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Sample GSM4544626 Query DataSets for GSM4544626
Status Public on Jul 09, 2021
Title P1CGP_ATAC_1000_cell_rep1
Sample type SRA
 
Source name cerebellum
Organism Mus musculus
Characteristics developmental stage: postnatal day 1
marker: Atoh1-GFP
Extracted molecule genomic DNA
Extraction protocol Atoh1-GFP positive cerebellar granule progenitor cells were FACS purified from postnatal day 1 animals. ATACseq was performed using 20,000 cells, and µATACseq was performed with 100, 500, 1000 cells. DNA fragments were extracted using MiniElute columns (Qiagen), and then amplified by PCR.
Libraries were prepared by PCR with indexed primers
 
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model Illumina NextSeq 500
 
Data processing For ATACseq, reads were trimmed based on quality score and then aligned to reference mouse genome (mm10) using bowtie2. PCR-duplicates were removed by Sambamba, and then peaks were called by MACS2 from individual replicate using filter p value < 0.01.
Genome_build: mm10
Supplementary_files_format_and_content: peak regions in narrowPeak format for ATACseq
 
Submission date May 11, 2020
Last update date Jul 10, 2021
Contact name Neil Segil
E-mail(s) nsegil@med.usc.edu
Phone 3234421549
Organization name University of Southern California
Department BCC
Lab 503K
Street address 1425 san pablo st, BCC 503K
City Los Angeles
State/province CA
ZIP/Postal code 90033
Country USA
 
Platform ID GPL19057
Series (2)
GSE150275 µATACseq: ATACseq with as few as 100 cells
GSE150391 POU4F3 Pioneer Activity Enables ATOH1 to Drive Diverse Mechanoreceptor Differentiation Through a Feed-Forward Epigenetic Mechanism
Relations
BioSample SAMN14886821
SRA SRX8321631

Supplementary file Size Download File type/resource
GSM4544626_P1CGP_ATAC_1000_cell_rep1.narrowPeak.gz 3.0 Mb (ftp)(http) NARROWPEAK
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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