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Sample GSM2142846 Query DataSets for GSM2142846
Status Public on Jan 01, 2017
Title Day 2.5 Trim33-deficient rep2
Sample type SRA
 
Source name Embryoid bodies - day2.5 in differentiation
Organism Mus musculus
Characteristics passages: 8 -10
strain: outbred
genotype/variation: Trim33-deficient
tissue: embryoid bodies
timepoint: day2.5 in differentiation
Treatment protocol Trim33-deficiency was induced with 4OH-Tamoxifen on day 1 (at 24 hours in differentiation).
Growth protocol ES cell lines were established from mouse embryos, which were homozygous for the Trim33-flox allele and carried the UbcCreERT2 transgene. Cells were cultured without feeder cells in the presence of LIF and 2i. Embryoid bodies were generated using the ATCC protocol on low attachment dishes under differentiating conditions. EBs were harvested at days 2 and 2.5 respectively.
Extracted molecule total RNA
Extraction protocol Equivalent amounts/number of embryoid bodies (EBs) were collected at days 2 and 2.5, comprising control and Trim33-deficient (n=3 independent pairs), in 100-200 μl commercially available (Qiagen) RLT buffer. Total RNA was isolated using Qiagen RNeasy Mini Kit Cat. No 74104.
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Data processing mRNA and sequencing libraries were prepared by the University of Michigan DNA Sequencing Core and single end reads generated on Illumina HiSeq2000.
After quality assessment per sample, single-end, 52 base pair reads were aligned to mm9 (Mus musculus assembly July 2007) using STAR RNA Seq aligner (Dobin et al., 2013).
Read counts for differential expression were obtained using HTSeq program. Differential expression analyses were performed using the DESeq program in R Statistical Package. https://bioconductor.org/packages/3.3/bioc/vignettes/DESeq/inst/doc/DESeq.pdf.
Genome_build: mm9
Supplementary_files_format_and_content: text files with raw counts from HT-seq (available on sample records) and excel files with DESeq output with differentially expressed genes p <=0.05 (available on series record)
 
Submission date May 04, 2016
Last update date May 15, 2019
Contact name Vesa Matti Kaartinen
E-mail(s) vesak@umich.edu
Phone 734 615 4726
Organization name University of Michigan
Department BMS
Lab Kaartinen
Street address 1011 N. University
City Ann Arbor
State/province MI
ZIP/Postal code 48109
Country USA
 
Platform ID GPL13112
Series (1)
GSE81095 RNA Sequencing Data in differentiating mouse embryonic stem cells [day2 and 2.5 in differentiation]
Relations
BioSample SAMN04940121
SRA SRX1742216

Supplementary file Size Download File type/resource
GSM2142846_53910_count.txt.gz 98.3 Kb (ftp)(http) TXT
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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