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| Status |
Public on Sep 29, 2023 |
| Title |
MCP IgG 1 |
| Sample type |
SRA |
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| Source name |
Myf6-Cre;Cdkn2a(Flox/Flox);Pax(3P3F/P3F);R26-tdTom (MCP)
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| Organism |
Mus musculus |
| Characteristics |
cell type: Myf6-Cre;Cdkn2a(Flox/Flox);Pax(3P3F/P3F);R26-tdTom (MCP)
antibody: IgG (NB810-56910, Novus)
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Tumors were manually dissociated and then digested for 1 hour at 37°C in 2 U/mL Collagenase B (#11088831001, Roche)/Dispase II (#04942078001, Roche), 50 mM HEPES/KOH pH 7.4; 150 mM NaCl. Cells were then spun down and resuspended in 2X volume 10% fetal bovine serum (FBS) (#SH30910.03, GE Hyclone) in phosphate buffered saline (PBS) to inactive digestion enzymes, samples were sequentially filtered through 70 μm (#22363548, Fisher) and 40 μm (#22363547, Fisher) filters to yield single cell suspensions. Data was acquired on a FACS Aria Cellsorter (BD Biosciences) and analyzed using FACSDiva software. DAPI used as a live/dead cell marker.
CUT&RUN libraries were prepared using the xGen ssDNA & Low-Input DNA Library Prep Kit (#10009859, IDT)
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
MCP IgG_2 - 2376821
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| Data processing |
CUT&RUN libraries were sequenced on NovaSeq6000 sequencer and generated 50 bp paired-end reads
The reads were aligned to mouse mm10 genome reference and fruit fly dm6 genome reference by BWA (version 0.7.170.7.12, default parameter). Duplicated reads were marked by the bamsormadup from the biobambam tool (version 2.0.87) available at https://www.sanger.ac.uk/tool/biobambam/. Uniquely mapped reads were kept by samtools (parameter “-q 1 -F 1804,” version 1.14). Fragments < 2000 bp were kept for peak calling and bigwig files were generated for visualization.
macs2 (PMID: 18798982) was used for peak calling
Assembly: mm10
Supplementary files format and content: narrowPeak,bw
Library strategy: CUT&RUN
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| Submission date |
Nov 17, 2022 |
| Last update date |
Sep 29, 2023 |
| Contact name |
Hongjian Jin |
| E-mail(s) |
hongjian.jin@STJUDE.ORG
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| Organization name |
St Jude Children's Research Hospital
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| Department |
Center for Applied Bioinformatics
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| Street address |
262 Danny Thomas Place
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| City |
Memphis |
| State/province |
TN |
| ZIP/Postal code |
38015 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE218265 |
PAX3-FOXO1 expression in endothelial progenitors dictates myogenic reprogramming and rhabdomyosarcoma identity[Cut&Run] |
| GSE218274 |
PAX3-FOXO1 expression in endothelial progenitors dictates myogenic reprogramming and rhabdomyosarcoma identity |
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| Relations |
| BioSample |
SAMN31776347 |
| SRA |
SRX18298893 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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