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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Dec 31, 2022 |
| Title |
ATACseq_NPC_4643_KO |
| Sample type |
SRA |
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| Source name |
Neurosphere culture from Ganglionic eminence
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| Organism |
Mus musculus |
| Characteristics |
cell type: Neural progenitor cells
strain: C57BL/6
genotype: Nestin-KO
gender: male
age: E15.5
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
ATAC-Seq: 50,000 to 100,000 nuclei from GE_NPC were used for ATAC-seq library preparation.
ATAC-seq library preparation using reagents from TruePrep DNA Library Preparation Kit V2 (Vazyme, TD501-02, China) following the manufactory's protocol with modifications.
RNA-seq: Total RNA was extracted from fresh frozen GE_NPCs and GE tissue at E15.5 by Direct-zolTM RNA MicroPrep kit (ZYMO RESEARCH, catalog #R2060) and RNeasy Lipid Tissue Mini Kit (Qiagen, catalog #74804), respectively.
mRNA-seq libraries from GE_NPCs were prepared by BGI Genomics, China. Total RNA-seq libraries from GE tissue were prepared using QIAseq™ Stranded Total RNA Lib Kit (Qiagen, Cat#180745) following the manufacturer’s instructions.
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
HiSeq X Ten |
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| Data processing |
ATACseq:
Sequenced reads were trimmed for adapter sequence, and masked for low-complexity or low-quality sequence (--quality 20 --phred33 --stringency 1 --length 20 --paired), then mapped to mm10 whole genome using Bowtie2 v2.3.4.3 with --phred33, --sensitive, look for multiple alignments and report best with MAPQ, --maxins 1000.
MACS2 was used for peak calling with --keep-dup 1 --shift -100 --extsize 200 –nomodel
RNA-seq:
Sequenced reads were trimmed for adapter sequence, and masked for low-complexity or low-quality sequence (--quality 20 --phred33 --stringency 1 --length 20 --paired), then mapped to mm10 whole genome using Tophat2 v2.1.1 with parameters --max-multihits 20 --transcriptome-max-hits 60.
The number of reads falling in the exons were counted by FeatureCounts v1.6.3 with GTF file (gencode.vM20.annotation.gtf).
Supplementary_files_format_and_content: Peak text files
Supplementary_files_format_and_content: Raw counts text files
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| Submission date |
Oct 29, 2021 |
| Last update date |
Dec 31, 2022 |
| Contact name |
Yan Jiang |
| E-mail(s) |
yan_jiang@fudan.edu.cn
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| Organization name |
Fudan University
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| Department |
Institutes of Brain Science
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| Street address |
131 Dongan rd
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| City |
Shanghai |
| ZIP/Postal code |
200032 |
| Country |
China |
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| Platform ID |
GPL21273 |
| Series (1) |
| GSE186806 |
Histone methyltransferase SETDB1 selectively regulates cortical HTR3A interneuron development and anxiety-like behavior in mice |
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| Relations |
| BioSample |
SAMN22771571 |
| SRA |
SRX12834319 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5661449_ATACseq_NPC_4643_KO_peaks.narrowPeak.gz |
2.6 Mb |
(ftp)(http) |
NARROWPEAK |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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