Protocol for transcriptomic and epigenomic analyses of tip-like endothelial cells using scRNA-seq and ChIP-seq
Summary: Angiogenesis begins as endothelial cells migrate, forming a sprouting tip and subsequent growth-rich stalk cells. Here, we present a protocol for transcriptomic and epigenomic analyses of tip-like cells in cultured endothelial cells. We describe steps for stimulating human umbilical vein en...
Saved in:
| Main Authors: | , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Elsevier
2025-03-01
|
| Series: | STAR Protocols |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S266616672400491X |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1841545544254619648 |
|---|---|
| author | Shintaro Funasaki Yuri Miyamura Shunsuke Kamei Akhinur Rahman Masaya Yamazaki Shingo Usuki Keiichiro Yasunaga Yorifumi Satou Hiroto Ohguchi Takashi Minami |
| author_facet | Shintaro Funasaki Yuri Miyamura Shunsuke Kamei Akhinur Rahman Masaya Yamazaki Shingo Usuki Keiichiro Yasunaga Yorifumi Satou Hiroto Ohguchi Takashi Minami |
| author_sort | Shintaro Funasaki |
| collection | DOAJ |
| description | Summary: Angiogenesis begins as endothelial cells migrate, forming a sprouting tip and subsequent growth-rich stalk cells. Here, we present a protocol for transcriptomic and epigenomic analyses of tip-like cells in cultured endothelial cells. We describe steps for stimulating human umbilical vein endothelial cells (HUVECs) with vascular endothelial cell growth factor (VEGF) to generate tip-like cells. We then detail procedures for library preparation for single-cell RNA sequencing (RNA-seq) and chromatin immunoprecipitation sequencing (ChIP-seq), and data analysis. This scalable protocol is also applicable to diverse omics studies, including proteomics and metabolomics.For complete details on the use and execution of this protocol, please refer to Miyamura et al.1 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. |
| format | Article |
| id | doaj-art-e0551648d9dd47ebbbc11dea43fa4734 |
| institution | Kabale University |
| issn | 2666-1667 |
| language | English |
| publishDate | 2025-03-01 |
| publisher | Elsevier |
| record_format | Article |
| series | STAR Protocols |
| spelling | doaj-art-e0551648d9dd47ebbbc11dea43fa47342025-01-12T05:25:46ZengElsevierSTAR Protocols2666-16672025-03-0161103326Protocol for transcriptomic and epigenomic analyses of tip-like endothelial cells using scRNA-seq and ChIP-seqShintaro Funasaki0Yuri Miyamura1Shunsuke Kamei2Akhinur Rahman3Masaya Yamazaki4Shingo Usuki5Keiichiro Yasunaga6Yorifumi Satou7Hiroto Ohguchi8Takashi Minami9Divison of Molecular and Vascular Biology, IRDA, Kumamoto University, Kumamoto 860-0811, JapanDivison of Molecular and Vascular Biology, IRDA, Kumamoto University, Kumamoto 860-0811, JapanDivison of Molecular and Vascular Biology, IRDA, Kumamoto University, Kumamoto 860-0811, JapanDivision of Genomics and Transcriptomics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 860-8556, JapanDivision of Medical Biochemistry, Graduate School of Medical Science, Kumamoto University, Kumamoto 860-8556, JapanLiaison Laboratory Research Promotion Center, IMEG, Kumamoto University, Kumamoto 860-8556, JapanLiaison Laboratory Research Promotion Center, IMEG, Kumamoto University, Kumamoto 860-8556, JapanDivision of Genomics and Transcriptomics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 860-8556, JapanDivision of Disease Epigenetics, IRDA, Kumamoto University, Kumamoto 860-0811, JapanDivison of Molecular and Vascular Biology, IRDA, Kumamoto University, Kumamoto 860-0811, Japan; Corresponding authorSummary: Angiogenesis begins as endothelial cells migrate, forming a sprouting tip and subsequent growth-rich stalk cells. Here, we present a protocol for transcriptomic and epigenomic analyses of tip-like cells in cultured endothelial cells. We describe steps for stimulating human umbilical vein endothelial cells (HUVECs) with vascular endothelial cell growth factor (VEGF) to generate tip-like cells. We then detail procedures for library preparation for single-cell RNA sequencing (RNA-seq) and chromatin immunoprecipitation sequencing (ChIP-seq), and data analysis. This scalable protocol is also applicable to diverse omics studies, including proteomics and metabolomics.For complete details on the use and execution of this protocol, please refer to Miyamura et al.1 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.http://www.sciencedirect.com/science/article/pii/S266616672400491XBioinformaticsSequence analysisSingle CellGenomicsRNAseqChIPseq |
| spellingShingle | Shintaro Funasaki Yuri Miyamura Shunsuke Kamei Akhinur Rahman Masaya Yamazaki Shingo Usuki Keiichiro Yasunaga Yorifumi Satou Hiroto Ohguchi Takashi Minami Protocol for transcriptomic and epigenomic analyses of tip-like endothelial cells using scRNA-seq and ChIP-seq STAR Protocols Bioinformatics Sequence analysis Single Cell Genomics RNAseq ChIPseq |
| title | Protocol for transcriptomic and epigenomic analyses of tip-like endothelial cells using scRNA-seq and ChIP-seq |
| title_full | Protocol for transcriptomic and epigenomic analyses of tip-like endothelial cells using scRNA-seq and ChIP-seq |
| title_fullStr | Protocol for transcriptomic and epigenomic analyses of tip-like endothelial cells using scRNA-seq and ChIP-seq |
| title_full_unstemmed | Protocol for transcriptomic and epigenomic analyses of tip-like endothelial cells using scRNA-seq and ChIP-seq |
| title_short | Protocol for transcriptomic and epigenomic analyses of tip-like endothelial cells using scRNA-seq and ChIP-seq |
| title_sort | protocol for transcriptomic and epigenomic analyses of tip like endothelial cells using scrna seq and chip seq |
| topic | Bioinformatics Sequence analysis Single Cell Genomics RNAseq ChIPseq |
| url | http://www.sciencedirect.com/science/article/pii/S266616672400491X |
| work_keys_str_mv | AT shintarofunasaki protocolfortranscriptomicandepigenomicanalysesoftiplikeendothelialcellsusingscrnaseqandchipseq AT yurimiyamura protocolfortranscriptomicandepigenomicanalysesoftiplikeendothelialcellsusingscrnaseqandchipseq AT shunsukekamei protocolfortranscriptomicandepigenomicanalysesoftiplikeendothelialcellsusingscrnaseqandchipseq AT akhinurrahman protocolfortranscriptomicandepigenomicanalysesoftiplikeendothelialcellsusingscrnaseqandchipseq AT masayayamazaki protocolfortranscriptomicandepigenomicanalysesoftiplikeendothelialcellsusingscrnaseqandchipseq AT shingousuki protocolfortranscriptomicandepigenomicanalysesoftiplikeendothelialcellsusingscrnaseqandchipseq AT keiichiroyasunaga protocolfortranscriptomicandepigenomicanalysesoftiplikeendothelialcellsusingscrnaseqandchipseq AT yorifumisatou protocolfortranscriptomicandepigenomicanalysesoftiplikeendothelialcellsusingscrnaseqandchipseq AT hirotoohguchi protocolfortranscriptomicandepigenomicanalysesoftiplikeendothelialcellsusingscrnaseqandchipseq AT takashiminami protocolfortranscriptomicandepigenomicanalysesoftiplikeendothelialcellsusingscrnaseqandchipseq |