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| Status |
Public on May 06, 2024 |
| Title |
e16smo_cn_k27m3_yz081 |
| Sample type |
SRA |
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| Source name |
cerebral cortex
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| Organism |
Mus musculus |
| Characteristics |
tissue: cerebral cortex
developmental stage: E16
antibody: rbh3k27m3
genotype: smoM2; no cre
treatment: Cut&Run
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Rosa26SmoM2/+ (smo_cn), and hGFAP-Cre; Rosa26SmoM2/+ cortices (smo_cy) (n=3 each group) were dissected, and cells were isolated with the Accumax (Sigma-Aldrich A7089) following the manufacturer’s instructions. For CUT&RUN, H3K27ac, H3K4me3, H3K27me3, and IgG (cntrl) antibodies were used. 10,000 cells were used for each experiment.
For CUT&RUN, DNA libraries were constructed using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB #E7645, E7103) with index primers (NEB, E7645-S).
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
e16smo_cn_k27m3_3samp_mm10.stringent.peaks.bed.trk.bb
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| Data processing |
Paired end reads were trimmed to 25x25bp and mapped using Bowtie2 against the set of mouse RepeatMasker elements.
Paired end reads that mapped to repeat elements were discarded. The remaining reads were mapped to the mm10 genome combined with the sacCer3 genome using Bowtie2.
Reads mapping to the sacCer3 genome were discarded. The remaining set of Bowtie2 paired-end mappings was filtered, retaining only mappings having genomic length less than or equal to 75bp.
The bam files of mappings were converted to coverage tracks across the genome using bedTools.
The coverage was merged over groups of 3 samples of the same genotype and antibody.
For each genotype, the coverage of an antibody was compared to the coverage of the control antibody using the SEACR program with the "norm" and "stringent" parameters.
The SEACR bed file of peaks was converted to a track in the bigBed format
Assembly: mm10
Supplementary files format and content: bigBed of SEACR peak loci
Library strategy: CUT&Tag
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| Submission date |
Jan 31, 2024 |
| Last update date |
May 06, 2024 |
| Contact name |
Bin Chen |
| Organization name |
University of California Santa Cruz
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| Department |
MCD Biology
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| Street address |
1156 High St.
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| City |
Santa Cruz |
| State/province |
CA |
| ZIP/Postal code |
95064 |
| Country |
USA |
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| Platform ID |
GPL21103 |
| Series (2) |
| GSE254691 |
A conserved molecular logic for neurogenesis to gliogenesis switch in the cerebral cortex [CUT&RUN] |
| GSE254693 |
A conserved molecular logic for neurogenesis to gliogenesis switch in the cerebral cortex |
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| Relations |
| BioSample |
SAMN39692590 |
| SRA |
SRX23462446 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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