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| Status |
Public on May 01, 2023 |
| Title |
ATAC-WT2 |
| Sample type |
SRA |
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| Source name |
cardiac muscle
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| Organism |
Rattus norvegicus |
| Characteristics |
genotype: wild type
cell line: H9c2
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| Treatment protocol |
The day before transfection, cells (1.0×106 cells/well) were seeded in six-well plates and cultured overnight until almost 70–80% cell confluence. The pSpCas9(BB)-2A-Puro(PX459) plasmid vector (available from our lab) was constructed in the sgRNA (5’- caccgATTTCCTCGGCCTGTGACTG), and the pEGFP-N1 plasmid vector (available from our lab) was used as control plasmid. 2 µg plasmid was diluted in 80 µL Opti-MEM (Sigma, cat. no. 408727), 6 µL PEI (Polysciences, cat. no. 23966-1) was diluted in 80 µL Opti-MEM, the two were mixed and incubated at room temperature for 10 minutes. PEI/plasmid mixture was then added to single well of 6-well plate. After 12 h, green fluorescence was examined under a fluorescence microscope (Nikon Eclipse TSZR). Then, Puromycin (Yeasen Biotechnology, cat. no. 60210ES60) was used to screen and achieve the stable cell lines.
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| Growth protocol |
Rat cardiomyocytes H9c2 were purchased from American Type Culture Collection (ATCC, cat. no. CRL-1446), cultured in DMEM (Gibco, cat. no. C11995500BT) supplemented with 10% fetal bovine serum (Hyclone, cat. no. SV30208.02) and maintained in a humidified incubator (Thermo Scientific, cat. no. 3131) with 5% CO2 atmosphere at 37℃. The medium was changed every 2-3 days.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nuclei were isolated from cells for each replicate, followed by the transposition reaction in the presence of Tn5 transposase (Vazyme) for 45 minutes at 37°C.
ATAC-seq libraries were prepared following a published protocol (Liu et al. 2017). Nuclei were isolated, permeabilized, and tagmented using Tn5 transposase (Vazyme), reverse-crosslinked, and amplified using NEBNext High-Fidelity 2 x PCR Master Mix (NEB). Library preparation and sequencing were performed by HiSeq X Ten (paired-end 150bp reads) .
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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 |
All reads for each sample were combined and aligned to Rn6 with bowtie2. Peaks were called for each sample using MACS2. The peak annotation was assessed using the ‘ChIPseeker’ library from R/Bioconductor. Motif analysis on peak regions was performed by HOMER function. Heatmaps and profile plots were generated using DeepTools. Visualization of genome-wide read coverage was performed by converting raw bam files to bigwig files using IGV tools.
Assembly: Rn6
Supplementary files format and content: bigwig files
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| Submission date |
Aug 16, 2022 |
| Last update date |
May 02, 2023 |
| Contact name |
Xinrui Wang |
| E-mail(s) |
wanxiru@sjtu.edu.cn
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| Organization name |
Rui-Jin Hospital affiliated to Shanghai Jiao Tong University School of Medicine
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| Street address |
197 Ruijin Rd II
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| City |
Shanghai |
| ZIP/Postal code |
200025 |
| Country |
China |
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| Platform ID |
GPL24688 |
| Series (2) |
| GSE211403 |
Nono deficiency impedes the proliferation and adhesion of H9c2 cardiomyocytes through Pi3k/Akt signaling pathway [ATAC-seq] |
| GSE211404 |
Nono deficiency impedes the proliferation and adhesion of H9c2 cardiomyocytes through Pi3k/Akt signaling pathway |
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| Relations |
| BioSample |
SAMN30351292 |
| SRA |
SRX17106377 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6469543_ATAC-WT2.bw |
45.8 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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