Group1
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE12 | GEO | 2001/11/21
SECONDARY ACCESSION(S): PRJNA84499
REPOSITORIES: GEO
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Project description:Replicate group 2 for GSE11. All samples were processed in parallel to minimize any variation introduced during target preparation. Keywords: parallel sample
2002-01-03 | GSE15 | GEO
Project description:We used high density oligonucleotide arrays to measure the relative expression levels of >39,000 genes and ESTs in the NOD mouse (a murine model of T1D and other autoimmune conditions), four NOD-derived diabetes resistant congenic strains and two nondiabetic control strains. Owing to the importance of T cells in the development of T1D we decided to target two organs, the spleen and thymus. We profiled gene expression in thymi from four week old female mice and spleens from three month old female mice. For each of the 14 strain-tissue combinations (7 strains x 2 tissues) we performed two independent replicate experiments, making the total number of hybridizations performed 28. In each case, an RNA population from a pool of two or three organs was generated to minimize the chances of within strain variation masking genuine variation between the strains. To minimize any variation introduced during target preparation, all samples within a given replicate group were processed in parallel. Three samples from group two (spleen: B10.H2g7_S2 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=gsm594 (GSM594); thymus: B10.H2g7_T2 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=gsm608 (GSM608), B10.H2g7 Idd3_T2 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=gsm609 (GSM609)) and one from group one (spleen B10.H2g7_S1 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=gsm587 (GSM587) failed a preliminary quality control check. Consequently, the steps involved in preparing labelled cRNA from the initial starting material had to be repeated for these four samples at a later date. A subsequent comparison of the variation seen between samples within the same replicate group (samples processed in parallel) versus samples in distinct replicate groups (samples processed at different times) revealed that the variation between the two groups (i.e. owing to independent sample preparation) was higher than the small amount of variation between the closely matched strains. Ignoring the variability introduced during sample preparation was therefore likely to result in spurious changes being detected and genuine strain-specific differences in gene expression being masked. Consequently, we decided to exclude the four samples that had had to be prepared independently owing to failing initial quality control. Keywords = NOD, diabetes, congenic Keywords: other
2001-11-21 | GSE11 | GEO
Project description:SW480 and SW620 are colon cancer cells lines derived from a primary tumor and a corresponding metastasis from the same individual. The numbers indicate the three indipendent replicate RNA samples processed. Three different software packages were used in parallel for signal calculation: Affymetrix microarray suite 5.0, DNA-Chip analyzer, and Robust multi-array analyses. Keywords = metastasis Keywords = colorectal cancer Keywords = tumor progression Keywords: repeat sample
2004-09-01 | GSE1323 | GEO
Project description:Female mice used were SvJ/129, 10-16 weeks of age; Hoxa-10+/+ and Hoxa-10-/- littermates were used in parallel experiments. 14 days after ovariectomy, mice were injected with sesame oil (Sigma; 0.1mL/mouse), followed by sacrifice and removal of uterine horns at 6 hours after injection. 8 uterine horns from 4 mice were pooled to form one sample. Total RNA preparation, cRNA labeling and hybridization were performed according to recommendations by Affymetrix. All 6 samples were collected and processed in parallel. Keywords: other
2002-12-10 | GSE109 | GEO
Project description:We carried out a parallel nested experiment performed simultaneously on RNA-Seq and microarrays that systematically split variation into four stages (treatment, biological variation, library preparation, and chip/lane noise), allowing a separation and comparison of the sources of variation in a well-controlled cellular system, Saccharomyces cerevisiae.
2015-01-31 | GSE65365 | GEO
Project description:Micorarray analysis was performed on RNA samples from hippocampal cultures infected with either Ad-aCaN or Ad-LacZ or uninfected. Each sample was applied to its own GeneChip (Rat RG-U34A; n=7-9 chips/group). Chips were then processed and scanned using Agilent Affymetrix GeneArray Scanner. MAS5 was used to determine signal intensity and presence/absence calls for the data. Keywords = bioinformatics Keywords = gene expression Keywords = calcineurin Keywords = calcium Keywords = Alzheimer's Keywords = inflamation Keywords = Adenovirus Keywords = astrocytes Keywords = microarray Keywords: parallel sample
2005-05-06 | GSE1978 | GEO
Project description:Total RNA was isolated from liver samples of C57/BL6 mice over a circadian time course, 3 biological replicate samples per time point were collected and processed individually. RNA from each individual biological replicate sample was extracted using RNeasy mini kit (Qiagen Cat# 74106) and hybridized on an Affymetrix mouse Gene ST1.0 microarray.
2013-01-01 | GSE37387 | GEO
Project description:Purpose: To compare the transcriptomes of HCC1937 vector and wtBRCA1 cells which were treated with OTX-015. Methods: HCC1937 vector and wtBRCA1 cells were treated with 5 micromolar OTX-015 for 24 hours. Total RNA was extracted and processed with NEBNext Ultra Directional RNA Library Prep Kit for cDNA library preparation. The data are in duplicate and raw data were generated by Illumina 2500 sequencer. The Fastq format data were then processed with Tophat for genome mapping. After getting the bam files, they were further analyzed with cuffdiff for gene expression of different groups. Results: From the transcriotome profiling and analysis, we got gene expression data of DMSO control group and OTX-015 treatment group for the HCC1937 BRCA1 isogenic cell lines. Conclusion: The gene expression data revealed the transcriptome variation by OTX-015 treatment.
2019-01-30 | GSE109809 | GEO
Project description:For each sample a matched total was prepared in parallel. For each biological replicate the cells were crosslinked on different days. Amplicons were prepared from each sample and hybridized on mouse 1.5 kb promoter arrays from Nimblegen. Keywords: ChIP-chip
2006-06-06 | GSE4908 | GEO
Project description:Every individual kidney was hybridised 4 times including 2 dye swaps: K1: 23557-23560 K2: 23561-23564 K3: 23565-23568 K4: 23569-23572 Only 2 of 4 hybridisations were made at one sample preparation. Keywords: parallel sample
2004-07-27 | GSE1585 | GEO