|
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 |