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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Feb 29, 2024 |
| Title |
ckit+WT ms BM, IgG, replicate 1, CUT&RUN |
| Sample type |
SRA |
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| Source name |
HSPCs
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| Organism |
Mus musculus |
| Characteristics |
cell type: HSPCs
genotype: IgG antibody
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
CUT&RUN was performed according to Epicypher CUT&RUN Protocol V2.0. Briefly, 0.5 million ckit + HSPCs from WT BL6 mice or Ctnnb1-Biotin-3xFLAG knockin mice (JAX:029511) were rinsed with wash buffer (20 mM HEPES, pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, and 1× Complete Protease Inhibitor Cocktail) and incubated with the activated Concanavalin A (ConA) beads (Bangs Laboratories BP531) at RT for 10 min. 0.5 μl antibody (HOXA9 Atlas HPA061982, FLAG Genscript A00170, IgG Cell Signaling Technology 3900S DA1E) was added and incubated at 4 °C overnight. After permeabilization with digitonin buffer (wash buffer plus 0.01% digitonin), 20 ng pAG-MNase (kindly provided by Dr Paul Lavender, King’s College London) was added and bound to antibody-labelled chromatin. MNase was subsequently activated by addition of CaCl 2 to cleave and release antibody-bound chromatin. DNA purification was performed using Monarch PCR cleanup kit (NEB, Monarch PCR & DNA Cleanup Kit, T1030).
DNA libraries were prepared using the NEB Ultra II DNA Library Prep Kit (NEB #E7103) and sequencing was carried out by Novogene UK.
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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 analysis was conducted using the CUT&RUNTools pipeline with default parameters,including read trimming, alignment, and peak calling. Reads were aligned to the reference mouse genome GRCm38.
Peak calling was carried out utilizing MACS2 (IgG used as control), and the identified peaks were used to generate heatmaps and profile plots.
Assembly: mm10
Supplementary files format and content: narrowPeak
Library strategy: CUT&RUN
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| Submission date |
Dec 01, 2023 |
| Last update date |
Feb 29, 2024 |
| Contact name |
Eric So |
| E-mail(s) |
eric.so@kcl.ac.uk
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| Organization name |
KCL
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| Lab |
So Lab
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| Street address |
School of Cancer and Pharmaceutical Sciences
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| City |
London |
| ZIP/Postal code |
SE5 9NU |
| Country |
United Kingdom |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE235821 |
β-catenin and Hoxa9 preserve DNA replication dynamics, genomic integrity and stem cell functionality in a Prmt1-dependent manner |
| GSE249199 |
β-catenin and Hoxa9 preserve DNA replication dynamics, genomic integrity and stem cell functionality in a Prmt1-dependent manner [CUT&RUN] |
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| Relations |
| BioSample |
SAMN38580601 |
| SRA |
SRX22715796 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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