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Sample GSM3356231 Query DataSets for GSM3356231
Status Public on Sep 03, 2018
Title In Vivo sci-ATAC-seq
Sample type SRA
 
Source name Murine hippocampus
Organism Mus musculus
Characteristics strain: C57BL/6
assay: sci-ATAC-seq
source: fresh tissue
Growth protocol In vitro cells were cultured in Neurobasal A containing 1xB27 and 2 mM glutamax
Extracted molecule genomic DNA
Extraction protocol Nuclei were extracted using nuclei isolation buffer and then washed
sci-ATAC-seq described in the associated publicaiton and supplementary protocol
single-cell combinatorial indexing ATAC-seq
 
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model Illumina NextSeq 500
 
Description ATAC DNA
Data processing Libraries were sequenced on an Illumina NextSeq 500 using custom chemistry
Fastq files were processed using 'scitools fastq-dump', in the provided fastq files the cell barcode is the entire 36bp read 3
Reads were aligned to the mm10 reference genome using bwa (via 'scitools align')
Peaks were called and processed using macs2 with default parameters specified by 'scitools callpeak'
Count matrixes were generated using 'scitools count'
Dimensionality reduction was performed using 'scitools tfidf', 'scitools lsi', and then 'scitools tsne'
Deviation scores were generated using ChromVAR
Peak links and co-accessbility networks were generted using Cicero
Combined data files were generated using 'scitools data-combine' and can be extracted into respective components via 'scitools data-split'
Genome_build: mm10
Supplementary_files_format_and_content: data.gz files that contain all primary analyses, extract by 'scitools data-split' or gunzip and parse by section headers
Supplementary_files_format_and_content: cell barcodes can be found at the bottom of each column in the data.gz files
 
Submission date Aug 23, 2018
Last update date Sep 04, 2018
Contact name Andrew Adey
E-mail(s) adey@ohsu.edu
Organization name Oregon Health & Science University
Department MMG
Lab Adey Lab
Street address 3181 S.W. Sam Jackson Park Rd, RHH, L103
City Portland
State/province OR
ZIP/Postal code 97239-3098
Country USA
 
Platform ID GPL19057
Series (1)
GSE118987 The accessible chromatin landscape of the murine hippocampus at single-cell resolution
Relations
BioSample SAMN09906899
SRA SRX4605447

Supplementary file Size Download File type/resource
GSM3356231_InVivo.data.txt.gz 62.7 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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