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Sample GSM3597743 Query DataSets for GSM3597743
Status Public on Jul 26, 2019
Title Foxa2.d4.FVFp.r1
Sample type SRA
Source name ES cells
Organism Mus musculus
Characteristics cell line: doxycycline (Dox) inducible Foxa2-Venus ES cell line (T128)
genotype: TetON-Foxa2-Venus
facs sorting markers: Venus-positive
chip antibody: anti-Foxa2 (SantaCruz; sc6554x)
Extracted molecule genomic DNA
Extraction protocol 1-2 million FACS-sorted cross-linked cells (1% formaldehyde, 10min RT) were lysed in 100 ul Buffer-B-0.3 (50 mM Tris-HCl, pH 8.0, 10 mM EDTA, 0,3%SDS, 1x protease inhibitors -Roche) and sonicated in a microtube (Covaris; 520045) using a Covaris S220 device until most of the DNA fragments were 200-500 base pairs long (settings: temperature 4°C, duty cycle 2%, peak incident power 105 Watts, cycles per burst 200). After shearing, lysates were centrifuged 10min, 4°C, 12000g and supernatant diluted with 1 volume of Dilution Buffer (1mM EGTA 300 mM NaCl, 2% Triton x-100, 0.2% sodium deoxycholate, 1x protease inhibitors-Roche). Sonicated chromatin was then incubated 4h at 4°C on a rotating wheel with 6 ug of antibody conjugated to 20 µl of magnetic beads  (Dynabeads, Life Technology). Beads were washed four times with Buffer-A (10 mM Tris-HCl, pH 7.5, 1 mM EDTA, 0.5 mM EGTA,1% Triton X-100, 0.1% SDS, 0.1% Na-deoxycholate, 140 mM NaCl, 1x protease inhibitors) and once with Buffer-C (10 mM Tris-HCl, pH 8.0, 10 mM EDTA). Beads were then incubated with 70 μl elution buffer (0.5% SDS, 300 mM NaCl, 5 mM EDTA, 10 mM Tris HCl pH 8.0) containing 2 μl of Proteinase K (20mg/ml) for 1 hour at 55°C and 8 hours at 65°C to revert formaldehyde crosslinking, and supernatant was transferred to a new tube. Another 30 μl of elution buffer was added to the beads for 1 minute and eluates were combined and incubated with another 1 μl of Proteinase K for 1 hour at 55°C. Finally, DNA was purified with SPRI AMPure XP beads (Beckman Coulter) (sample-to-beads ratio 1:2). Purified DNA was used as input for library preparation.
MicroPlex Library Preparation Kit v2 (Diagenode, cat. C05010012)
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 1500
Description ES cells were seeded without feedeers in gelatin-coated plates and grown for 96h in ES standard medium (LIF/serum) supplemented wiht 40ng/ml doxycycline.
Data processing reads were mapped to the mouse genome (mm10) using bowtie (Langmead et al., 2009)
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files were generated from Homer tag directories using
Submission date Feb 11, 2019
Last update date Sep 02, 2019
Contact name Filippo M. Cernilogar
Organization name LMU Munich
Department Biomedical Center
Street address Grosshaderner Strasse 9
City Planegg-Martinsried
ZIP/Postal code 82152
Country Germany
Platform ID GPL18480
Series (2)
GSE116258 Pre-marked chromatin and transcription factor co-binding shape the pioneering activity of Foxa2 [ChIP-seq Transcription Factors]
GSE116262 Pre-marked chromatin and transcription factor co-binding shape the pioneering activity of Foxa2
BioSample SAMN10910720
SRA SRX5360107

Supplementary file Size Download File type/resource
GSM3597743_Foxa2.d4.FVFp.r1_m1.ucsc.bigWig 114.5 Mb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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