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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Aug 10, 2020 |
| Title |
P28_V1_Dlx6pos |
| Sample type |
SRA |
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| Source name |
primary visual cortex
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| Organism |
Mus musculus |
| Characteristics |
age: P28
genotype/variation: Dlx6aCre::INTACT
tissue: primary visual cortex
cell type: cortical interneurons
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Male hemizygous Dlx6a-Cre mice (Jax stock #008199) were crossed with female homozygous INTACT mice (flox-Sun1-eGFP, Jax stock #021039) to yield Dlx6a-Cre::INTACT offspring for scATAC-seq experiments. Brains from P28 Dlx6aCre::INTACT mice were harvested, sectioned coronally on a mouse brain slicer (Zivic Instruments), and regions of interest were dissected in ice-cold ACSF. Tissue was then transferred to a dounce homogenizer containing Lysis Buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, 0.01% Tween-20, and 0.01% IGEPAL CA630, 0.001% Digitonin). Tissue was homogenized with 10 strokes of pestle A, 10 strokes of pestle B, and incubated for 5 min on ice before being filtered through a 30 μm filter and centrifuged at 500xg for 10 min at 4C. The pellet was resuspended in 1% BSA for sorting for GFP+ nuclei on a Sony SH800S cell sorter. Nuclei were sorted into Diluted Nuclei Buffer (10X Genomics).
scATAC-seq libraries were prepared using the Chromium Single Cell ATAC Solution (10X Genomics). Libraries were sequenced using a Nova-Seq S1 100 cycle kit (Illumina).
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Raw sequencing data were passed through the Cell Ranger ATAC pipeline (10X Genomics, v1.1.0). FASTQ files were generated from BCL files using cellranger-atac mkfastq.
Read filtering, alignment, and barcode counting were performed using cellranger-atac count.
Genome_build: mm10
Supplementary_files_format_and_content: The fragments.tsv.gz file contains 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 singlecell.csv file contains QC information associated with each barcode for cell-calling.
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| Submission date |
Jun 15, 2020 |
| Last update date |
Aug 10, 2020 |
| Contact name |
Kathryn Allaway |
| Organization name |
Broad Institute
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| Department |
Stanley Center for Psychiatric Disease
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| Lab |
Fishell Lab
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| Street address |
75 Ames St
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| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE152449 |
Viral manipulation of functionally distinct interneurons in mice, non-human primates and humans |
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| Relations |
| BioSample |
SAMN15236551 |
| SRA |
SRX8545741 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4616046_P28_V1_fragments.tsv.gz |
2.7 Gb |
(ftp)(http) |
TSV |
| GSM4616046_P28_V1_singlecell.csv.gz |
6.7 Mb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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