PMID- 37719153
OWN - NLM
STAT- PubMed-not-MEDLINE
LR  - 20240417
IS  - 2666-979X (Electronic)
IS  - 2666-979X (Linking)
VI  - 3
IP  - 9
DP  - 2023 Sep 13
TI  - A unified pipeline for FISH spatial transcriptomics.
PG  - 100384
LID - 10.1016/j.xgen.2023.100384 [doi]
LID - 100384
AB  - High-throughput spatial transcriptomics has emerged as a powerful tool for 
      investigating the spatial distribution of mRNA expression and its effects on 
      cellular function. There is a lack of standardized tools for analyzing spatial 
      transcriptomics data, leading many groups to write their own in-house tools that 
      are often poorly documented and not generalizable. To address this, we have 
      expanded and improved the starfish library and used those tools to create 
      PIPEFISH, a semi-automated and generalizable pipeline that performs transcript 
      annotation for fluorescence in situ hybridization (FISH)-based spatial 
      transcriptomics. We used this pipeline to annotate transcript locations from 
      three real datasets from three different common types of FISH image-based 
      experiments, MERFISH, seqFISH, and targeted in situ sequencing (ISS), and 
      verified that the results were high quality using the internal quality metrics of 
      the pipeline and also a comparison with an orthogonal method of measuring RNA 
      expression. PIPEFISH is a publicly available and open-source tool.
CI  - (c) 2023 The Authors.
FAU - Cisar, Cecilia
AU  - Cisar C
AD  - Department of Biomolecular Engineering, School of Engineering, University of 
      California, Santa Cruz, Santa Cruz, CA 95064, USA.
FAU - Keener, Nicholas
AU  - Keener N
AD  - Department of Biomolecular Engineering, School of Engineering, University of 
      California, Santa Cruz, Santa Cruz, CA 95064, USA.
FAU - Ruffalo, Mathew
AU  - Ruffalo M
AD  - Computational Biology Department, School of Computer Science, Carnegie Mellon 
      University, Pittsburgh, PA 15213, USA.
FAU - Paten, Benedict
AU  - Paten B
AD  - Department of Biomolecular Engineering, School of Engineering, University of 
      California, Santa Cruz, Santa Cruz, CA 95064, USA.
LA  - eng
GR  - U24 HG011853/HG/NHGRI NIH HHS/United States
PT  - Journal Article
DEP - 20230821
PL  - United States
TA  - Cell Genom
JT  - Cell genomics
JID - 9918284260106676
PMC - PMC10504669
OTO - NOTNLM
OT  - FISH
OT  - computational methods
OT  - genomics
OT  - spatial transcriptomics
OT  - transcriptomics
COIS- The authors declare no competing interests.
EDAT- 2023/09/18 06:42
MHDA- 2023/09/18 06:43
PMCR- 2023/08/21
CRDT- 2023/09/18 04:16
PHST- 2023/02/21 00:00 [received]
PHST- 2023/06/23 00:00 [revised]
PHST- 2023/07/24 00:00 [accepted]
PHST- 2023/09/18 06:43 [medline]
PHST- 2023/09/18 06:42 [pubmed]
PHST- 2023/09/18 04:16 [entrez]
PHST- 2023/08/21 00:00 [pmc-release]
AID - S2666-979X(23)00181-7 [pii]
AID - 100384 [pii]
AID - 10.1016/j.xgen.2023.100384 [doi]
PST - epublish
SO  - Cell Genom. 2023 Aug 21;3(9):100384. doi: 10.1016/j.xgen.2023.100384. eCollection 
      2023 Sep 13.