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Series GSE214611 Query DataSets for GSE214611
Status Public on Oct 03, 2022
Title Single Cell Spatial Transcriptomics Redefines the Borderzone induced by Myocardial Infarction and Mechanical Injury
Organisms Homo sapiens; Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary The ischemic borderzone (BZ) is a geographically complex and biologically enigmatic interface separating poorly perfused infarct zones (IZ) from comparatively healthy remote zones (RZ).  BZ cellular and molecular mechanisms are not well understood because efforts to dissect it inevitably include RZ and IZ in uncontrolled proportions. Here, we use single-cell/nuclei RNA-sequencing, spatial transcriptomics, and multiplexed RNA fluorescence in situ hybridization (mFISH) to identify BZ cardiomyocytes (CMs) subsets. BZ1 (Nppa+Xirp2­-) forms a hundreds-of-microns-thick transitional layer adjacent to RZ, while BZ2 (Nppa+Xirp2­+) forms a tens-of-microns-thick layer that the IZ edge. BZ2 CMs have reduced CM cell contact; colocalize with matricellular-protein-expressing myofibroblasts; and upregulate focal adhesion-, sarcomere-, and cytoskeletal-genes.  Surprisingly, the transcriptional BZ emerges within an hour of injury and is inducible by non-ischemic fine-needle-trauma. We suggest that mechanical instability and “loss of neighbor” at the BZ edge are the dominant inducers of the BZ transcriptional response.
 
Overall design Gene expression profiling of 10x Genomic Chromium single nuclei RNA-Seq or Visium spatial transcriptomics from the left ventricular myocardium or short axis sections of healthy and injured adult male C57BL6 mouse hearts (8-12 weeks). Injuries include MI (permanent ligation of the LAD coronary artery), I/R-30 (30 minutes of ischemia followed by reperfusion), transaortic constriction, isoproterenol injection, and traumatic needle injection.

Please note that the processed data files for GSM6613081, GSM6613087, GSM6613090 have been replaced on May 18, 2023 as the previous files were incomplete (missing spatial data folder and .h5 matrix file).
Web link https://www.nature.com/articles/s44161-022-00160-3
 
Contributor(s) Calcagno DM, Taghdiri N, Ninh VK, Mesfin JM, Toomu A, Sehgal R, Lee J, Liang Y, Duran JM, Adler E, Christman KL, Zhang K, Sheikh F, King KR
Citation DM Calcagno, N Taghdiri, VK Ninh, JM Mesfin, A Toomu, R Sehgal, J Lee, Y Liang, JM Duran, E Adler, KL Christman, K Zhang, F Sheikh, Z Fu and KR King. Single-cell and spatial transcriptomics of the infarcted heart define the dynamic onset of the border zone in response to mechanical destabilization. Nat Cardiovasc Res 2022, 1:1039-1055. doi:10.1038/s44161-022-00160-3
Submission date Oct 01, 2022
Last update date Jul 10, 2024
Contact name Kevin R King
Organization name UC San Diego
Department Medicine and Bioengineering
Lab King Lab
Street address 9500 Gilman Dr. MC 0412
City La Jolla
State/province CA
ZIP/Postal code 92093
Country USA
 
Platforms (2)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (32)
GSM6613059 Single nuclei, Day0 MI, biol rep 1
GSM6613060 Single nuclei, Day0 MI, biol rep 2
GSM6613061 Single nuclei, Day0 MI, biol rep 3
Relations
BioProject PRJNA886090

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

Supplementary file Size Download File type/resource
GSE214611_RAW.tar 2.7 Gb (http)(custom) TAR (of TAR, ZIP)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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