|
| Status |
Public on Jan 15, 2024 |
| Title |
BJ_cell_048_HiC |
| Sample type |
SRA |
| |
|
| Source name |
foreskin
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: foreskin
cell line: human fibroblast cell line
cell type: BJ
genotype: WT
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Viable cells were picked into a single tube containing 7 μL soft cell lysis buffer (25 mM Tris pH8.3, 30 mM NaCl, 0.45% IGEPAL-CA630, 1 U/μL SUPERaseIn) supplemented with 0.25 μL magnetic beads, then incubate on ice for 30 min, after incubation, vortex for 1 min. Centrifuge at 500 x g for 5 min at 4°C, then take 5 μL supernatant to a new tube. The supernatant was proceeded to Smart-seq2 reverse transcription and amplification5. Nuclei was proceeded to chromosome conformation capture.
simultaneous 3D genome and gene expression by LiMCA
Smart-seq2 for LiMCA RNA library; Dip-C protocol for LiMCA Hi-C library
|
| |
|
| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
Simultaneous single-cell three-dimensional genome and gene expression profiling Uncovers Dynamic Enhancer Connectivity Underlying Olfactory Receptor Choice
|
| Data processing |
RNA reads were mapped to hg38 transcriptome reference using hisat2.
Hi-C reads were processed and analysed using Dip-C and hickit package.
Files with .e.allValidPairs.gz and .e.hic suffixes were generated using the human genome assembly corrected for Philadelphia chromosome (ehap.hg38.genome.fa.gz).
We pooled Hi-C samples for each cell line.
We generated three replicate structures (_1.3dg.gz, _2.3dg.gz and _3.3dg.gz) per cell reconstructed with different random seeds (1-3).
Assembly: hg38
Supplementary files format and content: .hic
Supplementary files format and content: .3dg
Supplementary files format and content: .allValidPairs
|
| |
|
| Submission date |
Aug 04, 2023 |
| Last update date |
Jan 15, 2024 |
| Contact name |
Xiaoliang Sunney Xie |
| Organization name |
Peking University
|
| Lab |
Xiaoliang Sunney Xie
|
| Street address |
No.5 Yiheyuan Road, Haidian District
|
| City |
Beijing |
| State/province |
Beijing |
| ZIP/Postal code |
100871 |
| Country |
China |
| |
|
| Platform ID |
GPL20795 |
| Series (2) |
| GSE240114 |
Simultaneous single-cell three-dimensional genome and gene expression profiling Uncovers Dynamic Enhancer Connectivity Underlying Olfactory Receptor Choice [cell line, single-cell RNA-Seq & Hi-C] |
| GSE240128 |
Simultaneous single-cell three-dimensional genome and gene expression profiling uncovers dynamic enhancer connectivity underlying olfactory receptor choice |
|
| Relations |
| BioSample |
SAMN36844005 |
| SRA |
SRX21257576 |
