|
| Status |
Public on Jan 27, 2022 |
| Title |
scATAC-seq E14.5 somatosensory cortex rep2 |
| Sample type |
SRA |
| |
|
| Source name |
whole E14.5 somatosensory cortex
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
age: E14.5
cell type: whole tissue
technique: scATAC-seq
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
The somatosensory cortex of E14.5 mouse embryos was isolated and meninges removed. Single cell suspension was prepared using the papain-based neural dissociation kit (Miltenyi Biotec, Cat. N: 130-092-628) according to the manufacturer protocol with reduced dissociation times (5 min. instead of 15 min. at 37˚C). Cell number as well as the viability was assessed using the Countess™ II Automated Cell Counter (Invitrogen).
Directly after tissue dissociation scATAC-seq (10x Genomics, Cat. N: PN-1000110, PN-1000086, PN-1000084) libraries were generated according to the manual instructions with a targeted recovery of 6000 cells/nuclei per sample. Before sequencing, libraries were quantified by qPCR using the NEBNext® Library Quant Kit (New England Biolabs, Cat. N: E7630S). The size distribution of the obtained libraries was assessed using Agilent 2100 Bioanalyzer.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Raw sequencing data was converted to fastqs using cellranger-atac mkfastq (10x Genomics, v1.2.0). Reads were aligned to the GRCm38 reference genome (mm10) and quantified using cellranger-atac count (10x Genomics v1.2.0) using integrated doublet removal.
genome build: mm10
supplementary_files_format_and_content: Processed data files represent filtered peak-barcode matrix (*mtx.gz) stored in the Market Exchange Format (MEX) for sparse matrices as well as a BED file with peak. Furthermore the gzipped TSV files cotian barcode sequences as well as the genomic position of the obtained fragments, their barcodes and duplication count. A detailed described of the content of the processed data files can be found at https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/output/matrices and https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/output/fragments
|
| |
|
| Submission date |
Aug 04, 2020 |
| Last update date |
Jan 27, 2022 |
| Contact name |
Boyan Bonev |
| E-mail(s) |
[email protected]
|
| Organization name |
Helmholtz Zentrum München
|
| Lab |
Bonev Lab
|
| Street address |
Ingolstädter Landstr. 1
|
| City |
Neuherberg |
| State/province |
Deutschland |
| ZIP/Postal code |
85764 |
| Country |
Germany |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE155677 |
Multimodal profiling of the transcriptional regulatory landscape of the developing mouse cortex identifies Neurog2 as a key epigenome remodeler |
|
| Relations |
| BioSample |
SAMN15727710 |
| SRA |
SRX8884486 |
