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Sample GSM3495121 Query DataSets for GSM3495121
Status Public on Nov 28, 2021
Title Ring1a/b 2KO lingual epithelium rep2
Sample type SRA
 
Source name Lingual epithelium
Organism Mus musculus
Characteristics cell type: Lingual cells
tissue: Lingual epithelium
age: Embryonic day 16
genotype: Ring1a-/- Ring1bfl/fl K14-Cre+
Extracted molecule total RNA
Extraction protocol Basal lingual epithelial cells were purified from E16 embryos. Tongues were removed from the mandible and cut to exclude the posterior circumvallate papillae. For RNA and RNA-Seq analysis of control, Krt14-Cre Ring1a-/- Ring1b flox/flox mice, E16 tongues 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 ChIP analysis, control newborn P0 mice were collected. All cell isolations were performed on a FACS Influx instrument (BD, Franklin Lakes, NJ, USA). FACS-purified cells were collected directly into RLT Plus buffer (QIAGEN), and total RNA was isolated with the RNeasy Plus Micro Kit (QIAGEN). Complimentary DNA was reverse-transcribed from total RNA using qScript cDNA SuperMix (Quanta Biosciences, Gaithersburg, MD, USA) according to the manufacturer’s instructions.
15ng of RNA were reverse transcribed and amplified using the Ovation RNA-seq System V2 (Nugen). Libraries were constructed from 50ng of sonicated cDNA (Covaris) using the Ovation Ultra Low DR Multiplex system (Nugen). The concentration and quality of the libraries were determined using Qubit (Invitrogen) and Bioanalyzer (Agilent). Constructed RNA-seq libraries were sequenced at GENEWIZ on the Illumina HiSeq platform, obtaining 100-nucleotide single reads.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Data processing RNA-seq reads were aligned to the mouse reference genome (mm10) using the Tophat (v2.0.13)
Gene models of Refgene were downloaded from the UCSC genome browser on March 13, 2017. FPKM (Fragments Per Kilobase of transcript per Million mapped reads) values were generated using the cufflinks (v2.2.1). Lowly expressed genes (mean FPKM values < 1 in both groups under comparison) were excluded from differential expression analysis.
read counts from HTseq (v0.6.1)
DESeq2 (v1.6.3) was used to determine differentially expressed genes
genes with >2 fold change, false discovery rate (FDR) < 0.05, and FPKM>1 were identified as significantly differentially expressed
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited gene expression values (read counts from HTseq)
 
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 GPL21103
Series (2)
GSE123094 Polycomb repressive complex 1 (PRC1) role in lingual epithelium development [RNA-seq]
GSE123095 Polycomb repressive complex 1 (PRC1) role in lingual epithelium development
Relations
BioSample SAMN10497056
SRA SRX5077319

Supplementary file Size Download File type/resource
GSM3495121_Ring1ab_2KO_Rep2.tsv.gz 100.5 Kb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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