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| Status |
Public on Mar 26, 2024 |
| Title |
HFSCs, CNR IgG |
| Sample type |
SRA |
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| Source name |
Telogen (P55) skin mouse 1
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| Organism |
Mus musculus |
| Characteristics |
tissue: Telogen (P55) skin mouse 1
cell type: Hair follicle stem cells
genotype: wild-type
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
To resuspend HFSCs, 3D cultures were washed with sterile PBS, dissociated into single cell suspensions using TrpLE-Express (Gibco) for 15min at 37°C. After filtering, cells were pelleted and CNR was performed as previously described in Skene et al., 2018 with minor modifications. Briefly, cells were crosslinked with 1% formaldehyde and quenched with glycine. After washes, nuclei were incubated with concanavalin-A beads, followed by antibody incubation overnight. ConA-bead-bound nuclei were incubated with MNase to cut DNA and the fragments were relaesed by CaCl2 addition.
Sequencing libraries were generated using NEBNext Ultra II DNA Library Prep Kit for Illumina and NEBNext Multiplex Oligos for Illumina. PCR-amplified libraries were purified using 1× ratio of SPRI beads (Beckman) and eluted in 15 μl EB buffer (Qiagen).
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
CNR IgG
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| Data processing |
Reads were trimmed with Skewer, aligned to reference genome (mm10) using Bowtie (v.1.1.2), deduplicated with Java (v.2.3.0) Picard tools, and filtered to ≤120 bp using Samtools (v.1.3.1). BAM files for each replicate were combined using Samtools. Bigwig files were generated using Deeptools (v.3.1.2) with reads per kilobase of transcript per million mapped reads (RPKM) normalization and presented with Integrative Genomics Viewer (IGV) software. CNR peaks were called using SEACR (91) from bedGraph files generated from RPKM-normalized Bigwig files (UCSC Tools) using stringent setting and a numeric threshold of 0.001.
Assembly: mm10
Supplementary files format and content: BIGWIG file generated from combined bamfiles and peak files called from replicate pooled samples in bed format.
Library strategy: CUT&Run
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| Submission date |
Feb 29, 2024 |
| Last update date |
Mar 26, 2024 |
| Contact name |
Matthew T Tierney |
| E-mail(s) |
[email protected]
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| Phone |
5857974876
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| Organization name |
Rockefeller University
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| Street address |
1230 York Ave, Box 300
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| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
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| Platform ID |
GPL19057 |
| Series (1) |
| GSE231731 |
Retinoic acid promotes tissue regeneration by resolving stem cell lineage plasticity |
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| Relations |
| BioSample |
SAMN40207207 |
| SRA |
SRX23799846 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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