NDLI: Comparative transcriptomic analyses of thymocytes using 10x Genomics and Parse scRNA-seq technologies

Content Provider	Springer Nature : BioMed Central
Author	Filippov, Igor Philip, Chinna Susan Schauser, Leif Peterson, Pärt
Abstract	Background Single-cell RNA sequencing experiments commonly use 10x Genomics (10x) kits due to their high-throughput capacity and standardized protocols. Recently, Parse Biosciences (Parse) introduced an alternative technology that uses multiple in-situ barcoding rounds within standard 96-well plates. Parse enables the analysis of more cells from multiple samples in a single run without the need for additional reagents or specialized microfluidics equipment. To evaluate the performance of both platforms, we conducted a benchmark study using biological and technical replicates of mouse thymus as a complex immune tissue. Results We found that Parse detected nearly twice the number of genes compared to 10x, with each platform detecting a distinct set of genes. The comparison of multiplexed samples generated from 10x and Parse techniques showed 10x data to have lower technical variability and more precise annotation of biological states in the thymus compared to Parse. Conclusion Our results provide a comprehensive comparison of the suitability of both single-cell platforms for immunological studies.
Related Links	https://bmcgenomics.biomedcentral.com/counter/pdf/10.1186/s12864-024-10976-x.pdf
Ending Page	13
Page Count	13
Starting Page	1
File Format	HTM / HTML
ISSN	14712164
DOI	10.1186/s12864-024-10976-x
Journal	BMC Genomics
Issue Number	1
Volume Number	25
Language	English
Publisher	BioMed Central
Publisher Date	2024-11-11
Access Restriction	Open
Subject Keyword	Life Sciences Microarrays Proteomics Animal Genetics and Genomics Microbial Genetics and Genomics Plant Genetics and Genomics Transcriptomics 10x Parse scRNA-seq Thymus
Content Type	Text
Resource Type	Article
Subject	Biotechnology Genetics
Journal Impact Factor	3.5/2023
5-Year Journal Impact Factor	4.1/2023

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

A single-cell transcriptomic atlas of the developing chicken limb

ddSeeker: a tool for processing Bio-Rad ddSEQ single cell RNA-seq data

Using DenseFly algorithm for cell searching on massive scRNA-seq datasets

Comparative transcriptome analyses of flower development in four species of Achimenes (Gesneriaceae)

Transcriptomic analyses of regenerating adult feathers in chicken

Comparative genomics and transcriptomics of trait-gene association

spatialLIBD: an R/Bioconductor package to visualize spatially-resolved transcriptomics data

Choice of pre-processing pipeline influences clustering quality of scRNA-seq datasets

Comparative transcriptomic analyses revealed divergences of two agriculturally important aphid species

Comparative transcriptomic analyses of thymocytes using 10x Genomics and Parse scRNA-seq technologies

Similar Documents

A single-cell transcriptomic atlas of the developing chicken limb

ddSeeker: a tool for processing Bio-Rad ddSEQ single cell RNA-seq data

Using DenseFly algorithm for cell searching on massive scRNA-seq datasets

Comparative transcriptome analyses of flower development in four species of Achimenes (Gesneriaceae)

Transcriptomic analyses of regenerating adult feathers in chicken

Comparative genomics and transcriptomics of trait-gene association

spatialLIBD: an R/Bioconductor package to visualize spatially-resolved transcriptomics data

Choice of pre-processing pipeline influences clustering quality of scRNA-seq datasets

Comparative transcriptomic analyses revealed divergences of two agriculturally important aphid species

Comparative transcriptomic analyses of thymocytes using 10x Genomics and Parse scRNA-seq technologies