|
| 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 |
