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Sample GSM6738095 Query DataSets for GSM6738095
Status Public on Sep 29, 2023
Title MCP IgG 2
Sample type SRA
 
Source name Myf6-Cre;Cdkn2a(Flox/Flox);Pax(3P3F/P3F);R26-tdTom (MCP)
Organism Mus musculus
Characteristics cell type: Myf6-Cre;Cdkn2a(Flox/Flox);Pax(3P3F/P3F);R26-tdTom (MCP)
antibody: IgG (NB810-56910, Novus)
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)
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina NovaSeq 6000
 
Description MCP IgG_3 - 2379008
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
 
Submission date Nov 17, 2022
Last update date Sep 29, 2023
Contact name Hongjian Jin
E-mail(s) hongjian.jin@STJUDE.ORG
Organization name St Jude Children's Research Hospital
Department Center for Applied Bioinformatics
Street address 262 Danny Thomas Place
City Memphis
State/province TN
ZIP/Postal code 38015
Country USA
 
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
Relations
BioSample SAMN31776346
SRA SRX18298894

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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