| Sample_geo_accession | GSM931811
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| Sample_status | Public on May 01 2013
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| Sample_submission_date | May 16 2012
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| Sample_last_update_date | May 01 2013
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| Sample_type | RNA
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| Sample_channel_count | 1
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| Sample_organism_ch1 | Mus musculus
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| Sample_taxid_ch1 | 10090
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| Sample_treatment_protocol_ch1 | urogenital ridges were scored by using a YFP reporter for genotype
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| Sample_growth_protocol_ch1 | Embryos were collected from dams at E14.5
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| Sample_molecule_ch1 | total RNA
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| Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
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| Sample_label_ch1 | biotin
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| Sample_label_protocol_ch1 | For each experimental sample, RNA quality was assessed by RNA Nano LabChip analysis on an Agilent Bioanalyzer 2100. Concentrations may also be determined using a NanoDrop 1000 spectrophotometer. Under standard conditions processing of RNAs for GeneChip Analysis was in accordance with methods described in the Affymetrix GeneChip Expression Analysis Technical Manual, revision four, as subsequently detailed. Synthesis of cDNA first and second strand is performed using the GeneChip Expression 3’-Amplification Reagents One-Cycle cDNA Synthesis Kit (P/N 900431). Cleanup of the double stranded product is carried according to standard Affymetrix protocols using the Affymetrix GeneChip Cleanup Module (Affymetrix Catalog # 900371). In vitro transcription (IVT) is performed using the GeneChip Expression Amplification Reagents kit- 30 reactions (P/N 900449) and is carried out according to the standard Affymetrix protocols and quantification of the IVT samples is carried out on a Bio-Tek UV Plate Reader.
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| Sample_hyb_protocol | Hybridization is carried out in an Affymetrix Model 640 hybridization chamber according the Affymetrix GeneChip® Manual. Twenty micrograms of IVT material is the nominal amount used on the GeneChip® arrays. Affymetrix hybridization ovens are used to incubate the arrays at a constant temperature of 45oC overnight.
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| Sample_scan_protocol | Preparation of microarrays for scanning is carried out with Affymetrix appropriate wash protocols matched to the specific chip type on a Model 450 Fluidics station. Affymetrix GeneChip Operating Software (GCOS) operating system controls the Fluidics station process. Scanning is carried out on a GeneChip® Model 3000 7G scanner with autoloader. The Affymetrix GCOS v1.3 operating system controls the Model 3000 7G scanner and data acquisition functions. GCOS maintains the mediated first level data analysis and desktop data management for the entire GeneChip System. Chip library files specific to each array and necessary for scan interpretation are stored on the computer workstation controlling the scanner and are updated regularly as necessary when updates are made available from Affymetrix.
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| Sample_data_processing | GCOS was used with MAS5 algorithm
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| Sample_data_processing | GenePattern pipeline run requested on server http://genepattern.hpcgg.partners.org/ by user system@portal.hpcgg.org at Wed Nov 14 10:33:56 EST 2007
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| Sample_data_processing | Pipeline [name=AffxToFold; version=1.0; desc=Automated bioinformatics analysis for two class fold comparison; author=Eugene Clark, HPCGG; param-count=5]
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| Sample_data_processing | Input Parameters:
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| Sample_data_processing = AffxToFold1.classes | control:1170B;case:1170A
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| Sample_data_processing = AffxToFold1.comparisons | control,case
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| Sample_data_processing = AffxToFold1.input.filename | /udd/gigpad/research/Facilities/Affymetrix Microarrays_61/Batches/15223039-7_Teixeira_Teixeira/Project1170_ScaledTo500_no_rows_with_absent_calls_for_all_samples.xls
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| Sample_data_processing = AffxToFold1.foldLevel | 2
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| Sample_data_processing = AffxToFold1.sortOrder | ascending
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| Sample_data_processing | Result download directory: /udd/gigpad/research/Facilities/Affymetrix Microarrays_61/Batches/15223039-7_Teixeira_Teixeira/AffxToFold_case_vs_control
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| Sample_data_processing | Task 0 done at Wed Nov 14 10:34:11 EST 2007: AffxToFold
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| Sample_data_processing | Download AffxToFold output files done at Wed Nov 14 10:34:11 EST 2007
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| Sample_data_processing | All done at Wed Nov 14 10:34:11 EST 200
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| Sample_platform_id | GPL1261
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| Sample_contact_name | Jose,,Teixeira
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| Sample_contact_email | teixeira@helix.mgh.harvard.edu
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| Sample_contact_laboratory | Thier 931
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| Sample_contact_department | VCRB
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| Sample_contact_institute | Massachusetts General Hospital
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| Sample_contact_address | 55 Fruit St.
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| Sample_contact_city | Boston
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| Sample_contact_state | MA
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| Sample_contact_zip/postal_code | 02114
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| Sample_contact_country | USA
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| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM931nnn/GSM931811/suppl/GSM931811_MISRII_Homozygous_KO_UGR_1170B.CEL.gz
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| Sample_series_id | GSE38009
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| Sample_data_row_count | 45101
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