 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Dec 15, 2024 |
| Title |
3C_Tko_smc_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
KOD1
|
| Organism |
Thermococcus kodakarensis |
| Characteristics |
cell line: KOD1
genotype: smc deletion
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were crosslinked, permeabilized, and treated with AluI and HaeIII to digest genomic DNA. The insoluble fraction was collected and used for proximity ligation. After reversal of crosslinks, the DNA was extracted with phenol:chloroform:isoamyl alcohol, precipitated in ethanol, and sonicated.
Libraries were constructed using NEBNext Ultra II DNA Library Prep Kit for Illumina with Sample Purification Beads.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
*library strategy: 3C-seq
Data were processed using HiC-Pro version 3.0.0 (Servant et al., 2015). Normalized contact matrices were generated with MAX_ITER = 500. LOW_COUNT_PERC was set to 0.006 for Thermococcus kodakarensis.
Assembly: GCA_000009965.1, GCA_000195915.1
Supplementary files format and content: Tab-delimited tables. The first and second columns indicate genomic bins. The third column indicate normalized interaction frequencies between the bins.
|
| |
|
| Submission date |
May 13, 2024 |
| Last update date |
Dec 15, 2024 |
| Contact name |
Naomichi Takemata |
| Organization name |
Kyoto University
|
| Department |
Synthetic Chemistry and Biological Chemistry
|
| Street address |
Kyoto University, Katsura, Nishikyo-ku
|
| City |
Kyoto |
| ZIP/Postal code |
615-8510 |
| Country |
Japan |
| |
|
| Platform ID |
GPL28196 |
| Series (1) |
| GSE267297 |
Chromosomal domain formation by archaeal SMC, a roadblock protein, and DNA shape [3C-seq] |
|
| Relations |
| BioSample |
SAMN41381137 |
| SRA |
SRX24534409 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8263582_3C_Tko_smc_rep1.txt.gz |
640.8 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
|
|
|
|
 |
