitin-16h-Hi-C-rep2 |
| Sample type |
SRA |
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| Source name |
SSBO1 cells
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| Organism |
Breviolum minutum |
| Characteristics |
strain: SSBO1
treatment: a-amanitin treatment, 1ug/mL, 16h
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Symbiodinium minutum SSBO1 cells were first crosslinked using 37% formaldehyde (Sigma) at a final concentration of 1% for 15 minutes at room temperature. Formaldehyde was then quenched using 2.5 M Glycine at a final concentration of 0.25 M. Cells were subsequently centrifuged at 2,000 g for 5 minutes, washed once in 1X PBS, and stored at -80C.
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| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
L1242-SSB01-a_amanitin-16h-Hi-C-rep2
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| Data processing |
read alignment: juicer_tools.1.8.9
.hic file generation juicer_tools.1.8.9
Genome_build: custom
Supplementary_files_format_and_content: bedGraph of read coverage, normalized to RPM (Read Per Million) except for dSMF samples, where the bedGraph shows the methylation percentage
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| Submission date |
Jul 07, 2020 |
| Last update date |
Jul 08, 2020 |
| 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 |
GPL28838 |
| Series (1) |
| GSE153950 |
Transcription-dependent domain-scale 3D genome organization in dinoflagellates |
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| Relations |
| BioSample |
SAMN15464813 |
| SRA |
SRX8680454 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4658999_L1242-SSB01-a_amanitin-16h-Hi-C-rep2.inter.hic |
847.6 Mb |
(ftp)(http) |
HIC |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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