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Spatial Representation of Single Cell RNA-sequencing Data in Embryonic Kidneys
Summary Data Summary
Applicant Carroll, Thomas
E-Mail Address thomas.carroll@utsouthwestern.edu
Project Title Spatial Representation of Single Cell RNA-sequencing Data in Embryonic Kidneys
CBU ID 19AU4063
External SubContract ID 32307-64
Diabetic Complication Nephropathy
Funding Program Group Pilot & Feasibility [PF2019]
Abstract Single cell RNA sequencing datasets have become ubiquitous. Although these
datasets contain an enormous amount of data that can be used for hypothesis
generation, the data is frequently provided in the form of tSNE plots or Excel
datasheets that have limited utility. Neither of these methods provide
significant spatial information. We have adapted a technique that allows us to
present single cell data in a manner that includes spatial information. This
technique requires in situ hybridization of a relatively small number of cell
type specific genes to function as landmarks. However, these landmark genes must
be hybridized to the same or adjacent tissue sections to allow image
registration. This cannot be accomplished using current techniques. Here we
propose to establish a protocol for multiplexing mRNA expression (so-called in
situ single cell RNA-Seq) allowing us to visualize up to 1024 genes
simultaneously on a single tissue section. By carefully selecting a small number
of genes that represent a single cell sequencing cluster, we can the map the
entire transcriptome from one or more single cell datasets onto a reference
image of a kidney thus giving spatial resolution for all expressed genes.
Ultimately, this data will be provided as a searchable website that will allow
users to make multiple queries including simple gene expression data (virtual in
situ hybridization), spatial readout of signaling pathway or transcription
factor activity and spatial relationship of ligands and receptors. We feel
development of this technique will increase access to single cell RNA-seq data
and the facilitation of hypothesis generation and thus accelerate discovery and
potential cures for kidney disease.
Application PDF Application Research Plan
Status Contract Executed
Key Personnel thomas Carroll, PhD
Christopher Chaney, M.D.
Salary Total Costs 40331
Supply Total Costs 21397
Equipment Total Costs 0
Travel/Other Total Costs 0
Direct Costs 61728
Indirect Costs Proposed 38272
Total Costs Proposed 100000
Total Costs Approved 99999
Start Date 11/1/2019
End Date 10/31/2020
IFO Name Martinez, Diana
IFO E-Mail Address grants.mgt@utsouthwestern.edu
IACUC/IRB No. 2015-101169)
IACUC/IRB Institution UTSW Med Ctr.
Entity ID No.
Report Request Date 6/30/2022
T1D NO
TypeCount
Invoices 14
Progress Reports 2
Data Submission


Invoices
UrlCBU IDExternal IDInstitutionDateDirectIndirectInvoiceBalancePDF
  View  19AU406332307-64UTSW Med Ctr.9/12/2022$333.01$209.80$542.81$1.42View PDF
  View  19AU406332307-64UTSW Med Ctr.8/9/2022$149.81$94.38$244.19$1.42View PDF
  View  19AU406332307-64UTSW Med Ctr.7/20/2022$525.89$331.31$857.20$1.42View PDF
  View  19AU406332307-64UTSW Med Ctr.7/13/2021$4,905.06$3,149.84$8,054.90$1.42View PDF
  View  19AU406332307-64UTSW Med Ctr.6/15/2021$4,635.78$2,920.55$7,556.33$1.42View PDF
  View  19AU406332307-64UTSW Med Ctr.6/13/2022$2,100.14$1,323.09$3,423.23$1.42View PDF
  View  19AU406332307-64UTSW Med Ctr.5/18/2021$4,656.50$2,873.93$7,530.43$1.42View PDF
  View  19AU406332307-64UTSW Med Ctr.5/10/2022$2,585.69$1,628.99$4,214.68$1.42View PDF
  View  19AU406332307-64UTSW Med Ctr.4/14/2021$4,685.55$2,951.89$7,637.44$1.42View PDF
  View  19AU406332307-64UTSW Med Ctr.4/11/2022$1,409.84$888.20$2,298.04$1.42View PDF
  View  19AU406332307-64UTSW Med Ctr.3/16/2021$4,833.35$3,044.98$7,878.33$1.42View PDF
  View  19AU406332307-64UTSW Med Ctr.2/11/2021$4,628.81$2,916.15$7,544.96$1.42View PDF
  View  19AU406332307-64UTSW Med Ctr.12/14/2020$9,242.86$5,822.97$15,065.83$1.42View PDF
  View  19AU406332307-64UTSW Med Ctr.1/14/2021$16,655.95$10,493.26$27,149.21$1.42View PDF
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