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Sample GSM3223335 Query DataSets for GSM3223335
Status Public on Jul 26, 2019
Title RNA_d3F_r2
Sample type SRA
Source name mesendoderm cells
Organism Mus musculus
Characteristics cell line: double knock-in (DKI) mouse ES cell line carrying Foxa2-Venus and Sox17-Cherry gene fusions
genotype/variation: Foxa2-Venus heterozygous;Sox17-Cherry homozygous
facs sorting markers: Foxa2-Venus-pos/Sox17-Cherry-neg
time point: d3
antibody: none
Growth protocol The cells were cultured for few consecutive passages on gelatine and ES medium. On the day of differentiation, mESCs were seeded on 10 cm gelatine coated dishes directly in endoderm differentiation medium (EDM) supplemented with 1 ng/ml of murine Wnt3a and 10 ng/ml of Activin A. Freshly prepared EDM supplemented with Wnt3a and Activin A was added every day. Cells were collected on day0, day3 and day5 for FACS isolation.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted with Trizol and RNA clean and concentrator kit (Zymo research), including the on-column DNase step. Ribo-depletion with Ribozero goldkit (Illumina MRZG126).
Illumina TruSeq V2 RNA prep kit.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
Data processing Paired-end 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 GPL17021
Series (2)
GSE116259 Pre-marked chromatin and transcription factor co-binding shape the pioneering activity of Foxa2 [RNA-seq]
GSE116262 Pre-marked chromatin and transcription factor co-binding shape the pioneering activity of Foxa2
BioSample SAMN09486935
SRA SRX4298479

Supplementary file Size Download File type/resource
GSM3223335_RNA_d3F_r2_rsem.genes.results.txt.gz 442.4 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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