|
| Status |
Public on Jan 27, 2018 |
| Title |
P56_neun_neg_ATAC_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
adult mouse forebrain
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6NCrl
developmental stage: postnatal day 56
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nuclei were isolated from snap frozen forebrain tissues and stained with antibodies against NeuN. 20,000 NeuN nuclei were sorted.
Pelleted nuclei were resuspended in the tagmentation buffer. Tagmented DNA was PCR amplified for 8-10 cycles.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
1) Reads were mapped to the mm10 reference genome using Bowtie2 in paired-end mode; 2) poorly mapped, improperly paired and mitochondrial reads were filtered; 3) PCR duplications were further removed using Picards MarkDuplicates; 4) Mapping positions of reads were adjusted accounting for Tn5 insertion; ATAC-seq signal was normalized into RPKM using deepTools for visualization.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig, normalized read coverage file
|
| |
|
| Submission date |
Jun 14, 2017 |
| Last update date |
Aug 15, 2019 |
| Contact name |
Rongxin Fang |
| E-mail(s) |
r3fang@ucsd.edu
|
| Organization name |
Ludwig Institute for Cancer Research
|
| Lab |
Ren Lab
|
| Street address |
9500 Gilman Dr #3080
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE100033 |
Single-nucleus analysis of accessible chromatin in developing mouse forebrain reveals cell-type-specific transcriptional regulation |
|
| Relations |
| BioSample |
SAMN07237058 |
| SRA |
SRX3739255 |
