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| Status |
Public on Jul 26, 2024 |
| Title |
UiPSM Day9 ATAC |
| Sample type |
SRA |
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| Source name |
UiPSM Day9
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| Organism |
Homo sapiens |
| Characteristics |
cell type: UiPSM Day9
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| Treatment protocol |
A total of 50,000 cells cleaned up with ice-cold DPBS for 5 minutes and centrifuged at 500g for 5 minutes in 4℃.
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| Growth protocol |
Specific culture media for each cell type
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
The precipitation were lysed within 50 µL lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.2% (v/v) IGEPAL CA-630) and centrifuged at 500 g for 5 min at 4℃, then fragmentated with 50µL transposition reaction mix of TruePrep DNA Library Prep Kit V2 for Illumina® (TD501, Vazyme) under an 37℃ incubation condition for 30min, purified using a MinElute Kit (QIAGEN).
The fragmented genome suspension was amplificated 8-13 cycles with 50µL amplification mix of TruePrep DNA Library Prep Kit V2 for Illumina® (TD501, Vazyme), and purified using a MinElute Kit (QIAGEN).amplification mix of TruePrep DNA Library Prep Kit V2 for Illumina® (TD501, Vazyme), and purified using a MinElute Kit (QIAGEN).
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
bcl2fastq conversion software v2.17 used for basecalling.
Raw reads were trimmed with TrimGalore (v.0.6.4)
The data was mapped to human genome hg38 using bowtie22.
Low quality reads were filtered by SAMtools. Unique reads mapping to a single genomic location and strand were remained. Mitochondrial sequences were removed using “grep –v ‘chrM’”.
Genome_build: hg38
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| Submission date |
Oct 27, 2021 |
| Last update date |
Jul 26, 2024 |
| Contact name |
Xingnan Huang |
| E-mail(s) |
huangxingnan1994@gmail.com
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| Organization name |
Westlake University
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| Street address |
No.18 Shilongshan Road
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| City |
Hangzhou |
| ZIP/Postal code |
310024 |
| Country |
China |
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| Platform ID |
GPL24676 |
| Series (2) |
| GSE185137 |
Self-Renewing Presomitic Mesoderm Progenitor Lines Reprogrammed from human urine cells |
| GSE186671 |
Self-Renewing Presomitic Mesoderm Progenitor Lines Reprogrammed from human urine cells [Reprogramming ATAC-seq] |
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| Relations |
| BioSample |
SAMN22601095 |
| SRA |
SRX12798122 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5658823_UiMPC-4-d9_L4_801F0000256.sorted.multi.rmdup.bw |
281.8 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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