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Sample GSM3223346 Query DataSets for GSM3223346
Status Public on Jul 26, 2019
Title d2.Foxa2n.r1
Sample type SRA
 
Source name ES cells
Organism Mus musculus
Characteristics cell line: doxycycline (Dox) inducible Foxa2-VenusĀ  ES cell line (T119)
genotype/variation: TetON-Foxa2-Venus
facs sorting markers: Venus-negative
time point: d2

Growth protocol ES cells were seeded without feeders in gelatin-coated plates and grown for 48h in ES standard medium (LIF/serum) supplemented with 40ng/ml doxycycline.
Extracted molecule total RNA
Extraction protocol Trizol and RNA clean and concentrator kit (Zymo research).
Smarter ultra low input-v4 (Clontech 634888) and Microplex-v2 (Diagenode C05010012).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1500
 
Data processing RNA-seq reads were mapped to the mouse genome (mm10) using STAR (Dobin et al., 2013). Expression of genes in FPKM was calculated with RSEM (Li et al., 2011).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *_rsem.genes.results.txt: Tab-delimited text files were generated with RSEM.
 
Submission date Jun 25, 2018
Last update date Aug 12, 2019
Contact name Filippo M. Cernilogar
E-mail(s) filippo.cernilogar@med.uni-muenchen.de
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)
GSE116260 Pre-marked chromatin and transcription factor co-binding shape the pioneering activity of Foxa2 [RNA-seq low input]
GSE116262 Pre-marked chromatin and transcription factor co-binding shape the pioneering activity of Foxa2
Relations
BioSample SAMN09486954
SRA SRX4298491

Supplementary file Size Download File type/resource
GSM3223346_GS336_Doxy-FVF-_1_rsem.genes.results.txt.gz 453.8 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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