NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM7681857 Query DataSets for GSM7681857
Status Public on Jan 15, 2024
Title eHAP_cell_017_RNA
Sample type SRA
 
Source name eHAP
Organism Homo sapiens
Characteristics tissue: eHAP
cell line: eHAP
cell type: eHAP
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 SAMN36844299
SRA SRX21257522

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap