NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM4205748 Query DataSets for GSM4205748
Status Public on Jun 16, 2022
Title XEGs (CITE_Seq) replicate 2
Sample type SRA
 
Source name Cell culture
Organism Mus musculus
Characteristics starting cells: mouse ES cells, XEN-eGFP cells
Treatment protocol No treatment
Growth protocol Growth protocol P3 with chiron as described in van den Brink et al (2014) in Development. Differences: Gastruloids start with 200 E14 mouse embryonic stem cells (mESCs), PEGs start with a mixture 150 E14 mESCs and 50 Extra-embryonic-endoderm-like (XEN) cells and cells are collected after 4 days.
Extracted molecule total RNA
Extraction protocol Organoids were pooled and disociated with TrypLE. Spike-ins (see sample descriptions) were added before proceeding with single-cell RNA sequencing library preparation.
10X library: 10x RNA-seq libraries were prepared using the Chromium Single Cell 3' Reagent Kit, Version 3 Chemistry (10x Genomics) according to the manufacturer's protocol. CITE-seq libraries: CITE-seq libraries were prepared according to the CITE-seq protocol from New York Genome Center version 2019-02-13. Sequencing: Libraries were sequenced on an Illumina Novaseq6000 at 150bp paired end.
Paired end RNA-seq
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description Contains E14 mESC CITE-seq spike-ins (CD15 antibody) and XEN-eGFP CITE-seq spike-ins (CD140 antibody)
PEGs_rep2_barcodes.tsv
PEGs_rep2_features.tsv
PEGs_rep2_matrix.mtx.gz
PEGs_rep2_normCounts.tsv
Data processing Single-cell expression was quantified using unique molecular identifiers (UMIs) by 10x Genomics’ “Cell Ranger” software.
Counts were normalized with the scran package in R
Cell types were assigned by vote of the K-nearest-neighbors from the Pijuan-Sala dataset (GSE87038)
Genome_build: mm10 with mCherry and eGFP
CITE in the name indicates CITE-seq library preparation
Supplementary_files_format_and_content: fq.gz: compressed raw fastq file from illumina sequencing (CITE in the name indicates CITE-seq library preparation); matrix.mtx.gz:compressed matrix of UMI counts where cells are columns and genes rows; barcodes.tsv: compressed list of 16bp barcodes corresponding to the columns of matrix; features.fq.gz: compressed list of HUGO and ensembl identifiers corresponding to the rows of matrix; normCounts.tsv: Compressed table of normalized expression and cell type assignments.
 
Submission date Dec 05, 2019
Last update date Jun 16, 2022
Contact name Stefan Semrau
E-mail(s) semrau@physics.leidenuniv.nl
Phone 0031638304530
Organization name Leiden University
Department Physics
Street address Einsteinweg 55
City Leiden
State/province Zuid-Holland
ZIP/Postal code 2333CC
Country Netherlands
 
Platform ID GPL24247
Series (1)
GSE141530 A gastruloid model of the interaction between embryonic and extra-embryonic cell types
Relations
BioSample SAMN13491083
SRA SRX7276940

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap