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| Status |
Public on Mar 31, 2024 |
| Title |
Setd1a_CUTandRUN_rep2 |
| Sample type |
SRA |
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| Source name |
dentate gyrus
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| Organism |
Mus musculus |
| Characteristics |
tissue: dentate gyrus
antibody: Setd1a (Abcam, Ab70378)
cell type: Neural progenitor cells (NPCs)
genotype: WT
time: Day 5
treatment: BMP4/FGF2
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| Treatment protocol |
To induce quiescence, cells were plated into the proliferation medium at a density of 35,000-65,000 cells/cm2, and, after 16 h, fresh quiescence medium was added without EGF and with 20 ng/ml BMP4 and 20 ng/ml FGF2.
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| Growth protocol |
Adult NSCs were derived from the dentate gyrus of 7~8-week-old Hopx-CreERT2::Setd1afl/fl::H2B-GFP mice and cultured in the proliferation medium containing Neurobasal medium, 20 ng/ml FGF2, 20 ng/ml EGF, 2% B27, Glutamax, and Penicillin/Streptomycin, on culture dishes precoated with poly-D-lysine.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Material was prepared using a CUTANA™ ChIC/CUT&RUN Kit (EpiCypher, SKU: 14-1048) following manufactuer's protocols
Library was constructed following manufactuer's protocols (EpiCypher, SKU: 14-1048)
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
NextSeq 550 |
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| Data processing |
Raw sequencing data were demultiplexed with bcl2fastq2 v2.17.1.14 (Illumina).
Adaptors were trimmed using Trimmomatic v0.32 software
Trimeed sequence reads were uniquely mapped to mouse reference genome mm10 using Bowtie2 v2.1.0
Low mapping quality reads were filtered by SAMtools v0.1.18
Peak calling was performed using MACS2 v2.2.8
Assembly: mm10
Supplementary files format and content: txt file including Setd1 peaks
Library strategy: CUT&RUN
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| Submission date |
Dec 15, 2023 |
| Last update date |
Mar 31, 2024 |
| Contact name |
Ting Zhao |
| E-mail(s) |
ting820217@gmail.com
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| Organization name |
University of Pennsylvannia
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| Street address |
415 curie blvd
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| City |
philadelphia |
| ZIP/Postal code |
19104 |
| Country |
USA |
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| Platform ID |
GPL21626 |
| Series (2) |
| GSE250275 |
Epigenetic maintenance of neural stem cell quiescence in the adult mouse hippocampus via Setd1a [Cut & Run] |
| GSE250278 |
Epigenetic maintenance of neural stem cell quiescence in the adult mouse hippocampus via Setd1a |
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| Relations |
| BioSample |
SAMN38854263 |
| SRA |
SRX22897582 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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