|
| Status |
Public on Jul 17, 2024 |
| Title |
primary cortical neurons, WT, H3K27ac |
| Sample type |
SRA |
| |
|
| Source name |
primary cortical neurons
|
| Organism |
Mus musculus |
| Characteristics |
age: E16.5
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 were generated using SAMtools
NGSplot was used to generate metaplots
tdf files were generated using IGVtools
Assembly: mm10
Supplementary files format and content: tdf files generated by IGVtools from bam files aligned to bowtie2
Library strategy: CUT&TAG
|
| |
|
| Submission date |
Apr 26, 2024 |
| 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) |
| GSE246688 |
CUT&Tag, ATAC-seq, bulk RNA-seq and single-nucleus RNA-seq analysis of histone variant H2BE in cortical neurons |
| GSE246748 |
CUT&Tag seq analysis of histone variant H2BE in neurons [H2BE_CT_antibodyValidation] |
|
| Relations |
| BioSample |
SAMN41098216 |
| SRA |
SRX24382407 |
