Result

Search results for the GEO ID: GSE19618

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GSM ID

GPL ID

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Title

Source name

Description

Characteristics

GSM489248

GPL1261

Otocyst_EGFP-negative

EGFP-negative otocyst epithelial cells

age: E10.5 tissue: otocyst genotype: Tg(ETAR-EGFP)14Imeg heterozygous gfp status: negative

EGFP is not expressed in the dorsolateral otocyst.

Sample_geo_accession	GSM489248
Sample_status	Public on May 23 2011
Sample_submission_date	Dec 23 2009
Sample_last_update_date	May 23 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Otocysts dissected from heterozygous embryos were dissociated to a single-cell suspension by trypsin treatment (200 μl of 0.25% trypsin/ EDTA solution). 1 ml of Dulbecco’s Modified Eagle Medium (DMEM) and 10% fetal calf serum (FCS) was added to the single-cell suspension. After centrifugation, the cells were resuspended in 0.5 ml of PBS and 5% FCS. Propidium iodide (PI) was added to a final concentration of 1 μg/ml. By FACS experiment, the otocyst epithelial cells were sorted into EGFP-positive and EGFP-negative cells.
Sample_growth_protocol_ch1	The mice were housed with 12 hours of light and 12 hours of darkness in a controlled temperature (23 °C).
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Homogenization of cell lysates was performed using QIAshredder homogenizers (QIAGEN, Hilden, Germany). Total RNA was extracted using RNeasy Plus Mini Kit (QIAGEN) according to the manufacturers’ protocol.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA. The sample preparation protocol from the Affymetrix GeneChip Expression Analysis Manual (Affymetrix) was used.
Sample_hyb_protocol	The biotin-labeled cRNA was then hybridized to a high-density oligonucleotide array (GeneChip Mouse Genome 430 2.0 array; Affymetrix, Santa Clara, CA, USA). After washing, arrays were stained with streptavidin-phycoerythrin.
Sample_scan_protocol	Image data were collected and analyzed with an Affymetrix GeneChip Scanner 3000 (Affymetrix).
Sample_data_processing	Microarray Suite software 5.0 (Affymetrix) was used to calculate the average difference for each gene probe set, shown as the gene expression intensity value. The signal intensities were normalized so that the average of all of the genes on a GeneChip would be 100.
Sample_platform_id	GPL1261
Sample_contact_name	Chisato,,Fujimoto
Sample_contact_institute	The University of Tokyo
Sample_contact_address	7-3-1 Hongo
Sample_contact_city	Bunkyo-ku Tokyo
Sample_contact_zip/postal_code	113-0033
Sample_contact_country	Japan
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM489nnn/GSM489248/suppl/GSM489248.CEL.gz
Sample_series_id	GSE19618
Sample_data_row_count	45101

GSM489249

GPL1261

Otocyst_EGFP-positive

EGFP-positive otocyst epithelial cells

age: E10.5 tissue: otocyst genotype: Tg(ETAR-EGFP)14Imeg heterozygous gfp status: positive

EGFP is mainly expressed in the ventral and dorsomedial otocyst.

Sample_geo_accession	GSM489249
Sample_status	Public on May 23 2011
Sample_submission_date	Dec 23 2009
Sample_last_update_date	May 23 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Otocysts dissected from heterozygous embryos were dissociated to a single-cell suspension by trypsin treatment (200 μl of 0.25% trypsin/ EDTA solution). 1 ml of Dulbecco’s Modified Eagle Medium (DMEM) and 10% fetal calf serum (FCS) was added to the single-cell suspension. After centrifugation, the cells were resuspended in 0.5 ml of PBS and 5% FCS. Propidium iodide (PI) was added to a final concentration of 1 μg/ml. By FACS experiment, the otocyst epithelial cells were sorted into EGFP-positive and EGFP-negative cells.
Sample_growth_protocol_ch1	The mice were housed with 12 hours of light and 12 hours of darkness in a controlled temperature (23 °C).
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Homogenization of cell lysates was performed using QIAshredder homogenizers (QIAGEN, Hilden, Germany). Total RNA was extracted using RNeasy Plus Mini Kit (QIAGEN) according to the manufacturers’ protocol.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA. The sample preparation protocol from the Affymetrix GeneChip Expression Analysis Manual (Affymetrix) was used.
Sample_hyb_protocol	The biotin-labeled cRNA was then hybridized to a high-density oligonucleotide array (GeneChip Mouse Genome 430 2.0 array; Affymetrix, Santa Clara, CA, USA). After washing, arrays were stained with streptavidin-phycoerythrin.
Sample_scan_protocol	Image data were collected and analyzed with an Affymetrix GeneChip Scanner 3000 (Affymetrix).
Sample_data_processing	Microarray Suite software 5.0 (Affymetrix) was used to calculate the average difference for each gene probe set, shown as the gene expression intensity value. The signal intensities were normalized so that the average of all of the genes on a GeneChip would be 100.
Sample_platform_id	GPL1261
Sample_contact_name	Chisato,,Fujimoto
Sample_contact_institute	The University of Tokyo
Sample_contact_address	7-3-1 Hongo
Sample_contact_city	Bunkyo-ku Tokyo
Sample_contact_zip/postal_code	113-0033
Sample_contact_country	Japan
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM489nnn/GSM489249/suppl/GSM489249.CEL.gz
Sample_series_id	GSE19618
Sample_data_row_count	45101

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