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RNA differencial expression data between scrambled siRNA-treated mice and HN1L siRNA-treated mice tumor samples

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): synthetic construct Homo sapiens

PROVIDER: GSE106200 | GEO | 2017/12/20

SECONDARY ACCESSION(S): PRJNA415905

REPOSITORIES: GEO

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mRNA differencial expression data between scrambled siRNA-treated mice and HN1L siRNA-treated mice tumor samples

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MicroRNA differencial expression data between scrambled siRNA-treated mice and HN1L siRNA-treated mice tumor samples

Project description:(HN1L) is a targetable breast cancer stem cell (BCSC) gene that is altered in 25% of whole breast cancer and significantly correlated with shorter overall or relapse-free survival in triple negative breast cancer (TNBC) patients. HN1L silencing reduced the population of BCSCs, inhibited tumor initiation, re-sensitized chemo-resistant tumors to docetaxel, and hindered cancer progression in multiple TNBC cell line derived xenografts. We used miRNA array to compare miRNA expression profiles from PDX BCM2665 xenograft tumors with or without HN1L knockdown, to identify role of HN1L in regulating miRNA.

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RNA differencial expression data between scrambled siRNA-treated mice and HN1L siRNA-treated mice tumor samples

Project description:RNA differencial expression data between scrambled siRNA-treated mice and HN1L siRNA-treated mice tumor samples

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mRNA differencial expression data between scrambled siRNA-treated mice and HN1L siRNA-treated mice tumor samples

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MicroRNA differencial expression data between scrambled siRNA-treated mice and HN1L siRNA-treated mice tumor samples

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iTRAQ MS of mouse LbetaT2 cells transfected with Galphas siRNA vs. scrambled siRNA

Project description:Twenty million LbetaT2 cells were transfected with either control or Galphas siRNA, then were seeded in 100-mm cell culture plates in DMEM + 10% FBS. Two days later, cells were washed twice with pre-warmed PBS. Conditioned media was harvested another 24 h later, and centrifuged at 20,000 g for 10 min at 4°C to remove cell debris. To enrich secreted proteins in the conditioned media, conditioned media samples were centrifuged using Amicon centrifugal filters with a 3kDa cutoff (Millipore, Billerica, MA). A total of 8 concentrated conditioned media samples were independently prepared: 4 samples from control siRNA-treated cells, and 4 samples from Galphas siRNA-treated cells. Samples were stored at –70°C until they were sent to the Mount Sinai Proteomics Core Facility.HPLC-isobaric tags for relative and absolute quantitation mass-spectrometry (iTRAQ MS) - Data analysis ProteinPilot 3.0 (AB Sciex) was used to search the MS/MS spectra for protein identification and quantitation with its searching algorithm Paragon 3.0.0.0 (*Reference). The protein database used for searching was Uniprot mouse fasta file (release-2010_11). The search parameters include quantitation for iTRAQ 8-plex (peptide-labeled), MMTS for cysteine alkylation, trypsin for enzyme digestion, biological modifications for ID focus, and taxonomy set for Mus musculus. The detected protein threshold was set to 1.3 (95% confidence). Additionally, we converted our AB Sciex mass spectral data (TOF/TOF data) into an mzML format, using the AB Sciex MS Data Converter (beta version 1.3) tool. Finally, we used the command line tool group2xml, which is included with ProteinPilot Software, to convert the .group search engine result file to an XML file.

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Expression data of HeLa cells treated with CENP-E siRNA or Eg5 siRNA in the presence of BubR1 siRNA.

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Gene expression data from glioblastoma tumor samples

Project description:Glioblastoma (GBM) is an incurable brain tumor carrying a dismal prognosis, which displays considerable heterogeneity. We have recently identified recurrent H3F3A mutations affecting two critical positions of histone H3.3 (K27, G34) in one-third of pediatric GBM. Here we show that each of these H3F3A mutations defines an epigenetic subgroup of GBM with a distinct global methylation pattern, and are mutually exclusive with IDH1 mutation (characterizing a CpG-Island Methylator Phenotype (CIMP) subgroup). Three further epigenetic subgroups were enriched for hallmark genetic events of adult GBM (EGFR amplification, CDKN2A/B deletion) and/or known transcriptomic signatures. We also demonstrate that the two H3F3A mutations give rise to GBMs in separate anatomic compartments, with differential regulation of OLIG1/2 and FOXG1, possibly reflecting different cellular origins. To further dissect the biological differences between epigenetic glioblastoma subgroups, we looked at the transcriptomic profiles of glioblastoma samples. 46 glioblastoma samples from patients of various ages were selected for RNA extraction and hybridization on Affymetrix Affymetrix Human Genome U133 Plus 2.0 Arrays.

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