|
| Status |
Public on Jul 17, 2024 |
| Title |
WT biol rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
primary cortical neurons
|
| Organism |
Mus musculus |
| Characteristics |
cell type: primary cortical neurons
genotype: WT
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
At 12DIV, primary cortical neurons were collected in wash buffer (Kaya-Okur et al. 2019) and CUT&Tag was performed with anti-H2BE antibody (Millipore ABE1384)
Transposition reaction mix from Nextera Library Prep kit was used (Tagment DNA Enzyme 1 and Tagment DNA Buffer)
Nextera primer sets with NEBNext Master Mix was used to generate libraries with AMPure beads used for cleanup
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
Fastq files were aligned by Bowtie2
bam files from the two sequencing runs were merged for each biological replicate and 6 million reads were subset for each biol rep using SAMTools for downstream analysis
NGSplot was used to generate metaplots
deepTools was used to generate bigwig files
MACS3 was used for peak-calling
Assembly: mm10
Supplementary files format and content: bigwig files generated by deepTools from bam files aligned to bowtie2
Library strategy: CUT&Tag
|
| |
|
| Submission date |
Oct 31, 2023 |
| Last update date |
Jul 17, 2024 |
| Contact name |
Emily Feierman |
| E-mail(s) |
emily.feierman@gmail.com
|
| Organization name |
University of Pennsylvania
|
| Street address |
3400 Civic Center Blvd
|
| City |
Philadelphia |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL21626 |
| Series (2) |
| GSE246618 |
CUT&Tag seq analysis of histone variant H2BE in neurons |
| GSE246688 |
CUT&Tag, ATAC-seq, bulk RNA-seq and single-nucleus RNA-seq analysis of histone variant H2BE in cortical neurons |
|
| Relations |
| BioSample |
SAMN38047917 |
| SRA |
SRX22294046 |
