Search results for the GEO ID: GSE26076  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM640274 | GPL1261 |
|
Conjunctival fornix_PN9_sample_1
|
Epithelial layer of mouse conjunctival fornix
|
developmental stage: Post-natal day 9
genotype/variation: wild type
strain: mixed background
|
|
| Sample_geo_accession | GSM640274
| | Sample_status | Public on Jun 15 2011
| | Sample_submission_date | Dec 15 2010
| | Sample_last_update_date | Jun 15 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Epithelial layer of mouse conjunctival fornix isolated by laser capture microscopy.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 = Between 20 and 120 ng of total RNA was subjected to two cycles of transcriptional amplification using appropriate Affymetrix products (cited as catalog numbers) as follows. Eukaryote Poly A RNA internal standards (900433) were added to the samples, and the poly A containing mRNA component was reverse-transcribed in the presence of a T7-(dT)24 primer (900432). The resulting cDNA was extracted (900371) and subjected to transcriptional amplification using a MEGAscript T7 kit from Ambion (Austin, TX). The amplified cRNA product was extracted (900371) and copied back to cDNA using random primers (900432). Extracted cDNA was again transcribed in vitro, in the presence of biotin-labeled ribonucleotides (900449). The biotinylated cRNA product (107 ± 37 µg, mean ± SD, n | 11 with one outlier of 27 µg) was extracted and 20 μg was fragmented (900371: for 35 minutes at 94°C).
| | Sample_hyb_protocol | Hybridization controls (900454) were added, and each sample was hybridized overnight to a Mouse Genome 430 2.0 Array (900495).
| | Sample_scan_protocol | The chips were washed, developed and scanned in an Agilent ChipScanner (Affymetrix Inc., Santa Clara, CA).
| | Sample_data_processing | Raw data were processed and analyzed using Affymetrix GeneChip Operating System (GCOS) v1.4 software. GCOS was used to assess the presence or absence of the target sequence of each panel, its expression level, and then to make all relevant pair-wise statistical comparisons among samples. Unscaled 2% trimmed means (159 ± 52 mean ± SD, n=12) were scaled to 150. Processed data was sorted and inspected in the Microsoft Excel spreadsheet program (Microsoft, Redmond, WA) and further analyzed using BRB-Array Tools software (Biometric Research Branch, NCI, NIH, Bethesda, MD (www.nci.nih.gov/brb-arraytools.html/)). The Mouse Genome 430 2.0 chip contains 45,101 panels, each targeting a specific transcript sequence. Approximately 22,000 (21,996) transcripts identified by Entrez Gene numbers are redundantly targeted by 41,429 panels: the remaining 3,672 panels target products that currently have no Entrez Gene number. Panels showing consistent, GCOS-validated changes were submitted to Ingenuity Pathways Analysis (https://analysis.ingenuity.com) for classifying the genes according to Gene Ontology groups, functional interactive networks, or canonical pathways. The following conditions were used to designate genes as differentially expressed between any two groups of samples: (a) all three samples in the high-expression group have detectable transcripts (called Present), (b) of the nine pair-wise comparisons made by the GCOS software, at least 6 show valid differences, (c) group values do not overlap, i.e., the lowest value of the high-expression group is higher than the highest value of the low expression group, and (d) the average value of the high-expression group is >2 fold greater than the average value of the low-expression group.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Shivalingappa,Kottur,Swamynathan
| | Sample_contact_email | Swamynathansk@upmc.edu
| | Sample_contact_phone | 412-802-6437
| | Sample_contact_fax | 412-647-5880
| | Sample_contact_laboratory | Ocular Surface Development and Gene Expression
| | Sample_contact_department | Ophthalmology
| | Sample_contact_institute | University of Pittsburgh
| | Sample_contact_address | 203 Lothrop Street Room 1025
| | Sample_contact_city | Pittsburgh
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 15213
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM640nnn/GSM640274/suppl/GSM640274.CEL.gz
| | Sample_series_id | GSE26076
| | Sample_data_row_count | 45101
| | |
|
GSM640275 | GPL1261 |
|
Conjunctival fornix_PN9_sample_2
|
Epithelial layer of mouse conjunctival fornix
|
developmental stage: Post-natal day 9
genotype/variation: wild type
strain: mixed background
|
|
| Sample_geo_accession | GSM640275
| | Sample_status | Public on Jun 15 2011
| | Sample_submission_date | Dec 15 2010
| | Sample_last_update_date | Jun 15 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Epithelial layer of mouse conjunctival fornix isolated by laser capture microscopy.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 = Between 20 and 120 ng of total RNA was subjected to two cycles of transcriptional amplification using appropriate Affymetrix products (cited as catalog numbers) as follows. Eukaryote Poly A RNA internal standards (900433) were added to the samples, and the poly A containing mRNA component was reverse-transcribed in the presence of a T7-(dT)24 primer (900432). The resulting cDNA was extracted (900371) and subjected to transcriptional amplification using a MEGAscript T7 kit from Ambion (Austin, TX). The amplified cRNA product was extracted (900371) and copied back to cDNA using random primers (900432). Extracted cDNA was again transcribed in vitro, in the presence of biotin-labeled ribonucleotides (900449). The biotinylated cRNA product (107 ± 37 µg, mean ± SD, n | 11 with one outlier of 27 µg) was extracted and 20 μg was fragmented (900371: for 35 minutes at 94°C).
| | Sample_hyb_protocol | Hybridization controls (900454) were added, and each sample was hybridized overnight to a Mouse Genome 430 2.0 Array (900495).
| | Sample_scan_protocol | The chips were washed, developed and scanned in an Agilent ChipScanner (Affymetrix Inc., Santa Clara, CA).
| | Sample_data_processing | Raw data were processed and analyzed using Affymetrix GeneChip Operating System (GCOS) v1.4 software. GCOS was used to assess the presence or absence of the target sequence of each panel, its expression level, and then to make all relevant pair-wise statistical comparisons among samples. Unscaled 2% trimmed means (159 ± 52 mean ± SD, n=12) were scaled to 150. Processed data was sorted and inspected in the Microsoft Excel spreadsheet program (Microsoft, Redmond, WA) and further analyzed using BRB-Array Tools software (Biometric Research Branch, NCI, NIH, Bethesda, MD (www.nci.nih.gov/brb-arraytools.html/)). The Mouse Genome 430 2.0 chip contains 45,101 panels, each targeting a specific transcript sequence. Approximately 22,000 (21,996) transcripts identified by Entrez Gene numbers are redundantly targeted by 41,429 panels: the remaining 3,672 panels target products that currently have no Entrez Gene number. Panels showing consistent, GCOS-validated changes were submitted to Ingenuity Pathways Analysis (https://analysis.ingenuity.com) for classifying the genes according to Gene Ontology groups, functional interactive networks, or canonical pathways. The following conditions were used to designate genes as differentially expressed between any two groups of samples: (a) all three samples in the high-expression group have detectable transcripts (called Present), (b) of the nine pair-wise comparisons made by the GCOS software, at least 6 show valid differences, (c) group values do not overlap, i.e., the lowest value of the high-expression group is higher than the highest value of the low expression group, and (d) the average value of the high-expression group is >2 fold greater than the average value of the low-expression group.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Shivalingappa,Kottur,Swamynathan
| | Sample_contact_email | Swamynathansk@upmc.edu
| | Sample_contact_phone | 412-802-6437
| | Sample_contact_fax | 412-647-5880
| | Sample_contact_laboratory | Ocular Surface Development and Gene Expression
| | Sample_contact_department | Ophthalmology
| | Sample_contact_institute | University of Pittsburgh
| | Sample_contact_address | 203 Lothrop Street Room 1025
| | Sample_contact_city | Pittsburgh
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 15213
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM640nnn/GSM640275/suppl/GSM640275.CEL.gz
| | Sample_series_id | GSE26076
| | Sample_data_row_count | 45101
| | |
|
GSM640276 | GPL1261 |
|
Conjunctival fornix_PN9_sample_3
|
Epithelial layer of mouse conjunctival fornix
|
developmental stage: Post-natal day 9
genotype/variation: wild type
strain: mixed background
|
|
| Sample_geo_accession | GSM640276
| | Sample_status | Public on Jun 15 2011
| | Sample_submission_date | Dec 15 2010
| | Sample_last_update_date | Jun 15 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Epithelial layer of mouse conjunctival fornix isolated by laser capture microscopy.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 = Between 20 and 120 ng of total RNA was subjected to two cycles of transcriptional amplification using appropriate Affymetrix products (cited as catalog numbers) as follows. Eukaryote Poly A RNA internal standards (900433) were added to the samples, and the poly A containing mRNA component was reverse-transcribed in the presence of a T7-(dT)24 primer (900432). The resulting cDNA was extracted (900371) and subjected to transcriptional amplification using a MEGAscript T7 kit from Ambion (Austin, TX). The amplified cRNA product was extracted (900371) and copied back to cDNA using random primers (900432). Extracted cDNA was again transcribed in vitro, in the presence of biotin-labeled ribonucleotides (900449). The biotinylated cRNA product (107 ± 37 µg, mean ± SD, n | 11 with one outlier of 27 µg) was extracted and 20 μg was fragmented (900371: for 35 minutes at 94°C).
| | Sample_hyb_protocol | Hybridization controls (900454) were added, and each sample was hybridized overnight to a Mouse Genome 430 2.0 Array (900495).
| | Sample_scan_protocol | The chips were washed, developed and scanned in an Agilent ChipScanner (Affymetrix Inc., Santa Clara, CA).
| | Sample_data_processing | Raw data were processed and analyzed using Affymetrix GeneChip Operating System (GCOS) v1.4 software. GCOS was used to assess the presence or absence of the target sequence of each panel, its expression level, and then to make all relevant pair-wise statistical comparisons among samples. Unscaled 2% trimmed means (159 ± 52 mean ± SD, n=12) were scaled to 150. Processed data was sorted and inspected in the Microsoft Excel spreadsheet program (Microsoft, Redmond, WA) and further analyzed using BRB-Array Tools software (Biometric Research Branch, NCI, NIH, Bethesda, MD (www.nci.nih.gov/brb-arraytools.html/)). The Mouse Genome 430 2.0 chip contains 45,101 panels, each targeting a specific transcript sequence. Approximately 22,000 (21,996) transcripts identified by Entrez Gene numbers are redundantly targeted by 41,429 panels: the remaining 3,672 panels target products that currently have no Entrez Gene number. Panels showing consistent, GCOS-validated changes were submitted to Ingenuity Pathways Analysis (https://analysis.ingenuity.com) for classifying the genes according to Gene Ontology groups, functional interactive networks, or canonical pathways. The following conditions were used to designate genes as differentially expressed between any two groups of samples: (a) all three samples in the high-expression group have detectable transcripts (called Present), (b) of the nine pair-wise comparisons made by the GCOS software, at least 6 show valid differences, (c) group values do not overlap, i.e., the lowest value of the high-expression group is higher than the highest value of the low expression group, and (d) the average value of the high-expression group is >2 fold greater than the average value of the low-expression group.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Shivalingappa,Kottur,Swamynathan
| | Sample_contact_email | Swamynathansk@upmc.edu
| | Sample_contact_phone | 412-802-6437
| | Sample_contact_fax | 412-647-5880
| | Sample_contact_laboratory | Ocular Surface Development and Gene Expression
| | Sample_contact_department | Ophthalmology
| | Sample_contact_institute | University of Pittsburgh
| | Sample_contact_address | 203 Lothrop Street Room 1025
| | Sample_contact_city | Pittsburgh
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 15213
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM640nnn/GSM640276/suppl/GSM640276.CEL.gz
| | Sample_series_id | GSE26076
| | Sample_data_row_count | 45101
| | |
|
GSM640277 | GPL1261 |
|
Conjunctival fornix_PN14_sample_1
|
Epithelial layer of mouse conjunctival fornix
|
developmental stage: Post-natal day 14
genotype/variation: wild type
strain: mixed background
|
|
| Sample_geo_accession | GSM640277
| | Sample_status | Public on Jun 15 2011
| | Sample_submission_date | Dec 15 2010
| | Sample_last_update_date | Jun 15 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Epithelial layer of mouse conjunctival fornix isolated by laser capture microscopy.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 = Between 20 and 120 ng of total RNA was subjected to two cycles of transcriptional amplification using appropriate Affymetrix products (cited as catalog numbers) as follows. Eukaryote Poly A RNA internal standards (900433) were added to the samples, and the poly A containing mRNA component was reverse-transcribed in the presence of a T7-(dT)24 primer (900432). The resulting cDNA was extracted (900371) and subjected to transcriptional amplification using a MEGAscript T7 kit from Ambion (Austin, TX). The amplified cRNA product was extracted (900371) and copied back to cDNA using random primers (900432). Extracted cDNA was again transcribed in vitro, in the presence of biotin-labeled ribonucleotides (900449). The biotinylated cRNA product (107 ± 37 µg, mean ± SD, n | 11 with one outlier of 27 µg) was extracted and 20 μg was fragmented (900371: for 35 minutes at 94°C).
| | Sample_hyb_protocol | Hybridization controls (900454) were added, and each sample was hybridized overnight to a Mouse Genome 430 2.0 Array (900495).
| | Sample_scan_protocol | The chips were washed, developed and scanned in an Agilent ChipScanner (Affymetrix Inc., Santa Clara, CA).
| | Sample_data_processing | Raw data were processed and analyzed using Affymetrix GeneChip Operating System (GCOS) v1.4 software. GCOS was used to assess the presence or absence of the target sequence of each panel, its expression level, and then to make all relevant pair-wise statistical comparisons among samples. Unscaled 2% trimmed means (159 ± 52 mean ± SD, n=12) were scaled to 150. Processed data was sorted and inspected in the Microsoft Excel spreadsheet program (Microsoft, Redmond, WA) and further analyzed using BRB-Array Tools software (Biometric Research Branch, NCI, NIH, Bethesda, MD (www.nci.nih.gov/brb-arraytools.html/)). The Mouse Genome 430 2.0 chip contains 45,101 panels, each targeting a specific transcript sequence. Approximately 22,000 (21,996) transcripts identified by Entrez Gene numbers are redundantly targeted by 41,429 panels: the remaining 3,672 panels target products that currently have no Entrez Gene number. Panels showing consistent, GCOS-validated changes were submitted to Ingenuity Pathways Analysis (https://analysis.ingenuity.com) for classifying the genes according to Gene Ontology groups, functional interactive networks, or canonical pathways. The following conditions were used to designate genes as differentially expressed between any two groups of samples: (a) all three samples in the high-expression group have detectable transcripts (called Present), (b) of the nine pair-wise comparisons made by the GCOS software, at least 6 show valid differences, (c) group values do not overlap, i.e., the lowest value of the high-expression group is higher than the highest value of the low expression group, and (d) the average value of the high-expression group is >2 fold greater than the average value of the low-expression group.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Shivalingappa,Kottur,Swamynathan
| | Sample_contact_email | Swamynathansk@upmc.edu
| | Sample_contact_phone | 412-802-6437
| | Sample_contact_fax | 412-647-5880
| | Sample_contact_laboratory | Ocular Surface Development and Gene Expression
| | Sample_contact_department | Ophthalmology
| | Sample_contact_institute | University of Pittsburgh
| | Sample_contact_address | 203 Lothrop Street Room 1025
| | Sample_contact_city | Pittsburgh
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 15213
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM640nnn/GSM640277/suppl/GSM640277.CEL.gz
| | Sample_series_id | GSE26076
| | Sample_data_row_count | 45101
| | |
|
GSM640278 | GPL1261 |
|
Conjunctival fornix_PN14_sample_2
|
Epithelial layer of mouse conjunctival fornix
|
developmental stage: Post-natal day 14
genotype/variation: wild type
strain: mixed background
|
|
| Sample_geo_accession | GSM640278
| | Sample_status | Public on Jun 15 2011
| | Sample_submission_date | Dec 15 2010
| | Sample_last_update_date | Jun 15 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Epithelial layer of mouse conjunctival fornix isolated by laser capture microscopy.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 = Between 20 and 120 ng of total RNA was subjected to two cycles of transcriptional amplification using appropriate Affymetrix products (cited as catalog numbers) as follows. Eukaryote Poly A RNA internal standards (900433) were added to the samples, and the poly A containing mRNA component was reverse-transcribed in the presence of a T7-(dT)24 primer (900432). The resulting cDNA was extracted (900371) and subjected to transcriptional amplification using a MEGAscript T7 kit from Ambion (Austin, TX). The amplified cRNA product was extracted (900371) and copied back to cDNA using random primers (900432). Extracted cDNA was again transcribed in vitro, in the presence of biotin-labeled ribonucleotides (900449). The biotinylated cRNA product (107 ± 37 µg, mean ± SD, n | 11 with one outlier of 27 µg) was extracted and 20 μg was fragmented (900371: for 35 minutes at 94°C).
| | Sample_hyb_protocol | Hybridization controls (900454) were added, and each sample was hybridized overnight to a Mouse Genome 430 2.0 Array (900495).
| | Sample_scan_protocol | The chips were washed, developed and scanned in an Agilent ChipScanner (Affymetrix Inc., Santa Clara, CA).
| | Sample_data_processing | Raw data were processed and analyzed using Affymetrix GeneChip Operating System (GCOS) v1.4 software. GCOS was used to assess the presence or absence of the target sequence of each panel, its expression level, and then to make all relevant pair-wise statistical comparisons among samples. Unscaled 2% trimmed means (159 ± 52 mean ± SD, n=12) were scaled to 150. Processed data was sorted and inspected in the Microsoft Excel spreadsheet program (Microsoft, Redmond, WA) and further analyzed using BRB-Array Tools software (Biometric Research Branch, NCI, NIH, Bethesda, MD (www.nci.nih.gov/brb-arraytools.html/)). The Mouse Genome 430 2.0 chip contains 45,101 panels, each targeting a specific transcript sequence. Approximately 22,000 (21,996) transcripts identified by Entrez Gene numbers are redundantly targeted by 41,429 panels: the remaining 3,672 panels target products that currently have no Entrez Gene number. Panels showing consistent, GCOS-validated changes were submitted to Ingenuity Pathways Analysis (https://analysis.ingenuity.com) for classifying the genes according to Gene Ontology groups, functional interactive networks, or canonical pathways. The following conditions were used to designate genes as differentially expressed between any two groups of samples: (a) all three samples in the high-expression group have detectable transcripts (called Present), (b) of the nine pair-wise comparisons made by the GCOS software, at least 6 show valid differences, (c) group values do not overlap, i.e., the lowest value of the high-expression group is higher than the highest value of the low expression group, and (d) the average value of the high-expression group is >2 fold greater than the average value of the low-expression group.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Shivalingappa,Kottur,Swamynathan
| | Sample_contact_email | Swamynathansk@upmc.edu
| | Sample_contact_phone | 412-802-6437
| | Sample_contact_fax | 412-647-5880
| | Sample_contact_laboratory | Ocular Surface Development and Gene Expression
| | Sample_contact_department | Ophthalmology
| | Sample_contact_institute | University of Pittsburgh
| | Sample_contact_address | 203 Lothrop Street Room 1025
| | Sample_contact_city | Pittsburgh
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 15213
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM640nnn/GSM640278/suppl/GSM640278.CEL.gz
| | Sample_series_id | GSE26076
| | Sample_data_row_count | 45101
| | |
|
GSM640279 | GPL1261 |
|
Conjunctival fornix_PN14_sample_3
|
Epithelial layer of mouse conjunctival fornix
|
developmental stage: Post-natal day 14
genotype/variation: wild type
strain: mixed background
|
|
| Sample_geo_accession | GSM640279
| | Sample_status | Public on Jun 15 2011
| | Sample_submission_date | Dec 15 2010
| | Sample_last_update_date | Jun 15 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Epithelial layer of mouse conjunctival fornix isolated by laser capture microscopy.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 = Between 20 and 120 ng of total RNA was subjected to two cycles of transcriptional amplification using appropriate Affymetrix products (cited as catalog numbers) as follows. Eukaryote Poly A RNA internal standards (900433) were added to the samples, and the poly A containing mRNA component was reverse-transcribed in the presence of a T7-(dT)24 primer (900432). The resulting cDNA was extracted (900371) and subjected to transcriptional amplification using a MEGAscript T7 kit from Ambion (Austin, TX). The amplified cRNA product was extracted (900371) and copied back to cDNA using random primers (900432). Extracted cDNA was again transcribed in vitro, in the presence of biotin-labeled ribonucleotides (900449). The biotinylated cRNA product (107 ± 37 µg, mean ± SD, n | 11 with one outlier of 27 µg) was extracted and 20 μg was fragmented (900371: for 35 minutes at 94°C).
| | Sample_hyb_protocol | Hybridization controls (900454) were added, and each sample was hybridized overnight to a Mouse Genome 430 2.0 Array (900495).
| | Sample_scan_protocol | The chips were washed, developed and scanned in an Agilent ChipScanner (Affymetrix Inc., Santa Clara, CA).
| | Sample_data_processing | Raw data were processed and analyzed using Affymetrix GeneChip Operating System (GCOS) v1.4 software. GCOS was used to assess the presence or absence of the target sequence of each panel, its expression level, and then to make all relevant pair-wise statistical comparisons among samples. Unscaled 2% trimmed means (159 ± 52 mean ± SD, n=12) were scaled to 150. Processed data was sorted and inspected in the Microsoft Excel spreadsheet program (Microsoft, Redmond, WA) and further analyzed using BRB-Array Tools software (Biometric Research Branch, NCI, NIH, Bethesda, MD (www.nci.nih.gov/brb-arraytools.html/)). The Mouse Genome 430 2.0 chip contains 45,101 panels, each targeting a specific transcript sequence. Approximately 22,000 (21,996) transcripts identified by Entrez Gene numbers are redundantly targeted by 41,429 panels: the remaining 3,672 panels target products that currently have no Entrez Gene number. Panels showing consistent, GCOS-validated changes were submitted to Ingenuity Pathways Analysis (https://analysis.ingenuity.com) for classifying the genes according to Gene Ontology groups, functional interactive networks, or canonical pathways. The following conditions were used to designate genes as differentially expressed between any two groups of samples: (a) all three samples in the high-expression group have detectable transcripts (called Present), (b) of the nine pair-wise comparisons made by the GCOS software, at least 6 show valid differences, (c) group values do not overlap, i.e., the lowest value of the high-expression group is higher than the highest value of the low expression group, and (d) the average value of the high-expression group is >2 fold greater than the average value of the low-expression group.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Shivalingappa,Kottur,Swamynathan
| | Sample_contact_email | Swamynathansk@upmc.edu
| | Sample_contact_phone | 412-802-6437
| | Sample_contact_fax | 412-647-5880
| | Sample_contact_laboratory | Ocular Surface Development and Gene Expression
| | Sample_contact_department | Ophthalmology
| | Sample_contact_institute | University of Pittsburgh
| | Sample_contact_address | 203 Lothrop Street Room 1025
| | Sample_contact_city | Pittsburgh
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 15213
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM640nnn/GSM640279/suppl/GSM640279.CEL.gz
| | Sample_series_id | GSE26076
| | Sample_data_row_count | 45101
| | |
|
GSM640280 | GPL1261 |
|
Conjunctival fornix_PN20_sample_1
|
Epithelial layer of mouse conjunctival fornix
|
developmental stage: Post-natal day 20
genotype/variation: wild type
strain: mixed background
|
|
| Sample_geo_accession | GSM640280
| | Sample_status | Public on Jun 15 2011
| | Sample_submission_date | Dec 15 2010
| | Sample_last_update_date | Jun 15 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Epithelial layer of mouse conjunctival fornix isolated by laser capture microscopy.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 = Between 20 and 120 ng of total RNA was subjected to two cycles of transcriptional amplification using appropriate Affymetrix products (cited as catalog numbers) as follows. Eukaryote Poly A RNA internal standards (900433) were added to the samples, and the poly A containing mRNA component was reverse-transcribed in the presence of a T7-(dT)24 primer (900432). The resulting cDNA was extracted (900371) and subjected to transcriptional amplification using a MEGAscript T7 kit from Ambion (Austin, TX). The amplified cRNA product was extracted (900371) and copied back to cDNA using random primers (900432). Extracted cDNA was again transcribed in vitro, in the presence of biotin-labeled ribonucleotides (900449). The biotinylated cRNA product (107 ± 37 µg, mean ± SD, n | 11 with one outlier of 27 µg) was extracted and 20 μg was fragmented (900371: for 35 minutes at 94°C).
| | Sample_hyb_protocol | Hybridization controls (900454) were added, and each sample was hybridized overnight to a Mouse Genome 430 2.0 Array (900495).
| | Sample_scan_protocol | The chips were washed, developed and scanned in an Agilent ChipScanner (Affymetrix Inc., Santa Clara, CA).
| | Sample_data_processing | Raw data were processed and analyzed using Affymetrix GeneChip Operating System (GCOS) v1.4 software. GCOS was used to assess the presence or absence of the target sequence of each panel, its expression level, and then to make all relevant pair-wise statistical comparisons among samples. Unscaled 2% trimmed means (159 ± 52 mean ± SD, n=12) were scaled to 150. Processed data was sorted and inspected in the Microsoft Excel spreadsheet program (Microsoft, Redmond, WA) and further analyzed using BRB-Array Tools software (Biometric Research Branch, NCI, NIH, Bethesda, MD (www.nci.nih.gov/brb-arraytools.html/)). The Mouse Genome 430 2.0 chip contains 45,101 panels, each targeting a specific transcript sequence. Approximately 22,000 (21,996) transcripts identified by Entrez Gene numbers are redundantly targeted by 41,429 panels: the remaining 3,672 panels target products that currently have no Entrez Gene number. Panels showing consistent, GCOS-validated changes were submitted to Ingenuity Pathways Analysis (https://analysis.ingenuity.com) for classifying the genes according to Gene Ontology groups, functional interactive networks, or canonical pathways. The following conditions were used to designate genes as differentially expressed between any two groups of samples: (a) all three samples in the high-expression group have detectable transcripts (called Present), (b) of the nine pair-wise comparisons made by the GCOS software, at least 6 show valid differences, (c) group values do not overlap, i.e., the lowest value of the high-expression group is higher than the highest value of the low expression group, and (d) the average value of the high-expression group is >2 fold greater than the average value of the low-expression group.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Shivalingappa,Kottur,Swamynathan
| | Sample_contact_email | Swamynathansk@upmc.edu
| | Sample_contact_phone | 412-802-6437
| | Sample_contact_fax | 412-647-5880
| | Sample_contact_laboratory | Ocular Surface Development and Gene Expression
| | Sample_contact_department | Ophthalmology
| | Sample_contact_institute | University of Pittsburgh
| | Sample_contact_address | 203 Lothrop Street Room 1025
| | Sample_contact_city | Pittsburgh
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 15213
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM640nnn/GSM640280/suppl/GSM640280.CEL.gz
| | Sample_series_id | GSE26076
| | Sample_data_row_count | 45101
| | |
|
GSM640281 | GPL1261 |
|
Conjunctival fornix_PN20_sample_2
|
Epithelial layer of mouse conjunctival fornix
|
developmental stage: Post-natal day 20
genotype/variation: wild type
strain: mixed background
|
|
| Sample_geo_accession | GSM640281
| | Sample_status | Public on Jun 15 2011
| | Sample_submission_date | Dec 15 2010
| | Sample_last_update_date | Jun 15 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Epithelial layer of mouse conjunctival fornix isolated by laser capture microscopy.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 = Between 20 and 120 ng of total RNA was subjected to two cycles of transcriptional amplification using appropriate Affymetrix products (cited as catalog numbers) as follows. Eukaryote Poly A RNA internal standards (900433) were added to the samples, and the poly A containing mRNA component was reverse-transcribed in the presence of a T7-(dT)24 primer (900432). The resulting cDNA was extracted (900371) and subjected to transcriptional amplification using a MEGAscript T7 kit from Ambion (Austin, TX). The amplified cRNA product was extracted (900371) and copied back to cDNA using random primers (900432). Extracted cDNA was again transcribed in vitro, in the presence of biotin-labeled ribonucleotides (900449). The biotinylated cRNA product (107 ± 37 µg, mean ± SD, n | 11 with one outlier of 27 µg) was extracted and 20 μg was fragmented (900371: for 35 minutes at 94°C).
| | Sample_hyb_protocol | Hybridization controls (900454) were added, and each sample was hybridized overnight to a Mouse Genome 430 2.0 Array (900495).
| | Sample_scan_protocol | The chips were washed, developed and scanned in an Agilent ChipScanner (Affymetrix Inc., Santa Clara, CA).
| | Sample_data_processing | Raw data were processed and analyzed using Affymetrix GeneChip Operating System (GCOS) v1.4 software. GCOS was used to assess the presence or absence of the target sequence of each panel, its expression level, and then to make all relevant pair-wise statistical comparisons among samples. Unscaled 2% trimmed means (159 ± 52 mean ± SD, n=12) were scaled to 150. Processed data was sorted and inspected in the Microsoft Excel spreadsheet program (Microsoft, Redmond, WA) and further analyzed using BRB-Array Tools software (Biometric Research Branch, NCI, NIH, Bethesda, MD (www.nci.nih.gov/brb-arraytools.html/)). The Mouse Genome 430 2.0 chip contains 45,101 panels, each targeting a specific transcript sequence. Approximately 22,000 (21,996) transcripts identified by Entrez Gene numbers are redundantly targeted by 41,429 panels: the remaining 3,672 panels target products that currently have no Entrez Gene number. Panels showing consistent, GCOS-validated changes were submitted to Ingenuity Pathways Analysis (https://analysis.ingenuity.com) for classifying the genes according to Gene Ontology groups, functional interactive networks, or canonical pathways. The following conditions were used to designate genes as differentially expressed between any two groups of samples: (a) all three samples in the high-expression group have detectable transcripts (called Present), (b) of the nine pair-wise comparisons made by the GCOS software, at least 6 show valid differences, (c) group values do not overlap, i.e., the lowest value of the high-expression group is higher than the highest value of the low expression group, and (d) the average value of the high-expression group is >2 fold greater than the average value of the low-expression group.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Shivalingappa,Kottur,Swamynathan
| | Sample_contact_email | Swamynathansk@upmc.edu
| | Sample_contact_phone | 412-802-6437
| | Sample_contact_fax | 412-647-5880
| | Sample_contact_laboratory | Ocular Surface Development and Gene Expression
| | Sample_contact_department | Ophthalmology
| | Sample_contact_institute | University of Pittsburgh
| | Sample_contact_address | 203 Lothrop Street Room 1025
| | Sample_contact_city | Pittsburgh
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 15213
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM640nnn/GSM640281/suppl/GSM640281.CEL.gz
| | Sample_series_id | GSE26076
| | Sample_data_row_count | 45101
| | |
|
GSM640282 | GPL1261 |
|
Conjunctival fornix_PN20_sample_3
|
Epithelial layer of mouse conjunctival fornix
|
developmental stage: Post-natal day 20
genotype/variation: wild type
strain: mixed background
|
|
| Sample_geo_accession | GSM640282
| | Sample_status | Public on Jun 15 2011
| | Sample_submission_date | Dec 15 2010
| | Sample_last_update_date | Jun 15 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Epithelial layer of mouse conjunctival fornix isolated by laser capture microscopy.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 = Between 20 and 120 ng of total RNA was subjected to two cycles of transcriptional amplification using appropriate Affymetrix products (cited as catalog numbers) as follows. Eukaryote Poly A RNA internal standards (900433) were added to the samples, and the poly A containing mRNA component was reverse-transcribed in the presence of a T7-(dT)24 primer (900432). The resulting cDNA was extracted (900371) and subjected to transcriptional amplification using a MEGAscript T7 kit from Ambion (Austin, TX). The amplified cRNA product was extracted (900371) and copied back to cDNA using random primers (900432). Extracted cDNA was again transcribed in vitro, in the presence of biotin-labeled ribonucleotides (900449). The biotinylated cRNA product (107 ± 37 µg, mean ± SD, n | 11 with one outlier of 27 µg) was extracted and 20 μg was fragmented (900371: for 35 minutes at 94°C).
| | Sample_hyb_protocol | Hybridization controls (900454) were added, and each sample was hybridized overnight to a Mouse Genome 430 2.0 Array (900495).
| | Sample_scan_protocol | The chips were washed, developed and scanned in an Agilent ChipScanner (Affymetrix Inc., Santa Clara, CA).
| | Sample_data_processing | Raw data were processed and analyzed using Affymetrix GeneChip Operating System (GCOS) v1.4 software. GCOS was used to assess the presence or absence of the target sequence of each panel, its expression level, and then to make all relevant pair-wise statistical comparisons among samples. Unscaled 2% trimmed means (159 ± 52 mean ± SD, n=12) were scaled to 150. Processed data was sorted and inspected in the Microsoft Excel spreadsheet program (Microsoft, Redmond, WA) and further analyzed using BRB-Array Tools software (Biometric Research Branch, NCI, NIH, Bethesda, MD (www.nci.nih.gov/brb-arraytools.html/)). The Mouse Genome 430 2.0 chip contains 45,101 panels, each targeting a specific transcript sequence. Approximately 22,000 (21,996) transcripts identified by Entrez Gene numbers are redundantly targeted by 41,429 panels: the remaining 3,672 panels target products that currently have no Entrez Gene number. Panels showing consistent, GCOS-validated changes were submitted to Ingenuity Pathways Analysis (https://analysis.ingenuity.com) for classifying the genes according to Gene Ontology groups, functional interactive networks, or canonical pathways. The following conditions were used to designate genes as differentially expressed between any two groups of samples: (a) all three samples in the high-expression group have detectable transcripts (called Present), (b) of the nine pair-wise comparisons made by the GCOS software, at least 6 show valid differences, (c) group values do not overlap, i.e., the lowest value of the high-expression group is higher than the highest value of the low expression group, and (d) the average value of the high-expression group is >2 fold greater than the average value of the low-expression group.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Shivalingappa,Kottur,Swamynathan
| | Sample_contact_email | Swamynathansk@upmc.edu
| | Sample_contact_phone | 412-802-6437
| | Sample_contact_fax | 412-647-5880
| | Sample_contact_laboratory | Ocular Surface Development and Gene Expression
| | Sample_contact_department | Ophthalmology
| | Sample_contact_institute | University of Pittsburgh
| | Sample_contact_address | 203 Lothrop Street Room 1025
| | Sample_contact_city | Pittsburgh
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 15213
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM640nnn/GSM640282/suppl/GSM640282.CEL.gz
| | Sample_series_id | GSE26076
| | Sample_data_row_count | 45101
| | |
|
GSM640283 | GPL1261 |
|
Conjunctival fornix_PN14_Klf4CN_sample_1
|
Epithelial layer of mouse conjunctival fornix
|
developmental stage: Post-natal day 14
genotype/variation: KLf4 conditional knockout
strain: mixed background
|
|
| Sample_geo_accession | GSM640283
| | Sample_status | Public on Jun 15 2011
| | Sample_submission_date | Dec 15 2010
| | Sample_last_update_date | Jun 15 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Epithelial layer of mouse conjunctival fornix isolated by laser capture microscopy.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 = Between 20 and 120 ng of total RNA was subjected to two cycles of transcriptional amplification using appropriate Affymetrix products (cited as catalog numbers) as follows. Eukaryote Poly A RNA internal standards (900433) were added to the samples, and the poly A containing mRNA component was reverse-transcribed in the presence of a T7-(dT)24 primer (900432). The resulting cDNA was extracted (900371) and subjected to transcriptional amplification using a MEGAscript T7 kit from Ambion (Austin, TX). The amplified cRNA product was extracted (900371) and copied back to cDNA using random primers (900432). Extracted cDNA was again transcribed in vitro, in the presence of biotin-labeled ribonucleotides (900449). The biotinylated cRNA product (107 ± 37 µg, mean ± SD, n | 11 with one outlier of 27 µg) was extracted and 20 μg was fragmented (900371: for 35 minutes at 94°C).
| | Sample_hyb_protocol | Hybridization controls (900454) were added, and each sample was hybridized overnight to a Mouse Genome 430 2.0 Array (900495).
| | Sample_scan_protocol | The chips were washed, developed and scanned in an Agilent ChipScanner (Affymetrix Inc., Santa Clara, CA).
| | Sample_data_processing | Raw data were processed and analyzed using Affymetrix GeneChip Operating System (GCOS) v1.4 software. GCOS was used to assess the presence or absence of the target sequence of each panel, its expression level, and then to make all relevant pair-wise statistical comparisons among samples. Unscaled 2% trimmed means (159 ± 52 mean ± SD, n=12) were scaled to 150. Processed data was sorted and inspected in the Microsoft Excel spreadsheet program (Microsoft, Redmond, WA) and further analyzed using BRB-Array Tools software (Biometric Research Branch, NCI, NIH, Bethesda, MD (www.nci.nih.gov/brb-arraytools.html/)). The Mouse Genome 430 2.0 chip contains 45,101 panels, each targeting a specific transcript sequence. Approximately 22,000 (21,996) transcripts identified by Entrez Gene numbers are redundantly targeted by 41,429 panels: the remaining 3,672 panels target products that currently have no Entrez Gene number. Panels showing consistent, GCOS-validated changes were submitted to Ingenuity Pathways Analysis (https://analysis.ingenuity.com) for classifying the genes according to Gene Ontology groups, functional interactive networks, or canonical pathways. The following conditions were used to designate genes as differentially expressed between any two groups of samples: (a) all three samples in the high-expression group have detectable transcripts (called Present), (b) of the nine pair-wise comparisons made by the GCOS software, at least 6 show valid differences, (c) group values do not overlap, i.e., the lowest value of the high-expression group is higher than the highest value of the low expression group, and (d) the average value of the high-expression group is >2 fold greater than the average value of the low-expression group.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Shivalingappa,Kottur,Swamynathan
| | Sample_contact_email | Swamynathansk@upmc.edu
| | Sample_contact_phone | 412-802-6437
| | Sample_contact_fax | 412-647-5880
| | Sample_contact_laboratory | Ocular Surface Development and Gene Expression
| | Sample_contact_department | Ophthalmology
| | Sample_contact_institute | University of Pittsburgh
| | Sample_contact_address | 203 Lothrop Street Room 1025
| | Sample_contact_city | Pittsburgh
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 15213
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM640nnn/GSM640283/suppl/GSM640283.CEL.gz
| | Sample_series_id | GSE26076
| | Sample_data_row_count | 45101
| | |
|
GSM640284 | GPL1261 |
|
Conjunctival fornix_PN14_Klf4CN_sample_2
|
Epithelial layer of mouse conjunctival fornix
|
developmental stage: Post-natal day 14
genotype/variation: KLf4 conditional knockout
strain: mixed background
|
|
| Sample_geo_accession | GSM640284
| | Sample_status | Public on Jun 15 2011
| | Sample_submission_date | Dec 15 2010
| | Sample_last_update_date | Jun 15 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Epithelial layer of mouse conjunctival fornix isolated by laser capture microscopy.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 = Between 20 and 120 ng of total RNA was subjected to two cycles of transcriptional amplification using appropriate Affymetrix products (cited as catalog numbers) as follows. Eukaryote Poly A RNA internal standards (900433) were added to the samples, and the poly A containing mRNA component was reverse-transcribed in the presence of a T7-(dT)24 primer (900432). The resulting cDNA was extracted (900371) and subjected to transcriptional amplification using a MEGAscript T7 kit from Ambion (Austin, TX). The amplified cRNA product was extracted (900371) and copied back to cDNA using random primers (900432). Extracted cDNA was again transcribed in vitro, in the presence of biotin-labeled ribonucleotides (900449). The biotinylated cRNA product (107 ± 37 µg, mean ± SD, n | 11 with one outlier of 27 µg) was extracted and 20 μg was fragmented (900371: for 35 minutes at 94°C).
| | Sample_hyb_protocol | Hybridization controls (900454) were added, and each sample was hybridized overnight to a Mouse Genome 430 2.0 Array (900495).
| | Sample_scan_protocol | The chips were washed, developed and scanned in an Agilent ChipScanner (Affymetrix Inc., Santa Clara, CA).
| | Sample_data_processing | Raw data were processed and analyzed using Affymetrix GeneChip Operating System (GCOS) v1.4 software. GCOS was used to assess the presence or absence of the target sequence of each panel, its expression level, and then to make all relevant pair-wise statistical comparisons among samples. Unscaled 2% trimmed means (159 ± 52 mean ± SD, n=12) were scaled to 150. Processed data was sorted and inspected in the Microsoft Excel spreadsheet program (Microsoft, Redmond, WA) and further analyzed using BRB-Array Tools software (Biometric Research Branch, NCI, NIH, Bethesda, MD (www.nci.nih.gov/brb-arraytools.html/)). The Mouse Genome 430 2.0 chip contains 45,101 panels, each targeting a specific transcript sequence. Approximately 22,000 (21,996) transcripts identified by Entrez Gene numbers are redundantly targeted by 41,429 panels: the remaining 3,672 panels target products that currently have no Entrez Gene number. Panels showing consistent, GCOS-validated changes were submitted to Ingenuity Pathways Analysis (https://analysis.ingenuity.com) for classifying the genes according to Gene Ontology groups, functional interactive networks, or canonical pathways. The following conditions were used to designate genes as differentially expressed between any two groups of samples: (a) all three samples in the high-expression group have detectable transcripts (called Present), (b) of the nine pair-wise comparisons made by the GCOS software, at least 6 show valid differences, (c) group values do not overlap, i.e., the lowest value of the high-expression group is higher than the highest value of the low expression group, and (d) the average value of the high-expression group is >2 fold greater than the average value of the low-expression group.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Shivalingappa,Kottur,Swamynathan
| | Sample_contact_email | Swamynathansk@upmc.edu
| | Sample_contact_phone | 412-802-6437
| | Sample_contact_fax | 412-647-5880
| | Sample_contact_laboratory | Ocular Surface Development and Gene Expression
| | Sample_contact_department | Ophthalmology
| | Sample_contact_institute | University of Pittsburgh
| | Sample_contact_address | 203 Lothrop Street Room 1025
| | Sample_contact_city | Pittsburgh
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 15213
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM640nnn/GSM640284/suppl/GSM640284.CEL.gz
| | Sample_series_id | GSE26076
| | Sample_data_row_count | 45101
| | |
|
GSM640285 | GPL1261 |
|
Conjunctival fornix_PN14_Klf4CN_sample_3
|
Epithelial layer of mouse conjunctival fornix
|
developmental stage: Post-natal day 14
genotype/variation: KLf4 conditional knockout
strain: mixed background
|
|
| Sample_geo_accession | GSM640285
| | Sample_status | Public on Jun 15 2011
| | Sample_submission_date | Dec 15 2010
| | Sample_last_update_date | Jun 15 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Epithelial layer of mouse conjunctival fornix isolated by laser capture microscopy.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 = Between 20 and 120 ng of total RNA was subjected to two cycles of transcriptional amplification using appropriate Affymetrix products (cited as catalog numbers) as follows. Eukaryote Poly A RNA internal standards (900433) were added to the samples, and the poly A containing mRNA component was reverse-transcribed in the presence of a T7-(dT)24 primer (900432). The resulting cDNA was extracted (900371) and subjected to transcriptional amplification using a MEGAscript T7 kit from Ambion (Austin, TX). The amplified cRNA product was extracted (900371) and copied back to cDNA using random primers (900432). Extracted cDNA was again transcribed in vitro, in the presence of biotin-labeled ribonucleotides (900449). The biotinylated cRNA product (107 ± 37 µg, mean ± SD, n | 11 with one outlier of 27 µg) was extracted and 20 μg was fragmented (900371: for 35 minutes at 94°C).
| | Sample_hyb_protocol | Hybridization controls (900454) were added, and each sample was hybridized overnight to a Mouse Genome 430 2.0 Array (900495).
| | Sample_scan_protocol | The chips were washed, developed and scanned in an Agilent ChipScanner (Affymetrix Inc., Santa Clara, CA).
| | Sample_data_processing | Raw data were processed and analyzed using Affymetrix GeneChip Operating System (GCOS) v1.4 software. GCOS was used to assess the presence or absence of the target sequence of each panel, its expression level, and then to make all relevant pair-wise statistical comparisons among samples. Unscaled 2% trimmed means (159 ± 52 mean ± SD, n=12) were scaled to 150. Processed data was sorted and inspected in the Microsoft Excel spreadsheet program (Microsoft, Redmond, WA) and further analyzed using BRB-Array Tools software (Biometric Research Branch, NCI, NIH, Bethesda, MD (www.nci.nih.gov/brb-arraytools.html/)). The Mouse Genome 430 2.0 chip contains 45,101 panels, each targeting a specific transcript sequence. Approximately 22,000 (21,996) transcripts identified by Entrez Gene numbers are redundantly targeted by 41,429 panels: the remaining 3,672 panels target products that currently have no Entrez Gene number. Panels showing consistent, GCOS-validated changes were submitted to Ingenuity Pathways Analysis (https://analysis.ingenuity.com) for classifying the genes according to Gene Ontology groups, functional interactive networks, or canonical pathways. The following conditions were used to designate genes as differentially expressed between any two groups of samples: (a) all three samples in the high-expression group have detectable transcripts (called Present), (b) of the nine pair-wise comparisons made by the GCOS software, at least 6 show valid differences, (c) group values do not overlap, i.e., the lowest value of the high-expression group is higher than the highest value of the low expression group, and (d) the average value of the high-expression group is >2 fold greater than the average value of the low-expression group.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Shivalingappa,Kottur,Swamynathan
| | Sample_contact_email | Swamynathansk@upmc.edu
| | Sample_contact_phone | 412-802-6437
| | Sample_contact_fax | 412-647-5880
| | Sample_contact_laboratory | Ocular Surface Development and Gene Expression
| | Sample_contact_department | Ophthalmology
| | Sample_contact_institute | University of Pittsburgh
| | Sample_contact_address | 203 Lothrop Street Room 1025
| | Sample_contact_city | Pittsburgh
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 15213
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM640nnn/GSM640285/suppl/GSM640285.CEL.gz
| | Sample_series_id | GSE26076
| | Sample_data_row_count | 45101
| | |
|
| |
| |
Make groups for comparisons |
(2 groups will be compared at a time) |
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| Select GSMs and click on "Add groups" |
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