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Sample GSM3223341 Query DataSets for GSM3223341
Status Public on Jul 26, 2019
Title d0.homo.r2
Sample type SRA
 
Source name ES 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: Cherry-negative
time point: d0

Growth protocol ES cells were split on red-fluorescent mitomycin-treated MEFs in ESC medium without LIF. The following day were collected 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
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 SAMN09486959
SRA SRX4298486

Supplementary file Size Download File type/resource
GSM3223341_GS159_d0_Foxa2-V_KO_homo_C17_rsem.genes.results.txt.gz 457.9 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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