|
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 |