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Sample GSM5680573 Query DataSets for GSM5680573
Status Public on Nov 15, 2021
Title 66_2020_9_H8_iXEN
Sample type SRA
 
Source name mESC
Organism Mus musculus
Characteristics cell type: iXEN
Treatment protocol Cell lines with doxycycline-inducible transgenes were incubated with 2 µg/ml doxycycline
Extracted molecule total RNA
Extraction protocol Rosette-to-Lumen stage embryoids and 2D mono-culturestem cells were harvested by washing with PBS and incubation in StemPro Accutase Cell Dissociation Reagent to create a single-cell solution
Cells lysed in Guanidine Hydrochloride (50 mM), dNTPs (17.4mM), 2.2µM SMART dT30VN primer lysis buffer
Nextera XT DNA Library Preparation Kit (Illumina)
NextSeq500 system SR 75bp with 2*8bp index reads
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description matrix_Seurat_imput_RtL_3D_2D
Data processing Single-cell data were demultiplexed using bcl2fastq2 v2.20.
raw reads were pseudoaligned using Kallisto with default settings (v0.44.0)78. Based on the pseudo alignment estimated by Kallisto
reads mapped to each transcript against the mouse transcriptome GRCm38, Gencode vM16 primary assembly
Normalization using Seurat
Genome_build: transcriptome GRCm38, Gencode vM16
Supplementary_files_format_and_content: tab separated txt files; containing raw seurat input matrices
 
Submission date Nov 08, 2021
Last update date Nov 15, 2021
Contact name Joachim Schultze
E-mail(s) j.schultze@uni-bonn.de
Organization name LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)
Department Genomics and Immunoregulation
Street address Carl-Troll-Strasse 31
City Bonn
State/province NRW
ZIP/Postal code 53115
Country Germany
 
Platform ID GPL19057
Series (1)
GSE188394 Induction of Rosette-to-Lumen stage embryoids using reprogramming paradigms in ESCs
Relations
BioSample SAMN22984035
SRA SRX13047451

Supplementary data files not provided
SRA Run SelectorHelp
Processed data are available on Series record
Raw data are available in SRA

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