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| Status |
Public on Jun 01, 2024 |
| Title |
WT_NPC_H3K9me3_Rep3 |
| Sample type |
SRA |
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| Source name |
Neural progenitor cells
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| Organism |
Mus musculus |
| Characteristics |
cell type: Neural progenitor cells from ganglionic eminence
strain: C57BL/6
chip antibody: H3K9me3 (Abcam, Ab8898, lot 1039691-1)
genotype: Wildtype
age: Embryonic day 15.5
fetus id: 5871-1WT
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| Growth protocol |
Ganglionic eminences of fetal brains were harvested, dissociated with Accutase solution (Sigma A6964), and cultured in ultra-low attachment plates (Corning 3471) with advanced DMEM/F-12 (Gibco 12634-010) supplemented with N-2 (Gibco 17502048), B-27 (Gibco 12587010), GlutaMAX (Gibco 35050061), P/S (Sigma V900929), heparin (5 ug/ml), EGF (20 ng/ml) and FGF (20 ng/ml). Fresh medium was added every 3 days, and neurospheres were dissociated with Accutase and passed every 5 days.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Three million NPCs were harvested, washed in PBS and lysed with NP40 lysis buffer (0.32 M sucrose, 5 mM CaCl2, 3 mM Mg(Ace)2, 0.1 mM EDTA, 10 mM Tris pH8, 0.1% NP40). For native ChIP (nChIP, for H3K9me3), nuclei were collected through centrifugation, resuspended in douncing buffer (10 mM Tris pH8, 4 mM MgCl2, 1 mM CaCl2) and chromatin was fragmentized with micrococcal nuclease (Sigma N3755). Hypotonic solution (0.2 mM EDTA, cOmplete inhibitor (Roche 11697498001), 0.1% NP40) was added for nuclei lysis and chromatin release. For fixed ChIP (xChIP, for CTCF), nuclei were collected through centrifugation, fixed in 1% formaldehyde (Sigma 252549) at room temperature for 5 minutes with rotation, and quenched in 0.125 M glycine at RT for 10 minutes with rotation. After collected with centrifugation, the fixed nuclei were resuspended in FSB solution (5 mM EDTA, 20 mM Tris pH8, 500 mM NaCl) supplemented with 0.1% SDS and cOmplete inhibitor, and sonicated with Covaris E220 ultrasonicator system to 300~500 bp. For both nChIP and xChIP, protein-DNA complexes were isolated with antibody.
ChIP DNA was blunted with End-it DNA Repair Kit (Epicentre ER0720), A-tailed with Klenow Exo-minus (Epicentre KL06041K), ligated with adapter (Vazyme N802-01) using Fast-Link kit (Epicentre LK11025) and amplified with VAHTS HiFi Universal Amplification Mix for Illumina (Vazyme N618-02). The library was size-selected with SPRIselect beads (Beckman B23318) and sent for sequencing on Illumina NovaSeq 6000 (paired-end, 150 bp).
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Quality control of ChIP-seq reads was conducted with FastQC (version 0.11.9).
Reads were trimmed with Trim Galore (version 0.6.7, --quality 20 --phred33 --stringency 1 --length 20 --fastqc --paired).
Reads were aligned to mm10 with Bowtie2 (version 2.4.1) in default settings.
Reads were binarized, sorted, deduplicated and indexed with SAMtools (version 1.6).
Narrow peaks were called with MACS2 (version 2.2.7.1) in default settings.
Assembly: mm10
Supplementary files format and content: NARROWPEAK: Narrow peak text files, tab delimited
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| Submission date |
Nov 13, 2023 |
| Last update date |
Jun 01, 2024 |
| 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 |
GPL24247 |
| Series (2) |
| GSE247618 |
Histone methyltransferase SETDB1 silenced SINE B2 retrotransposons and maintained mitotic cell cycle of neural progenitor cells (ChIP-Seq) |
| GSE247620 |
Histone methyltransferase SETDB1 silenced SINE B2 retrotransposons and maintained mitotic cell cycle of neural progenitor cells |
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| Relations |
| BioSample |
SAMN38236064 |
| SRA |
SRX22512354 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7898075_WT_NPC_H3K9me3_Rep3_peaks.narrowPeak.gz |
199.5 Kb |
(ftp)(http) |
NARROWPEAK |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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