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Status |
Public on Sep 22, 2021 |
Title |
E13_MGE_Dlx6neg_2_ATAC |
Sample type |
SRA |
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Source name |
Medial Ganglionic Eminence
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Organism |
Mus musculus |
Characteristics |
cell type: MGE progenitor cells age: E13
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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).
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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 |
Jan 18, 2021 |
Last update date |
Sep 22, 2021 |
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 (2) |
GSE165031 |
Single-cell ATAC-seq of developing cortical interneurons. |
GSE165233 |
Genetic and epigenetic coordination of cortical interneuron development |
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Relations |
BioSample |
SAMN17373766 |
SRA |
SRX9891026 |
Supplementary file |
Size |
Download |
File type/resource |
GSM5024885_E13_MGE_dlxneg_2_ATAC_fragments.tsv.gz |
1.7 Gb |
(ftp)(http) |
TSV |
GSM5024885_E13_MGE_dlxneg_2_ATAC_singlecell.csv.gz |
6.6 Mb |
(ftp)(http) |
CSV |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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