|
| Status |
Public on Aug 06, 2024 |
| Title |
CN34_e11.5_R2 |
| Sample type |
SRA |
| |
|
| Source name |
CN3/4 e11.5 GFP-positive-R2
|
| Organism |
Mus musculus |
| Characteristics |
cell type: CN3/4 e11.5 GFP-positive-R2
genotype: WILDTYPE
|
| Treatment protocol |
N/A
|
| Growth protocol |
N/A
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
GFP positive cells FACS purified from e10.5 or e11.5 cells
“Single Cell CUT and Tag on 10X genomics platform” protocol from www.protocol.io and 10x Genomics Chromium Next GEM Single Cell ATAC Kit
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
scCUT&Tag using antibody H3K27Ac (ab177178)
|
| 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
CUT&Tag fragment counts were tabulated using the Cell Ranger count function using default parameters
.bam and/or fragment files were processed for peak calling using R ArchR package (https://github.com/GreenleafLab/ArchR)
Calculation of activity by contact (ABC) enhancer scores (https://github.com/broadinstitute/ABC-Enhancer-Gene-Prediction)
Assembly: mm10
Supplementary files format and content: .bam binary file containing aligned fragments
Supplementary files format and content: .bigwig track format to visualise histone modification profiles along the genome
Library strategy: scCUT&Tag
|
| |
|
| 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) |
| GSE254088 |
Noncoding Mendelian epigenomics - single cell CUT&Tag mouse cMN data |
| GSE254090 |
A cell type-aware framework for nominating non-coding variants in Mendelian regulatory disorders |
|
| Relations |
| BioSample |
SAMN39597315 |
| SRA |
SRX23381760 |
