 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Mar 17, 2021 |
| Title |
L1334-SSB01-a_amanitin_high-48h-Hi-C 2 |
| Sample type |
SRA |
| |
|
| Source name |
L1334-SSB01-a_amanitin_high-48h-Hi-C
|
| Organism |
Breviolum minutum |
| Characteristics |
strain: SSBO1
treatment: a-amanitin treatment, 4ug/mL, 48h
|
| 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.
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.
|
| |
|
| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
L1334-SSB01-a_amanitin_high-48h-Hi-C
|
| Data processing |
read alignment: 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
|
| |
|
| Submission date |
Mar 16, 2021 |
| Last update date |
Mar 17, 2021 |
| 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 |
GPL28838 |
| Series (1) |
| GSE153950 |
Transcription-dependent domain-scale 3D genome organization in dinoflagellates |
|
| Relations |
| BioSample |
SAMN18320176 |
| SRA |
SRX10355448 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5173885_L1334-SSB01-a_amanitin_high-48h-Hi-C.inter.hic |
314.6 Mb |
(ftp)(http) |
HIC |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
