NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM8002635 Query DataSets for GSM8002635
Status Public on Mar 13, 2024
Title clone4_k9me3_R2 (Cut&Run)
Sample type SRA
 
Source name UPS (3672-3)
Organism Homo sapiens
Characteristics cell line: UPS (3672-3)
cell type: undifferentiated pleomorphic sarcoma cell line
genotype: Atrx knockout
chip antibody: H3K9me3 (Abcam,8898)
Extracted molecule genomic DNA
Extraction protocol Cells were collected by trypsin. Washed by PBS and followed the protocol from EpiCypher.
Libraries were generated using NEBNext Ultra II kits.
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina NextSeq 500
 
Data processing Cut and run reads were aligned using Rsubread’s align method and predicted fragment lengths were calculated by the ChIPQC R Bioconductor package. Normalized, fragment extended signal bigWigs were created using the rtracklayer R Bioconductor package. Peak calls were made using the SEACR software.
Assembly: hg38
Supplementary files format and content: bigwig files normalized to read depth
Supplementary files format and content: bed files generated by SEACR
Library strategy: CUT&RUN
 
Submission date Jan 04, 2024
Last update date Mar 13, 2024
Contact name Douglas Barrows
E-mail(s) dbarrows@rockefeller.edu
Phone 7749940981
Organization name Rockefeller University
Street address 1230 York Ave
City New York
State/province NY
ZIP/Postal code 10065
Country USA
 
Platform ID GPL18573
Series (2)
GSE240030 ATRX guards against aberrant differentiation in mesenchymal progenitor cells
GSE252531 ATRX guards against aberrant differentiation in mesenchymal progenitor cells [CUT&RUN]
Relations
BioSample SAMN39255913
SRA SRX23095796

Supplementary file Size Download File type/resource
GSM8002635_Sorted_UPS_clone4_k9me3_R2Normalised.bw 193.1 Mb (ftp)(http) BW
GSM8002635_UPS_clone4_k9me3_R2_overIgG.relaxed.bed.gz 9.4 Mb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap