NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM7813999 Query DataSets for GSM7813999
Status Public on Jun 09, 2024
Title E90_rep_2_scMultiome_RNA
Sample type SRA
 
Source name prefrontal cortex
Organism Macaca mulatta
Characteristics tissue: prefrontal cortex
genotype: WT
Extracted molecule nuclear RNA
Extraction protocol Transfer fresh frozen tissue sample to a pre-chilled 1.5 mL Eppendorf tube, add 500 μL of chilled Nuclei Lysis Buffer, and then transfer to a Douncer. Dounce the tissue with A and B pestle for complete homogenization, filter with a 40 μm strainer, and add 500 μL of chilled Nuclei Lysis Buffer. Mix gently and incubate on ice for 5 min. Centrifuge the nuclei at 500 x g for 5 min at 4°C. Remove supernatant without disturbing the pellet. Isolate pure nuclei using gradient centrifugation, and quantify the nuclei using Trypan blue staining on a hemocytometer.
For single-nucleus multi-omics library construction, the isolated nuclei were resuspended with 500 μL diltuted nuclei buffer (1 x nuclei buffer (10X Genomics, PN-2000207), 1mM DTT, 1U/μL RNase inhibitor, nuclease-free Water). The nuclei were counted using Trypan blue staining on a hemocytometer, and 6,000 nuclei were loaded per lane. All libraries were constructed based on the user guide of Chromium Next GEM Single Cell Multiome ATAC + GEX kit (10X Genomics). Libraries were sequenced on the Illumina NovaSeq 6000 platform.
 
Library strategy RNA-Seq
Library source transcriptomic single cell
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description 10x Genomics scMultiome transcriptom part
Data processing The demultiplexing, barcode processing and fragment generation were made using the Cell Ranger software v6.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest?). Peak calling and insertion counts were made in ArchR.
Assembly: Mmul_10
Supplementary files format and content: bed format, peak called using scMultiome data from all samples
Supplementary files format and content: Tab-seperated table format, gene counts matrix
Supplementary files format and content: Matrix market format, Tn5 insertion counts matrix
Supplementary files format and content: Tab-seperated table format, meta data for each cell
 
Submission date Sep 29, 2023
Last update date Jun 09, 2024
Contact name Yiming Sun
E-mail(s) yimingsun@pku.edu.cn
Organization name Peking University
Department School of Life Sciences
Street address NO.5, Yiheyuan Road, Haidian District
City Beijing
State/province Beijing
ZIP/Postal code 100871
Country China
 
Platform ID GPL27943
Series (1)
GSE241429 Comparative single-cell multiome reveals evolutionary innovations in neural progenitor cells during primate corticogenesis
Relations
BioSample SAMN37622058
SRA SRX21941623

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

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