{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"submitter":["Marcus Breese"],"study_type":["transcription profiling by array"],"organism":["Xenopus laevis"],"species":["Xenopus laevis"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-GEOD-29795"],"description":["This dataset was used to as a filter to annotate the results from another experiment (GSE29791). We used these results to find genes that were enriched in the head regions. In this way, we could eliminate more ubiquitously expressed genes. St. 18 embryos were bisected and RNA was collected from head and tail fragments. 3 individual heads and 3 tails were run, as well as 1 pool of heads and 1 pool of tails  comparison of gene expression profiles for tissues"],"repository":["biostudies-arrayexpress"],"sample_protocol":["Hybridization - Following fragmentation, 10 ug of cRNA were hybridized for 17 hr at 45C on Xenopus Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station.","Labeling - Biotinylated cRNA were prepared according to the standard 2-cycle Affymetrix protocol from 100ng of total RNA (Expression Analysis Technical Manual, Affymetrix).","Nucleic Acid Extraction - Total RNA was collected by homogenization in Invitrogen TRIzol reagent and further purified using an Qiagen RNeasy micro kit."],"figure_sub":["MIAME Score","Raw Data","Organization","Assays and Data","Processed Data","MAGE-TAB Files","Array Designs"],"pubmed_authors":["Matthew Grow","Marcus Breese","Howard Edenberg"],"data_protocol":["Feature Extraction - The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 1000.","Assay Data Transformation - ID_REF = <br>VALUE = MAS5.0 signal<br>ABS_CALL = indicating whether the transcript was present (P), absent (A), or marginal (M)<br>DETECTION P-VALUE =","Image Adquisition - GeneChips were scanned using the standard Affymetrix protocol."],"additional_accession":[]},"is_claimable":false,"name":"Gene expression profile for X.laevis embryo head vs.tail","description":"This dataset was used to as a filter to annotate the results from another experiment (GSE29791). We used these results to find genes that were enriched in the head regions. In this way, we could eliminate more ubiquitously expressed genes. St. 18 embryos were bisected and RNA was collected from head and tail fragments. 3 individual heads and 3 tails were run, as well as 1 pool of heads and 1 pool of tails  comparison of gene expression profiles for tissues","dates":{"release":"2011-12-01T00:00:00Z","modification":"2023-08-15T22:10:17.917Z","creation":"2022-01-31T15:38:57.303Z"},"accession":"E-GEOD-29795","cross_references":{"GEO":["GSE29795"],"EFO":["EFO_0002768"]}}