|
Status |
Public on Jan 15, 2024 |
Title |
BJ_cell_058_RNA |
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 |
polyA RNA |
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 |
RNA-Seq |
Library source |
transcriptomic single cell |
Library selection |
cDNA |
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 |
SAMN36844384 |
SRA |
SRX21256967 |