NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM7300273 Query DataSets for GSM7300273
Status Public on Feb 19, 2024
Title ED210204_t
Sample type SRA
 
Source name Transcriptomic dataset of tCROP-seq
Organism Mus musculus
Characteristics tissue: Forebrain
strain: C57bl/6
treatment: FACSorted for GFP
age: E16
Extracted molecule total RNA
Extraction protocol embryonic tissue was collected in ice-cold Leibowitz medium and papain dissociation was carried out (Wortington, #LK003150). Postnatal tissue was dissected in ice-cold bubbled ACSF and dissociatedwas carried out with the Miltenyi BioTech Neural Tissue Dissociation Kit (P) (#130-092-628)
Transcriptomic libraries were prepared for sequencing using standard Illumina protocols. Barcode libraries were prepared from PCR cDNA to amplify barcode regions with custom primers with standard Illumina adapters.
 
Library strategy RNA-Seq
Library source transcriptomic single cell
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description total RNA
Data processing Transcritpomic dataset: Sequencing reads in FASTQ files were aligned to a reference transcriptome (mm10-2.1.0) and collapsed into unique molecular identifier counts using the 10x Genomics Cell Ranger software (version 3.0.2 and 5.0.1).Data were read into R (version 3.6.0) as a count matrix and cells wer filtered using Seurat v3 with cut-offs for: max/min gene expression, max nCount_RNA, and percentage of total reads that aligned to the mitochondrial genome (applied cut-offs see Supplementary Data 1, Bandler et al. 2021).
Filtered count matrix
Assembly: mm10-2.1.0
 
Submission date May 05, 2023
Last update date Feb 19, 2024
Contact name Christian Mayer
Organization name Max Planck Institute of Neurobiology.
Lab Mayerlab
Street address Am Klopferspitz 18
City Martinsried
ZIP/Postal code 82152
Country Germany
 
Platform ID GPL24247
Series (2)
GSE231774 Spatial enhancer activation determines inhibitory neuron identity (scRNAseq)
GSE231779 Spatial enhancer activation determines inhibitory neuron identity
Relations
BioSample SAMN34718710
SRA SRX20742156

Supplementary file Size Download File type/resource
GSM7300273_ED210204_filtered.rds.gz 79.6 Mb (ftp)(http) RDS
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