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| Status |
Public on May 08, 2024 |
| Title |
IPSCs, control, CUT&Tag, rep01 |
| Sample type |
SRA |
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| Source name |
Peripheral blood
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Peripheral blood
cell line: IPSCs
cell type: IPSCs
genotype: Normal
treatment: H3K27ac antibody (Active motif, #39133)
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells was rinsed with PBS and dissociated with 0.5mM EDTA.
Resuspended cells were attached to Concanavalin A beads (Bangs Laboratories, IN, USA) and then were incubated with primary antibody against H3K27ac (Active motif, CA, USA). After washed, cells were incubated with pA-Tn5 (Vazyme, China). After quenching the fragmentation, the cells were added with proteinase K. Post-incubation, a phenol–chloroform–isoamyl alcohol mix wasused to extract DNA. The samples were incubated at -80°C freezer and subsequently centrifuged. The pellet was air dried and resuspended in a desired amount of EB buffer. DNA concentration was estimated using the Qubit. PCR amplification was performed using universal N5 primer and indexed N7 primer and PCR cycle number was optimized. Amplified products were purified using 1: 1.3X Ampure bead.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Cut&Tag data were aligned to the human reference genome (hg38) using 'bwa mem' of BWA (v0.7.15) with default parameters.
Reads with low mapping quality (MAPQ<20) reads were filtered out using ‘samtools view’ function of samtools (v1.3.1).
PCR duplicates were removed using ‘MarkDuplicates’ function of Picard.
H3K27ac modification peaks were identified using 'macs2 callpeak' function of MACS2 (v2.2.7.1) with default parameters.
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak
Library strategy: CUT&Tag
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| Submission date |
May 03, 2024 |
| Last update date |
May 08, 2024 |
| Contact name |
Qingjiong Zhang |
| E-mail(s) |
zhangqji@mail.sysu.edu.cn
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| Phone |
13609718372
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| Organization name |
Zhongshan Ophthalmic Center
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| Street address |
Sun Yat-sen University
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| City |
Guangzhou |
| State/province |
Guangdong |
| ZIP/Postal code |
510060 |
| Country |
China |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE266513 |
Altered chromatin topologies caused by balanced chromosomal translocation lead to central iris hypoplasia [Cut & Tag] |
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| Relations |
| BioSample |
SAMN41200289 |
| SRA |
SRX24452010 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8248704_IPSCcontrol_CutTag_H3K27ac_B1.merge.rpkm.bw |
119.7 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
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