|
| Status |
Public on Nov 03, 2022 |
| Title |
Embryo, E13.5, single nuclei ATAC |
| Sample type |
SRA |
| |
|
| Source name |
Embryo
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Embryo
age: E13.5
strain: C57BL/6JRj
genotype: WT
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
We prepared single nuclei suspensions from fresh frozen embryos (E12.5, E13.5 and E15.5) that were littermates to those used for spatial ATAC. Three to five 70 µm frozen sections were obtained for each embryonic stage matching the anatomical landmarks from spatial ATAC sections. Frozen sections were then dissociated according to the 10X Chromium Single Nuclei Isolation kit (1000494) omitting the debris removal step to avoid cell loss.
Nuclei suspensions were stained with 7-AAD (Miltenyi; 1:50) and sorted on a BD Fusion flow cytometer with a 100 µm nozzle. Nuclei were then immediately processed according to the 10X Genomics’ Single Cell ATAC Next GEM kit v1.1
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic single cell |
| Library selection |
other |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
snATAC-seq
|
| Data processing |
Raw reads were pre-processed using 10X Genomics’ CellRanger ATAC pipeline (v2.0.0).
We obtained age-specific fragment files from ENCODE and merged them using GenomicRanges’s (v1.46.1) ´reduce()´ function.
Next, we calculated new count matrices for each sample separately using FeatureMatrix() function from Seurat (v4.1.0) and merged the data into a single dataset.
We normalized data and performed clustering following Signac (v1.6.0) standard workflow.
Assembly: mm10
Supplementary files format and content: h5 (feature-barcode matrix)
Supplementary files format and content: csv (metadata with spatial coordinates, sample, and clustering)
Supplementary files format and content: tsv (fragments)
|
| |
|
| Submission date |
Oct 07, 2022 |
| Last update date |
Nov 03, 2022 |
| Contact name |
Margherita Zamboni |
| E-mail(s) |
margherita.zamboni@ki.se
|
| Organization name |
Karolinska Institutet
|
| Department |
Cell and Molecular Biology
|
| Lab |
Jonas Frisen
|
| Street address |
Solnavägen 9
|
| City |
Stockholm |
| ZIP/Postal code |
171 65 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL21626 |
| Series (2) |
| GSE214988 |
Chromatin accessibility profiling of the developing mouse embryo at the single nulceus level |
| GSE214991 |
Developing mouse embryo |
|
| Relations |
| BioSample |
SAMN31206660 |
| SRA |
SRX17825931 |
