organism: Homo sapiens
description: 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.
attributes.tag: ENA-FIRST-PUBLIC
attributes.value: 2022-12-31
attributes.tag: ENA-LAST-UPDATE
attributes.value: 2022-12-31
attributes.tag: External Id
attributes.value: SAMEA111348588
attributes.tag: INSDC center alias
attributes.value: St. John's Medical College Hospital
attributes.tag: INSDC center name
attributes.value: St. John's Medical College Hospital
attributes.tag: INSDC first public
attributes.value: 2022-12-31T00:58:37Z
attributes.tag: INSDC last update
attributes.value: 2022-12-31T00:58:37Z
attributes.tag: INSDC status
attributes.value: public
attributes.tag: Submitter Id
attributes.value: E-MTAB-12164:RhoC pull down 1
attributes.tag: broker name
attributes.value: ArrayExpress
attributes.tag: cell_line
attributes.value: SiHa
attributes.tag: common name
attributes.value: human
attributes.tag: developmental stage
attributes.value: adult
attributes.tag: disease
attributes.value: squamous cell carcinoma
attributes.tag: genotype
attributes.value: RhoC overexpression
attributes.tag: isolate
attributes.value: not applicable
attributes.tag: organism part
attributes.value: uterine cervix
attributes.tag: sample name
attributes.value: E-MTAB-12164:RhoC pull down 1