 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on May 18, 2023 |
| Title |
ChIPseq_H3K27ac_NPC_2982-1KO |
| Sample type |
SRA |
| |
|
| Source name |
Neurosphere culture from Ganglionic eminence
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Neural progenitor cells
strain: C57BL/6
genotype: Nestin-KO
gender: male
age: E15.5
chip antibody: H3K27ac
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
100,000 nuclei from GE_NPC were used for ChIPseq library preparation.
Native ChIP-seq were perform according to previous publication (Kundakovic et al., 2017). After incubated with A/G Magnetic beads (Thermo Scientific™, #88803), ChIP DNA was went through end repairing (End-it DNA Repair Kit, Epicentre, ER0720), A-tailing (Klenow Exo-minus, Epicentre, KL06041K), adapter ligation (Fast-Link kit (Epicentre, LK11025) using VAHTS DNA Adapters set2 (Vazyme, N802-01), and then PCR amplified using NEBNext 2X master mix (E7335S). SPRIselect beads (Beckman, B23318) was used for library size selection (1:0.55 followed by 1:1.12). The final library concentration was measured with Qubit4, and the quality was evaluated on Agilent 4200 TapeStation, and then sent for sequencing.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
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 500.
diffReps was used for differential analysis with 1KB window and other default parameters.
Assembly: mm10
Supplementary files format and content: annotated text files
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 500.
MACS2 was used for peak calling with --keep-dup 1; default shifting model.
Assembly: mm10
Supplementary files format and content: peak text files
|
| |
|
| Submission date |
Apr 13, 2022 |
| Last update date |
May 18, 2023 |
| Contact name |
Yan Jiang |
| E-mail(s) |
yan_jiang@fudan.edu.cn
|
| Organization name |
Fudan University
|
| Department |
Institutes of Brain Science
|
| Street address |
131 Dongan rd
|
| City |
Shanghai |
| ZIP/Postal code |
200032 |
| Country |
China |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE200726 |
Histone methyltransferase SETDB1 selectively regulates cortical HTR3A interneuron development and anxiety-like behavior in mice [ChIP-seq] |
|
| Relations |
| BioSample |
SAMN27562150 |
| SRA |
SRX14841480 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6042816_ChIPseq_H3K27ac_NPC_2982-1KO_peaks.narrowPeak.gz |
1.0 Mb |
(ftp)(http) |
NARROWPEAK |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
