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| Status |
Public on Jul 09, 2021 |
| Title |
Pten KO Cardiomyocyte (Sample_K1) |
| Sample type |
SRA |
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| Source name |
cardiomyocytes
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| Organism |
Mus musculus |
| Characteristics |
cell type: ES-derived cardiomyocytes
strain: cell line
genotype: Pten-/-
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| Treatment protocol |
The Pten-/- ESCs were generated by the CRISPR-Cas9 system. ESCs were cultured in 6-well plates and transfected with donor plasmid and constructs containing Cas9 and target sequences using lipofectamine 3000, and these were then subjected to cell sorting of GFP-positive cells after transfection for 48 h. The enriched gene-modified cell populations were cultured in 60-mm dishes for 4-5 days, and each cell clone was passaged into 24-well plates. Finally, the Pten-/- cell lines were identified by sequencing, and the cells were stored in liquid nitrogen.
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| Growth protocol |
ESCs were cultured in ESC culture medium withdraw of 2iL (2i, PD0325901 and CHIR99021; L, LIF) to form EBs for 5 days. EBs were formed using the hanging drop method with 250 cells/drop in DMEM/F12 media containing GlutaMAX and sodium pyruvate with 15% fetal bovine serum, nonessential amino acid solution, and b-mercaptoethanol. Then EBs were collected and transferred to petri dishes with NM medium containing DMEM/F12 (Life Technologies, 10565), nonessential amino acid solution (Life Technologies, 11140), Heparin (Sigma, H3149), and N2 (Life Technologies, 17502). After 2 days suspension culture in NM medium, EBs could be collected and transferred to tissue culture plate with NM medium. At about 9 days, the beating cardiomyocytes will be generated and could be collected to perform the downstream experiments.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA from WT and Pten-/- embryoid bodies and cardiomyocytes were extracted by the genomic DNA extraction Kit.
The DNA was fragmented by sonication using a Bioruptor (Diagenode, Belgium) to a mean size of approximately 250 bp, followed by the blunt-ending, dA addition to 3'-end, finally, adaptor ligation (in this case of methylated adaptors to protect from bisulfite conversion), essentially according to the manufacturer’s instructions. Ligated DNA was bisulfite converted using the EZ DNA Methylation-Gold kit (ZYMO). Different Insert size fragments were excised from the same lane of a 2% TAE agarose gel. Products were purified by using QIAquick Gel Extraction kit (Qiagen) and amplified by PCR. At last, Sequencing was performed using the DNBseq platforms.
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
BGISEQ-500 |
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| Description |
Whole-Genome Bisulfite Seq
MGI2000- PE100
DMR_info.tar.gz
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| Data processing |
The raw data was filtered first to remove those low-quality data and get clean data.
The clean data was mapped to the reference genome when we made sure the data quantity of clean data was sufficient. Meanwhile, we needed to make a quality test about the alignment.
We used those mapped data to get methylation information of the cytosine through the whole genome after we made sure that the alignment result was qualified.
We used the cytosine information for standard bioinformatics analysis and personalized bioinformatics analysis.
Genome_build: NA
Supplementary_files_format_and_content: Count format and DMR format.
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| Submission date |
Oct 27, 2020 |
| Last update date |
Jul 09, 2021 |
| Contact name |
Gang Lu |
| E-mail(s) |
[email protected]
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| Organization name |
The Chinese University of Hong Kong
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| Street address |
Sha Tin
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| City |
Hong Kong |
| ZIP/Postal code |
852 |
| Country |
China |
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| Platform ID |
GPL23479 |
| Series (2) |
| GSE160236 |
Whole-genome bisulfite sequencing analysis of Pten's function in regulating cardiomyocyte differentiation |
| GSE160237 |
Pten's function in regulating cardiomyocyte differentiation |
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| Relations |
| BioSample |
SAMN16575552 |
| SRA |
SRX9379285 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4869590_Sample_K1_Control.cout.txt.gz |
259.0 Kb |
(ftp)(http) |
TXT |
| GSM4869590_Sample_K1_chr1.cout.txt.gz |
544.2 Mb |
(ftp)(http) |
TXT |
| GSM4869590_Sample_K1_chr10.cout.txt.gz |
359.1 Mb |
(ftp)(http) |
TXT |
| GSM4869590_Sample_K1_chr11.cout.txt.gz |
357.4 Mb |
(ftp)(http) |
TXT |
| GSM4869590_Sample_K1_chr12.cout.txt.gz |
329.8 Mb |
(ftp)(http) |
TXT |
| GSM4869590_Sample_K1_chr13.cout.txt.gz |
331.5 Mb |
(ftp)(http) |
TXT |
| GSM4869590_Sample_K1_chr14.cout.txt.gz |
334.3 Mb |
(ftp)(http) |
TXT |
| GSM4869590_Sample_K1_chr15.cout.txt.gz |
285.7 Mb |
(ftp)(http) |
TXT |
| GSM4869590_Sample_K1_chr16.cout.txt.gz |
262.7 Mb |
(ftp)(http) |
TXT |
| GSM4869590_Sample_K1_chr17.cout.txt.gz |
266.1 Mb |
(ftp)(http) |
TXT |
| GSM4869590_Sample_K1_chr18.cout.txt.gz |
245.7 Mb |
(ftp)(http) |
TXT |
| GSM4869590_Sample_K1_chr19.cout.txt.gz |
170.2 Mb |
(ftp)(http) |
TXT |
| GSM4869590_Sample_K1_chr2.cout.txt.gz |
506.7 Mb |
(ftp)(http) |
TXT |
| GSM4869590_Sample_K1_chr3.cout.txt.gz |
424.5 Mb |
(ftp)(http) |
TXT |
| GSM4869590_Sample_K1_chr4.cout.txt.gz |
431.9 Mb |
(ftp)(http) |
TXT |
| GSM4869590_Sample_K1_chr5.cout.txt.gz |
424.8 Mb |
(ftp)(http) |
TXT |
| GSM4869590_Sample_K1_chr6.cout.txt.gz |
437.0 Mb |
(ftp)(http) |
TXT |
| GSM4869590_Sample_K1_chr7.cout.txt.gz |
406.6 Mb |
(ftp)(http) |
TXT |
| GSM4869590_Sample_K1_chr8.cout.txt.gz |
359.3 Mb |
(ftp)(http) |
TXT |
| GSM4869590_Sample_K1_chr9.cout.txt.gz |
351.4 Mb |
(ftp)(http) |
TXT |
| GSM4869590_Sample_K1_chrM.cout.txt.gz |
90.4 Kb |
(ftp)(http) |
TXT |
| GSM4869590_Sample_K1_chrX.cout.txt.gz |
381.7 Mb |
(ftp)(http) |
TXT |
| GSM4869590_Sample_K1_chrY.cout.txt.gz |
179.5 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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