NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM6890984 Query DataSets for GSM6890984
Status Public on Feb 24, 2023
Title mBD2(SKY)-PBRM1-H3K14Ac ChIP-seq- Replicate 2
Sample type SRA
 
Source name Renal cancer cell line
Organism Homo sapiens
Characteristics cell line: Caki2
genotype: Caki2 with mBD2(SKY)-PBRM1
antibody: H3K14Ac Ab (Millipore Sigma 07-353)
Treatment protocol Caki2 cell line transduced with lentiviral particles for either empty vector, wtPBRM1 or mBD2(SKY)-PBRM1 contsructs were treated with doxycycline for 6 days to induce protein expression
Growth protocol Caki2 renal cancer cell lines were grown under normal conditions: McCoy's 5A with 10% FBS
Extracted molecule genomic DNA
Extraction protocol Cells were fixed, washed, and lysed. The chromatin was sheared using a probe sonicator and protein/DNA complexes were isolated with antibody.
Libraries were constructed using OvationĀ® Ultralow V2 UDI DNA-Seq Library Preparation Kit from Tecan, according the manufacturer's instructions. Libraries were double size selected before sequencing
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NovaSeq 6000
 
Data processing Data quality control, trimming and filtering were performed with Partek Flow Software Tools
ChIP-seq reads were mapped to the human (hg38) genome with bowtie2
Aligned reads were converted to bigwig format using deeptools bamCoverage
Peaks were called using MACS
Spike-in normalization was performed as described in the manuscript
Assembly: Hg38
Supplementary files format and content: BigWig files are in an indexed binary format and contain genome-wide coverage information
 
Submission date Dec 22, 2022
Last update date Feb 24, 2023
Contact name Emily C. Dykhuizen
E-mail(s) edykhui@purdue.edu
Organization name Purdue University
Department Medicinal Chemistry and Molecular Pharmacology
Street address 201 S. University St.
City West Lafayette
State/province IN
ZIP/Postal code 47907
Country USA
 
Platform ID GPL24676
Series (2)
GSE221618 PBRM1 bromodomains associate with RNA to facilitate chromatin association (ChIP-seq)
GSE221620 PBRM1 bromodomains associate with RNA to facilitate chromatin association
Relations
BioSample SAMN32374684
SRA SRX18828526

Supplementary file Size Download File type/resource
GSM6890984_SYK_K14_2_CKDL220026704-1A_HFW3CDSX5_L2_filtered.bw 155.2 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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