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Series GSE146397 Query DataSets for GSE146397
Status Public on Jan 07, 2021
Title Diploid chromatin conformation capture (Dip-C) of single cells from the developing mouse cortex and hippocampus
Organism Mus musculus
Experiment type Other
Summary To study the dynamics of 3D genome structure during postnatal development of the mouse forebrain, we performed Dip-C on 1,954 single cells from the mouse cortex and hippocampus at different ages throughout the first postnatal year.
 
Overall design We performed Dip-C on 1,954 single cells and analyzed them with dip-c and hickit packages. We amplified 2544 samples (=26.5 96-well plates), and then filtered out 590 samples with fewer than 100K contacts per sample, which are considered as "empty wells" that were missed by the flow cytometer. The file GSE146397_metadata.excluded_samples.txt lists all excluded sample titles. The 1954 samples included in this study are listed in the file GSE146397_metadata.cells_contacts_100k.txt.gz.
 
Contributor(s) Tan L
Citation(s) 33484631
BioProject PRJNA607329
Submission date Mar 04, 2020
Last update date Apr 06, 2021
Contact name Longzhi Tan
E-mail(s) tanlongzhi@gmail.com
Organization name Harvard University
Department Chemistry and Chemical Biology
Lab Xiaoliang Sunney Xie
Street address 12 Oxford St
City Cambridge
State/province MA
ZIP/Postal code 02138
Country USA
 
Platforms (2)
GPL21103 Illumina HiSeq 4000 (Mus musculus)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (2544)
GSM4382149 Cortex P1 CASTxB6 Cell 001
GSM4382150 Cortex P1 CASTxB6 Cell 002
GSM4382151 Cortex P1 CASTxB6 Cell 003
This SubSeries is part of SuperSeries:
GSE162511 Single-cell transcriptome and 3D genome atlas of the developing mouse brain
Relations
SRA SRP249897

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE146397_00README.md.txt 7.7 Kb (ftp)(http) TXT
GSE146397_RAW.tar 183.3 Gb (http)(custom) TAR (of HIC, TXT)
GSE146397_aggregated_data.C.colors.txt.gz 1.2 Gb (ftp)(http) TXT
GSE146397_aggregated_data.allele_maternal_maternal.contacts.hic 737.7 Mb (ftp)(http) HIC
GSE146397_aggregated_data.allele_maternal_maternal.contacts.pairs.txt.gz 733.1 Mb (ftp)(http) TXT
GSE146397_aggregated_data.allele_paternal_paternal.contacts.hic 714.0 Mb (ftp)(http) HIC
GSE146397_aggregated_data.allele_paternal_paternal.contacts.pairs.txt.gz 684.5 Mb (ftp)(http) TXT
GSE146397_aggregated_data.cluster_N8.contacts.hic 683.5 Mb (ftp)(http) HIC
GSE146397_aggregated_data.cluster_N8.contacts.pairs.txt.gz 522.0 Mb (ftp)(http) TXT
GSE146397_aggregated_data.cluster_adult_astrocyte.contacts.hic 513.6 Mb (ftp)(http) HIC
GSE146397_aggregated_data.cluster_adult_astrocyte.contacts.pairs.txt.gz 294.4 Mb (ftp)(http) TXT
GSE146397_aggregated_data.cluster_cortical_l2-5_pyramidal_cell.contacts.hic 886.5 Mb (ftp)(http) HIC
GSE146397_aggregated_data.cluster_cortical_l2-5_pyramidal_cell.contacts.pairs.txt.gz 821.4 Mb (ftp)(http) TXT
GSE146397_aggregated_data.cluster_cortical_l6_pyramidal_cell.contacts.hic 548.8 Mb (ftp)(http) HIC
GSE146397_aggregated_data.cluster_cortical_l6_pyramidal_cell.contacts.pairs.txt.gz 372.9 Mb (ftp)(http) TXT
GSE146397_aggregated_data.cluster_hippocampal_pyramidal_cell.contacts.hic 777.0 Mb (ftp)(http) HIC
GSE146397_aggregated_data.cluster_hippocampal_pyramidal_cell.contacts.pairs.txt.gz 700.5 Mb (ftp)(http) TXT
GSE146397_aggregated_data.cluster_interneuron.contacts.hic 581.0 Mb (ftp)(http) HIC
GSE146397_aggregated_data.cluster_interneuron.contacts.pairs.txt.gz 395.6 Mb (ftp)(http) TXT
GSE146397_aggregated_data.cluster_mature_oligodendrocyte.contacts.hic 698.1 Mb (ftp)(http) HIC
GSE146397_aggregated_data.cluster_mature_oligodendrocyte.contacts.pairs.txt.gz 467.4 Mb (ftp)(http) TXT
GSE146397_aggregated_data.cluster_medium_spiny_neuron.contacts.hic 299.1 Mb (ftp)(http) HIC
GSE146397_aggregated_data.cluster_medium_spiny_neuron.contacts.pairs.txt.gz 132.3 Mb (ftp)(http) TXT
GSE146397_aggregated_data.cluster_microglia_etc.contacts.hic 515.3 Mb (ftp)(http) HIC
GSE146397_aggregated_data.cluster_microglia_etc.contacts.pairs.txt.gz 292.5 Mb (ftp)(http) TXT
GSE146397_aggregated_data.cluster_neonatal_astrocyte.contacts.hic 511.7 Mb (ftp)(http) HIC
GSE146397_aggregated_data.cluster_neonatal_astrocyte.contacts.pairs.txt.gz 276.9 Mb (ftp)(http) TXT
GSE146397_aggregated_data.cluster_neonatal_neuron_1.contacts.hic 1.2 Gb (ftp)(http) HIC
GSE146397_aggregated_data.cluster_neonatal_neuron_1.contacts.pairs.txt.gz 1.2 Gb (ftp)(http) TXT
GSE146397_aggregated_data.cluster_neonatal_neuron_2.contacts.hic 892.2 Mb (ftp)(http) HIC
GSE146397_aggregated_data.cluster_neonatal_neuron_2.contacts.pairs.txt.gz 824.4 Mb (ftp)(http) TXT
GSE146397_aggregated_data.cluster_oligodendrocyte_progenitor.contacts.hic 556.0 Mb (ftp)(http) HIC
GSE146397_aggregated_data.cluster_oligodendrocyte_progenitor.contacts.pairs.txt.gz 331.2 Mb (ftp)(http) TXT
GSE146397_aggregated_data.clusters_adult_neurons.contacts.hic 2.0 Gb (ftp)(http) HIC
GSE146397_aggregated_data.clusters_adult_neurons.contacts.pairs.txt.gz 2.7 Gb (ftp)(http) TXT
GSE146397_aggregated_data.clusters_neonatal_neurons.contacts.hic 1.7 Gb (ftp)(http) HIC
GSE146397_aggregated_data.clusters_neonatal_neurons.contacts.pairs.txt.gz 2.0 Gb (ftp)(http) TXT
GSE146397_aggregated_data.cpg_b100k.color2s.txt.gz 214.5 Mb (ftp)(http) TXT
GSE146397_aggregated_data.cpg_b1m.color2s.txt.gz 35.9 Mb (ftp)(http) TXT
GSE146397_genomic_data.b6_cast.chr.txt.gz 76.1 Mb (ftp)(http) TXT
GSE146397_genomic_data.cast_b6.chr.txt.gz 76.1 Mb (ftp)(http) TXT
GSE146397_genomic_data.mm10.cpg.100k.txt.gz 119.2 Kb (ftp)(http) TXT
GSE146397_genomic_data.mm10.cpg.1m.txt.gz 13.9 Kb (ftp)(http) TXT
GSE146397_genomic_data.mm10.cpg.20k.txt.gz 515.0 Kb (ftp)(http) TXT
GSE146397_genomic_data.mm10.par.bed.gz 77 b (ftp)(http) BED
GSE146397_metadata.cells_contacts_100k.txt.gz 7.2 Kb (ftp)(http) TXT
GSE146397_metadata.cells_contacts_100k_rmsd_1.5.txt.gz 3.3 Kb (ftp)(http) TXT
GSE146397_metadata.excluded_samples.txt.gz 1.7 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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