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Sample GSM5024884 Query DataSets for GSM5024884
Status Public on Sep 22, 2021
Title E13_MGE_Dlx6pos_2_ATAC
Sample type SRA
 
Source name Medial Ganglionic Eminence
Organism Mus musculus
Characteristics cell type: MGE postmitotic cells
age: E13
Extracted molecule genomic DNA
Extraction protocol For embryonic timepoints, male hemizygous Dlx6a-Cre mice (Jax stock #008199) were crossed with female homozygous Ai9 or Ai14 mice (Rosa-LSL-tdtomato, Jax stock # 007909 or 007914) and checked daily for the presence of a vaginal plug, with the morning a plug was found being considered embryonic day 0. Embryos were screened using a fluorescent microscope for the presence of tdTomato. For embryonic timepoints using wild-type mice, timed pregnant CD-1 mice were used (Charles River #022). For postnatal timepoints, male hemizygous Dlx6a-Cre mice were crossed with female homozygous INTACT mice (flox-Sun1-eGFP, Jax stock #021039) to yield Dlx6a-Cre;INTACT offspring. For the P2 Mef2c conditional knockout (Mef2c_cKO), mice with the Lhx6-iCre (Jax stock #026555) and Mef2c-Fl/+ (Jax stock #025556) alleles were crossed with mice with the Mef2c-Fl/Fl and INTACT alleles to yield Lhx6-iCre;INTACT;Mef2c-Fl/Fl offspring. For embryonic timepoints, embryos were harvested from pregnant dams and relevant brain regions were 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, centrifuged at 300xg for 5 min at 4C, and, where cell-sorting was required, resuspended in 1% BSA in PBS for cell sorting of tdTomato+ cells. For postnatal timepoints, brains were harvested, sectioned coronally on a stainless-steel 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 CA-630, 0.001% Digitonin). Tissue was homogenized with 10 strokes of pestle A, 10 strokes of pestle B, and incubated for 5 minutes on ice before being filtered through a 30 μm filter and centrifuged at 500xg for 10 minutes at 4C. The pellet was resuspended in 1% BSA in PBS for sorting for GFP+ nuclei. For all timepoints, cells or nuclei were sorted into Diluted Nuclei Buffer (10x Genomics) on a Sony SH800S cell sorter with a 100 µm chip.
scATAC-seq libraries were prepared using the Chromium Single Cell ATAC Solution v1 (10X Genomics). Libraries were sequenced using a Nova-Seq 100 cycle kit (Illumina).
 
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model Illumina NovaSeq 6000
 
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.
 
Submission date Jan 18, 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)
GSE165031 Single-cell ATAC-seq of developing cortical interneurons.
GSE165233 Genetic and epigenetic coordination of cortical interneuron development
Relations
BioSample SAMN17373767
SRA SRX9891025

Supplementary file Size Download File type/resource
GSM5024884_E13_MGE_dlxpos_2_ATAC_fragments.tsv.gz 1.7 Gb (ftp)(http) TSV
GSM5024884_E13_MGE_dlxpos_2_ATAC_singlecell.csv.gz 6.8 Mb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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