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Sample GSM7882922 Query DataSets for GSM7882922
Status Public on Dec 01, 2023
Title Pancreatic Tumor Tissue, IPI-926, 2 days, KA003
Sample type SRA
 
Source name Pancreatic Tumor Tissue
Organism Mus musculus
Characteristics tissue: Pancreatic Tumor Tissue
genotype: KrasLSL.G12D/+; P53LSL.R172H/+; Pdx1-Cre
treatment: IPI-926, 2 days
Treatment protocol Treatment with the vehicle hydroxypropyl-beta-cyclodextrin (HPBCD, Acros Organics; 5% w/w in water for injection (WFI)), or IPI-926 (kindly provided by PellePharm; 5 mg/ml) was performed daily via oral gavage at 40 mg/kg. Tumor tissue was collected 2 hours after final dose.
Growth protocol Tumor tissue was collected following humane euthanasia and trimmed of healthy pancreas tissue in a sterile petri dish. The tumor pieces were dissociated using a modified protocol based on Miltenyi (mouse) Tumor Dissociation Kit (Miltenyi Biotec, 130-096-730)
Extracted molecule total RNA
Extraction protocol Tumor tissue was placed in a digestion buffer containing trypsin, DNase, and an enzymatic cocktail (Supplementary Table 7) and digested at 37°C for 42 minutes (37C_m_TDK_2 program) on a gentleMACS Octo Dissociator (Miltenyi Biotec, 130-096-427). Cell suspensions were then filtered through a 40 μm cell strainer (Corning, 431750) and red blood cells were removed by incubation with red cell lysis buffer (Millipore Sigma, 11814389001), before a final resuspension in 100 μL PBS + 0.01% BSA.
Single Cell 3' v3, 10x Genomics
 
Library strategy RNA-Seq
Library source transcriptomic single cell
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description 10x Genomics
Data processing The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
 
Submission date Nov 06, 2023
Last update date Dec 01, 2023
Contact name Lukas Vlahos
E-mail(s) lv2395@cumc.columbia.edu
Organization name Columbia University
Department Systems Biology
Lab Andrea Califano
Street address 1130 St Nicholas Ave
City New York City
State/province New York
ZIP/Postal code 10032
Country USA
 
Platform ID GPL19057
Series (1)
GSE247072 Tumor Explants Elucidate a Cascade of Paracrine SHH, WNT, and VEGF Signals Driving Pancreatic Cancer Angiosuppression
Relations
BioSample SAMN38117152
SRA SRX22381255

Supplementary file Size Download File type/resource
GSM7882922_KA003_barcodes.tsv.gz 52.6 Kb (ftp)(http) TSV
GSM7882922_KA003_features.tsv.gz 284.1 Kb (ftp)(http) TSV
GSM7882922_KA003_matrix.mtx.gz 64.7 Mb (ftp)(http) MTX
SRA Run SelectorHelp
Raw data are available in SRA

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