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Sample GSM958754 Query DataSets for GSM958754
Status Public on Mar 31, 2013
Title FoxA1 ChIP-seq in Asynchronous Cells 3
Sample type SRA
Source name HuH7 cells, asynchronously cycling
Organism Homo sapiens
Characteristics cell type: HuH7
cycling state: asynchronous
antibody: FoxA1
vendor/catalog/lot: Abcam ab23738 (lot #737921)
Treatment protocol Cells were blocked in S phase by addition of fresh medium containing 2 mM thymidine (Sigma; St. Louis, MO; T1895). After 24 hours, cells were washed three times with PBS and released into medium containing 0.06 µg/mL nocodazole (Sigma; M1404). After 18 h, about 94% of the cells were blocked in metaphase (Fig. S5a) and used for imaging or ChIP. For mitotic block-release studies, arrested cells were either: 1) harvested by gentle shaking and replated into fresh medium, or 2) washed 3 times with PBS (2 minutes incubation at room temperature per wash) and fresh medium was added to the cells.
Growth protocol HuH7 cells were plated in fresh DMEM High Glucose with L-glutamine (Invitrogen; Carlsbad, CA; 11965) containing 10% FBS (HyClone, Logan, UT) and 1% penicillin-streptomycin (Invitrogen) and grown overnight to 75% confluence.
Extracted molecule genomic DNA
Extraction protocol Triplicate immunoprecipitation samples were adjusted to 335 µg and then divided into two aliquots. The incubation with FoxA1 antibodies were performed with 18 µg. ChIP products were used to generate libraries using a ChIP-Seq sample preparation kit (illumina IP-102-1001, San Diego CA). Amplicons between 100 and 200 bp were validated on a Bioanalyzer (Agilent Technologies 2100, Santa Clara CA) before being used for sequencing on an Illumina Sequencer.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer IIx
Description DNA immunoprecipitated by FoxA1
Data processing ELAND was used to perform base-calls (default parameters)
Quality control and alignment was performed using ELAND (default parameters)
MACS was used to detect peaks in FoxA1 binding (MFOLD=16, FDR=0.05 for mitotic and 0.0005 for asynchronous cells after pooling replicates
Track views were generated by pooling replicates, then binning all aligned tags into 25bp bins and normalizing by the total number of bases sequenced, then subtracting input
Genome_build: hg18 (NCBI 36)
Supplementary_files_format_and_content: BED6 files are included for called peaks
Submission date Jul 10, 2012
Last update date May 15, 2019
Contact name Kenneth S. Zaret
Phone 2155735813
Organization name University of Pennsylvania School of Medicine
Department Cell and Developmental Biology
Lab Zaret lab
Street address 9-132, SCTR, 3400 Civic Center Boulevard
City Philadelphia
State/province PA
ZIP/Postal code 19104-5157
Country USA
Platform ID GPL10999
Series (2)
GSE39241 FoxA1 binding in asynchronous and mitotic HUH7 cells
GSE39243 Expression and FoxA1 binding in asynchronous and mitotic HUH7 cells
SRA SRX159091
BioSample SAMN01086976

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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