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Search results for the GEO ID: GSE12631

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GSM315841

GPL570

HuCNJE-SP1

Side population (Hoechst 33342-transporting cells; SP)

Side population (Hoechst 33342-transporting cells; SP) from freshly isolated epithelial cells cultured for 12 hr.

Human conjunctiva (CNJ) from donor cadaver- Sample #1. Caucasian dead at 62 from a brain embolism.

Sample_geo_accession	GSM315841
Sample_status	Public on Oct 30 2009
Sample_submission_date	Aug 28 2008
Sample_last_update_date	Aug 20 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_biomaterial_provider_ch1	NDRI
Sample_treatment_protocol_ch1	Whole human conjunctivae from an unidentifiable cadaver donor was obtained from the National Disease Research Interchange (NDRI, Philadelphia, PA) within 48 hours of collection. No donor details apart from age, and cause of death were released and stored. The use of human tissue in the study was in accordance with the provisions of the Declaration of Helsinki and sanctioned by the Institutional Review Board. The conjunctiva was quartered and incubated for 16-20 hr at 4°C in a culture flask containing 5 mg/ml Dispase (Roche, Nutley, NJ) dissolved in -(2-hydroxyethyl)-1-piperazine-ethanesulfonic acid-buffered (hb), penicillin-streptomycin-complemented Dulbecco’s modified Eagle’s medium and Ham-F12 1:1 mix (D/F-12) under slow (20-30 cycles/min) side-to-side tilting motion . At the end of this incubation the epithelial sheet is essentially separated from the underlying stroma and can be floated into the bathing solution with gentle mechanical prodding. Epithelial sheets were transferred to 50 ml conical tube containing 15 ml trypsin solution and incubated for 20-25 min at 37º C under 40 cycles/ min orbital agitation. After trypsin neutralization with hbDF/12-20 % fetal bovine serum (FBS), suspensions were sequentially sieved through 100 and 40 μm filters.
Sample_growth_protocol_ch1	Sieved single cells were centrifuged at 200 g, the cell pellet was resuspended in SHEM medium (D/F12 complemented with, 5 % FBS, 10ng/ml cholera toxin, 10 ng/ml epidermal growth factor (EGF), plated in 75 cm2 flasks at a density of 80,000-100,000 cells/cm2 and cultured overnight (14-16 hr) at 37 ºC in a 5% CO2 incubator.
Sample_growth_protocol_ch1	After overnight culture the medium was refreshed with pre-warmed solution to remove floating cells (60- 70 % of total plated) and complemented with 5 μg/ml Hoechst 33342 for 1.5 hr. The treated cells were then released by trypsinization (2 min-37º C), spun down and resuspended in ice-cold phenol red-free D/F12 complemented with 5% serum and 1 μg/ml propidium iodide.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Cell sorting was performed in an INFLUX (Cytopeia, Seattle, WA) flow cytometer. The source tube was maintained at 4 ºC at all times. Light scattering gates that has been previously determined to exclude non epithelial cells from the sorting populations were applied and the cohort of non side population cells from the Hoechst blue/red emission plot was collected in 750 μl of Tri-Reagent LS (Molecular Research Center, Cincinnati, OH) solutions that was continuously stirred by means of mini-magnets and a custom-designed stirrer Tri-Reagent LS solutions containing the collected SP and nSP cells volumes were adjusted to 1.0 ml by the addition of H2O and 0.5 μl polycryl RNA carrier (MRC). RNA was isolated according to the manufacturer instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	RNAs was adjusted by either addition of water or evaporative concentration to a 3 ng/ul and 10 ul were converted into cDNA using SuperScript Choice reverse transcriptase ( Gibco BRL, Bethesda, MD). After two rounds of RNA amplicfication the final cDNA was synthetized was transcribed in vitro transcription to generate biotin labeled cRNA using the ENZO BioArray™ HighYield™ Kit (Affymetrix).
Sample_hyb_protocol	Appropriately fragmented biotin-labeled cRNA was hybridized to HG-U133 plus 2.0 GeneChips® (Affymetrix) oligonucleotide microarray following the manufacture protocol.
Sample_scan_protocol	Hybridized microarrays were stained with a streptavidin-phycoerythrin reagent and fluorescence images were captured using a G2500A (Agilent, Santa Clara CA) laser scanner.
Sample_data_processing = Expression data was extracted from the fluorescent images using Affymetrix Microarray Suite, version 5.0 (MAS 5.0). The MAS 5.0 signal intensity (SI) values, the P/A/M detection ‘calls’ representing the chances that the SI value is a true (P, for present), a false (A for absent) or a marginal (M) positive for all 4 pairs of SP/nSP microarrays and the MAS5.0 p-values for these detection calls, were collected in a single Excel (Microsoft, Redmont, WA) file containing 8x3 = 24 columns. The average signal intensity value per transcripts in each sample (SnAv) and the all sample average (Av-SnAv	299.97/transcript) were calculated. Each SI value was then multiplied by the corresponding 299.97/SnAv quotient to generate normalized experiments in which each the average SI value/transcript is 299.97. The submitted data includes these normalized SI values and the MAS 5.0 P/A/M calls and p-values for the SP cells.
Sample_platform_id	GPL570
Sample_contact_name	J. Mario,,Wolosin
Sample_contact_email	jmario.wolosin@mssm.edu
Sample_contact_phone	212-241-8980
Sample_contact_fax	212-289-5945
Sample_contact_laboratory	Stem Cells
Sample_contact_department	Ophthalmology
Sample_contact_institute	Mount Siani School of Medicine
Sample_contact_address	One Gustave levy Pl
Sample_contact_city	New York
Sample_contact_state	NY
Sample_contact_zip/postal_code	07666
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM315nnn/GSM315841/suppl/GSM315841.CEL.gz
Sample_series_id	GSE12631
Sample_data_row_count	54675

GSM315897

GPL570

HuCNJE-nSP1

Non side population (Hoechst 33342-stained cells; nSP)

Non side population (Hoechst 33342-stained;nSP) from freshly isolated epithelial cells cultured for 12 hr.

Human conjunctiva (CNJ) from donor cadaver- Sample #1. Caucasian dead at 62 from a brain embolism.

Sample_geo_accession	GSM315897
Sample_status	Public on Oct 30 2009
Sample_submission_date	Aug 29 2008
Sample_last_update_date	Aug 20 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_biomaterial_provider_ch1	NDRI
Sample_treatment_protocol_ch1	Whole human conjunctivae from an unidentifiable cadaver donor was obtained from the National Disease Research Interchange (NDRI, Philadelphia, PA) within 48 hours of collection. No donor details apart from age, and cause of death were released and stored. The use of human tissue in the study was in accordance with the provisions of the Declaration of Helsinki and sanctioned by the Institutional Review Board. The conjunctiva was quartered and incubated for 16-20 hr at 4°C in a culture flask containing 5 mg/ml Dispase (Roche, Nutley, NJ) dissolved in -(2-hydroxyethyl)-1-piperazine-ethanesulfonic acid-buffered (hb), penicillin-streptomycin-complemented Dulbecco’s modified Eagle’s medium and Ham-F12 1:1 mix (D/F-12) under slow (20-30 cycles/min) side-to-side tilting motion . At the end of this incubation the epithelial sheet is essentially separated from the underlying stroma and can be floated into the bathing solution with gentle mechanical prodding. Epithelial sheets were transferred to 50 ml conical tube containing 15 ml trypsin solution and incubated for 20-25 min at 37º C under 40 cycles/ min orbital agitation. After trypsin neutralization with hbDF/12-20 % fetal bovine serum (FBS), suspensions were sequentially sieved through 100 and 40 μm filters.
Sample_growth_protocol_ch1	Sieved single cells were centrifuged at 200 g, the cell pellet was resuspended in SHEM medium (D/F12 complemented with, 5 % FBS, 10ng/ml cholera toxin, 10 ng/ml epidermal growth factor (EGF), plated in 75 cm2 flasks at a density of 80,000-100,000 cells/cm2 and cultured overnight (14-16 hr) at 37 ºC in a 5% CO2 incubator.
Sample_growth_protocol_ch1	After overnight culture the medium was refreshed with pre-warmed solution to remove floating cells (60- 70 % of total plated) and complemented with 5 μg/ml Hoechst 33342 for 1.5 hr. The treated cells were then released by trypsinization (2 min-37º C), spun down and resuspended in ice-cold phenol red-free D/F12 complemented with 5% serum and 1 μg/ml propidium iodide.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Cell sorting was performed in an INFLUX (Cytopeia, Seattle, WA) flow cytometer. The source tube was maintained at 4 ºC at all times. Light scattering gates that has been previously determined to exclude non epithelial cells from the sorting populations were applied and the cohort of non side population cells from the Hoechst blue/red emission plot was collected in 750 μl of Tri-Reagent LS (Molecular Research Center, Cincinnati, OH) solutions that was continuously stirred by means of mini-magnets and a custom-designed stirrer Tri-Reagent LS solutions containing the collected SP and nSP cells volumes were adjusted to 1.0 ml by the addition of H2O and 0.5 μl polycryl RNA carrier (MRC). RNA was isolated according to the manufacturer instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	RNAs was adjusted by either addition of water or evaporative concentration to a 3 ng/ul and 10 ul were converted into cDNA using SuperScript Choice reverse transcriptase ( Gibco BRL, Bethesda, MD). After two rounds of RNA amplification the final cDNA was synthetized was transcribed in vitro transcription to generate biotin labeled cRNA using the ENZO BioArray™ HighYield™ Kit (Affymetrix).
Sample_hyb_protocol	Appropriately fragmented biotin-labeled cRNA was hybridized to HG-U133 plus 2.0 GeneChips® (Affymetrix) oligonucleotide microarray following the manufacture protocol.
Sample_scan_protocol	Hybridized microarrays were stained with a streptavidin-phycoerythrin reagent and fluorescence images were captured using a G2500A (Agilent, Santa Clara CA) laser scanner.
Sample_data_processing = Expression data was extracted from the fluorescent images using Affymetrix Microarray Suite, version 5.0 (MAS 5.0). The MAS 5.0 signal intensity (SI) values, the P/A/M detection ‘calls’ representing the chances that the SI value is a true (P, for present), a false (A for absent) or a marginal (M) positive for all 4 pairs of SP/nSP microarrays and the MAS5.0 p-values for these detection calls, were collected in a single Excel (Microsoft, Redmont, WA) file containing 8x3 = 24 columns. The average signal intensity value per transcripts in each sample (SnAv) and the all sample average (Av-SnAv	299.97/transcript) were calculated. Each SI value was then multiplied by the corresponding 299.97/SnAv quotient to generate normalized experiments in which each the average SI value/transcript is 299.97. The submitted data includes these normalized SI values and the MAS 5.0 P/A/M calls and p-values for the nSP cells sorted along with the SP cells.
Sample_platform_id	GPL570
Sample_contact_name	J. Mario,,Wolosin
Sample_contact_email	jmario.wolosin@mssm.edu
Sample_contact_phone	212-241-8980
Sample_contact_fax	212-289-5945
Sample_contact_laboratory	Stem Cells
Sample_contact_department	Ophthalmology
Sample_contact_institute	Mount Siani School of Medicine
Sample_contact_address	One Gustave levy Pl
Sample_contact_city	New York
Sample_contact_state	NY
Sample_contact_zip/postal_code	07666
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM315nnn/GSM315897/suppl/GSM315897.CEL.gz
Sample_series_id	GSE12631
Sample_data_row_count	54675

GSM317171

GPL570

HuCNJE-SP2

Side population (Hoechst 33342-transporting cells; SP)

Side population (Hoechst 33342-transporting cells; SP) from freshly isolated epithelial cells cultured for 12 hr

Human conjunctiva (CNJ) from donor cadaver- Sample #2. Caucasian. Dead from heart infarct at age 58

Sample_geo_accession	GSM317171
Sample_status	Public on Oct 30 2009
Sample_submission_date	Aug 30 2008
Sample_last_update_date	Aug 20 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_biomaterial_provider_ch1	NDRI
Sample_treatment_protocol_ch1	Whole human conjunctivae from an unidentifiable cadaver donor was obtained from the National Disease Research Interchange (NDRI, Philadelphia, PA) within 48 hours of collection. No donor details apart from age, and cause of death were released and stored. The use of human tissue in the study was in accordance with the provisions of the Declaration of Helsinki and sanctioned by the Institutional Review Board. The conjunctiva was quartered and incubated for 16-20 hr at 4°C in a culture flask containing 5 mg/ml Dispase (Roche, Nutley, NJ) dissolved in -(2-hydroxyethyl)-1-piperazine-ethanesulfonic acid-buffered (hb), penicillin-streptomycin-complemented Dulbecco’s modified Eagle’s medium and Ham-F12 1:1 mix (D/F-12) under slow (20-30 cycles/min) side-to-side tilting motion . At the end of this incubation the epithelial sheet is essentially separated from the underlying stroma and can be floated into the bathing solution with gentle mechanical prodding. Epithelial sheets were transferred to 50 ml conical tube containing 15 ml trypsin solution and incubated for 20-25 min at 37º C under 40 cycles/ min orbital agitation. After trypsin neutralization with hbDF/12-20 % fetal bovine serum (FBS), suspensions were sequentially sieved through 100 and 40 μm filters
Sample_growth_protocol_ch1	Sieved single cells were centrifuged at 200 g, the cell pellet was resuspended in SHEM medium (D/F12 complemented with, 5 % FBS, 10ng/ml cholera toxin, 10 ng/ml epidermal growth factor (EGF), plated in 75 cm2 flasks at a density of 80,000-100,000 cells/cm2 and cultured overnight (14-16 hr) at 37 ºC in a 5% CO2 incubator.
Sample_growth_protocol_ch1	After overnight culture the medium was refreshed with pre-warmed solution to remove floating cells (60- 70 % of total plated) and complemented with 5 μg/ml Hoechst 33342 for 1.5 hr. The treated cells were then released by trypsinization (2 min-37º C), spun down and resuspended in ice-cold phenol red-free D/F12 complemented with 5% serum and 1 μg/ml propidium iodide.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Cell sorting was performed in an INFLUX (Cytopeia, Seattle, WA) flow cytometer. The source tube was maintained at 4 ºC at all times. Light scattering gates that has been previously determined to exclude non epithelial cells from the sorting populations were applied and the cohort of non side population cells from the Hoechst blue/red emission plot was collected in 750 μl of Tri-Reagent LS (Molecular Research Center, Cincinnati, OH) solutions that was continuously stirred by means of mini-magnets and a custom-designed stirrer Tri-Reagent LS solutions containing the collected SP and nSP cells volumes were adjusted to 1.0 ml by the addition of H2O and 0.5 μl polycryl RNA carrier (MRC). RNA was isolated according to the manufacturer instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	RNAs was adjusted by either addition of water or evaporative concentration to a 3 ng/ul and 10 ul were converted into cDNA using SuperScript Choice reverse transcriptase ( Gibco BRL, Bethesda, MD). After two rounds of RNA amplicfication the final cDNA was synthetized was transcribed in vitro transcription to generate biotin labeled cRNA using the ENZO BioArray™ HighYield™ Kit (Affymetr
Sample_hyb_protocol	Appropriately fragmented biotin-labeled cRNA was hybridized to HG-U133 plus 2.0 GeneChips® (Affymetrix) oligonucleotide microarray following the manufacture protocol.
Sample_scan_protocol	Hybridized microarrays were stained with a streptavidin-phycoerythrin reagent and fluorescence images were captured using a G2500A (Agilent, Santa Clara CA) laser scanner.
Sample_data_processing = Expression data was extracted from the fluorescent images using Affymetrix Microarray Suite, version 5.0 (MAS 5.0). The MAS 5.0 signal intensity (SI) values, the P/A/M detection ‘calls’ representing the chances that the SI value is a true (P, for present), a false (A for absent) or a marginal (M) positive for all 4 pairs of SP/nSP microarrays and the MAS5.0 p-values for these detection calls, were collected in a single Excel (Microsoft, Redmont, WA) file containing 8x3 = 24 columns. The average signal intensity value per transcripts in each sample (SnAv) and the all sample average (Av-SnAv	299.97/transcript) were calculated. Each SI value was then multiplied by the corresponding 299.97/SnAv quotient to generate normalized experiments in which each the average SI value/transcript is 299.97. The submitted data includes these normalized SI values and the MAS 5.0 P/A/M calls and p-values. for SP cells.
Sample_platform_id	GPL570
Sample_contact_name	J. Mario,,Wolosin
Sample_contact_email	jmario.wolosin@mssm.edu
Sample_contact_phone	212-241-8980
Sample_contact_fax	212-289-5945
Sample_contact_laboratory	Stem Cells
Sample_contact_department	Ophthalmology
Sample_contact_institute	Mount Siani School of Medicine
Sample_contact_address	One Gustave levy Pl
Sample_contact_city	New York
Sample_contact_state	NY
Sample_contact_zip/postal_code	07666
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM317nnn/GSM317171/suppl/GSM317171.CEL.gz
Sample_series_id	GSE12631
Sample_data_row_count	54675

GSM317172

GPL570

HuCNJE-nSP2

Non side population (Hoechst 33342-stained cells; nSP)

Non Side population (Hoechst 33342-stained cells; nSP) from freshly isolated epithelial cells cultured for 12 hr.

Human conjunctiva (CNJ) from donor cadaver- Sample #2. Caucasian. Dead from heart infarct at age 58.

Sample_geo_accession	GSM317172
Sample_status	Public on Oct 30 2009
Sample_submission_date	Aug 30 2008
Sample_last_update_date	Aug 20 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_biomaterial_provider_ch1	NDRI
Sample_treatment_protocol_ch1	Whole human conjunctivae from an unidentifiable cadaver donor was obtained from the National Disease Research Interchange (NDRI, Philadelphia, PA) within 48 hours of collection. No donor details apart from age, and cause of death were released and stored. The use of human tissue in the study was in accordance with the provisions of the Declaration of Helsinki and sanctioned by the Institutional Review Board. The conjunctiva was quartered and incubated for 16-20 hr at 4°C in a culture flask containing 5 mg/ml Dispase (Roche, Nutley, NJ) dissolved in -(2-hydroxyethyl)-1-piperazine-ethanesulfonic acid-buffered (hb), penicillin-streptomycin-complemented Dulbecco’s modified Eagle’s medium and Ham-F12 1:1 mix (D/F-12) under slow (20-30 cycles/min) side-to-side tilting motion . At the end of this incubation the epithelial sheet is essentially separated from the underlying stroma and can be floated into the bathing solution with gentle mechanical prodding. Epithelial sheets were transferred to 50 ml conical tube containing 15 ml trypsin solution and incubated for 20-25 min at 37º C under 40 cycles/ min orbital agitation. After trypsin neutralization with hbDF/12-20 % fetal bovine serum (FBS), suspensions were sequentially sieved through 100 and 40 μm filters.
Sample_growth_protocol_ch1	Sieved single cells were centrifuged at 200 g, the cell pellet was resuspended in SHEM medium (D/F12 complemented with, 5 % FBS, 10ng/ml cholera toxin, 10 ng/ml epidermal growth factor (EGF), plated in 75 cm2 flasks at a density of 80,000-100,000 cells/cm2 and cultured overnight (14-16 hr) at 37 ºC in a 5% CO2 incubator.
Sample_growth_protocol_ch1	After overnight culture the medium was refreshed with pre-warmed solution to remove floating cells (60- 70 % of total plated) and complemented with 5 μg/ml Hoechst 33342 for 1.5 hr. The treated cells were then released by trypsinization (2 min-37º C), spun down and resuspended in ice-cold phenol red-free D/F12 complemented with 5% serum and 1 μg/ml propidium iodide.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Cell sorting was performed in an INFLUX (Cytopeia, Seattle, WA) flow cytometer. The source tube was maintained at 4 ºC at all times. Light scattering gates that has been previously determined to exclude non epithelial cells from the sorting populations were applied and the cohort of non side population cells from the Hoechst blue/red emission plot was collected in 750 μl of Tri-Reagent LS (Molecular Research Center, Cincinnati, OH) solutions that was continuously stirred by means of mini-magnets and a custom-designed stirrer Tri-Reagent LS solutions containing the collected SP and nSP cells volumes were adjusted to 1.0 ml by the addition of H2O and 0.5 μl polycryl RNA carrier (MRC). RNA was isolated according to the manufacturer instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	RNAs was adjusted by either addition of water or evaporative concentration to a 3 ng/ul and 10 ul were converted into cDNA using SuperScript Choice reverse transcriptase ( Gibco BRL, Bethesda, MD). After two rounds of RNA amplicfication the final cDNA was synthetized was transcribed in vitro transcription to generate biotin labeled cRNA using the ENZO BioArray™ HighYield™ Kit (Affymetrix).
Sample_hyb_protocol	Appropriately fragmented biotin-labeled cRNA was hybridized to HG-U133 plus 2.0 GeneChips® (Affymetrix) oligonucleotide microarray following the manufacture protocol.
Sample_scan_protocol	Hybridized microarrays were stained with a streptavidin-phycoerythrin reagent and fluorescence images were captured using a G2500A (Agilent, Santa Clara CA) laser scanner.
Sample_data_processing = Expression data was extracted from the fluorescent images using Affymetrix Microarray Suite, version 5.0 (MAS 5.0). The MAS 5.0 signal intensity (SI) values, the P/A/M detection ‘calls’ representing the chances that the SI value is a true (P, for present), a false (A for absent) or a marginal (M) positive for all 4 pairs of SP/nSP microarrays and the MAS5.0 p-values for these detection calls, were collected in a single Excel (Microsoft, Redmont, WA) file containing 8x3 = 24 columns. The average signal intensity value per transcripts in each sample (SnAv) and the all sample average (Av-SnAv	299.97/transcript) were calculated. Each SI value was then multiplied by the corresponding 299.97/SnAv quotient to generate normalized experiments in which each the average SI value/transcript is 299.97. The submitted data includes these normalized SI values and the MAS 5.0 P/A/M calls and p-values for nSP cells sorted along with the SP cells.
Sample_platform_id	GPL570
Sample_contact_name	J. Mario,,Wolosin
Sample_contact_email	jmario.wolosin@mssm.edu
Sample_contact_phone	212-241-8980
Sample_contact_fax	212-289-5945
Sample_contact_laboratory	Stem Cells
Sample_contact_department	Ophthalmology
Sample_contact_institute	Mount Siani School of Medicine
Sample_contact_address	One Gustave levy Pl
Sample_contact_city	New York
Sample_contact_state	NY
Sample_contact_zip/postal_code	07666
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM317nnn/GSM317172/suppl/GSM317172.CEL.gz
Sample_series_id	GSE12631
Sample_data_row_count	54675

GSM317173

GPL570

HuCNJE-SP3

Side population (Hoechst 33342-transporting cells; SP)

Side population (Hoechst 33342-transporting cells; SP) from freshly isolated epithelial cells cultured for 12 hr.

Human conjunctiva (CNJ) from donor cadaver. Sample #3. Caucasian. Dead from lung cancer at age 64.

Sample_geo_accession	GSM317173
Sample_status	Public on Oct 30 2009
Sample_submission_date	Aug 30 2008
Sample_last_update_date	Aug 20 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_biomaterial_provider_ch1	NDRI
Sample_treatment_protocol_ch1	Whole human conjunctivae from an unidentifiable cadaver donor was obtained from the National Disease Research Interchange (NDRI, Philadelphia, PA) within 48 hours of collection. No donor details apart from age, and cause of death were released and stored. The use of human tissue in the study was in accordance with the provisions of the Declaration of Helsinki and sanctioned by the Institutional Review Board. The conjunctiva was quartered and incubated for 16-20 hr at 4°C in a culture flask containing 5 mg/ml Dispase (Roche, Nutley, NJ) dissolved in -(2-hydroxyethyl)-1-piperazine-ethanesulfonic acid-buffered (hb), penicillin-streptomycin-complemented Dulbecco’s modified Eagle’s medium and Ham-F12 1:1 mix (D/F-12) under slow (20-30 cycles/min) side-to-side tilting motion . At the end of this incubation the epithelial sheet is essentially separated from the underlying stroma and can be floated into the bathing solution with gentle mechanical prodding. Epithelial sheets were transferred to 50 ml conical tube containing 15 ml trypsin solution and incubated for 20-25 min at 37º C under 40 cycles/ min orbital agitation. After trypsin neutralization with hbDF/12-20 % fetal bovine serum (FBS), suspensions were sequentially sieved through 100 and 40 μm filters.
Sample_growth_protocol_ch1	Sieved single cells were centrifuged at 200 g, the cell pellet was resuspended in SHEM medium (D/F12 complemented with, 5 % FBS, 10ng/ml cholera toxin, 10 ng/ml epidermal growth factor (EGF), plated in 75 cm2 flasks at a density of 80,000-100,000 cells/cm2 and cultured overnight (14-16 hr) at 37 ºC in a 5% CO2 incubator.
Sample_growth_protocol_ch1	After overnight culture the medium was refreshed with pre-warmed solution to remove floating cells (60- 70 % of total plated) and complemented with 5 μg/ml Hoechst 33342 for 1.5 hr. The treated cells were then released by trypsinization (2 min-37º C), spun down and resuspended in ice-cold phenol red-free D/F12 complemented with 5% serum and 1 μg/ml propidium iodide.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Cell sorting was performed in an INFLUX (Cytopeia, Seattle, WA) flow cytometer. The source tube was maintained at 4 ºC at all times. Light scattering gates that has been previously determined to exclude non epithelial cells from the sorting populations were applied and the cohort of non side population cells from the Hoechst blue/red emission plot was collected in 750 μl of Tri-Reagent LS (Molecular Research Center, Cincinnati, OH) solutions that was continuously stirred by means of mini-magnets and a custom-designed stirrer Tri-Reagent LS solutions containing the collected SP and nSP cells volumes were adjusted to 1.0 ml by the addition of H2O and 0.5 μl polycryl RNA carrier (MRC). RNA was isolated according to the manufacturer instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	RNAs was adjusted by either addition of water or evaporative concentration to a 3 ng/ul and 10 ul were converted into cDNA using SuperScript Choice reverse transcriptase ( Gibco BRL, Bethesda, MD). After two rounds of RNA amplicfication the final cDNA was synthetized was transcribed in vitro transcription to generate biotin labeled cRNA using the ENZO BioArray™ HighYield™ Kit (Affymetrix).
Sample_hyb_protocol	Appropriately fragmented biotin-labeled cRNA was hybridized to HG-U133 plus 2.0 GeneChips® (Affymetrix) oligonucleotide microarray following the manufacture protocol.
Sample_scan_protocol	Hybridized microarrays were stained with a streptavidin-phycoerythrin reagent and fluorescence images were captured using a G2500A (Agilent, Santa Clara CA) laser scanner.
Sample_data_processing = Expression data was extracted from the fluorescent images using Affymetrix Microarray Suite, version 5.0 (MAS 5.0). The MAS 5.0 signal intensity (SI) values, the P/A/M detection ‘calls’ representing the chances that the SI value is a true (P, for present), a false (A for absent) or a marginal (M) positive for all 4 pairs of SP/nSP microarrays and the MAS5.0 p-values for these detection calls, were collected in a single Excel (Microsoft, Redmont, WA) file containing 8x3 = 24 columns. The average signal intensity value per transcripts in each sample (SnAv) and the all sample average (Av-SnAv	299.97/transcript) were calculated. Each SI value was then multiplied by the corresponding 299.97/SnAv quotient to generate normalized experiments in which each the average SI value/transcript is 299.97. The submitted data includes these normalized SI values and the MAS 5.0 P/A/M calls and p-values for the SP cells.
Sample_platform_id	GPL570
Sample_contact_name	J. Mario,,Wolosin
Sample_contact_email	jmario.wolosin@mssm.edu
Sample_contact_phone	212-241-8980
Sample_contact_fax	212-289-5945
Sample_contact_laboratory	Stem Cells
Sample_contact_department	Ophthalmology
Sample_contact_institute	Mount Siani School of Medicine
Sample_contact_address	One Gustave levy Pl
Sample_contact_city	New York
Sample_contact_state	NY
Sample_contact_zip/postal_code	07666
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM317nnn/GSM317173/suppl/GSM317173.CEL.gz
Sample_series_id	GSE12631
Sample_data_row_count	54675

GSM317174

GPL570

HuCNJE-nSP3

Non side population (Hoechst 33342-stained cells; nSP)

Non side population (Hoechst 33342-stained cells; nSP) from freshly isolated epithelial cells cultured for 12 hr

Human conjunctiva (CNJ) from donor cadaver- Sample #3. Caucasian. Dead from lung cancer at age 64.

Sample_geo_accession	GSM317174
Sample_status	Public on Oct 30 2009
Sample_submission_date	Aug 30 2008
Sample_last_update_date	Aug 20 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_biomaterial_provider_ch1	NDRI
Sample_treatment_protocol_ch1	Whole human conjunctivae from an unidentifiable cadaver donor was obtained from the National Disease Research Interchange (NDRI, Philadelphia, PA) within 48 hours of collection. No donor details apart from age, and cause of death were released and stored. The use of human tissue in the study was in accordance with the provisions of the Declaration of Helsinki and sanctioned by the Institutional Review Board. The conjunctiva was quartered and incubated for 16-20 hr at 4°C in a culture flask containing 5 mg/ml Dispase (Roche, Nutley, NJ) dissolved in -(2-hydroxyethyl)-1-piperazine-ethanesulfonic acid-buffered (hb), penicillin-streptomycin-complemented Dulbecco’s modified Eagle’s medium and Ham-F12 1:1 mix (D/F-12) under slow (20-30 cycles/min) side-to-side tilting motion . At the end of this incubation the epithelial sheet is essentially separated from the underlying stroma and can be floated into the bathing solution with gentle mechanical prodding. Epithelial sheets were transferred to 50 ml conical tube containing 15 ml trypsin solution and incubated for 20-25 min at 37º C under 40 cycles/ min orbital agitation. After trypsin neutralization with hbDF/12-20 % fetal bovine serum (FBS), suspensions were sequentially sieved through 100 and 40 μm filters.
Sample_growth_protocol_ch1	Sieved single cells were centrifuged at 200 g, the cell pellet was resuspended in SHEM medium (D/F12 complemented with, 5 % FBS, 10ng/ml cholera toxin, 10 ng/ml epidermal growth factor (EGF), plated in 75 cm2 flasks at a density of 80,000-100,000 cells/cm2 and cultured overnight (14-16 hr) at 37 ºC in a 5% CO2 incubator.
Sample_growth_protocol_ch1	After overnight culture the medium was refreshed with pre-warmed solution to remove floating cells (60- 70 % of total plated) and complemented with 5 μg/ml Hoechst 33342 for 1.5 hr. The treated cells were then released by trypsinization (2 min-37º C), spun down and resuspended in ice-cold phenol red-free D/F12 complemented with 5% serum and 1 μg/ml propidium iodide.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Cell sorting was performed in an INFLUX (Cytopeia, Seattle, WA) flow cytometer. The source tube was maintained at 4 ºC at all times. Light scattering gates that has been previously determined to exclude non epithelial cells from the sorting populations were applied and the cohort of non side population cells from the Hoechst blue/red emission plot was collected in 750 μl of Tri-Reagent LS (Molecular Research Center, Cincinnati, OH) solutions that was continuously stirred by means of mini-magnets and a custom-designed stirrer Tri-Reagent LS solutions containing the collected SP and nSP cells volumes were adjusted to 1.0 ml by the addition of H2O and 0.5 μl polycryl RNA carrier (MRC). RNA was isolated according to the manufacturer instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	RNAs was adjusted by either addition of water or evaporative concentration to a 3 ng/ul and 10 ul were converted into cDNA using SuperScript Choice reverse transcriptase ( Gibco BRL, Bethesda, MD). After two rounds of RNA amplicfication the final cDNA was synthetized was transcribed in vitro transcription to generate biotin labeled cRNA using the ENZO BioArray™ HighYield™ Kit (Affymetrix).
Sample_hyb_protocol	Appropriately fragmented biotin-labeled cRNA was hybridized to HG-U133 plus 2.0 GeneChips® (Affymetrix) oligonucleotide microarray following the manufacture protocol.
Sample_scan_protocol	Hybridized microarrays were stained with a streptavidin-phycoerythrin reagent and fluorescence images were captured using a G2500A (Agilent, Santa Clara CA) laser scanner.
Sample_data_processing = Expression data was extracted from the fluorescent images using Affymetrix Microarray Suite, version 5.0 (MAS 5.0). The MAS 5.0 signal intensity (SI) values, the P/A/M detection ‘calls’ representing the chances that the SI value is a true (P, for present), a false (A for absent) or a marginal (M) positive for all 4 pairs of SP/nSP microarrays and the MAS5.0 p-values for these detection calls, were collected in a single Excel (Microsoft, Redmont, WA) file containing 8x3 = 24 columns. The average signal intensity value per transcripts in each sample (SnAv) and the all sample average (Av-SnAv	299.97/transcript) were calculated. Each SI value was then multiplied by the corresponding 299.97/SnAv quotient to generate normalized experiments in which each the average SI value/transcript is 299.97. The submitted data includes these normalized SI values and the MAS 5.0 P/A/M calls and p-values for the nSP cells sorted along with SP cells in the third (#3) experiment.
Sample_platform_id	GPL570
Sample_contact_name	J. Mario,,Wolosin
Sample_contact_email	jmario.wolosin@mssm.edu
Sample_contact_phone	212-241-8980
Sample_contact_fax	212-289-5945
Sample_contact_laboratory	Stem Cells
Sample_contact_department	Ophthalmology
Sample_contact_institute	Mount Siani School of Medicine
Sample_contact_address	One Gustave levy Pl
Sample_contact_city	New York
Sample_contact_state	NY
Sample_contact_zip/postal_code	07666
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM317nnn/GSM317174/suppl/GSM317174.CEL.gz
Sample_series_id	GSE12631
Sample_data_row_count	54675

GSM317175

GPL570

HuCNJE-SP4

Side population (Hoechst 33342-transporting cells; SP)

Side population (Hoechst 33342-transporting cells; SP) from freshly isolated epithelial cells cultured for 12 hr B

Human conjunctiva (CNJ) from donor cadaver- Sample #4. Caucasian. Dead from heart infarct at age 55.

Sample_geo_accession	GSM317175
Sample_status	Public on Oct 30 2009
Sample_submission_date	Aug 30 2008
Sample_last_update_date	Aug 20 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_biomaterial_provider_ch1	NDRI
Sample_treatment_protocol_ch1	Whole human conjunctivae from an unidentifiable cadaver donor was obtained from the National Disease Research Interchange (NDRI, Philadelphia, PA) within 48 hours of collection. No donor details apart from age, and cause of death were released and stored. The use of human tissue in the study was in accordance with the provisions of the Declaration of Helsinki and sanctioned by the Institutional Review Board. The conjunctiva was quartered and incubated for 16-20 hr at 4°C in a culture flask containing 5 mg/ml Dispase (Roche, Nutley, NJ) dissolved in -(2-hydroxyethyl)-1-piperazine-ethanesulfonic acid-buffered (hb), penicillin-streptomycin-complemented Dulbecco’s modified Eagle’s medium and Ham-F12 1:1 mix (D/F-12) under slow (20-30 cycles/min) side-to-side tilting motion . At the end of this incubation the epithelial sheet is essentially separated from the underlying stroma and can be floated into the bathing solution with gentle mechanical prodding. Epithelial sheets were transferred to 50 ml conical tube containing 15 ml trypsin solution and incubated for 20-25 min at 37º C under 40 cycles/ min orbital agitation. After trypsin neutralization with hbDF/12-20 % fetal bovine serum (FBS), suspensions were sequentially sieved through 100 and 40 μm filters.
Sample_growth_protocol_ch1	Sieved single cells were centrifuged at 200 g, the cell pellet was resuspended in SHEM medium (D/F12 complemented with, 5 % FBS, 10ng/ml cholera toxin, 10 ng/ml epidermal growth factor (EGF), plated in 75 cm2 flasks at a density of 80,000-100,000 cells/cm2 and cultured overnight (14-16 hr) at 37 ºC in a 5% CO2 incubator.
Sample_growth_protocol_ch1	After overnight culture the medium was refreshed with pre-warmed solution to remove floating cells (60- 70 % of total plated) and complemented with 5 μg/ml Hoechst 33342 for 1.5 hr. The treated cells were then released by trypsinization (2 min-37º C), spun down and resuspended in ice-cold phenol red-free D/F12 complemented with 5% serum and 1 μg/ml propidium iodide.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Cell sorting was performed in an INFLUX (Cytopeia, Seattle, WA) flow cytometer. The source tube was maintained at 4 ºC at all times. Light scattering gates that has been previously determined to exclude non epithelial cells from the sorting populations were applied and the cohort of non side population cells from the Hoechst blue/red emission plot was collected in 750 μl of Tri-Reagent LS (Molecular Research Center, Cincinnati, OH) solutions that was continuously stirred by means of mini-magnets and a custom-designed stirrer Tri-Reagent LS solutions containing the collected SP and nSP cells volumes were adjusted to 1.0 ml by the addition of H2O and 0.5 μl polycryl RNA carrier (MRC). RNA was isolated according to the manufacturer instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	RNAs was adjusted by either addition of water or evaporative concentration to a 3 ng/ul and 10 ul were converted into cDNA using SuperScript Choice reverse transcriptase ( Gibco BRL, Bethesda, MD). After two rounds of RNA amplicfication the final cDNA was synthetized was transcribed in vitro transcription to generate biotin labeled cRNA using the ENZO BioArray™ HighYield™ Kit (Affymetrix).
Sample_hyb_protocol	Appropriately fragmented biotin-labeled cRNA was hybridized to HG-U133 plus 2.0 GeneChips® (Affymetrix) oligonucleotide microarray following the manufacture protocol.
Sample_scan_protocol	Hybridized microarrays were stained with a streptavidin-phycoerythrin reagent and fluorescence images were captured using a G2500A (Agilent, Santa Clara CA) laser scanner.
Sample_data_processing = Expression data was extracted from the fluorescent images using Affymetrix Microarray Suite, version 5.0 (MAS 5.0). The MAS 5.0 signal intensity (SI) values, the P/A/M detection ‘calls’ representing the chances that the SI value is a true (P, for present), a false (A for absent) or a marginal (M) positive for all 4 pairs of SP/nSP microarrays and the MAS5.0 p-values for these detection calls, were collected in a single Excel (Microsoft, Redmont, WA) file containing 8x3 = 24 columns. The average signal intensity value per transcripts in each sample (SnAv) and the all sample average (Av-SnAv	299.97/transcript) were calculated. Each SI value was then multiplied by the corresponding 299.97/SnAv quotient to generate normalized experiments in which each the average SI value/transcript is 299.97. The submitted data includes these normalized SI values and the MAS 5.0 P/A/M calls and p-values from the SP cells.
Sample_platform_id	GPL570
Sample_contact_name	J. Mario,,Wolosin
Sample_contact_email	jmario.wolosin@mssm.edu
Sample_contact_phone	212-241-8980
Sample_contact_fax	212-289-5945
Sample_contact_laboratory	Stem Cells
Sample_contact_department	Ophthalmology
Sample_contact_institute	Mount Siani School of Medicine
Sample_contact_address	One Gustave levy Pl
Sample_contact_city	New York
Sample_contact_state	NY
Sample_contact_zip/postal_code	07666
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM317nnn/GSM317175/suppl/GSM317175.CEL.gz
Sample_series_id	GSE12631
Sample_data_row_count	54675

GSM317176

GPL570

HuCNJE-nSP4

Non side population (Hoechst 33342-stained cells; nSP)

Non side population (Hoechst 33342-stained;nSP) from freshly isolated epithelial cells cultured for 12 hr.

Human conjunctiva (CNJ) from donor cadaver- Sample #4. Caucasian. Dead from heart infarct at age 55.

Sample_geo_accession	GSM317176
Sample_status	Public on Oct 30 2009
Sample_submission_date	Aug 30 2008
Sample_last_update_date	Aug 20 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_biomaterial_provider_ch1	NDRI
Sample_treatment_protocol_ch1	Whole human conjunctivae from an unidentifiable cadaver donor was obtained from the National Disease Research Interchange (NDRI, Philadelphia, PA) within 48 hours of collection. No donor details apart from age, and cause of death were released and stored. The use of human tissue in the study was in accordance with the provisions of the Declaration of Helsinki and sanctioned by the Institutional Review Board. The conjunctiva was quartered and incubated for 16-20 hr at 4°C in a culture flask containing 5 mg/ml Dispase (Roche, Nutley, NJ) dissolved in -(2-hydroxyethyl)-1-piperazine-ethanesulfonic acid-buffered (hb), penicillin-streptomycin-complemented Dulbecco’s modified Eagle’s medium and Ham-F12 1:1 mix (D/F-12) under slow (20-30 cycles/min) side-to-side tilting motion . At the end of this incubation the epithelial sheet is essentially separated from the underlying stroma and can be floated into the bathing solution with gentle mechanical prodding. Epithelial sheets were transferred to 50 ml conical tube containing 15 ml trypsin solution and incubated for 20-25 min at 37º C under 40 cycles/ min orbital agitation. After trypsin neutralization with hbDF/12-20 % fetal bovine serum (FBS), suspensions were sequentially sieved through 100 and 40 μm filters.
Sample_growth_protocol_ch1	Sieved single cells were centrifuged at 200 g, the cell pellet was resuspended in SHEM medium (D/F12 complemented with, 5 % FBS, 10ng/ml cholera toxin, 10 ng/ml epidermal growth factor (EGF), plated in 75 cm2 flasks at a density of 80,000-100,000 cells/cm2 and cultured overnight (14-16 hr) at 37 ºC in a 5% CO2 incubator.
Sample_growth_protocol_ch1	After overnight culture the medium was refreshed with pre-warmed solution to remove floating cells (60- 70 % of total plated) and complemented with 5 μg/ml Hoechst 33342 for 1.5 hr. The treated cells were then released by trypsinization (2 min-37º C), spun down and resuspended in ice-cold phenol red-free D/F12 complemented with 5% serum and 1 μg/ml propidium iodide.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Cell sorting was performed in an INFLUX (Cytopeia, Seattle, WA) flow cytometer. The source tube was maintained at 4 ºC at all times. Light scattering gates that has been previously determined to exclude non epithelial cells from the sorting populations were applied and the cohort of non side population cells from the Hoechst blue/red emission plot was collected in 750 μl of Tri-Reagent LS (Molecular Research Center, Cincinnati, OH) solutions that was continuously stirred by means of mini-magnets and a custom-designed stirrer Tri-Reagent LS solutions containing the collected SP and nSP cells volumes were adjusted to 1.0 ml by the addition of H2O and 0.5 μl polycryl RNA carrier (MRC). RNA was isolated according to the manufacturer instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	RNAs was adjusted by either addition of water or evaporative concentration to a 3 ng/ul and 10 ul were converted into cDNA using SuperScript Choice reverse transcriptase ( Gibco BRL, Bethesda, MD). After two rounds of RNA amplicfication the final cDNA was synthetized was transcribed in vitro transcription to generate biotin labeled cRNA using the ENZO BioArray™ HighYield™ Kit (Affymetrix).
Sample_hyb_protocol	Appropriately fragmented biotin-labeled cRNA was hybridized to HG-U133 plus 2.0 GeneChips® (Affymetrix) oligonucleotide microarray following the manufacture protocol.
Sample_scan_protocol	Hybridized microarrays were stained with a streptavidin-phycoerythrin reagent and fluorescence images were captured using a G2500A (Agilent, Santa Clara CA) laser scanner.
Sample_data_processing = Expression data was extracted from the fluorescent images using Affymetrix Microarray Suite, version 5.0 (MAS 5.0). The MAS 5.0 signal intensity (SI) values, the P/A/M detection ‘calls’ representing the chances that the SI value is a true (P, for present), a false (A for absent) or a marginal (M) positive for all 4 pairs of SP/nSP microarrays and the MAS5.0 p-values for these detection calls, were collected in a single Excel (Microsoft, Redmont, WA) file containing 8x3 = 24 columns. The average signal intensity value per transcripts in each sample (SnAv) and the all sample average (Av-SnAv	299.97/transcript) were calculated. Each SI value was then multiplied by the corresponding 299.97/SnAv quotient to generate normalized experiments in which each the average SI value/transcript is 299.97. The submitted data includes these normalized SI values and the MAS 5.0 P/A/M calls and p-values from the nSP cells sorted along with the SP cells in the fourth (#4) experiment.
Sample_platform_id	GPL570
Sample_contact_name	J. Mario,,Wolosin
Sample_contact_email	jmario.wolosin@mssm.edu
Sample_contact_phone	212-241-8980
Sample_contact_fax	212-289-5945
Sample_contact_laboratory	Stem Cells
Sample_contact_department	Ophthalmology
Sample_contact_institute	Mount Siani School of Medicine
Sample_contact_address	One Gustave levy Pl
Sample_contact_city	New York
Sample_contact_state	NY
Sample_contact_zip/postal_code	07666
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM317nnn/GSM317176/suppl/GSM317176.CEL.gz
Sample_series_id	GSE12631
Sample_data_row_count	54675

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