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Sample GSM7872428 Query DataSets for GSM7872428
Status Public on Jun 12, 2024
Title Ccm3 KORapa, scRNAseq
Sample type SRA
 
Source name Retina
Organism Mus musculus
Characteristics tissue: Retina
genotype: Mfsd2a-CreERT2:Pdcd10fl/fl
treatment: Tamoxifen+Rapamycin
Extracted molecule total RNA
Extraction protocol Standard cell disscoiaiton followed by FACS sorting
Library was performed according to the manufacter's instructions (single cell 3' v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains illumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SRPIselect reagent for subsequent library construction. During the library construction Illumina R2 primer sequence, pair-end construct with P5 and P7 sequences and a sample index were added.
 
Library strategy RNA-Seq
Library source transcriptomic single cell
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description KO-RapaP9
10x Genomics
Data processing The demultiplexing, barcode processing, gene counting and aggregation were made using Cell Ranger software v6.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: tab-separated value files and matrix files produced with CellRanger
 
Submission date Oct 30, 2023
Last update date Jun 12, 2024
Contact name Francesc Lopez
E-mail(s) francesc.lopez@yale.edu
Organization name Yale University
Department Department of Genetics
Lab YCGA
Street address P.O. Box 27386
City West Haven
State/province CT
ZIP/Postal code 06516
Country USA
 
Platform ID GPL24247
Series (1)
GSE246598 mTORC1 signaling in brain endothelial progenitors contributes to CCM pathogenesis in a Pdcd10-deficient mouse model
Relations
BioSample SAMN38042149
SRA SRX22289115

Supplementary file Size Download File type/resource
GSM7872428_KO-RapaP9_barcodes.tsv.gz 12.5 Kb (ftp)(http) TSV
GSM7872428_KO-RapaP9_features.tsv.gz 284.1 Kb (ftp)(http) TSV
GSM7872428_KO-RapaP9_matrix.mtx.gz 21.2 Mb (ftp)(http) MTX
SRA Run SelectorHelp
Raw data are available in SRA

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