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Series GSE211895 Query DataSets for GSE211895
Status Public on Nov 01, 2022
Title Assessment of Spatial Genomics for Oncology Discovery
Organisms Homo sapiens; Mus musculus; Rattus norvegicus
Experiment type Expression profiling by high throughput sequencing
Summary Tumor heterogeneity is a major challenge for oncology drug discovery and development. Understanding of the spatial tumor landscape is key to identifying new targets and impactful model systems. Here, we test the utility of spatial transcriptomics (ST) for Oncology Discovery by profiling 40 tissue sections and 80,024 capture spots across a diverse set of tissue types, sample formats, and RNA capture chemistries. We verify the accuracy and fidelity of ST by leveraging matched pathology analysis that provide a ground truth for tissue section composition. We then use spatial data to demonstrate the capture of key tumor depth features, identifying hypoxia, necrosis, vasculature, and extracellular matrix variation. We also leverage spatial context to identify relative cell type locations showing the anti-correlation of tumor and immune cells in syngeneic cancer models. Lastly, we demonstrate target identification approaches in clinical pancreatic adenocarcinoma samples, highlighting tumor intrinsic biomarkers and paracrine signaling.
 
Overall design Anna, Lyubetskaya
 
Contributor(s) Rabe B, Fisher A, Lewin A, Neuhaus I, Brett C, Brett T, Pereira E, Golhar R, Kebede S, Font-Tello A, Mosure K, Van Wittenberghe N, Mavrakis K, MacIsaac K, Chen B, Drokhlyansky E
Citation(s) 36452860
Submission date Aug 23, 2022
Last update date Mar 20, 2024
Contact name Anna Lyubetskaya
E-mail(s) anna.lyubetskaya@bms.com
Organization name Bristol-Myers Squibb
Street address 100 Binney St
City Cambridge
ZIP/Postal code 02142
Country USA
 
Platforms (3)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
GPL25947 Illumina NovaSeq 6000 (Rattus norvegicus)
Samples (29)
GSM6505118 rat colon, fresh frozen, with coverslip, rep A, experiment 4
GSM6505119 rat colon, fresh frozen, with coverslip, rep B, experiment 4
GSM6505120 rat colon, fresh frozen, rep C, experiment 4
Relations
BioProject PRJNA872761
SRA SRP393519

Download family Format
SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE211895_RAW.tar 102.4 Gb (http)(custom) TAR (of CSV, H5, JSON, PNG, TIFF)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
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