Protocol for identification and validation of IGF2BP1 target genes in pluripotent human embryonic carcinoma cells

We present a detailed protocol to identify and validate IGF2BP1 target genes in pluripotent human embryonic carcinoma cells (NTERA-2). We first identify the target genes through RNA-immunoprecipitation (RIP) sequencing. We then validate the identified targets through the use of RIP-qPCR assays, dete...

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Detalles Bibliográficos
Autores principales: Myint, Khine, Chuang, Linda Shyue Huey, Matsuo, Junichi, Ito, Yoshiaki
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier 2023
Materias:
Protocol
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10227443/
https://www.ncbi.nlm.nih.gov/pubmed/37243602
http://dx.doi.org/10.1016/j.xpro.2023.102338
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author Myint, Khine
Chuang, Linda Shyue Huey
Matsuo, Junichi
Ito, Yoshiaki
author_facet Myint, Khine
Chuang, Linda Shyue Huey
Matsuo, Junichi
Ito, Yoshiaki
author_sort Myint, Khine
collection PubMed
description We present a detailed protocol to identify and validate IGF2BP1 target genes in pluripotent human embryonic carcinoma cells (NTERA-2). We first identify the target genes through RNA-immunoprecipitation (RIP) sequencing. We then validate the identified targets through the use of RIP-qPCR assays, determine the m(6)A status of target genes by m(6)A-IP, and perform functional validation by quantifying changes in mRNA or protein expression levels upon knockdown of IGF2BP1 or methyltransferases in NTERA-2. For complete details on the use and execution of this protocol, please refer to Myint et al. (2022).(1)
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spelling pubmed-102274432023-05-31 Protocol for identification and validation of IGF2BP1 target genes in pluripotent human embryonic carcinoma cells Myint, Khine Chuang, Linda Shyue Huey Matsuo, Junichi Ito, Yoshiaki STAR Protoc Protocol We present a detailed protocol to identify and validate IGF2BP1 target genes in pluripotent human embryonic carcinoma cells (NTERA-2). We first identify the target genes through RNA-immunoprecipitation (RIP) sequencing. We then validate the identified targets through the use of RIP-qPCR assays, determine the m(6)A status of target genes by m(6)A-IP, and perform functional validation by quantifying changes in mRNA or protein expression levels upon knockdown of IGF2BP1 or methyltransferases in NTERA-2. For complete details on the use and execution of this protocol, please refer to Myint et al. (2022).(1) Elsevier 2023-05-26 /pmc/articles/PMC10227443/ /pubmed/37243602 http://dx.doi.org/10.1016/j.xpro.2023.102338 Text en © 2023 The Author(s) https://creativecommons.org/licenses/by-nc-nd/4.0/This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
spellingShingle Protocol
Myint, Khine
Chuang, Linda Shyue Huey
Matsuo, Junichi
Ito, Yoshiaki
Protocol for identification and validation of IGF2BP1 target genes in pluripotent human embryonic carcinoma cells
title Protocol for identification and validation of IGF2BP1 target genes in pluripotent human embryonic carcinoma cells
title_full Protocol for identification and validation of IGF2BP1 target genes in pluripotent human embryonic carcinoma cells
title_fullStr Protocol for identification and validation of IGF2BP1 target genes in pluripotent human embryonic carcinoma cells
title_full_unstemmed Protocol for identification and validation of IGF2BP1 target genes in pluripotent human embryonic carcinoma cells
title_short Protocol for identification and validation of IGF2BP1 target genes in pluripotent human embryonic carcinoma cells
title_sort protocol for identification and validation of igf2bp1 target genes in pluripotent human embryonic carcinoma cells
topic Protocol
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10227443/
https://www.ncbi.nlm.nih.gov/pubmed/37243602
http://dx.doi.org/10.1016/j.xpro.2023.102338
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