NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM8057838 Query DataSets for GSM8057838
Status Public on Mar 12, 2024
Title Mouse cells, WT, replicate 2, Ser5P CTD
Sample type SRA
 
Source name n/a
Organism Mus musculus
Characteristics cell line: n/a
cell type: lineage -ve marrow cells
genotype: WT
Treatment protocol Modified allele expression induced with doxycycline (1ug/ml) and maintained for 4 days
Growth protocol K562 cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.
Extracted molecule genomic DNA
Extraction protocol Formaldehyde was directly added to the media to a final concentration of 1% and 10 million cells were incubated for 15 min. Glycine was added to quench the reaction for 5 min. Cells were spun down and pellet was washed twice with PBS . The cell pellet was lysed on ice in cell lysis buffer, pelleted and resuspended in MNase digestion buffer containing MNase, followed by nuclear lysis in nuclear lysis buffer. Sonication was performed with a sonic Dismembranator.100 μg of chromatin was used for each IP. Either pan-Pol2 CTD, Ser5P CTD, or Ser2P CTD antibodies was mixed with diluted chromatin and subjected to IP performed on a rotating wheel at 4°C overnight. Pierce Protein A/G Magnetic beads were added to the chromatin-antibody mixture and 4°C rotation continued for 3 more hours. Beads were washed with wash buffers. Immuno-bound chromatin was eluted at 55°C for 1 hour with elution buffer and de-crosslinked overnight at 65°C. DNA was extracted with phenol:chloroform:isoamyl alcohol and precipitated for 60 min at −20°C with sodium acetate and ethanol. Pellet was washed with 70% ethanol and resuspended in TE buffer. DNA quality and size distribution were checked on Fragment Analyzer.
10 ng of DNA was used for library preparation according to NEBNext® Ultra II DNA Library Prep Kit. Purity and size distribution of the libraries were estimated using Fragment Analyzer.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2500
 
Data processing Sequence reads were trimmed for adaptors with Cutadaptv4.1
Trimmed sequence reads were mapped to hg38 using Bowtie2 aligners
The respective IP and Input BAM files were compared to each other while being simultaneously normalized for sequencing depth (using RPKM), and reformatting to the bigWig file format using deepTools BamCompare program.
Assembly: hg38
Supplementary files format and content: bigWig
 
Submission date Jan 31, 2024
Last update date Mar 12, 2024
Contact name MANOJ PILLAI
E-mail(s) MANOJ.PILLAI@YALE.EDU
Organization name YALE UNIVERSITY
Lab PILLAI LAB
Street address 300 GEORGE STREET #786
City NEW HAVEN
State/province CT
ZIP/Postal code 06511
Country USA
 
Platform ID GPL17021
Series (2)
GSE226003 Disruption of RNAPII transcription elongation links Oncogenic splicing factor mutations to replciation stress and targetable alterations in chromatin landscape.
GSE254792 Disruption of RNAPII transcription elongation links Oncogenic splicing factor mutations to replciation stress and targetable alterations in chromatin landscape [Murine ChIP-Seq]
Relations
BioSample SAMN39710325
SRA SRX23484912

Supplementary file Size Download File type/resource
GSM8057838_Ser5PPol2CTDChIPseq_murine_WT_IP_replicate2.bw 220.8 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