| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| PE mouse anti-human CD117 | BD Biosciences | Cat# 555714; RRID:AB_396058, clone YB5.B8 |
| Critical commercial assays | ||
| SMARTer Stranded Total RNA-Seq Kit | Takara Bio | Cat# 634412 |
| MethylCode Bisulfite Conversion Kit | ThermoFisher | MECOV-50 |
| EpiArt DNA Methylation Library Kit for Illumina V3 | Vazyme | NE103 |
| Deposited data | ||
| RNA-seq data | This paper | GSA: HRA005278 |
| WGBS-seq data | This paper | GSA: HRA005277 |
| Software and algorithms | ||
| FastQC (v0.11.8) | Babraham Institute | https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ |
| Cutadapt (v2.5) | Martin42 | http://cutadapt.readthedocs.io/en/stable/ |
| Hisat2 (v2.1.0) | Pertea et al.43 | http://ccb.jhu.edu/software/hisat2 |
| SAMtools (v1.9) | Li et al.44 | http://www.htslib.org/ |
| featureCounts (v2.0.1) | Liao et al.45 | http://subread.sourceforge.net/ |
| Homer (v4.11) | Heinz et al.46 | http://homer.ucsd.edu/homer/index.html |
| Bismark (v0.22.1) | Krueger and Andrews47 | https://www.bioinformatics.babraham.ac.uk/projects/bismark/ |
| Bedtools (v2.28.0) | Quinlan and Hall48 | http://bedtools.readthedocs.io/en/latest/ |
| IGV (v2.16.0) | Broad Institute | http://software.broadinstitute.org/software/igv/ |
| R (v4.2.3) | R Core Team | https://www.r-project.org/ |
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