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Sample GSM3223345 Query DataSets for GSM3223345
Status Public on Jul 26, 2019
Title d3.homo.r2
Sample type SRA
Source name endoderm cells
Organism Mus musculus
Characteristics cell line: Foxa2 knock-in/knock-out (Foxa2-Venus) KO mouse ES cell line
genotype/variation: Foxa2-Venus-KO/Foxa2-Venus-KO
facs sorting markers: Venus-positive
time point: d3

Growth protocol ES cells were split on mitomycin-treated MEFs in ESC medium without LIF. The following day, the ESCs were preplated twice to isolate the ESCs from the mitomycin-treated feeder cells and subsequently were seeded on the Wnt3a feeders cells in Endoderm Differentiation Mmedium containing Activin A (12ng/ml), refreshed every day. Cells were collected 3 days later for FACS isolation.
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
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
BioSample SAMN09486955
SRA SRX4298490

Supplementary file Size Download File type/resource
GSM3223345_GS162_d3F_Foxa2-V_KO_homo_C17_rsem.genes.results.txt.gz 456.1 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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