characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2022-12-31T00:58:37Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2022-12-31T00:58:37Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA111348591
characteristics.characteristic: External Id
characteristics.text: St. John's Medical College Hospital
characteristics.characteristic: INSDC center name
characteristics.text: 2022-12-31T00:58:37Z
characteristics.characteristic: INSDC first public
characteristics.text: 2022-12-31T00:58:37Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS13446138
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-12164:WDR5 pull down 2
characteristics.characteristic: Submitter Id
characteristics.text: ArrayExpress
characteristics.characteristic: broker name
characteristics.text: SiHa
characteristics.characteristic: cell_line
characteristics.text: human
characteristics.characteristic: common name
characteristics.text: Protocols: Sample used was SiHa cells. The cells were grown in a CO2 incubator in DMEM supplemented with 10%FBS. ChIP was performed using the Simple ChIP Enzymatic Chromatin IP Kit (CST 9003S) as per the manufacturer’s protocol. Briefly, proteins were crosslinked to the DNA by adding PFA to the media at a final concentration of 4% (w/v). Excess PFA was quenched using glycine. The media was removed and the cells were washed twice with cold 1XPBS and collected in 2ml of ice cold 1XPBS by scraping. The DNA from these cells was fragmented using both micrococcal nuclease and sonication. The cross-linked chromatin samples were treated with RNase A and DNA was purified using the column method. The DNA was then quantified and equal amounts of DNA was incubated with magnetic beads and the desired antibody overnight at 4°C. The beads were then washed thrice with high salt buffer and the DNA bound to the beads was collected using elution buffer and the cross-links reversed using sodium chloride and proteinase K. The pulled-down DNA was again purified using the column method and quantified using the DNA Qubit High sensitivity assay kit (Life technologies, Invitrogen). Libraries were prepared using NEB Next Ultra II DNA Library preparation kit. In brief, ChIP DNA was subjected to various enzymatic steps for repairing the ends and attaching the dA-tail, followed by ligation of adapter sequences. These adapter ligated fragments were then size selected using SPRI beads. Next, the size selected fragments were indexed during limited cycle PCR to generate final libraries for paired-end sequencing.
characteristics.characteristic: description
characteristics.text: adult
characteristics.characteristic: developmental stage
characteristics.text: squamous cell carcinoma
characteristics.characteristic: disease
characteristics.text: RhoC overexpression
characteristics.characteristic: genotype
characteristics.text: Homo sapiens
characteristics.characteristic: organism
characteristics.text: Homo sapiens
characteristics.characteristic: organism
characteristics.text: uterine cervix
characteristics.characteristic: organism part
characteristics.text: Homo sapiens
characteristics.characteristic: scientific_name
characteristics.text: WDR5 pull down 2
characteristics.characteristic: title