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| Status |
Public on Jul 17, 2024 |
| Title |
KO biol rep 2 ATAC-Seq |
| Sample type |
SRA |
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| Source name |
primary cortical neurons
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| Organism |
Mus musculus |
| Characteristics |
developmental stage: E16.5
cell type: primary cortical neurons
genotype: H2BE-KO/mCherry-KI
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were collected in cell lysis buffer (10mM TrisHCl ph7.5, 10mM NaCl, 3mM MgCl2, 0.1% NP-40, 0.1% Tween20, 0.1% Digitonin)
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
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
NextSeq 550 |
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| Data processing |
Fastq files were aligned by Bowtie2
bam files from the two sequencing runs were merged for each biological replicate and 50 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 and DiffBind was used to identify differential peaks
Assembly: mm10
Supplementary files format and content: bigwig files generated by deepTools from bam files aligned to bowtie2
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| Submission date |
Oct 31, 2023 |
| Last update date |
Jul 17, 2024 |
| Contact name |
Emily Feierman |
| E-mail(s) |
emily.feierman@gmail.com
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| Organization name |
University of Pennsylvania
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| Street address |
3400 Civic Center Blvd
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| City |
Philadelphia |
| ZIP/Postal code |
19104 |
| Country |
USA |
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| Platform ID |
GPL21626 |
| Series (2) |
| GSE246687 |
Analysis of histone variant H2BE in neuronal chromatin |
| GSE246688 |
CUT&Tag, ATAC-seq, bulk RNA-seq and single-nucleus RNA-seq analysis of histone variant H2BE in cortical neurons |
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| Relations |
| BioSample |
SAMN38053523 |
| SRA |
SRX22323609 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7874614_KO1B_50M.bw |
146.0 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
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