|
| Status |
Public on Jan 15, 2021 |
| Title |
sciATAC Mouse Brain |
| Sample type |
SRA |
| |
|
| Source name |
Mouse whole brain
|
| Organism |
Mus musculus |
| Characteristics |
tissue: whole brain
region: Whole brain
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 |
SAMN17316235 |
| SRA |
SRX9850743 |
