NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM8033185 Query DataSets for GSM8033185
Status Public on Aug 06, 2024
Title CN7_e10.5_R2
Sample type SRA
 
Source name CN7 e10.5 GFP-positive
Organism Mus musculus
Characteristics cell type: CN7 e10.5 GFP-positive
genotype: WILDTYPE
Treatment protocol N/A
Growth protocol N/A
Extracted molecule genomic DNA
Extraction protocol GFP positive and negative cells FACS purified from e10.5 or e11.5 cells
10x Genomics scATAC
 
Library strategy ATAC-seq
Library source genomic single cell
Library selection other
Instrument model Illumina NextSeq 500
 
Data processing NextSeq 500 software (Illumina) used for basecalling
bcl outputs from NextSeq 500 were processed using 10x Cell Ranger ATAC mkfastq pipeline (https://www.10xgenomics.com/support/software/cell-ranger/) for demultiplexing and fastq file generation
ATAC fragment counts were tabulated using the Cell Ranger count function using default parameters
.bam and/or fragment files were processed for peak calling and differential accessibility analysis using R ArchR package (https://github.com/GreenleafLab/ArchR)
Assembly: mm10
Supplementary files format and content: .bam binary file containing aligned fragments
Supplementary files format and content: .bw bigwig track format to visualise accessibility profiles along the genome
 
Submission date Jan 24, 2024
Last update date Aug 06, 2024
Contact name Elizabeth C Engle
E-mail(s) elizabeth.engle@childrens.harvard.edu
Phone 6179194030
Organization name Boston Childrens Hospital
Street address 3 Blackfan Circle
City Boston
ZIP/Postal code 02115
Country USA
 
Platform ID GPL19057
Series (2)
GSE254086 Noncoding Mendelian epigenomics - single cell ATACseq mouse cMN data
GSE254090 A cell type-aware framework for nominating non-coding variants in Mendelian regulatory disorders
Relations
BioSample SAMN39596313
SRA SRX23380201

Supplementary file Size Download File type/resource
GSM8033185_CN12neg-R1-e11-5.nodups.bam.bw 196.3 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA

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