|
| Status |
Public on Sep 22, 2021 |
| Title |
E13_MGE_multi_atac |
| Sample type |
SRA |
| |
|
| Source name |
medial ganglionic eminence
|
| Organism |
Mus musculus |
| Characteristics |
strain: CD-1
cell type: MGE cells
age: E13
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
E13.5 embryos were harvested from timed pregnant CD-1 mice and the MGE was dissected in ice-cold Leibovitz's L-15 medium. Pooled tissue from several embryos were dissociated using the Neural Tissue Dissociation Kit (T) (Miltyeni Biotec, PN-130-093-231) according to the manufacturer’s instructions. Dissociated cells were then filtered through a 70 um filter, and centrifuged at 300xg for 5 min at 4C. Nuclei then were isolated as described in the 10x Genomics demonstrated protocols ‘Nuclei Isolation from Embryonic Mouse Brain for Single Cell Multiome ATAC + Gene Expression Sequencing ’ for fresh tissue for input to single-cell Multiome library preparation.
Single-cell multiomic (ATAC + Gene Expression) libraries were prepared on the 10x Genomics platform using the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle (PN-1000285), Chromium Next GEM Chip J Single Cell Kit (PN-1000230), Single Index Kit N Set A (Pn- PN-1000212) and Dual Index Kit TT Set A (PN-1000215) as instructed by the manufacturer. Libraries were sequenced using the Nova-Seq 100 cycle kit (ATAC library) and Next-Seq 150 cycle kit (Gene Expression library) (Illumina) by Broad Institute Genomic Services.
Dual scRNA/scATAC-seq
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
ATAC from the same barcoded cells as Gene expression (RNA) sample
|
| Data processing |
Raw multiomic data was processed using the Cell Ranger ARC v1.0.0 pipeline (10x Genomics). Reads were aligned to the GRCm38 (mm10) mus musculus genome.
Read filtering, alignment, and barcode counting were performed using cellranger-arc count.
Genome_build: mm10
Supplementary_files_format_and_content: barcodes.tsv file containing cell barcodes present in the corresponding expression matrix.
Supplementary_files_format_and_content: features.tsv file containing gene IDs and names present in the corresponding expression matrix.
Supplementary_files_format_and_content: matrix.mtx file is sparse matrix containing feature-barcode matrices.
Supplementary_files_format_and_content: The fragments.tsv.gz file is a tabular file where each line represents a unique ATAC-seq fragment. Duplicate reads are collapsed into a single fragment record.
Supplementary_files_format_and_content: The per_barcode_metrics.csv file contains QC information associated with each barcode for cell-calling.
|
| |
|
| Submission date |
Jan 19, 2021 |
| Last update date |
Sep 22, 2021 |
| Contact name |
Kathryn Allaway |
| Organization name |
Broad Institute
|
| Department |
Stanley Center for Psychiatric Disease
|
| Lab |
Fishell Lab
|
| Street address |
75 Ames St
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE165114 |
Multiomic sequencing of the MGE |
| GSE165233 |
Genetic and epigenetic coordination of cortical interneuron development |
|
| Relations |
| BioSample |
SAMN17383959 |
| SRA |
SRX9897323 |
