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Effects of Id1 depletion in TAMs on the genes expression of MC38 cells.

ABSTRACT: Effects of Id1 depletion in TAMs on the genes expression of MC38 cells.

PROVIDER: PRJNA779424 | ENA |

REPOSITORIES: ENA

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Effects of Id1 depletion in TAMs on the genes expression of MC38 cells.

Project description:We report the application of high-throughput mRNA sequencing to explore the effect of Id1 depletion in TAMs on gene expression of MC38 cells. Different groups of TAMs were isolated from the subcutaneous tumors in Id1f/f or myeloid cell lineage speciﬁc Id1 deficient mice (Id1-Lyz-KO) . MC38 cells were then mixed with two groups of TAMs and be implanted in C57BL/6J mice. CD45- cells were then isolated from the subcutaneous tumors described above to do the transcriptome sequencing.

2023-10-15 | GSE188572 | GEO

Effects of Id1 depletion in TAMs on the genes expression of MC38 cells.

Project description:We report the application of high-throughput mRNA sequencing to explore the effect of Id1 depletion in TAMs on its gene expression . Different groups of TAMs were isolated from the subcutaneous tumors in Id1f/f or myeloid cell lineage speciﬁc Id1 deficient mice (Id1-Lyz-KO) .

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Effects of Id1 depletion in TAMs on the genes expression of MC38 cells.

Project description:Effects of Id1 depletion in TAMs on the genes expression of MC38 cells.

| PRJNA827027 | ENA

Gene expression profiles of mouse embryonic stem cells (mESCs) after genetic depletion of Id1 and knock-down of Zrf1

Project description:Id proteins are dominant negative regulators within the HLH family of proteins. In embryonic stem cells (ESCs), Id1 and Id3 maintain the pluripotent state by preventing neural differentiation. The Id1-interacting protein Zrf1 plays a crucial role as a chromatin-bound factor in specification of the neural fate from ESCs. Here, we show that Id1 blocks Zrf1 recruitment to chromatin, thus preventing the activation of neural genes during ESC differentiation. Moreover, genetic deletion of Id1 in ESCs caused misexpression of more than 6000 genes. Interestingly, the expression of almost half of those genes was restored upon further depletion of Zrf1. We therefore identified Zrf1 as a transcriptional regulator downstream of Id1 in ESCs. In Id1KO mESCs, Zrf1 expression was depleted by using shRNAs. Four replicates corresponding to four independent biological samples per group were collected.

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Gene expression profiles of mouse embryonic stem cells (mESCs) after genetic depletion of Id1 and knock-down of Zrf1

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Heme-TAMs prevent cancer cell apoptosis and drive growth, invasiveness, and metastasis

Project description:To study the impact of heme-TAMs on the growth, phenotype, and function of cancer cells, we cultured GFP-MC38 cells either alone or mixed with heme-treated macrophages in microwell plates, enabling us to collect large numbers of uniform spheroids for scRNA-seq. We observed that after four days, the size of GFP-MC38 spheroids regressed, and the tumor cells underwent apoptosis and decayed metabolically. In contrast, the presence of heme-TAMs within spheroids prevented apoptosis, supporting the extended growth of metabolically viable spheroids beyond 10 days of culture.

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Transcriptomic profiling of 4T1 cells depleted for Id1/3 and Robo1

Project description:Id1 and its closely related family member Id3 are expressed by a diversity of stem and progenitor cells. We show that Id1/3 are required for the self-renewal and proliferation of triple negative breast cancer (TNBC) cells both in vitro and in vivo. Furthermore, we identified that Id1/3 negatively regulates the tumour suppressor gene Robo1. Depletion of Robo1 could rescue the proliferative defect induced by Id1/3 knockdown. To understand the mechanisms by which Robo1 rescues cell proliferation in Id1/3 depleted cells, we performed RNA-Sequencing on 4T1 cells with Dox-inducible Id1/3 KD and/or Robo1 depletion using siRNA. We conclude that following Id1/3 knockdown, Robo1 is induced and exerts anti-proliferative effects via suppression of a Myc transcriptional program.

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Quantitative analysis of Id1 Wild Type and Id1 knockout hematopoietic stem cells transcriptome

Project description:To explore the molecular basis by which Id1 loss promotes HSC quiescence under stress we compared the transcriptome of Id1-/- and Id1+/+ HSCs isolated from primary BMT recipient mice by RNA-seq. We found 179 upregulated and 1476 downregulated genes in Id1-/- HSCs compared to Id1+/+ HSCs using a fold-change cut-off of 2 . Collectively, the IPA analysis shows that Id1-/- HSCs have gene expression profiles consistent with reduced response to stress, reduced cycling and proliferation, and reduced ribosomal biogenesis and protein synthesis, which is consistent with our hypothesis that Id1-/- HSCs have molecular signature of quiescent HSCs compared to Id1+/+ HSCs.

2018-08-09 | GSE114533 | GEO

Id1 overexpressing BMDC

Project description:Trascriptional profiling by array of bone marrow derived murine cells trasduced with control and Id1-overexpressing vectors to identify genes changes induced by increased expression of the transcriptional regulator Id1

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Transcription profiling by array of human BCPAP thyroid tumor cells transfected with a plasmid coding for Id1 to identify Id1 target genes

Project description:BCPAP thyroid tumor cells were transfected with a plasmid coding for Id1 or with empty plasmid as control and single clones were derived by antibiotics selection. <br><br>The gene expression profile of the clone Id1A (which expresses high levels of Id1) was compared with the expression profiles of 3 control clones to identify genes that are regulated by Id1 in thyroid tumor cells.

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