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Sample GSM5021071 Query DataSets for GSM5021071
Status Public on Jan 15, 2021
Title sciMAP Mouse SSp
Sample type SRA
 
Source name Mouse whole brain - cryosectioned
Organism Mus musculus
Characteristics tissue: whole brain - cryosectioned
region: SSp
exposure: none
strain: C57BL/6
Extracted molecule genomic DNA
Extraction protocol Nuclei isolation using sciMAP-ATAC protocols
sci-ATAC-seq protocol
sciMAP-ATAC and sci-ATAC-seq
 
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model Illumina NextSeq 500
 
Data processing scitools fastq-dump to generate index-matched fastq files
bwa mem to align to respective genome (mm10 for mouse, hg38 for human)
scitools count to generate count matrixes
cistopic v3 for dimensionality reduction
Genome_build: mm10 for mouse, hg38 for human
Supplementary_files_format_and_content: Count matrixes in sparse matrix format with row and column files along with a triplet matrix values file
Supplementary_files_format_and_content: Aggregate metadata is a csv file with additional informaiton on all cells
 
Submission date Jan 14, 2021
Last update date Jan 17, 2021
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)
GSE164849 Spatially mapped single-cell chromatin accessibility
Relations
BioSample SAMN17316233
SRA SRX9850745

Supplementary file Size Download File type/resource
GSM5021071_sciMAP.CortexExperiment.counts.sparseMatrix.cols.txt.gz 42.4 Kb (ftp)(http) TXT
GSM5021071_sciMAP.CortexExperiment.counts.sparseMatrix.rows.txt.gz 1.0 Mb (ftp)(http) TXT
GSM5021071_sciMAP.CortexExperiment.counts.sparseMatrix.values.txt.gz 42.0 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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