Result

Search results for the GEO ID: GSE31004

(Click on the check boxes provided under "Select for analysis", to initiate grouping)

(Once the selection is made, click on "Add groups" in "Make groups for comparison", to make a group. Scroll down)

GSM ID

GPL ID

Select for analysis

Title

Source name

Description

Characteristics

GSM768225

GPL1261

Saline control, biological rep1

Mouse newborn palate

tissue: Newborn Palate strain: BALB/c age: Newborn - P1 treatment: saline-treated fetuses

Gene expression data from saline-treated fetuses

Sample_geo_accession	GSM768225
Sample_status	Public on Dec 15 2011
Sample_submission_date	Jul 27 2011
Sample_last_update_date	Dec 15 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Sterile physiological saline or nicotine (1.5 mg/kg/day, 3.0 mg/kg/day, or 4.5 mg/kg/day)
Sample_growth_protocol_ch1	A small incision of 0.5 cm was made in the skin posterior to the shoulder of pregnant mice and an osmotic mini-pump (Model 1004 - Alzet Corp, CA) was implanted subcutaneously. The incision was closed with a wound clip and covered with an antibiotic. The clip was removed after 14 days and dams were allowed to give birth naturally at/around 21 days
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was isolated from the posterior one-third of palatal tissues from newborn pups (n=2) using the RNeasy spin column RNA purification kit (Qiagen)
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	The UNMC Microarray Core uses a variety of commercially available assays for generating biotin-labeled samples for hybridization to Affymetrix GeneChip
Sample_hyb_protocol	The GeneChip arrays are hybridized overnight in the Affymetrix hybridization oven at 42oC. The Affymetrix GeneChip Fluidics Station 450 performs the automated Affymetrix wash and stain protocols.
Sample_scan_protocol	The Affymetrix GeneChip Scanner 3000 7G is used to generate the resultant GeneChip array image
Sample_data_processing	Scanned array images were analyzed by dChip applying a smoothing spline normalization method prior to obtaining model-based gene expression indices, a.k.a. signal values. There were no outliers identified by dChip, so all samples were carried on for subsequent analysis. When comparing two groups of samples to identify enriched genes in a given group, we used the lower confidence bound (LCB) of the fold change (FC) between the two groups as the cut-off criteria. If 90% LCB of FC between the two groups was above 1.2, the corresponding gene was considered to be differentially expressed.
Sample_platform_id	GPL1261
Sample_contact_name	Ali,,Nawshad
Sample_contact_email	anawshad@unmc.edu
Sample_contact_phone	402-472-1378
Sample_contact_fax	402-472-2551
Sample_contact_laboratory	Nawshad Lab
Sample_contact_department	Oral Biology
Sample_contact_institute	Unviersity of Nebraska Medical Center
Sample_contact_address	40th and Holdrege
Sample_contact_city	Lincoln
Sample_contact_state	NE
Sample_contact_zip/postal_code	68583
Sample_contact_country	USA
Sample_contact_web_link	http://www.unmc.edu/dentistry/nawshad.htm
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM768nnn/GSM768225/suppl/GSM768225.CEL.gz
Sample_series_id	GSE31004
Sample_data_row_count	45101

GSM768226

GPL1261

Saline control, biological rep2

Mouse newborn palate

tissue: Newborn Palate strain: BALB/c age: Newborn - P1 treatment: saline-treated fetuses

Gene expression data from saline-treated fetuses

Sample_geo_accession	GSM768226
Sample_status	Public on Dec 15 2011
Sample_submission_date	Jul 27 2011
Sample_last_update_date	Dec 15 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Sterile physiological saline or nicotine (1.5 mg/kg/day, 3.0 mg/kg/day, or 4.5 mg/kg/day)
Sample_growth_protocol_ch1	A small incision of 0.5 cm was made in the skin posterior to the shoulder of pregnant mice and an osmotic mini-pump (Model 1004 - Alzet Corp, CA) was implanted subcutaneously. The incision was closed with a wound clip and covered with an antibiotic. The clip was removed after 14 days and dams were allowed to give birth naturally at/around 21 days
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was isolated from the posterior one-third of palatal tissues from newborn pups (n=2) using the RNeasy spin column RNA purification kit (Qiagen)
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	The UNMC Microarray Core uses a variety of commercially available assays for generating biotin-labeled samples for hybridization to Affymetrix GeneChip
Sample_hyb_protocol	The GeneChip arrays are hybridized overnight in the Affymetrix hybridization oven at 42oC. The Affymetrix GeneChip Fluidics Station 450 performs the automated Affymetrix wash and stain protocols.
Sample_scan_protocol	The Affymetrix GeneChip Scanner 3000 7G is used to generate the resultant GeneChip array image
Sample_data_processing	Scanned array images were analyzed by dChip applying a smoothing spline normalization method prior to obtaining model-based gene expression indices, a.k.a. signal values. There were no outliers identified by dChip, so all samples were carried on for subsequent analysis. When comparing two groups of samples to identify enriched genes in a given group, we used the lower confidence bound (LCB) of the fold change (FC) between the two groups as the cut-off criteria. If 90% LCB of FC between the two groups was above 1.2, the corresponding gene was considered to be differentially expressed.
Sample_platform_id	GPL1261
Sample_contact_name	Ali,,Nawshad
Sample_contact_email	anawshad@unmc.edu
Sample_contact_phone	402-472-1378
Sample_contact_fax	402-472-2551
Sample_contact_laboratory	Nawshad Lab
Sample_contact_department	Oral Biology
Sample_contact_institute	Unviersity of Nebraska Medical Center
Sample_contact_address	40th and Holdrege
Sample_contact_city	Lincoln
Sample_contact_state	NE
Sample_contact_zip/postal_code	68583
Sample_contact_country	USA
Sample_contact_web_link	http://www.unmc.edu/dentistry/nawshad.htm
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM768nnn/GSM768226/suppl/GSM768226.CEL.gz
Sample_series_id	GSE31004
Sample_data_row_count	45101

GSM768227

GPL1261

Nic 1.5mg/kg/day, biological rep1

Mouse newborn palate

tissue: Newborn Palate strain: BALB/c age: Newborn - P1 treatment: 1.5mg/kg/day nicotine-treated fetuses

Gene expression data from 1.5mg/kg/day nicotine-treated fetuses

Sample_geo_accession	GSM768227
Sample_status	Public on Dec 15 2011
Sample_submission_date	Jul 27 2011
Sample_last_update_date	Dec 15 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Sterile physiological saline or nicotine (1.5 mg/kg/day, 3.0 mg/kg/day, or 4.5 mg/kg/day)
Sample_growth_protocol_ch1	A small incision of 0.5 cm was made in the skin posterior to the shoulder of pregnant mice and an osmotic mini-pump (Model 1004 - Alzet Corp, CA) was implanted subcutaneously. The incision was closed with a wound clip and covered with an antibiotic. The clip was removed after 14 days and dams were allowed to give birth naturally at/around 21 days
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was isolated from the posterior one-third of palatal tissues from newborn pups (n=2) using the RNeasy spin column RNA purification kit (Qiagen)
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	The UNMC Microarray Core uses a variety of commercially available assays for generating biotin-labeled samples for hybridization to Affymetrix GeneChip
Sample_hyb_protocol	The GeneChip arrays are hybridized overnight in the Affymetrix hybridization oven at 42oC. The Affymetrix GeneChip Fluidics Station 450 performs the automated Affymetrix wash and stain protocols.
Sample_scan_protocol	The Affymetrix GeneChip Scanner 3000 7G is used to generate the resultant GeneChip array image
Sample_data_processing	Scanned array images were analyzed by dChip applying a smoothing spline normalization method prior to obtaining model-based gene expression indices, a.k.a. signal values. There were no outliers identified by dChip, so all samples were carried on for subsequent analysis. When comparing two groups of samples to identify enriched genes in a given group, we used the lower confidence bound (LCB) of the fold change (FC) between the two groups as the cut-off criteria. If 90% LCB of FC between the two groups was above 1.2, the corresponding gene was considered to be differentially expressed.
Sample_platform_id	GPL1261
Sample_contact_name	Ali,,Nawshad
Sample_contact_email	anawshad@unmc.edu
Sample_contact_phone	402-472-1378
Sample_contact_fax	402-472-2551
Sample_contact_laboratory	Nawshad Lab
Sample_contact_department	Oral Biology
Sample_contact_institute	Unviersity of Nebraska Medical Center
Sample_contact_address	40th and Holdrege
Sample_contact_city	Lincoln
Sample_contact_state	NE
Sample_contact_zip/postal_code	68583
Sample_contact_country	USA
Sample_contact_web_link	http://www.unmc.edu/dentistry/nawshad.htm
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM768nnn/GSM768227/suppl/GSM768227.CEL.gz
Sample_series_id	GSE31004
Sample_data_row_count	45101

GSM768228

GPL1261

Nic 1.5mg/kg/day, biological rep2

Mouse newborn palate

tissue: Newborn Palate strain: BALB/c age: Newborn - P1 treatment: 1.5mg/kg/day nicotine-treated fetuses

Gene expression data from 1.5mg/kg/day nicotine-treated fetuses

Sample_geo_accession	GSM768228
Sample_status	Public on Dec 15 2011
Sample_submission_date	Jul 27 2011
Sample_last_update_date	Dec 15 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Sterile physiological saline or nicotine (1.5 mg/kg/day, 3.0 mg/kg/day, or 4.5 mg/kg/day)
Sample_growth_protocol_ch1	A small incision of 0.5 cm was made in the skin posterior to the shoulder of pregnant mice and an osmotic mini-pump (Model 1004 - Alzet Corp, CA) was implanted subcutaneously. The incision was closed with a wound clip and covered with an antibiotic. The clip was removed after 14 days and dams were allowed to give birth naturally at/around 21 days
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was isolated from the posterior one-third of palatal tissues from newborn pups (n=2) using the RNeasy spin column RNA purification kit (Qiagen)
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	The UNMC Microarray Core uses a variety of commercially available assays for generating biotin-labeled samples for hybridization to Affymetrix GeneChip
Sample_hyb_protocol	The GeneChip arrays are hybridized overnight in the Affymetrix hybridization oven at 42oC. The Affymetrix GeneChip Fluidics Station 450 performs the automated Affymetrix wash and stain protocols.
Sample_scan_protocol	The Affymetrix GeneChip Scanner 3000 7G is used to generate the resultant GeneChip array image
Sample_data_processing	Scanned array images were analyzed by dChip applying a smoothing spline normalization method prior to obtaining model-based gene expression indices, a.k.a. signal values. There were no outliers identified by dChip, so all samples were carried on for subsequent analysis. When comparing two groups of samples to identify enriched genes in a given group, we used the lower confidence bound (LCB) of the fold change (FC) between the two groups as the cut-off criteria. If 90% LCB of FC between the two groups was above 1.2, the corresponding gene was considered to be differentially expressed.
Sample_platform_id	GPL1261
Sample_contact_name	Ali,,Nawshad
Sample_contact_email	anawshad@unmc.edu
Sample_contact_phone	402-472-1378
Sample_contact_fax	402-472-2551
Sample_contact_laboratory	Nawshad Lab
Sample_contact_department	Oral Biology
Sample_contact_institute	Unviersity of Nebraska Medical Center
Sample_contact_address	40th and Holdrege
Sample_contact_city	Lincoln
Sample_contact_state	NE
Sample_contact_zip/postal_code	68583
Sample_contact_country	USA
Sample_contact_web_link	http://www.unmc.edu/dentistry/nawshad.htm
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM768nnn/GSM768228/suppl/GSM768228.CEL.gz
Sample_series_id	GSE31004
Sample_data_row_count	45101

GSM768229

GPL1261

Nic 3.0mg/kg/day, biological rep1

Mouse newborn palate

tissue: Newborn Palate strain: BALB/c age: Newborn - P1 treatment: 3.0mg/kg/day nicotine-treated fetuses

Gene expression data from 3.0mg/kg/day nicotine-treated fetuses

Sample_geo_accession	GSM768229
Sample_status	Public on Dec 15 2011
Sample_submission_date	Jul 27 2011
Sample_last_update_date	Dec 15 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Sterile physiological saline or nicotine (1.5 mg/kg/day, 3.0 mg/kg/day, or 4.5 mg/kg/day)
Sample_growth_protocol_ch1	A small incision of 0.5 cm was made in the skin posterior to the shoulder of pregnant mice and an osmotic mini-pump (Model 1004 - Alzet Corp, CA) was implanted subcutaneously. The incision was closed with a wound clip and covered with an antibiotic. The clip was removed after 14 days and dams were allowed to give birth naturally at/around 21 days
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was isolated from the posterior one-third of palatal tissues from newborn pups (n=2) using the RNeasy spin column RNA purification kit (Qiagen)
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	The UNMC Microarray Core uses a variety of commercially available assays for generating biotin-labeled samples for hybridization to Affymetrix GeneChip
Sample_hyb_protocol	The GeneChip arrays are hybridized overnight in the Affymetrix hybridization oven at 42oC. The Affymetrix GeneChip Fluidics Station 450 performs the automated Affymetrix wash and stain protocols.
Sample_scan_protocol	The Affymetrix GeneChip Scanner 3000 7G is used to generate the resultant GeneChip array image
Sample_data_processing	Scanned array images were analyzed by dChip applying a smoothing spline normalization method prior to obtaining model-based gene expression indices, a.k.a. signal values. There were no outliers identified by dChip, so all samples were carried on for subsequent analysis. When comparing two groups of samples to identify enriched genes in a given group, we used the lower confidence bound (LCB) of the fold change (FC) between the two groups as the cut-off criteria. If 90% LCB of FC between the two groups was above 1.2, the corresponding gene was considered to be differentially expressed.
Sample_platform_id	GPL1261
Sample_contact_name	Ali,,Nawshad
Sample_contact_email	anawshad@unmc.edu
Sample_contact_phone	402-472-1378
Sample_contact_fax	402-472-2551
Sample_contact_laboratory	Nawshad Lab
Sample_contact_department	Oral Biology
Sample_contact_institute	Unviersity of Nebraska Medical Center
Sample_contact_address	40th and Holdrege
Sample_contact_city	Lincoln
Sample_contact_state	NE
Sample_contact_zip/postal_code	68583
Sample_contact_country	USA
Sample_contact_web_link	http://www.unmc.edu/dentistry/nawshad.htm
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM768nnn/GSM768229/suppl/GSM768229.CEL.gz
Sample_series_id	GSE31004
Sample_data_row_count	45101

GSM768230

GPL1261

Nic 3.0mg/kg/day, biological rep2

Mouse newborn palate

tissue: Newborn Palate strain: BALB/c age: Newborn - P1 treatment: 3.0mg/kg/day nicotine-treated fetuses

Gene expression data from 3.0mg/kg/day nicotine-treated fetuses

Sample_geo_accession	GSM768230
Sample_status	Public on Dec 15 2011
Sample_submission_date	Jul 27 2011
Sample_last_update_date	Dec 15 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Sterile physiological saline or nicotine (1.5 mg/kg/day, 3.0 mg/kg/day, or 4.5 mg/kg/day)
Sample_growth_protocol_ch1	A small incision of 0.5 cm was made in the skin posterior to the shoulder of pregnant mice and an osmotic mini-pump (Model 1004 - Alzet Corp, CA) was implanted subcutaneously. The incision was closed with a wound clip and covered with an antibiotic. The clip was removed after 14 days and dams were allowed to give birth naturally at/around 21 days
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was isolated from the posterior one-third of palatal tissues from newborn pups (n=2) using the RNeasy spin column RNA purification kit (Qiagen)
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	The UNMC Microarray Core uses a variety of commercially available assays for generating biotin-labeled samples for hybridization to Affymetrix GeneChip
Sample_hyb_protocol	The GeneChip arrays are hybridized overnight in the Affymetrix hybridization oven at 42oC. The Affymetrix GeneChip Fluidics Station 450 performs the automated Affymetrix wash and stain protocols.
Sample_scan_protocol	The Affymetrix GeneChip Scanner 3000 7G is used to generate the resultant GeneChip array image
Sample_data_processing	Scanned array images were analyzed by dChip applying a smoothing spline normalization method prior to obtaining model-based gene expression indices, a.k.a. signal values. There were no outliers identified by dChip, so all samples were carried on for subsequent analysis. When comparing two groups of samples to identify enriched genes in a given group, we used the lower confidence bound (LCB) of the fold change (FC) between the two groups as the cut-off criteria. If 90% LCB of FC between the two groups was above 1.2, the corresponding gene was considered to be differentially expressed.
Sample_platform_id	GPL1261
Sample_contact_name	Ali,,Nawshad
Sample_contact_email	anawshad@unmc.edu
Sample_contact_phone	402-472-1378
Sample_contact_fax	402-472-2551
Sample_contact_laboratory	Nawshad Lab
Sample_contact_department	Oral Biology
Sample_contact_institute	Unviersity of Nebraska Medical Center
Sample_contact_address	40th and Holdrege
Sample_contact_city	Lincoln
Sample_contact_state	NE
Sample_contact_zip/postal_code	68583
Sample_contact_country	USA
Sample_contact_web_link	http://www.unmc.edu/dentistry/nawshad.htm
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM768nnn/GSM768230/suppl/GSM768230.CEL.gz
Sample_series_id	GSE31004
Sample_data_row_count	45101

GSM768231

GPL1261

Nic 4.5mg/kg/day, biological rep1

Mouse newborn palate

tissue: Newborn Palate strain: BALB/c age: Newborn - P1 treatment: 4.5mg/kg/day nicotine-treated fetuses

Gene expression data from 4.5mg/kg/day nicotine-treated fetuses

Sample_geo_accession	GSM768231
Sample_status	Public on Dec 15 2011
Sample_submission_date	Jul 27 2011
Sample_last_update_date	Dec 15 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Sterile physiological saline or nicotine (1.5 mg/kg/day, 3.0 mg/kg/day, or 4.5 mg/kg/day)
Sample_growth_protocol_ch1	A small incision of 0.5 cm was made in the skin posterior to the shoulder of pregnant mice and an osmotic mini-pump (Model 1004 - Alzet Corp, CA) was implanted subcutaneously. The incision was closed with a wound clip and covered with an antibiotic. The clip was removed after 14 days and dams were allowed to give birth naturally at/around 21 days
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was isolated from the posterior one-third of palatal tissues from newborn pups (n=2) using the RNeasy spin column RNA purification kit (Qiagen)
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	The UNMC Microarray Core uses a variety of commercially available assays for generating biotin-labeled samples for hybridization to Affymetrix GeneChip
Sample_hyb_protocol	The GeneChip arrays are hybridized overnight in the Affymetrix hybridization oven at 42oC. The Affymetrix GeneChip Fluidics Station 450 performs the automated Affymetrix wash and stain protocols.
Sample_scan_protocol	The Affymetrix GeneChip Scanner 3000 7G is used to generate the resultant GeneChip array image
Sample_data_processing	Scanned array images were analyzed by dChip applying a smoothing spline normalization method prior to obtaining model-based gene expression indices, a.k.a. signal values. There were no outliers identified by dChip, so all samples were carried on for subsequent analysis. When comparing two groups of samples to identify enriched genes in a given group, we used the lower confidence bound (LCB) of the fold change (FC) between the two groups as the cut-off criteria. If 90% LCB of FC between the two groups was above 1.2, the corresponding gene was considered to be differentially expressed.
Sample_platform_id	GPL1261
Sample_contact_name	Ali,,Nawshad
Sample_contact_email	anawshad@unmc.edu
Sample_contact_phone	402-472-1378
Sample_contact_fax	402-472-2551
Sample_contact_laboratory	Nawshad Lab
Sample_contact_department	Oral Biology
Sample_contact_institute	Unviersity of Nebraska Medical Center
Sample_contact_address	40th and Holdrege
Sample_contact_city	Lincoln
Sample_contact_state	NE
Sample_contact_zip/postal_code	68583
Sample_contact_country	USA
Sample_contact_web_link	http://www.unmc.edu/dentistry/nawshad.htm
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM768nnn/GSM768231/suppl/GSM768231.CEL.gz
Sample_series_id	GSE31004
Sample_data_row_count	45101

GSM768232

GPL1261

Nic 4.5mg/kg/day, biological rep2

Mouse newborn palate

tissue: Newborn Palate strain: BALB/c age: Newborn - P1 treatment: 4.5mg/kg/day nicotine-treated fetuses

Gene expression data from 4.5mg/kg/day nicotine-treated fetuses

Sample_geo_accession	GSM768232
Sample_status	Public on Dec 15 2011
Sample_submission_date	Jul 27 2011
Sample_last_update_date	Dec 15 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Sterile physiological saline or nicotine (1.5 mg/kg/day, 3.0 mg/kg/day, or 4.5 mg/kg/day)
Sample_growth_protocol_ch1	A small incision of 0.5 cm was made in the skin posterior to the shoulder of pregnant mice and an osmotic mini-pump (Model 1004 - Alzet Corp, CA) was implanted subcutaneously. The incision was closed with a wound clip and covered with an antibiotic. The clip was removed after 14 days and dams were allowed to give birth naturally at/around 21 days
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was isolated from the posterior one-third of palatal tissues from newborn pups (n=2) using the RNeasy spin column RNA purification kit (Qiagen)
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	The UNMC Microarray Core uses a variety of commercially available assays for generating biotin-labeled samples for hybridization to Affymetrix GeneChip
Sample_hyb_protocol	The GeneChip arrays are hybridized overnight in the Affymetrix hybridization oven at 42oC. The Affymetrix GeneChip Fluidics Station 450 performs the automated Affymetrix wash and stain protocols.
Sample_scan_protocol	The Affymetrix GeneChip Scanner 3000 7G is used to generate the resultant GeneChip array image
Sample_data_processing	Scanned array images were analyzed by dChip applying a smoothing spline normalization method prior to obtaining model-based gene expression indices, a.k.a. signal values. There were no outliers identified by dChip, so all samples were carried on for subsequent analysis. When comparing two groups of samples to identify enriched genes in a given group, we used the lower confidence bound (LCB) of the fold change (FC) between the two groups as the cut-off criteria. If 90% LCB of FC between the two groups was above 1.2, the corresponding gene was considered to be differentially expressed.
Sample_platform_id	GPL1261
Sample_contact_name	Ali,,Nawshad
Sample_contact_email	anawshad@unmc.edu
Sample_contact_phone	402-472-1378
Sample_contact_fax	402-472-2551
Sample_contact_laboratory	Nawshad Lab
Sample_contact_department	Oral Biology
Sample_contact_institute	Unviersity of Nebraska Medical Center
Sample_contact_address	40th and Holdrege
Sample_contact_city	Lincoln
Sample_contact_state	NE
Sample_contact_zip/postal_code	68583
Sample_contact_country	USA
Sample_contact_web_link	http://www.unmc.edu/dentistry/nawshad.htm
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM768nnn/GSM768232/suppl/GSM768232.CEL.gz
Sample_series_id	GSE31004
Sample_data_row_count	45101

Make groups for comparisons

(2 groups will be compared at a time)

Select GSMs and click on "Add groups"

Enter the group name here:

Select expression type

Transcripts profile based on;

A. Differential status (Up/Down regulation)

B. Absolute calls (Transcribed/Not-detected)

Filter results by number of probes