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Sample GSM6341916 Query DataSets for GSM6341916
Status Public on May 24, 2024
Title Metastatic mouse UPS cell lacking Setd1a, H3K4Me3, rep1
Sample type SRA
 
Source name Mouse Setd1a KO UPS cell
Organism Mus musculus
Characteristics cell line: Mouse Setd1a KO UPS cell
cell type: sarcoma
chip antibody: H3K4Me3(CST)
Growth protocol DMEM, 10% fetal bovine serum, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.
Extracted molecule genomic DNA
Extraction protocol Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris).
ChIP-seq libraries were prepared using the SimpleChIP Plus Sonication Chromatin IP kit (CST). 10 ug of DNA was used as starting material for input and ip samples. Libraries were amplified using 10 cycles on the thermocycler. Libraries were validated using the Agilent High Sensitivity DNA Kit and 2% Agarose gel
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NovaSeq 6000
 
Data processing ChIP-seq reads were trimmed using TrimGalore (v 0.6.6) and then aligned to GRCm38/mm10 reference genome by bwa (v 0.7.17-r1188).
Unmapped reads reads aligned to multiple locations were removed using samtools (v 1.11).
Duplicated reads were marked by picard (v 2.26.0).
The genomic coverage was saved in bigwig format and normalized by CPM method by bedTools (v 2.29.2) and UCSC Utilities bedGraphToBigWig (v 377).
Assembly: GRCm38/mm10
Supplementary files format and content: bigWig normalized by total reads
 
Submission date Jul 18, 2022
Last update date May 24, 2024
Contact name jianhong ou
E-mail(s) jianhong.ou@duke.edu
Phone 5084102796
Organization name Duke University
Department Cell Biology
Lab Regeneromics
Street address 465 Nanaline Duke Building, Duke University Medical Center
City Durham
State/province North Carolina
ZIP/Postal code 27710
Country USA
 
Platform ID GPL24247
Series (2)
GSE208365 Identify H3K4Me3 occupancy on genome in Setd1a Knock out (KO) mouse undifferentiated pleomorphic sarcoma cells
GSE208367 COMPASS complex inhibition targets the metastasis initiating cell in undifferentiated pleomorphic sarcoma
Relations
BioSample SAMN29794403
SRA SRX16314658

Supplementary file Size Download File type/resource
GSM6341916_Setd1a-H3K4Me3_R1.mLb.clN.bigWig 189.5 Mb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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