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Sample GSM2668126 Query DataSets for GSM2668126
Status Public on Jan 27, 2018
Title P56_neun_neg_ATAC_rep1
Sample type SRA
Source name adult mouse forebrain
Organism Mus musculus
Characteristics strain: C57BL/6NCrl
developmental stage: postnatal day 56
Extracted molecule genomic DNA
Extraction protocol Nuclei were isolated from snap frozen forebrain tissues and stained with antibodies against NeuN. 20,000 NeuN nuclei were sorted.
Pelleted nuclei were resuspended in the tagmentation buffer. Tagmented DNA was PCR amplified for 8-10 cycles.
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model Illumina HiSeq 4000
Data processing 1) Reads were mapped to the mm10 reference genome using Bowtie2 in paired-end mode; 2) poorly mapped, improperly paired and mitochondrial reads were filtered; 3) PCR duplications were further removed using Picards MarkDuplicates; 4) Mapping positions of reads were adjusted accounting for Tn5 insertion; ATAC-seq signal was normalized into RPKM using deepTools for visualization.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig, normalized read coverage file
Submission date Jun 14, 2017
Last update date Aug 15, 2019
Contact name Rongxin Fang
Organization name Ludwig Institute for Cancer Research
Lab Ren Lab
Street address 9500 Gilman Dr #3080
City La Jolla
State/province CA
ZIP/Postal code 92093
Country USA
Platform ID GPL21103
Series (1)
GSE100033 Single-nucleus analysis of accessible chromatin in developing mouse forebrain reveals cell-type-specific transcriptional regulation
BioSample SAMN07237058
SRA SRX3739255

Supplementary file Size Download File type/resource 131.8 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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