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Sample GSM6596556 Query DataSets for GSM6596556
Status Public on Jun 07, 2023
Title PCN organoid 2 of 2
Sample type SRA
Source name esophagus
Organism Mus musculus
Characteristics tissue: organoid
cell type: epithelial cell
genotype: Trp53;Cdkn2a;Notch1 KO
treatment: none
Extracted molecule total RNA
Extraction protocol organoids from WT, PC, PN, and PCN were collected 7 days after seeding and digested with 0.05% trypsin-EDTA at 37 ℃ for 30 min.
Each group was tagged with 2 CMO tags from CellPlex kit (10x Genomics). The tagged cells of each group were pooled together with same number of cells after counting cells. cDNA library was prepared with the 10x Genomics 3’ v2 kit.
Library strategy RNA-Seq
Library source transcriptomic single cell
Library selection cDNA
Instrument model Illumina NovaSeq 6000
Description Multiplexed
Data processing The demultiplexing, barcoded processing, and gene counting were performed using the Cell Ranger ( v6.1.2)
Assembly: GRCm38/mm10
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)
Submission date Sep 22, 2022
Last update date Jun 07, 2023
Contact name Jae-Il Park
Organization name M.D. Anderson Cancer Center
Department Dept. of Experimental Radiation Oncology
Street address 6565 MD Anderson BLVD
City Houston
State/province Texas
ZIP/Postal code 77030
Country USA
Platform ID GPL24247
Series (2)
GSE213927 Key Genetic Determinants Driving Esophageal Squamous Cell Carcinoma Initiation and Immune Evasion [scRNAseq]
GSE213929 Key Genetic Determinants Driving Esophageal Squamous Cell Carcinoma Initiation and Immune Evasion
BioSample SAMN30961497
SRA SRX17673802

Supplementary file Size Download File type/resource
GSM6596556_PCN2_barcodes.tsv.gz 11.1 Kb (ftp)(http) TSV
GSM6596556_PCN2_features.tsv.gz 284.2 Kb (ftp)(http) TSV
GSM6596556_PCN2_matrix.mtx.gz 18.3 Mb (ftp)(http) MTX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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