Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Integrative analysis of genomic amplification-dependent expression and loss-of-function screen identifies ASAP1 as a driver gene in triple negative breast cancer progression

ABSTRACT: Purpose: To investigate the impact of ASAP1 depletion on the transcriptomic profile of TNBC cells using TempO-Seq-based high-throughput RNA sequencing. Methods: Three TNBC cell lines (BT549, SUM149PT and Hs578T) were treated with siRNA control or siRNA targeting ASAP1 for 72 hours. RNA was isolated with RNeasy Plus Mini Kit as described by manufacturer (QIAGEN, Cat. 74136). Transcriptome RNA-Sequencing (TempO-Seq) was performed using Illumina high-throughput RNA sequencing. Results: We mapped about 7 million sequence reads per sample to the human genome. Normalization and differential expression analysis were performed using DESeq2 package. Genes with significant down- or up-regulation (Log2 FC ≥ |1|) under indicated conditions were analysed by web-based functional analysis tool Metascape to visualise and annotate their biological functions and pathways. Conclusions: Genes with 2-fold changes (absolute Log2 FC ≥ 1) in down- or up-regulation were selected in BT549 (311 down / 495 up), Hs578T (133 down / 117 up) and SUM149PT (500 down / 401 up) cells, respectively. Consequently, 95 DEGs were downregulated, and 79 DEGs upregulated in ≥ 2/3 of the TNBC cell lines, in total 174 DEGs, which were considered as common DEGs that were susceptible to the depletion of the amplification-dependent ASAP1. 53 of these commonly differentially expressed transcripts were linked to relapse-free survival in TNBC patients.

ORGANISM(S): Homo sapiens

PROVIDER: GSE134803 | GEO | 2020/05/19

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

A kinase inhibitor screen identifies a dual cdc7/CDK9 inhibitor to sensitise triple-negative breast cancer to EGFR-targeted therapy

Project description:Purpose: To investigate the impact of combined cdc7, CDK9 and EGFR inhibition on the transcriptomic profile of EGFR-TKI-resistant TNBC cells using high-throughput RNA sequencing. Methods: EGFR-TKI-resistant TNBC cell lines (Hs578T and SKBR7) were treated with DMSO, lapatinib (3.16 µM), PHA-767491 (1 µM) or co-treated with lapatinib (3.16 µM) & PHA-767491 (1 µM) for 6 hours. RNA was isolated with RNeasy Plus Mini Kit as described by manufacturer (QIAGEN, Cat. 74136). Transcriptome RNA-Sequencing (RNA-Seq) was performed using Illumina high-throughput RNA sequencing. Results:we mapped about 40 million sequence reads per sample to the human genome (build hg38). RNA-Seq data was normalised by TMM using EdgeR’s normalisation-factor followed by quantile normalisation and presented in Log2 fold change (Log2 FC) scales.Genes with significant down- or up-regulation (Log2 FC ≥ |0.5|) under indicated conditions were analysed by web-based functional analysis tool Ingenuity pathway Analysis (IPA) to visualise and annotate their biological functions and pathways. Conclusions: 1387 and 2747 genes were down-regulated in co-treated Hs578T and SKBR7 cells, respectively. 2614 genes were up-regulated by co-treatment in Hs578T cells, whilst 243 genes were up-regulated by the same treatment in SKBR7 cells. We identified 845 commonly differentially expressed transcripts in both HS578T and SKBR7 cells after co-treatment of which 141 transcripts were up-regulated and 704 transcripts were down-regulated. 34 of these commonly differentially expressed transcripts were linked to metastasis-free survival in TNBC patients.

2019-07-21 | GSE131375 | GEO

search for downstream target genes of HTG3 based on RNA seq data

Project description:With the threshold of absolute value of log2 (Fold Change) ≥1 and P < 0.05, 4122 and 4100 differentially expressed genes (DEGs) were up-regulated and down-regulated, respectively by HS in ZH11; 4725 genes(H-DEGs) were up or down-regulated in the htg3 mutant under normal or stress conditions; Among the H-DEGs, 1025 and 947 genes were up- and down-regulated, respectively, by HS in ZH11.

2022-02-28 | GSE197401 | GEO

to investigate the changes of the gene of glioma mice after Bifidobacterium administration

Project description:Differentially expressed genes (DEGs) between the Glioma and BIF groups were identified based on P < 0.05 and |log2 (fold change)| ≥1, among which 441 were up-regulated and 520 were down-regulated

2023-10-31 | GSE246028 | GEO

Gene expression profile at single cell level of SUM149PT, SUM185PE, SUM229PE, SUM159PT and SUM1315MO2 cell lines

Project description:SUM149PT, SUM185PE, SUM229PE, SUM159PT and SUM1315MO2 are triple negative breast cancer cell lines. They were sequenced to test the contrastive learning-based algorithm we developed to predict Afatinib sensitivity in TNBC.

2024-03-25 | GSE228275 | GEO

miR-200c induction in BT549 TNBC cells

Project description:miR-200c induction in BT549 TNBC cells

| PRJNA423021 | ENA

Global gene expression profiles of GATA6-AS1 knockdown cultures and control shRNA cultures at cardiomyocyte differentiation day 2 and day 5

Project description:Methods: RNA-seq libraries were prepared using the Illumina TruSeq technology. The libraries were quantified and samples were multiplexed in each lane of the flowcell. Cluster generation was performed and then sequenced on the Illumina HiSeq2500 system. Reads were mapped on the Human Genome Reference (GRCh38) and normalized expression table was generated. Results: At day 2, GATA6-AS1 knockdown resulted in 499 down-regulated and 1086 up-regulated differentially expressed genes (DEGs, set at -log10 p-value = 1.996; log2 changes <-1 or >1). At day 5, GATA6-AS1 knockdown resulted in 1457 down-regulated and 1166 up-regulated DEGs Conclusions: Data demonstrate GATA6-AS1 knockdown inhibits mesoderm induction and cardiomyocyte differentiation in hPSCs.

2020-09-03 | GSE157369 | GEO

RNA-Seq from zmknl1 and WT kernels at 14 DAP (day after pollination) with each two independent biological replicates

Project description:To further understand the basis of the phenotypic defects in the zmknl1 mutant, we performed RNA-Seq from zmknl1 and WT kernels at 14 DAP with each two independent biological replicates. Totally 555 significantly differentially expressed genes (DEGs) were identified according to these RNA-Seq data (q-value <0.05, log2(fold change) >= 1.5), with 317 down- and 238 up-regulated genes.

2019-12-21 | GSE124245 | GEO

Global Analysis of the Transcriptional Response of Chinese cabbage (Brassica rapa ssp. pekinensis) to Methyl Jasmonate Reveals JA Signaling on Enhancement of Secondary Metabolism Pathways

Project description:We conducted a RNA-Seq analysis of MeJA-treated Chinese cabbage leaf transcriptome. Total 14,619,469 sequence reads were generated to produce 27,461 detected genes, among which 1,451 genes were up-regulated and 991 genes were down-regulated as differentially expressed genes (DEGs) (log2 ratio â¥1, false discovery rate â¤0.001). More than 90% of the DEGs (2,278) were between 1.0- and 3.0-fold (log2 ratio). The most highly represented pathways by 1,674 annotated DEGs were related to âmetabolic pathwaysâ (333 members), âribosomeâ (314 members), âbiosynthesis of secondary metabolitesâ (218 members), âplant-pathogen interactionâ (146 members), and âplant hormone signal transductionâ (99 members). Fourteen genes involved in JA biosynthesis pathway were up-regulated. As many as 182 genes for the biosynthesis of several secondary metabolites were induced, and the level of indole glucosinolate was highly increased by MeJA treatment. The genes encoding sugar catabolism and some amino acids synthesis were up-regulated, which could supply structural intermediates and energy for the biosynthesis of secondary metabolites. The results demonstrated a high degree of transcriptional complexity with dynamic coordinated changes in global gene expression of Chinese cabbage in response to MeJA treatment. It expands our understanding of the complex molecular events on JA-induced plant resistance and accumulation of secondary metabolites. It also provides a foundation for further studies on the molecular mechanisms of different pathways in other Brassica crops under MeJA treatment. Transcriptomic analysis of MeJA-treated Chinese cabbage leaf

2015-12-31 | E-GEOD-51363 | biostudies-arrayexpress

RNA-seq analysis of murine Sox4+/+ versus Sox4-/- 4T1 TNBC cells

Project description:We identified the SOX4 transcription factor and integrin alpha V encoded by the ITGAV gene as important resistance mechanisms to T cell-mediated cytotoxicity of TNBC cells. Here, we performed RNA seq. analysis of SOX4 and ITGAV deficient (CRISPR knockout) BT549 human and 4T1 murine TNBC cells as compared to control edited counterparts. Additionally, we performed SOX4 specific ChIP-seq studies in BT549 human TNBC cells. The objective of the study was to identify the molecular regulators and signaling pathways that mediate resistance to T cell mediated immunity. GSEA analysis of RNA-seq data showed that the 'interferon response' represented one of the top pathways for genes upregulated in SOX4 or ITGAV edited compared to control TNBC cells. In contrast, gene sets associated with TGF beta and TNF alpha/NF kappa b were negatively enriched in both Sox4 and Itgav edited TNBC cells. Further analysis of RNA-seq data showed that SOX4 or ITGAV edited TNBC cells contained higher mRNA levels of many interferon-stimulated genes (ISGs), including genes associated with important innate immune pathways such as RIG-I/MDA-5, cGAS - STING and the AIM2 inflammasome

2021-01-01 | GSE144013 | GEO

Genome wide SOX4 specific binding sites in BT549 human TNBC cells

2021-01-01 | GSE144012 | GEO