|
| Status |
Public on Nov 18, 2023 |
| Title |
H3K4me3 exc rep2 |
| Sample type |
SRA |
| |
|
| Source name |
whole brain
|
| Organism |
Mus musculus |
| Characteristics |
tissue: whole brain
cell type: excitatory neuron
genotype: Sun1 f/f | Emx1Cre (+)
age: 8 weeks
chip antibody: H3K4me3
|
| Growth protocol |
Mice were maintained and bred in a 12-hour light/dark cycle under standard pathogen-free conditions.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nuclei were isolated from adult mouse brain tissue and subjected to FACS-sorting. The FACS-sorted nuclei were used for Cut&Run with the CUTANA CUT&RUN Kit. The Cut&Run enriched DNA fragments were used for DNA library construction.
Cut&Run libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) following the manufacturer's instructions.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Sequencing adapters and low-quality bases were first trimed with cutadapt(v1.18) and trim_galore(v0.5.0) for all cun&run libraries. The retained reads were aligned to mouse genome(mm10) using bowtie2(v2.3.5) in pair-end mode with option “-N 1 -L 25”.
PCR duplications were removed using picard(v2.25.0) with the option “REMOVE_DUPLICATES=true”. Non-redundant reads were further filtered for minimal mapping quality (MAPQ ≥ 30) using samtools(v1.12) view with option “-q30”.
Peak calling for histone modifications was performed by MACS2(v2.2.5) using option “-p 0.05” for H3K27ac and H3K4me3, “--broad -p 0.05” for H3K4me1 and H3K27me3. The reproducible peaks between biological replicates was further identified following irreproducible discovery rate (IDR, v2.0.4.2) framework with parameters “--rank signal.value”.
Stricter parameters were adopted for EGR1 cun&run datasets peak calling to generate the reliable transcription factor binding sites，with option “-p 0.005” for MACS2 and “--rank signal.value --idr-threshold 0.02” for IDR framework.
Assembly: mm10
Supplementary files format and content: narrowPeak, broad Peak
Library strategy: Cut&Run
|
| |
|
| Submission date |
Nov 18, 2022 |
| Last update date |
Nov 18, 2023 |
| Contact name |
Xiguang Xu |
| E-mail(s) |
xiguang@vt.edu
|
| Organization name |
Virginia Tech
|
| Department |
Department of Biomedical Sciences and Pathobiology
|
| Lab |
Epigenomics and Computational Biology Laboratory
|
| Street address |
1015 Life Science Circle
|
| City |
Blacksburg |
| State/province |
VA |
| ZIP/Postal code |
24060 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE218312 |
Histone modifications mediate transcription factor regulation and contribute to neuronal subtype identity |
|
| Relations |
| BioSample |
SAMN31785159 |
| SRA |
SRX18306225 |
