Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcriptome profiling of breast cancer cells with Insulin like growth factor binding protein 2 (IGFBP2) knockdown

ABSTRACT: The study was carried out to identify the genes regulated upon IGFBP2 modulation in breast cancer. This will help to understand the molecular targets and biological pathways targeted by IGFBP2 in breast cancer. C5 (Cy5) Vs. Vector(Cy3), C5 (Cy5) Vs. Vector(Cy3), C12 (Cy5) Vs. Vector(Cy3), C12 (Cy5) vs. Vector(Cy3)

ORGANISM(S): Homo sapiens

SUBMITTER: Neeraj KUMAR

PROVIDER: E-GEOD-40682 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Regulation of protumorigenic pathways by insulin like growth factor binding protein2 and its association along with β-catenin in breast cancer lymph node metastasis.

Sehgal Priyanka P Kumar Neeraj N Praveen Kumar Varuvar Rajesh VR Patil Shilpa S Bhattacharya Animesh A Vijaya Kumar Manavalan M Mukherjee Geetashree G Kondaiah Paturu P

Molecular cancer 20130616

<h4>Background</h4>Insulin like growth factor binding proteins modulate the mitogenic and pro survival effects of IGF. Elevated expression of IGFBP2 is associated with progression of tumors that include prostate, ovarian, glioma among others. Though implicated in the progression of breast cancer, the molecular mechanisms involved in IGFBP2 actions are not well defined. This study investigates the molecular targets and biological pathways targeted by IGFBP2 in breast cancer.<h4>Methods</h4>Transc ...[more]

PMID: 23767917

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Project description:Sample groupings for this project are as follows: Cauline leaf vs Cultured Cell : - Cauline leaf, p1; Exp:Red; Ref: Green (Cy5:Cy3) - Cauline leaf, p2; Exp:Red; Ref: Green (Cy5:Cy3) - Cauline leaf, p3; Exp:Red; Ref: Green (Cy5:Cy3) Cotyledon light vs Cotyledon dark : - Cotyledon, CP1; Exp:Red; Ref: Green (Cy5:Cy3) - Cotyledon, CP2; Exp:Red; Ref: Green (Cy5:Cy3) Cotyledon light vs Cultured cell : - Cotyledon, cn1; Exp:Green; Ref: Red (Cy3:Cy5) - Cotyledon, cn2; Exp:Green; Ref: Red (Cy3:Cy5) Cotyledon dark vs Cultured cell : - Cotyledon dark, n1; Exp:Green; Ref: Red (Cy3:Cy5) - Cotyledon dark, n2; Exp:Green; Ref: Red (Cy3:Cy5) - Cotyledon dark, n3; Exp:Green; Ref: Red (Cy3:Cy5) Germinating seed vs Cultured cell : - Germinating seed, gn1; Exp:Green; Ref: Red (Cy3:Cy5) - Germinating seed, gn2; Exp:Green; Ref: Red (Cy3:Cy5) - Germinating seed, gn3; Exp:Green; Ref: Red (Cy3:Cy5) Hypocotyl light vs Hypocotyl dark : - Hypocotyl, hldn1; Exp:Red; Ref: Green (Cy5:Cy3) - Hypocotyl, hldn2; Exp:Red; Ref: Green (Cy5:Cy3) Hypocotyl light vs Cultured cell : - Hypocotyl light, hln1; Exp:Green; Ref: Red (Cy3:Cy5) - Hypocotyl light, hln2; Exp:Green; Ref: Red (Cy3:Cy5) Petal vs Cultured cell : - Petal, pn1; Exp:Green; Ref: Red (Cy3:Cy5) - Petal, pn2; Exp:Green; Ref: Red (Cy3:Cy5) - Petal, pn3; Exp:Green; Ref: Red (Cy3:Cy5) 1DBP vs Cultured cell : - Pistil 1DBP, pin1; Exp:Green; Ref: Red (Cy3:Cy5) - Pistil 1DBP, pin2; Exp:Green; Ref: Red (Cy3:Cy5) - Pistil 1DBP, pin3; Exp:Green; Ref: Red (Cy3:Cy5) Pistil 1DPP vs Cultured cell : - Pistil 1DPP, psn1; Exp:Green; Ref: Red (Cy3:Cy5) - Pistil 1DPP, psn2; Exp:Green; Ref: Red (Cy3:Cy5) - Pistil 1DPP, psn3; Exp:Green; Ref: Red (Cy3:Cy5) - Pistil 1DPP, psn4; Exp:Green; Ref: Red (Cy3:Cy5) Root dark vs Cultured cell : - Root dark, rdn1; Exp:Green; Ref: Red (Cy3:Cy5) - Root dark, rdn2; Exp:Green; Ref: Red (Cy3:Cy5) Root light vs Cultured cell : - Root light, rln1; Exp:Green; Ref: Red (Cy3:Cy5) - Root light, rlp1; Exp:Red; Ref: Green (Cy5:Cy3) Root light vs Root dark : - Root light vs dark, rldp1; Exp:Red; Ref: Green (Cy5:Cy3) - Root light vs dark, rldp2; Exp:Red; Ref: Green (Cy5:Cy3) Rosette leaf vs Cultured cell : - Rosette leaf, rfp1; Exp:Red; Ref: Green (Cy5:Cy3) - Rosette leaf, rfp2; Exp:Red; Ref: Green (Cy5:Cy3) - Rosette leaf, rfp3; Exp:Red; Ref: Green (Cy5:Cy3) Sepal vs Cultured cell : - Sepal, sn1; Exp:Green; Ref: Red (Cy3:Cy5) - Sepal, sn2; Exp:Green; Ref: Red (Cy3:Cy5) Silique 3DPP vs Cultured cell : - Silique 3DPP, s3n1; Exp:Green; Ref: Red (Cy3:Cy5) - Silique 3DPP, s3n2; Exp:Green; Ref: Red (Cy3:Cy5) - Silique 3DPP, s3n3; Exp:Green; Ref: Red (Cy3:Cy5) Silique 8DPP vs Cultured cell : - Silique 8DPP, s8n1; Exp:Green; Ref: Red (Cy3:Cy5) - Silique 8DPP, s8n2; Exp:Green; Ref: Red (Cy3:Cy5) - Silique 8DPP, s8n3; Exp:Green; Ref: Red (Cy3:Cy5) Stamen vs Cultured cell : - Stamen, smn1; Exp:Green; Ref: Red (Cy3:Cy5) - Stamen, smn2; Exp:Green; Ref: Red (Cy3:Cy5) - Stamen, smn3; Exp:Green; Ref: Red (Cy3:Cy5) Hypocotyl dark vs Cultured cell : - Hypocotyl dark, hn1; Exp:Green; Ref: Red (Cy3:Cy5) - Hypocotyl dark, hn2; Exp:Green; Ref: Red (Cy3:Cy5) Stem vs Cultured cell : - Stem, stp1; Exp:Red; Ref: Green (Cy5:Cy3) - Stem, stp2; Exp:Red; Ref: Green (Cy5:Cy3) - Stem, stp3; Exp:Red; Ref: Green (Cy5:Cy3) Keywords: other

Project description:Medium chain fatty acids (MCFA) have been shown to inhibit methanogenesis, disrupt the cell envelope, and decrease survival of Methanobrevibacter ruminantium M1 in a dose-, time-, and protonation level dependent way. However, the exact mechanisms behind these observations are still unknown. Although the biochemistry of the metabolic processes of M. ruminantium has been well studied and its genome sequence is now available, little is known about the overall transcriptome regulation of M. ruminantium in response to inhibitors like MCFA. In the present study, we used RNA Sequencing to evaluate the effects of lauric acid (C12) on M. ruminantium. Pure M. ruminantium cell cultures in the mid-exponential growth phase were exposed to C12 in concentrations of 0.4 mg/mL, dissolved in DMSO for 1 h, and the transcriptomic changes compared to DMSO-only treated control samples (final DMSO concentration 0.2 %), were investigated. Gene expression changes upon exposure to C12 were not dramatic in magnitude (log2 fold change mostly below +/- 3) and in gene number (214 genes). However, the observed expression changes affected mostly genes which encoded cell-surface associated proteins (adhesion-like proteins, membrane-associated transporters and hydrogenases), or proteins, which were involved in detoxification or DNA repair processes. The transcriptional response of M. ruminantium M1 to C12 did not specifically inhibit methanogenesis. Instead, the data indicated a non-specific antimicrobial action by lauric acid, which involves destruction of the cell membrane and interferences with cellular energetics in M. ruminantium. To date, there has been no systematic characterization of a ruminal methanogen transcriptome by deep sequencing. Our results give first hints on the molecular inhibitory mechanism of C12 on M. ruminantium. RNA profiles of M. ruminantium treated in vitro (lauric acid disolved in DMSO), non-treated=controls (DMSO supplementation) and non-treated=blanks (no supplementation) were generated by deep sequencing, in triplicates, by using Illumina HiSeq2500

Dataset Information

Transcriptome profiling of breast cancer cells with Insulin like growth factor binding protein 2 (IGFBP2) knockdown

Publications

Regulation of protumorigenic pathways by insulin like growth factor binding protein2 and its association along with β-catenin in breast cancer lymph node metastasis.

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