|
| Status |
Public on Oct 20, 2023 |
| Title |
B14804_KO_neuron_HiC_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
iPSC-derived human neurons
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: iPSC-derived human neurons
cell line: WTC11 Ngn2 derived
genotype: homozygous B14804 KO
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
We used the Arima HiC kit to process the samples. Briefly, frozen cell pellets were lysed and conditioned before chromatin digestion. The digested chromatin was then filled in and biotinylated before ligation. Next, chromatin was protein-digested and reverse crosslinking overnight, followed by purification. The purified DNA was then sonicated using the bioruptor pico (Diagenode) and size selected before library preparation using the NEB DNA Ultra II, following Arima’s protocol.
The Hi-C DNA was bound to streptavidin beads before enzymatic end prep, adaptor ligation, DNA release by heat incubation, and lastly, PCR to barcode and amplify the libraries.
|
| |
|
| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Raw Hi-C sequencing was processed using the HiCUP pipeline.
Alignments were converted to a multi-resolution Hi-C matrix using pairtools.
Hi-C data between biological replicates.
Insulation scores were calculated using the hicFindTADs command from HiCExplorer.
hg38
Bedfiles containing genome-wide insulation scores based on the HiC data merged between replicates of wild-type and knock-out neurons.
|
| |
|
| Submission date |
Mar 16, 2023 |
| Last update date |
Oct 20, 2023 |
| Contact name |
Mariam Okhovat |
| Organization name |
Oregon Health and Science University
|
| Department |
Medicine
|
| Street address |
3030 S Moody Ave.
|
| City |
Portland |
| State/province |
Oregon |
| ZIP/Postal code |
97239 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE197926 |
TAD Evolutionary and functional characterization reveals diversity in mammalian TAD boundary properties and function |
|
| Relations |
| BioSample |
SAMN33787991 |
| SRA |
SRX19695804 |
