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E-MEXP-3500
Mus musculus
6 Downloadable Samples
Affymetrix Mouse Genome 430 2.0 Array (mouse4302), UNKNOWN
Description
In total 3 mice brain tissues were used for this experiment. Tissue from each mouse brain was divided for immunoprecipitation with 5ug of either rabbit anti-TDP-43 antibody (Abcam) or normal rabbit IgG (Sigma) .The antibodies were first incubated with the lysate overnight at 4 degrees C, after which 50 uL of protein G Dynabeads(tm) (Invitrogen(tm)) added and the solution incubated for 1 hour at 4 degrees C with rotation. Following several washing with washing buffer (Invitrogen(tm)), the protein-RNA complex was eluted from 20 uL of bead-protein complex using 10 uL of elution buffer (Invitrogen(tm)) and seperated on a 10% NuPage(tm) Bis-Tris gel (Invitrogen(tm)). RNA was isolated from the remaining 30 uL of protein-bead complex using TRIzol reagent (Invitrogen) followed by DNaseI treatment (Ambion). The TDP-43 immunoprecipitated RNA was converted to cDNA, fragmented and biotin labelled using WT cDNA synthesis & amplification kit and Terminal Labeling Kit (Affymetrix(tm)) for Affymetrix(tm) GeneChip(tm) Mouse Gene 1.0 ST and 3'-IVT expression analysis kit (Affymetrix(tm)) for GeneChip(tm) Mouse 430_2 arrays according to the standard protocol. Labelled RNA was hybridised to arrays in a hybridization oven (Affymetrix(tm)) at 45 degrees C rotating at 60 rpm for 17 hours and scanned using the Affymetrix(tm) GeneChip Scanner. Successful hybridisation to the microarray was checked using Expression Console software (Affymetrix(tm)) and the data (.CEL files) transferred to Partek Genomics Suite for statistical analysis. TDP-43 and IgG immunoprecipitated RNA samples were each hybridised to 3 GeneChip Mouse Gene 1.0 ST and 3 GeneChip Mouse 430 (n = 6 for each group).
Publication Title
No associated publication
Sample Metadata Fields
Sex, Specimen part, Subject
View Samples- Homo sapiens
- 359 Downloadable Samples
- Illumina HumanHT-12 V3.0 expression beadchip
Description
We carried out blood transcriptome-wide association studies and replicated results to identify genes whose expression differs across the human aging spectrum.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Age, Specimen part, Treatment, Race
View Samples- Homo sapiens
- 24 Downloadable Samples
- Illumina HumanHT-12 V4.0 expression beadchip
Description
Comparison of the gene expression profiles of a recombinant protein producing Hek 293 cell line (referred to as producer) and its non-producing parental cell line Hek293F (referred to as non-producer). The parental cell line was obtained from Invitrogen, Carlsbad, CA. The producer was transfected with a heavy chain variable region fused to the Fc region of a human IgG (dAb-Fc). The aim of this study was to gain a better understanding of the process of recombinant protein production in Hek293 cells and to identify targets for the engineering of an improved host cell line.
Publication Title
A multi-omics analysis of recombinant protein production in Hek293 cells.
Sample Metadata Fields
Cell line, Time
View Samples- Escherichia coli
- 18 Downloadable Samples
- Affymetrix E. coli Genome 2.0 Array (ecoli2)
Description
Gene expression profiling of two different E. coli CAUTI strains during biofilm growth in human urine.<br></br>
Publication Title
Escherichia coli isolates causing asymptomatic bacteriuria in catheterized and noncatheterized individuals possess similar virulence properties.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 36 Downloadable Samples
- Illumina human-6 v2.0 expression beadchip
Description
In the following experiment, three different hESC cell lines (HES2, MEL1 and H9) were grown in the presence of KOSR, KOSR or mTESR containing media respectively. KOSR (Knockout serum replacement medium) is a standard media allowing the growth of hESC without the need for manual passaging - Enzymatic passaging is used instread. mTESR (Ludwig et al., 2007) is a media allowing the growth of hESC on matrigel with enzymatic passaging. At day 7 after passaging, these cells were FACs sorted for the presence of GCTM-2 and CD9 into 4 distinct fractions (p4: GCTM-2-neg, CD9-neg; p5: GCTM-2-low, CD9-low; p6: GCTM-2-medium, CD9-medium and p7: GCTM-2-high, CD9-high). For each cell line-subfraction combination, RNA was harvested and subject to microarray.
Publication Title
Identification of human embryonic stem cell surface markers by combined membrane-polysome translation state array analysis and immunotranscriptional profiling.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 31 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Following sex determination, XY and XX gonads develop into a testis and an ovary, respectively. Depending on the sex of the gonad, resident germ cells will subsequently be committed to either spermatogenesis or oogenesis. In this study we took advantage of the Wv/Wv mouse genetic model, in which gonads are almost devoided of germ cells, to uncover gene expression underlying fetal germ cell development.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Age, Specimen part
View Samples- Homo sapiens
- 24 Downloadable Samples
- Illumina HumanWG-6 v3.0 expression beadchip
Description
Two independent induced pluripotent stem cell lines: ES4CL1 (derived from foreskin) and MR90C2 (derived from lung Fibroblast) were maintained on inactivated mouse embryonic fibroblast (MEF) feeder cells in the presence of ESC media containing DMEM, 20% knock-out serum replacement with 100ng/mL of bFGF. 7 days after seeding, cells were harvested in TrypLE Express and FACs sorted using antibodies detecting the presence of cell surface antigens GCTM-2 and CD9.
Publication Title
Identification of unsafe human induced pluripotent stem cell lines using a robust surrogate assay for pluripotency.
Sample Metadata Fields
Specimen part
View Samples- Bos indicus, Bos taurus
- 12 Downloadable Samples
- Affymetrix Bovine Genome Array (bovine)
Description
This experiment was undertaken to document changes in gene expression in the skin of tick-resistant Brahman (Bos indicus) and tick-susceptible Holstein-Friesian (Bos taurus) cattle prior to, and following, infestation with the cattle tick Rhipicephalus (Boophilus) microplus
Publication Title
No associated publication
Sample Metadata Fields
Sex, Age, Specimen part, Disease, Disease stage
View Samples- Homo sapiens
- 12 Downloadable Samples
- Illumina human-6 v2.0 expression beadchip
Description
HES4 hESC were cultured in serum media and maintained on a layer of mouse embryonic fibroblast feeder cells at a density of 6 x 104 cells/cm2. For differentiation: hESC were differentiated for a total of 14 days. Differentiation was induced by passaging 4 human ES cell pieces onto 12 well plates seeded with 0.67 x 10E4 cells/cm2. Cells were maintained in media containing 20% FCS for 2 days before media containing 5% FCS was used. Reduced serum media was changed every second day for the remaining 12 days
Publication Title
Subfractionation of differentiating human embryonic stem cell populations allows the isolation of a mesodermal population enriched for intermediate mesoderm and putative renal progenitors.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 12 Downloadable Samples
- Illumina human-6 v2.0 expression beadchip
Description
HES2 ESCs were grown in standard ES culture conditions. After 1 week, these cells were FACs sorted for the presence of GCTM-2 and CD9.
Publication Title
Identification of human embryonic stem cell surface markers by combined membrane-polysome translation state array analysis and immunotranscriptional profiling.
Sample Metadata Fields
No sample metadata fields
View Samples