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| Status |
Public on May 01, 2024 |
| Title |
hCNCC_IgG_rep2 |
| Sample type |
SRA |
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| Source name |
H9-derived cranial neural crest cells
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| Organism |
Homo sapiens |
| Characteristics |
cell line: H9-derived cranial neural crest cells
cell type: Stem cells
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
The CUT&RUN assay was conducted in hCNCCs using the ChIC/CUT&RUN Kit (EpiCypher, catalog no. 14-1048). Approximately 500,000 cells were harvested using Accutase and subsequently incubated with activated ConA Beads for 10 minutes at room temperature. Primary antibodies were then added to each 50 µL reaction: IgG (EpiCypher, 13-0042k, 0.5 µg), H3K27ac (Active Motif, 39133, 0.5 µg), TCF7L2 (Cell Signaling, 2569S, 1 µg), and the mixture was incubated overnight on a nutator at 4°C. On the second day, pAG-MNase and cold calcium chloride were used to activate the cleavage of target DNA. E. coli Spike-in DNA (0.1 ng) was also added for normalization in downstream analyses. DNA purification involved phenol/chloroform extraction and ethanol precipitation.
Library preparation for histone proteins was performed using the CUT&RUN Library Prep Kit (EpiCypher, 14-1001). For TFs, modified procedures, as previously reported (https:// doi.org/10.17504/protocols.io.bagaibse), were employed to enhance the preservation of small DNA fragments
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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&RUN sequencing data were analyzed employing the CUT&RUNTools 2.0 pipeline (https://github.com/fl-yu/CUT-RUNTools-2.0). For histone peak calling, the fragment size filter was deactivated, while for TFs, fragments larger than 120 bp were filtered out. Normalized bigwig files were generated using an alignment scale factor based on spike-in reads from E. coli K12 strain MG1655
Assembly: hg38/GRCh38
Supplementary files format and content: bigWig
Library strategy: CUT&RUN
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| Submission date |
Apr 02, 2024 |
| Last update date |
May 01, 2024 |
| Contact name |
Xu Xiaopeng |
| E-mail(s) |
xu_xiaopeng@gzlab.ac.cn
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| Organization name |
Guangzhou National Laboratory
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| Street address |
96 Xingdao South Road, Guangzhou International Bio Island, Haizhu District
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| City |
Guangzhou |
| ZIP/Postal code |
510320 |
| Country |
China |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE263084 |
Regulatory Functional Landscape of the HMX1 Gene for Normal Ear Development [CUT&RUN] |
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| Relations |
| BioSample |
SAMN40731349 |
| SRA |
SRX24137083 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8185634_hCNCC_IgG_rep2.spikein_normalized.bw |
68.5 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
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