Result

Search results for the GEO ID: GSE7964

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GSM ID

GPL ID

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Title

Source name

Description

Characteristics

GSM197170

GPL570

SEG1_vehicle pretreated_acid pulsed

Derived from human esophageal cancer

Human esophageal cancer cell line SEG-1

Gene expression data from acid-pulsed cells pretreated with vehicle

Sample_geo_accession	GSM197170
Sample_status	Public on Jul 30 2007
Sample_submission_date	May 31 2007
Sample_last_update_date	Jun 20 2007
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Cells were pretreated with vehicle or HDAC-42 (1.6 uM) in DMEM phenol red-free medium containing 5% FBS for 24 hours. Cells were then rinsed and pulsed with serum-free acidified medium (pH 3.5) or vehicle for 20 mins in a humidified chamber (37C). Cells were rinsed again and replenished with serum-free media or HDAC-42 (1.6 uM) in serum-free media. Cells were harvested 6 hours post vehicle or acid exposure.
Sample_growth_protocol_ch1	SEG-1 esophageal adenocarcinoma cells were plated at 2 x 10^6 cells/T75 flask.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Trizol extraction of total RNA was performed per the manufacterer's instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	The Ovation™ Biotin RNA Amplification and Labeling System (NuGen Technologies, Inc., San Carlos, CA) was used to prepare amplified, biotin-labeled cDNA from total RNA for following manufacturer’s instructions. Briefly, first strand cDNA was synthesized from 25 ng of total RNA using a unique first strand DNA/RNA chimeric primer and reverse transcriptase. Following double strand cDNA generation, amplification of cDNA was achieved by utilizing an isothermal DNA amplification process that involves repeated SPIA™ DNA/RNA primer binding, DNA duplication, strand displacement and RNA cleavage. The amplified SPIA™ cDNA was purified and subjected to a two-step fragmentation and labeling process. The fragmented/biotinylated cDNA content was measured in a ND-1000 spectrophotometer and the quality was analyzed on an RNA 6000 Nano LabChip (Agilent) using Agilent Bioanalyzer 2100.
Sample_hyb_protocol	Following fragmentation, labeled cRNA was hybridized to the human genoma gene chip U133 2.0 Plus. Hybridization was allowed to continue for 16 hours at 45ºC followed by washing and staining of microarrays in a Fluidics Station 450 (Affymetrix Inc., USA).
Sample_scan_protocol	GeneChips were scanned in a GeneChip Scanner 3000 (Affymetrix Inc., USA)
Sample_data_processing	CEL files were generated from DAT files using GeneChip® Operating Software (GCOS) software (Affymetrix Inc., USA). The probe set signals were generated using the RMA algorithm in ArrayAssist 3.4 (Stratagene) and were used to determine differential gene expression by pair-wise comparisons. The genes that were altered by two-fold either ways were sorted and used for further interpretation of the microarray data.
Sample_platform_id	GPL570
Sample_contact_name	Laura,A,Kresty
Sample_contact_email	kresty.1@osu.edu
Sample_contact_department	Internal Medicine
Sample_contact_institute	The Ohio State University
Sample_contact_address	CCC Building, Rm 302B
Sample_contact_city	Columbus
Sample_contact_state	OH
Sample_contact_zip/postal_code	43201
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM197nnn/GSM197170/suppl/GSM197170.CEL.gz
Sample_series_id	GSE7964
Sample_data_row_count	54675

GSM197171

GPL570

SEG1_HDAC42 pretreated_acid pulsed

Derived from human esophageal cancer

Human esophageal cancer cell line SEG-1

Gene expression data from acid-pulsed cells pretreated with HDAC-42

Sample_geo_accession	GSM197171
Sample_status	Public on Jul 30 2007
Sample_submission_date	May 31 2007
Sample_last_update_date	Jun 20 2007
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Cells were pretreated with vehicle or HDAC-42 (1.6 uM) in DMEM phenol red-free medium containing 5% FBS for 24 hours. Cells were then rinsed and pulsed with serum-free acidified medium (pH 3.5) or vehicle for 20 mins in a humidified chamber (37C). Cells were rinsed again and replenished with serum-free media or HDAC-42 (1.6 uM) in serum-free media. Cells were harvested 6 hours post vehicle or acid exposure.
Sample_growth_protocol_ch1	SEG-1 esophageal adenocarcinoma cells were plated at 2 x 10^6 cells/T75 flask.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Trizol extraction of total RNA was performed per the manufacterer's instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	The Ovation™ Biotin RNA Amplification and Labeling System (NuGen Technologies, Inc., San Carlos, CA) was used to prepare amplified, biotin-labeled cDNA from total RNA for following manufacturer’s instructions. Briefly, first strand cDNA was synthesized from 25 ng of total RNA using a unique first strand DNA/RNA chimeric primer and reverse transcriptase. Following double strand cDNA generation, amplification of cDNA was achieved by utilizing an isothermal DNA amplification process that involves repeated SPIA™ DNA/RNA primer binding, DNA duplication, strand displacement and RNA cleavage. The amplified SPIA™ cDNA was purified and subjected to a two-step fragmentation and labeling process. The fragmented/biotinylated cDNA content was measured in a ND-1000 spectrophotometer and the quality was analyzed on an RNA 6000 Nano LabChip (Agilent) using Agilent Bioanalyzer 2100.
Sample_hyb_protocol	Following fragmentation, labeled cRNA was hybridized to the human genoma gene chip U133 2.0 Plus. Hybridization was allowed to continue for 16 hours at 45ºC followed by washing and staining of microarrays in a Fluidics Station 450 (Affymetrix Inc., USA).
Sample_scan_protocol	GeneChips were scanned in a GeneChip Scanner 3000 (Affymetrix Inc., USA)
Sample_data_processing	CEL files were generated from DAT files using GeneChip® Operating Software (GCOS) software (Affymetrix Inc., USA). The probe set signals were generated using the RMA algorithm in ArrayAssist 3.4 (Stratagene) and were used to determine differential gene expression by pair-wise comparisons. The genes that were altered by two-fold either ways were sorted and used for further interpretation of the microarray data.
Sample_platform_id	GPL570
Sample_contact_name	Laura,A,Kresty
Sample_contact_email	kresty.1@osu.edu
Sample_contact_department	Internal Medicine
Sample_contact_institute	The Ohio State University
Sample_contact_address	CCC Building, Rm 302B
Sample_contact_city	Columbus
Sample_contact_state	OH
Sample_contact_zip/postal_code	43201
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM197nnn/GSM197171/suppl/GSM197171.CEL.gz
Sample_series_id	GSE7964
Sample_data_row_count	54675

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