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Sample GSM3495116 Query DataSets for GSM3495116
Status Public on Nov 28, 2021
Title Non gustatory epithelium P0 control- Rep2
Sample type SRA
 
Source name Lingual epithelium
Organism Mus musculus
Characteristics cell type: Lingual cells
tissue: Lingual epithelium
age: postnatal day 0
genotype: Control
chip antibody: H2AK119ub (Cell Signaling, Cat# 8240S)
Extracted molecule genomic DNA
Extraction protocol Basal lingual epithelial cells were purified from P0 newborn mice. Tongues were removed from the mandible and cut to exclude the posterior circumvallate papillae. For ChIP, only control mice were collected. Tissues were cut into small pieces and incubated with 1.26U/mL dispase (Invitrogen) and 0.3% type 1 collagenase (Worthington) for 45 minutes at 37ºC with 80 rpm shaking. Tissues were washed with 1xPBS, dissociated with 0.25% Trypsin with 2.21mM EDTA (Corning Cellgro; Manassas, VA, USA), and then washed twice with 1xPBS. Cells were stained with 1:200 EpCAM-APC antibodies (Biolegend; San Diego, CA, USA) for 30 min on ice and washed twice with 1x HBSS prior to cell sorting.
For high-throughput ChIP sequencing, libraries were constructed from 4ng of Purified DNA using the DNA SMART ChIP-Seq Kit (Clontech; Palo Alto, CA, USA) according to the manufacturer’s instructions. Constructed ChIP-seq libraries were sequenced on the Illumina NextSeq 500 platform. Two biological replicates were used for ChIP experiments.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
 
Data processing ChIP-seq reads were aligned to the mm10 reference genome using bowtie2 (v2.3.3, default parameters).
Duplicate reads were removed by the Samtools software v0.1.19 (Li et al. 2009).
Peaks (mostly broad) in H2AK119ub1 ChIP samples were called as previously described (Goldberg et al. 2010) for the two replicates independently.
To visualize ChIP-seq signals, we used the Integrative Genomics Viewer (IGV; http://software.broadinstitute.org/software/igv/) and TDF files from the igvtools (v2.3.57; https://software.broadinstitute.org/software/igv/igvtools).
Genome_build: mm10
Supplementary_files_format_and_content: IGV tdf and peaks
 
Submission date Nov 29, 2018
Last update date Nov 28, 2021
Contact name Dejian Zhao
E-mail(s) dejian.zhao@yale.edu
Organization name Yale School of Medicine
Department Genetics
Street address 333 Cedar St
City New Haven
State/province CT
ZIP/Postal code 06510
Country USA
 
Platform ID GPL19057
Series (2)
GSE123093 Polycomb repressive complex 1 (PRC1) role in lingual epithelium development [ChIP-Seq]
GSE123095 Polycomb repressive complex 1 (PRC1) role in lingual epithelium development
Relations
BioSample SAMN10497061
SRA SRX5077342

Supplementary file Size Download File type/resource
GSM3495116_H2AK119ub_Rep2.tdf 169.6 Mb (ftp)(http) TDF
GSM3495116_H2AK119ub_Rep2_peaks.ann.txt.gz 108.1 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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