Search results for the GEO ID: GSE18811  |
(Click on the check boxes provided under "Select for analysis", to initiate grouping) |
(Once the selection is made, click on "Add groups" in "Make groups for comparison", to make a group. Scroll down) |
|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM466520 | GPL570 |
|
292FW1
|
fetal RPE cultures
|
cell type: fetal RPE
gestational age: 16 weeks
|
Fetal RPE were cultured on Primaria® flasks and assages 1-2 were used for all studies. The confluent monolayers used in these experiments have the morphology, pigmentation, polarity, and physiology of native RPE.
|
| Sample_geo_accession | GSM466520
| | Sample_status | Public on Apr 15 2010
| | Sample_submission_date | Oct 29 2009
| | Sample_last_update_date | Apr 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Fetal RPE were cultured on Primaria® flasks for 6 weeks using MEM-α modified medium with additional supplements. Passages 1-2 were used for all studies. The confluent monolayers used in these experiments have the morphology, pigmentation, polarity, and physiology of native RPE.ARPE-19 spontaneously transformed cell line was cultured using MEM-α modified medium with additional supplements on flasks and inserts to match fetal RPE culturing conditions.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Fetal and adult RPE cells were collected, homogenized in TRIzol reagent (Invitrogen, Carlsbad, CA) and RNA was subsequently purified using an RNeasy Mini kit (Qiagen Inc, Valencia, CA). Double-stranded cDNA was synthesized from 6µg of total RNA using the SuperScript Choice system (Invitrogen, Carlsbad, CA) and the T7-Oligo (dT) promoter primer kit (Affymetrix, Santa Clara, CA). cDNA was purified using Phase Lock Gels (Eppendorf, Westbury, NY). Concentration and quality of RNA samples was determined on the Agilent bioanalyzer (Agilent Technologies, Palo Alto, CA). The integrity of RNA is assessed by looking at 18 & 28s rRNA peaks and though the RIN (RNA integrity number). RNA concentrations were measured using the Nano drop spectrophotometer (Wilmington, DE) and all samples used for the study had 260/280 ratios above 2.0 and 260/230 ratios above 1.7.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Ten micrograms of total RNA was reverse transcribed with Superscript II reverse transcriptase (Invitrogen, Carlsbad, CA) using T7-(dT) 24 primer (Geneset Oligos, La Jolla, CA, USA) containing T7 RNA polymerase promoter. After synthesis of the second cDNA strand, this product was used in an in vitro transcription reaction to generate biotinylated cRNA using a BioArray High Yield RNA Transcript Labeling Kit (Affymetrix, Santa Clara, CA). The biotinylated cRNA was cleaned with the RNAeasy Mini Kit (Qiagen, Valencia, CA).
| | Sample_hyb_protocol | Biotin-labeled cRNA was then fragmented at 94oC for 35 min with 5X fragmentation buffer (200 mM Tris-acetate, pH 8.1, 500 mM potassium acetate, 150 mM magnesium acetate) and then hybridized (10 ug) to Affymetrix (Santa Clara, CA) mouse 430_2 oligonucleotide probe arrays for 16 h at 45oC
| | Sample_scan_protocol | Hybridization fluid was removed and the arrays were washed and stained with streptavidin-phycoerythrin (SAPE), and the signal amplified by anti-streptavidin antibody using Affymetrix Fluidics Station 400. Probe set signals were measured using Agilent GeneArray Scanner (Affymetrix).
| | Sample_data_processing | Affymetrix Microarray Suite version 5.0
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jennifer,,Barb
| | Sample_contact_email | barbj@mail.nih.gov
| | Sample_contact_phone | 3014359232
| | Sample_contact_fax | 3014024544
| | Sample_contact_laboratory | MSCL
| | Sample_contact_department | DCB
| | Sample_contact_institute | NIH
| | Sample_contact_address | 12 South Drive Bldg 12A Room 2001
| | Sample_contact_city | Bethesda
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 20892
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM466nnn/GSM466520/suppl/GSM466520.CEL.gz
| | Sample_series_id | GSE18811
| | Sample_data_row_count | 54675
| | |
|
GSM466521 | GPL570 |
|
292FW10
|
fetal RPE cultures
|
cell type: fetal RPE
gestational age: 16 weeks
|
Fetal RPE were cultured on Primaria® flasks and assages 1-2 were used for all studies. The confluent monolayers used in these experiments have the morphology, pigmentation, polarity, and physiology of native RPE.
|
| Sample_geo_accession | GSM466521
| | Sample_status | Public on Apr 15 2010
| | Sample_submission_date | Oct 29 2009
| | Sample_last_update_date | Apr 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Fetal RPE were cultured on Primaria® flasks for 6 weeks using MEM-α modified medium with additional supplements. Passages 1-2 were used for all studies. The confluent monolayers used in these experiments have the morphology, pigmentation, polarity, and physiology of native RPE.ARPE-19 spontaneously transformed cell line was cultured using MEM-α modified medium with additional supplements on flasks and inserts to match fetal RPE culturing conditions.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Fetal and adult RPE cells were collected, homogenized in TRIzol reagent (Invitrogen, Carlsbad, CA) and RNA was subsequently purified using an RNeasy Mini kit (Qiagen Inc, Valencia, CA). Double-stranded cDNA was synthesized from 6µg of total RNA using the SuperScript Choice system (Invitrogen, Carlsbad, CA) and the T7-Oligo (dT) promoter primer kit (Affymetrix, Santa Clara, CA). cDNA was purified using Phase Lock Gels (Eppendorf, Westbury, NY). Concentration and quality of RNA samples was determined on the Agilent bioanalyzer (Agilent Technologies, Palo Alto, CA). The integrity of RNA is assessed by looking at 18 & 28s rRNA peaks and though the RIN (RNA integrity number). RNA concentrations were measured using the Nano drop spectrophotometer (Wilmington, DE) and all samples used for the study had 260/280 ratios above 2.0 and 260/230 ratios above 1.7.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Ten micrograms of total RNA was reverse transcribed with Superscript II reverse transcriptase (Invitrogen, Carlsbad, CA) using T7-(dT) 24 primer (Geneset Oligos, La Jolla, CA, USA) containing T7 RNA polymerase promoter. After synthesis of the second cDNA strand, this product was used in an in vitro transcription reaction to generate biotinylated cRNA using a BioArray High Yield RNA Transcript Labeling Kit (Affymetrix, Santa Clara, CA). The biotinylated cRNA was cleaned with the RNAeasy Mini Kit (Qiagen, Valencia, CA).
| | Sample_hyb_protocol | Biotin-labeled cRNA was then fragmented at 94oC for 35 min with 5X fragmentation buffer (200 mM Tris-acetate, pH 8.1, 500 mM potassium acetate, 150 mM magnesium acetate) and then hybridized (10 ug) to Affymetrix (Santa Clara, CA) mouse 430_2 oligonucleotide probe arrays for 16 h at 45oC
| | Sample_scan_protocol | Hybridization fluid was removed and the arrays were washed and stained with streptavidin-phycoerythrin (SAPE), and the signal amplified by anti-streptavidin antibody using Affymetrix Fluidics Station 400. Probe set signals were measured using Agilent GeneArray Scanner (Affymetrix).
| | Sample_data_processing | Affymetrix Microarray Suite version 5.0
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jennifer,,Barb
| | Sample_contact_email | barbj@mail.nih.gov
| | Sample_contact_phone | 3014359232
| | Sample_contact_fax | 3014024544
| | Sample_contact_laboratory | MSCL
| | Sample_contact_department | DCB
| | Sample_contact_institute | NIH
| | Sample_contact_address | 12 South Drive Bldg 12A Room 2001
| | Sample_contact_city | Bethesda
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 20892
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM466nnn/GSM466521/suppl/GSM466521.CEL.gz
| | Sample_series_id | GSE18811
| | Sample_data_row_count | 54675
| | |
|
GSM466522 | GPL570 |
|
292FW11
|
fetal RPE cultures
|
cell type: fetal RPE
gestational age: 17 weeks
|
Fetal RPE were cultured on Primaria® flasks and assages 1-2 were used for all studies. The confluent monolayers used in these experiments have the morphology, pigmentation, polarity, and physiology of native RPE.
|
| Sample_geo_accession | GSM466522
| | Sample_status | Public on Apr 15 2010
| | Sample_submission_date | Oct 29 2009
| | Sample_last_update_date | Apr 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Fetal RPE were cultured on Primaria® flasks for 6 weeks using MEM-α modified medium with additional supplements. Passages 1-2 were used for all studies. The confluent monolayers used in these experiments have the morphology, pigmentation, polarity, and physiology of native RPE.ARPE-19 spontaneously transformed cell line was cultured using MEM-α modified medium with additional supplements on flasks and inserts to match fetal RPE culturing conditions.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Fetal and adult RPE cells were collected, homogenized in TRIzol reagent (Invitrogen, Carlsbad, CA) and RNA was subsequently purified using an RNeasy Mini kit (Qiagen Inc, Valencia, CA). Double-stranded cDNA was synthesized from 6µg of total RNA using the SuperScript Choice system (Invitrogen, Carlsbad, CA) and the T7-Oligo (dT) promoter primer kit (Affymetrix, Santa Clara, CA). cDNA was purified using Phase Lock Gels (Eppendorf, Westbury, NY). Concentration and quality of RNA samples was determined on the Agilent bioanalyzer (Agilent Technologies, Palo Alto, CA). The integrity of RNA is assessed by looking at 18 & 28s rRNA peaks and though the RIN (RNA integrity number). RNA concentrations were measured using the Nano drop spectrophotometer (Wilmington, DE) and all samples used for the study had 260/280 ratios above 2.0 and 260/230 ratios above 1.7.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Ten micrograms of total RNA was reverse transcribed with Superscript II reverse transcriptase (Invitrogen, Carlsbad, CA) using T7-(dT) 24 primer (Geneset Oligos, La Jolla, CA, USA) containing T7 RNA polymerase promoter. After synthesis of the second cDNA strand, this product was used in an in vitro transcription reaction to generate biotinylated cRNA using a BioArray High Yield RNA Transcript Labeling Kit (Affymetrix, Santa Clara, CA). The biotinylated cRNA was cleaned with the RNAeasy Mini Kit (Qiagen, Valencia, CA).
| | Sample_hyb_protocol | Biotin-labeled cRNA was then fragmented at 94oC for 35 min with 5X fragmentation buffer (200 mM Tris-acetate, pH 8.1, 500 mM potassium acetate, 150 mM magnesium acetate) and then hybridized (10 ug) to Affymetrix (Santa Clara, CA) mouse 430_2 oligonucleotide probe arrays for 16 h at 45oC
| | Sample_scan_protocol | Hybridization fluid was removed and the arrays were washed and stained with streptavidin-phycoerythrin (SAPE), and the signal amplified by anti-streptavidin antibody using Affymetrix Fluidics Station 400. Probe set signals were measured using Agilent GeneArray Scanner (Affymetrix).
| | Sample_data_processing | Affymetrix Microarray Suite version 5.0
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jennifer,,Barb
| | Sample_contact_email | barbj@mail.nih.gov
| | Sample_contact_phone | 3014359232
| | Sample_contact_fax | 3014024544
| | Sample_contact_laboratory | MSCL
| | Sample_contact_department | DCB
| | Sample_contact_institute | NIH
| | Sample_contact_address | 12 South Drive Bldg 12A Room 2001
| | Sample_contact_city | Bethesda
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 20892
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM466nnn/GSM466522/suppl/GSM466522.CEL.gz
| | Sample_series_id | GSE18811
| | Sample_data_row_count | 54675
| | |
|
GSM466523 | GPL570 |
|
292FW12
|
fetal RPE cultures
|
cell type: fetal RPE
gestational age: 17 weeks
|
Fetal RPE were cultured on Primaria® flasks and assages 1-2 were used for all studies. The confluent monolayers used in these experiments have the morphology, pigmentation, polarity, and physiology of native RPE.
|
| Sample_geo_accession | GSM466523
| | Sample_status | Public on Apr 15 2010
| | Sample_submission_date | Oct 29 2009
| | Sample_last_update_date | Apr 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Fetal RPE were cultured on Primaria® flasks for 6 weeks using MEM-α modified medium with additional supplements. Passages 1-2 were used for all studies. The confluent monolayers used in these experiments have the morphology, pigmentation, polarity, and physiology of native RPE.ARPE-19 spontaneously transformed cell line was cultured using MEM-α modified medium with additional supplements on flasks and inserts to match fetal RPE culturing conditions.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Fetal and adult RPE cells were collected, homogenized in TRIzol reagent (Invitrogen, Carlsbad, CA) and RNA was subsequently purified using an RNeasy Mini kit (Qiagen Inc, Valencia, CA). Double-stranded cDNA was synthesized from 6µg of total RNA using the SuperScript Choice system (Invitrogen, Carlsbad, CA) and the T7-Oligo (dT) promoter primer kit (Affymetrix, Santa Clara, CA). cDNA was purified using Phase Lock Gels (Eppendorf, Westbury, NY). Concentration and quality of RNA samples was determined on the Agilent bioanalyzer (Agilent Technologies, Palo Alto, CA). The integrity of RNA is assessed by looking at 18 & 28s rRNA peaks and though the RIN (RNA integrity number). RNA concentrations were measured using the Nano drop spectrophotometer (Wilmington, DE) and all samples used for the study had 260/280 ratios above 2.0 and 260/230 ratios above 1.7.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Ten micrograms of total RNA was reverse transcribed with Superscript II reverse transcriptase (Invitrogen, Carlsbad, CA) using T7-(dT) 24 primer (Geneset Oligos, La Jolla, CA, USA) containing T7 RNA polymerase promoter. After synthesis of the second cDNA strand, this product was used in an in vitro transcription reaction to generate biotinylated cRNA using a BioArray High Yield RNA Transcript Labeling Kit (Affymetrix, Santa Clara, CA). The biotinylated cRNA was cleaned with the RNAeasy Mini Kit (Qiagen, Valencia, CA).
| | Sample_hyb_protocol | Biotin-labeled cRNA was then fragmented at 94oC for 35 min with 5X fragmentation buffer (200 mM Tris-acetate, pH 8.1, 500 mM potassium acetate, 150 mM magnesium acetate) and then hybridized (10 ug) to Affymetrix (Santa Clara, CA) mouse 430_2 oligonucleotide probe arrays for 16 h at 45oC
| | Sample_scan_protocol | Hybridization fluid was removed and the arrays were washed and stained with streptavidin-phycoerythrin (SAPE), and the signal amplified by anti-streptavidin antibody using Affymetrix Fluidics Station 400. Probe set signals were measured using Agilent GeneArray Scanner (Affymetrix).
| | Sample_data_processing | Affymetrix Microarray Suite version 5.0
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jennifer,,Barb
| | Sample_contact_email | barbj@mail.nih.gov
| | Sample_contact_phone | 3014359232
| | Sample_contact_fax | 3014024544
| | Sample_contact_laboratory | MSCL
| | Sample_contact_department | DCB
| | Sample_contact_institute | NIH
| | Sample_contact_address | 12 South Drive Bldg 12A Room 2001
| | Sample_contact_city | Bethesda
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 20892
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM466nnn/GSM466523/suppl/GSM466523.CEL.gz
| | Sample_series_id | GSE18811
| | Sample_data_row_count | 54675
| | |
|
GSM466524 | GPL570 |
|
292FW13
|
fetal RPE cultures
|
cell type: fetal RPE
gestational age: 17 weeks
|
Fetal RPE were cultured on Primaria® flasks and assages 1-2 were used for all studies. The confluent monolayers used in these experiments have the morphology, pigmentation, polarity, and physiology of native RPE.
|
| Sample_geo_accession | GSM466524
| | Sample_status | Public on Apr 15 2010
| | Sample_submission_date | Oct 29 2009
| | Sample_last_update_date | Apr 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Fetal RPE were cultured on Primaria® flasks for 6 weeks using MEM-α modified medium with additional supplements. Passages 1-2 were used for all studies. The confluent monolayers used in these experiments have the morphology, pigmentation, polarity, and physiology of native RPE.ARPE-19 spontaneously transformed cell line was cultured using MEM-α modified medium with additional supplements on flasks and inserts to match fetal RPE culturing conditions.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Fetal and adult RPE cells were collected, homogenized in TRIzol reagent (Invitrogen, Carlsbad, CA) and RNA was subsequently purified using an RNeasy Mini kit (Qiagen Inc, Valencia, CA). Double-stranded cDNA was synthesized from 6µg of total RNA using the SuperScript Choice system (Invitrogen, Carlsbad, CA) and the T7-Oligo (dT) promoter primer kit (Affymetrix, Santa Clara, CA). cDNA was purified using Phase Lock Gels (Eppendorf, Westbury, NY). Concentration and quality of RNA samples was determined on the Agilent bioanalyzer (Agilent Technologies, Palo Alto, CA). The integrity of RNA is assessed by looking at 18 & 28s rRNA peaks and though the RIN (RNA integrity number). RNA concentrations were measured using the Nano drop spectrophotometer (Wilmington, DE) and all samples used for the study had 260/280 ratios above 2.0 and 260/230 ratios above 1.7.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Ten micrograms of total RNA was reverse transcribed with Superscript II reverse transcriptase (Invitrogen, Carlsbad, CA) using T7-(dT) 24 primer (Geneset Oligos, La Jolla, CA, USA) containing T7 RNA polymerase promoter. After synthesis of the second cDNA strand, this product was used in an in vitro transcription reaction to generate biotinylated cRNA using a BioArray High Yield RNA Transcript Labeling Kit (Affymetrix, Santa Clara, CA). The biotinylated cRNA was cleaned with the RNAeasy Mini Kit (Qiagen, Valencia, CA).
| | Sample_hyb_protocol | Biotin-labeled cRNA was then fragmented at 94oC for 35 min with 5X fragmentation buffer (200 mM Tris-acetate, pH 8.1, 500 mM potassium acetate, 150 mM magnesium acetate) and then hybridized (10 ug) to Affymetrix (Santa Clara, CA) mouse 430_2 oligonucleotide probe arrays for 16 h at 45oC
| | Sample_scan_protocol | Hybridization fluid was removed and the arrays were washed and stained with streptavidin-phycoerythrin (SAPE), and the signal amplified by anti-streptavidin antibody using Affymetrix Fluidics Station 400. Probe set signals were measured using Agilent GeneArray Scanner (Affymetrix).
| | Sample_data_processing | Affymetrix Microarray Suite version 5.0
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jennifer,,Barb
| | Sample_contact_email | barbj@mail.nih.gov
| | Sample_contact_phone | 3014359232
| | Sample_contact_fax | 3014024544
| | Sample_contact_laboratory | MSCL
| | Sample_contact_department | DCB
| | Sample_contact_institute | NIH
| | Sample_contact_address | 12 South Drive Bldg 12A Room 2001
| | Sample_contact_city | Bethesda
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 20892
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM466nnn/GSM466524/suppl/GSM466524.CEL.gz
| | Sample_series_id | GSE18811
| | Sample_data_row_count | 54675
| | |
|
GSM466525 | GPL570 |
|
292FW14
|
fetal RPE cultures
|
cell type: fetal RPE
gestational age: 16 weeks
|
Fetal RPE were cultured on Primaria® flasks and assages 1-2 were used for all studies. The confluent monolayers used in these experiments have the morphology, pigmentation, polarity, and physiology of native RPE.
|
| Sample_geo_accession | GSM466525
| | Sample_status | Public on Apr 15 2010
| | Sample_submission_date | Oct 29 2009
| | Sample_last_update_date | Apr 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Fetal RPE were cultured on Primaria® flasks for 6 weeks using MEM-α modified medium with additional supplements. Passages 1-2 were used for all studies. The confluent monolayers used in these experiments have the morphology, pigmentation, polarity, and physiology of native RPE.ARPE-19 spontaneously transformed cell line was cultured using MEM-α modified medium with additional supplements on flasks and inserts to match fetal RPE culturing conditions.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Fetal and adult RPE cells were collected, homogenized in TRIzol reagent (Invitrogen, Carlsbad, CA) and RNA was subsequently purified using an RNeasy Mini kit (Qiagen Inc, Valencia, CA). Double-stranded cDNA was synthesized from 6µg of total RNA using the SuperScript Choice system (Invitrogen, Carlsbad, CA) and the T7-Oligo (dT) promoter primer kit (Affymetrix, Santa Clara, CA). cDNA was purified using Phase Lock Gels (Eppendorf, Westbury, NY). Concentration and quality of RNA samples was determined on the Agilent bioanalyzer (Agilent Technologies, Palo Alto, CA). The integrity of RNA is assessed by looking at 18 & 28s rRNA peaks and though the RIN (RNA integrity number). RNA concentrations were measured using the Nano drop spectrophotometer (Wilmington, DE) and all samples used for the study had 260/280 ratios above 2.0 and 260/230 ratios above 1.7.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Ten micrograms of total RNA was reverse transcribed with Superscript II reverse transcriptase (Invitrogen, Carlsbad, CA) using T7-(dT) 24 primer (Geneset Oligos, La Jolla, CA, USA) containing T7 RNA polymerase promoter. After synthesis of the second cDNA strand, this product was used in an in vitro transcription reaction to generate biotinylated cRNA using a BioArray High Yield RNA Transcript Labeling Kit (Affymetrix, Santa Clara, CA). The biotinylated cRNA was cleaned with the RNAeasy Mini Kit (Qiagen, Valencia, CA).
| | Sample_hyb_protocol | Biotin-labeled cRNA was then fragmented at 94oC for 35 min with 5X fragmentation buffer (200 mM Tris-acetate, pH 8.1, 500 mM potassium acetate, 150 mM magnesium acetate) and then hybridized (10 ug) to Affymetrix (Santa Clara, CA) mouse 430_2 oligonucleotide probe arrays for 16 h at 45oC
| | Sample_scan_protocol | Hybridization fluid was removed and the arrays were washed and stained with streptavidin-phycoerythrin (SAPE), and the signal amplified by anti-streptavidin antibody using Affymetrix Fluidics Station 400. Probe set signals were measured using Agilent GeneArray Scanner (Affymetrix).
| | Sample_data_processing | Affymetrix Microarray Suite version 5.0
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jennifer,,Barb
| | Sample_contact_email | barbj@mail.nih.gov
| | Sample_contact_phone | 3014359232
| | Sample_contact_fax | 3014024544
| | Sample_contact_laboratory | MSCL
| | Sample_contact_department | DCB
| | Sample_contact_institute | NIH
| | Sample_contact_address | 12 South Drive Bldg 12A Room 2001
| | Sample_contact_city | Bethesda
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 20892
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM466nnn/GSM466525/suppl/GSM466525.CEL.gz
| | Sample_series_id | GSE18811
| | Sample_data_row_count | 54675
| | |
|
GSM466526 | GPL570 |
|
292FW17
|
native fetal RPE
|
cell type: native fetal RPE
gestational age: 16 weeks
|
Fetal RPE were cultured on Primaria® flasks and assages 1-2 were used for all studies. The confluent monolayers used in these experiments have the morphology, pigmentation, polarity, and physiology of native RPE.
|
| Sample_geo_accession | GSM466526
| | Sample_status | Public on Apr 15 2010
| | Sample_submission_date | Oct 29 2009
| | Sample_last_update_date | Apr 13 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Fetal RPE were cultured on Primaria® flasks for 6 weeks using MEM-α modified medium with additional supplements. Passages 1-2 were used for all studies. The confluent monolayers used in these experiments have the morphology, pigmentation, polarity, and physiology of native RPE.ARPE-19 spontaneously transformed cell line was cultured using MEM-α modified medium with additional supplements on flasks and inserts to match fetal RPE culturing conditions.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Fetal and adult RPE cells were collected, homogenized in TRIzol reagent (Invitrogen, Carlsbad, CA) and RNA was subsequently purified using an RNeasy Mini kit (Qiagen Inc, Valencia, CA). Double-stranded cDNA was synthesized from 6µg of total RNA using the SuperScript Choice system (Invitrogen, Carlsbad, CA) and the T7-Oligo (dT) promoter primer kit (Affymetrix, Santa Clara, CA). cDNA was purified using Phase Lock Gels (Eppendorf, Westbury, NY). Concentration and quality of RNA samples was determined on the Agilent bioanalyzer (Agilent Technologies, Palo Alto, CA). The integrity of RNA is assessed by looking at 18 & 28s rRNA peaks and though the RIN (RNA integrity number). RNA concentrations were measured using the Nano drop spectrophotometer (Wilmington, DE) and all samples used for the study had 260/280 ratios above 2.0 and 260/230 ratios above 1.7.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Ten micrograms of total RNA was reverse transcribed with Superscript II reverse transcriptase (Invitrogen, Carlsbad, CA) using T7-(dT) 24 primer (Geneset Oligos, La Jolla, CA, USA) containing T7 RNA polymerase promoter. After synthesis of the second cDNA strand, this product was used in an in vitro transcription reaction to generate biotinylated cRNA using a BioArray High Yield RNA Transcript Labeling Kit (Affymetrix, Santa Clara, CA). The biotinylated cRNA was cleaned with the RNAeasy Mini Kit (Qiagen, Valencia, CA).
| | Sample_hyb_protocol | Biotin-labeled cRNA was then fragmented at 94oC for 35 min with 5X fragmentation buffer (200 mM Tris-acetate, pH 8.1, 500 mM potassium acetate, 150 mM magnesium acetate) and then hybridized (10 ug) to Affymetrix (Santa Clara, CA) mouse 430_2 oligonucleotide probe arrays for 16 h at 45oC
| | Sample_scan_protocol | Hybridization fluid was removed and the arrays were washed and stained with streptavidin-phycoerythrin (SAPE), and the signal amplified by anti-streptavidin antibody using Affymetrix Fluidics Station 400. Probe set signals were measured using Agilent GeneArray Scanner (Affymetrix).
| | Sample_data_processing | Affymetrix Microarray Suite version 5.0
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jennifer,,Barb
| | Sample_contact_email | barbj@mail.nih.gov
| | Sample_contact_phone | 3014359232
| | Sample_contact_fax | 3014024544
| | Sample_contact_laboratory | MSCL
| | Sample_contact_department | DCB
| | Sample_contact_institute | NIH
| | Sample_contact_address | 12 South Drive Bldg 12A Room 2001
| | Sample_contact_city | Bethesda
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 20892
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM466nnn/GSM466526/suppl/GSM466526.CEL.gz
| | Sample_series_id | GSE18811
| | Sample_data_row_count | 54675
| | |
|
GSM466527 | GPL570 |
|
292FW18
|
native fetal RPE
|
cell type: native fetal RPE
gestational age: 18 weeks
|
Fetal RPE were cultured on Primaria® flasks and assages 1-2 were used for all studies. The confluent monolayers used in these experiments have the morphology, pigmentation, polarity, and physiology of native RPE.
|
| Sample_geo_accession | GSM466527
| | Sample_status | Public on Apr 15 2010
| | Sample_submission_date | Oct 29 2009
| | Sample_last_update_date | Apr 13 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Fetal RPE were cultured on Primaria® flasks for 6 weeks using MEM-α modified medium with additional supplements. Passages 1-2 were used for all studies. The confluent monolayers used in these experiments have the morphology, pigmentation, polarity, and physiology of native RPE.ARPE-19 spontaneously transformed cell line was cultured using MEM-α modified medium with additional supplements on flasks and inserts to match fetal RPE culturing conditions.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Fetal and adult RPE cells were collected, homogenized in TRIzol reagent (Invitrogen, Carlsbad, CA) and RNA was subsequently purified using an RNeasy Mini kit (Qiagen Inc, Valencia, CA). Double-stranded cDNA was synthesized from 6µg of total RNA using the SuperScript Choice system (Invitrogen, Carlsbad, CA) and the T7-Oligo (dT) promoter primer kit (Affymetrix, Santa Clara, CA). cDNA was purified using Phase Lock Gels (Eppendorf, Westbury, NY). Concentration and quality of RNA samples was determined on the Agilent bioanalyzer (Agilent Technologies, Palo Alto, CA). The integrity of RNA is assessed by looking at 18 & 28s rRNA peaks and though the RIN (RNA integrity number). RNA concentrations were measured using the Nano drop spectrophotometer (Wilmington, DE) and all samples used for the study had 260/280 ratios above 2.0 and 260/230 ratios above 1.7.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Ten micrograms of total RNA was reverse transcribed with Superscript II reverse transcriptase (Invitrogen, Carlsbad, CA) using T7-(dT) 24 primer (Geneset Oligos, La Jolla, CA, USA) containing T7 RNA polymerase promoter. After synthesis of the second cDNA strand, this product was used in an in vitro transcription reaction to generate biotinylated cRNA using a BioArray High Yield RNA Transcript Labeling Kit (Affymetrix, Santa Clara, CA). The biotinylated cRNA was cleaned with the RNAeasy Mini Kit (Qiagen, Valencia, CA).
| | Sample_hyb_protocol | Biotin-labeled cRNA was then fragmented at 94oC for 35 min with 5X fragmentation buffer (200 mM Tris-acetate, pH 8.1, 500 mM potassium acetate, 150 mM magnesium acetate) and then hybridized (10 ug) to Affymetrix (Santa Clara, CA) mouse 430_2 oligonucleotide probe arrays for 16 h at 45oC
| | Sample_scan_protocol | Hybridization fluid was removed and the arrays were washed and stained with streptavidin-phycoerythrin (SAPE), and the signal amplified by anti-streptavidin antibody using Affymetrix Fluidics Station 400. Probe set signals were measured using Agilent GeneArray Scanner (Affymetrix).
| | Sample_data_processing | Affymetrix Microarray Suite version 5.0
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jennifer,,Barb
| | Sample_contact_email | barbj@mail.nih.gov
| | Sample_contact_phone | 3014359232
| | Sample_contact_fax | 3014024544
| | Sample_contact_laboratory | MSCL
| | Sample_contact_department | DCB
| | Sample_contact_institute | NIH
| | Sample_contact_address | 12 South Drive Bldg 12A Room 2001
| | Sample_contact_city | Bethesda
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 20892
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM466nnn/GSM466527/suppl/GSM466527.CEL.gz
| | Sample_series_id | GSE18811
| | Sample_data_row_count | 54675
| | |
|
GSM466528 | GPL570 |
|
292FW19
|
native fetal RPE
|
cell type: native fetal RPE
gestational age: 18 weeks
|
Fetal RPE were cultured on Primaria® flasks for 6 weeks using MEM-α modified medium with additional supplements. Passages 1-2 were used for all studies. The confluent monolayers used in these experiments have the morphology, pigmentation, polarity, and physiology of native RPE.
|
| Sample_geo_accession | GSM466528
| | Sample_status | Public on Apr 15 2010
| | Sample_submission_date | Oct 29 2009
| | Sample_last_update_date | Apr 13 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Fetal RPE were cultured on Primaria® flasks for 6 weeks using MEM-α modified medium with additional supplements. Passages 1-2 were used for all studies. The confluent monolayers used in these experiments have the morphology, pigmentation, polarity, and physiology of native RPE.ARPE-19 spontaneously transformed cell line was cultured using MEM-α modified medium with additional supplements on flasks and inserts to match fetal RPE culturing conditions.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Fetal and adult RPE cells were collected, homogenized in TRIzol reagent (Invitrogen, Carlsbad, CA) and RNA was subsequently purified using an RNeasy Mini kit (Qiagen Inc, Valencia, CA). Double-stranded cDNA was synthesized from 6µg of total RNA using the SuperScript Choice system (Invitrogen, Carlsbad, CA) and the T7-Oligo (dT) promoter primer kit (Affymetrix, Santa Clara, CA). cDNA was purified using Phase Lock Gels (Eppendorf, Westbury, NY). Concentration and quality of RNA samples was determined on the Agilent bioanalyzer (Agilent Technologies, Palo Alto, CA). The integrity of RNA is assessed by looking at 18 & 28s rRNA peaks and though the RIN (RNA integrity number). RNA concentrations were measured using the Nano drop spectrophotometer (Wilmington, DE) and all samples used for the study had 260/280 ratios above 2.0 and 260/230 ratios above 1.7.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Ten micrograms of total RNA was reverse transcribed with Superscript II reverse transcriptase (Invitrogen, Carlsbad, CA) using T7-(dT) 24 primer (Geneset Oligos, La Jolla, CA, USA) containing T7 RNA polymerase promoter. After synthesis of the second cDNA strand, this product was used in an in vitro transcription reaction to generate biotinylated cRNA using a BioArray High Yield RNA Transcript Labeling Kit (Affymetrix, Santa Clara, CA). The biotinylated cRNA was cleaned with the RNAeasy Mini Kit (Qiagen, Valencia, CA).
| | Sample_hyb_protocol | Biotin-labeled cRNA was then fragmented at 94oC for 35 min with 5X fragmentation buffer (200 mM Tris-acetate, pH 8.1, 500 mM potassium acetate, 150 mM magnesium acetate) and then hybridized (10 ug) to Affymetrix (Santa Clara, CA) mouse 430_2 oligonucleotide probe arrays for 16 h at 45oC
| | Sample_scan_protocol | Hybridization fluid was removed and the arrays were washed and stained with streptavidin-phycoerythrin (SAPE), and the signal amplified by anti-streptavidin antibody using Affymetrix Fluidics Station 400. Probe set signals were measured using Agilent GeneArray Scanner (Affymetrix).
| | Sample_data_processing | Affymetrix Microarray Suite version 5.0
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jennifer,,Barb
| | Sample_contact_email | barbj@mail.nih.gov
| | Sample_contact_phone | 3014359232
| | Sample_contact_fax | 3014024544
| | Sample_contact_laboratory | MSCL
| | Sample_contact_department | DCB
| | Sample_contact_institute | NIH
| | Sample_contact_address | 12 South Drive Bldg 12A Room 2001
| | Sample_contact_city | Bethesda
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 20892
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM466nnn/GSM466528/suppl/GSM466528.CEL.gz
| | Sample_series_id | GSE18811
| | Sample_data_row_count | 54675
| | |
|
GSM466529 | GPL570 |
|
292FW2
|
fetal RPE cultures
|
cell type: fetal RPE
gestational age: 16 weeks
|
Fetal RPE were cultured on Primaria® flasks and assages 1-2 were used for all studies. The confluent monolayers used in these experiments have the morphology, pigmentation, polarity, and physiology of native RPE.
|
| Sample_geo_accession | GSM466529
| | Sample_status | Public on Apr 15 2010
| | Sample_submission_date | Oct 29 2009
| | Sample_last_update_date | Apr 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Fetal RPE were cultured on Primaria® flasks for 6 weeks using MEM-α modified medium with additional supplements. Passages 1-2 were used for all studies. The confluent monolayers used in these experiments have the morphology, pigmentation, polarity, and physiology of native RPE.ARPE-19 spontaneously transformed cell line was cultured using MEM-α modified medium with additional supplements on flasks and inserts to match fetal RPE culturing conditions.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Fetal and adult RPE cells were collected, homogenized in TRIzol reagent (Invitrogen, Carlsbad, CA) and RNA was subsequently purified using an RNeasy Mini kit (Qiagen Inc, Valencia, CA). Double-stranded cDNA was synthesized from 6µg of total RNA using the SuperScript Choice system (Invitrogen, Carlsbad, CA) and the T7-Oligo (dT) promoter primer kit (Affymetrix, Santa Clara, CA). cDNA was purified using Phase Lock Gels (Eppendorf, Westbury, NY). Concentration and quality of RNA samples was determined on the Agilent bioanalyzer (Agilent Technologies, Palo Alto, CA). The integrity of RNA is assessed by looking at 18 & 28s rRNA peaks and though the RIN (RNA integrity number). RNA concentrations were measured using the Nano drop spectrophotometer (Wilmington, DE) and all samples used for the study had 260/280 ratios above 2.0 and 260/230 ratios above 1.7.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Ten micrograms of total RNA was reverse transcribed with Superscript II reverse transcriptase (Invitrogen, Carlsbad, CA) using T7-(dT) 24 primer (Geneset Oligos, La Jolla, CA, USA) containing T7 RNA polymerase promoter. After synthesis of the second cDNA strand, this product was used in an in vitro transcription reaction to generate biotinylated cRNA using a BioArray High Yield RNA Transcript Labeling Kit (Affymetrix, Santa Clara, CA). The biotinylated cRNA was cleaned with the RNAeasy Mini Kit (Qiagen, Valencia, CA).
| | Sample_hyb_protocol | Biotin-labeled cRNA was then fragmented at 94oC for 35 min with 5X fragmentation buffer (200 mM Tris-acetate, pH 8.1, 500 mM potassium acetate, 150 mM magnesium acetate) and then hybridized (10 ug) to Affymetrix (Santa Clara, CA) mouse 430_2 oligonucleotide probe arrays for 16 h at 45oC
| | Sample_scan_protocol | Hybridization fluid was removed and the arrays were washed and stained with streptavidin-phycoerythrin (SAPE), and the signal amplified by anti-streptavidin antibody using Affymetrix Fluidics Station 400. Probe set signals were measured using Agilent GeneArray Scanner (Affymetrix).
| | Sample_data_processing | Affymetrix Microarray Suite version 5.0
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jennifer,,Barb
| | Sample_contact_email | barbj@mail.nih.gov
| | Sample_contact_phone | 3014359232
| | Sample_contact_fax | 3014024544
| | Sample_contact_laboratory | MSCL
| | Sample_contact_department | DCB
| | Sample_contact_institute | NIH
| | Sample_contact_address | 12 South Drive Bldg 12A Room 2001
| | Sample_contact_city | Bethesda
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 20892
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM466nnn/GSM466529/suppl/GSM466529.CEL.gz
| | Sample_series_id | GSE18811
| | Sample_data_row_count | 54675
| | |
|
GSM466530 | GPL570 |
|
292FW20
|
adult native RPE
|
cell type: adult native RPE from 76 y.o. donor
|
Adult native RPE (anRPE) were collected from donors of Caucasian decent and total RNA was extracted right after.
|
| Sample_geo_accession | GSM466530
| | Sample_status | Public on Apr 15 2010
| | Sample_submission_date | Oct 29 2009
| | Sample_last_update_date | Apr 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Fetal RPE were cultured on Primaria® flasks for 6 weeks using MEM-α modified medium with additional supplements. Passages 1-2 were used for all studies. The confluent monolayers used in these experiments have the morphology, pigmentation, polarity, and physiology of native RPE.ARPE-19 spontaneously transformed cell line was cultured using MEM-α modified medium with additional supplements on flasks and inserts to match fetal RPE culturing conditions.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Fetal and adult RPE cells were collected, homogenized in TRIzol reagent (Invitrogen, Carlsbad, CA) and RNA was subsequently purified using an RNeasy Mini kit (Qiagen Inc, Valencia, CA). Double-stranded cDNA was synthesized from 6µg of total RNA using the SuperScript Choice system (Invitrogen, Carlsbad, CA) and the T7-Oligo (dT) promoter primer kit (Affymetrix, Santa Clara, CA). cDNA was purified using Phase Lock Gels (Eppendorf, Westbury, NY). Concentration and quality of RNA samples was determined on the Agilent bioanalyzer (Agilent Technologies, Palo Alto, CA). The integrity of RNA is assessed by looking at 18 & 28s rRNA peaks and though the RIN (RNA integrity number). RNA concentrations were measured using the Nano drop spectrophotometer (Wilmington, DE) and all samples used for the study had 260/280 ratios above 2.0 and 260/230 ratios above 1.7.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Ten micrograms of total RNA was reverse transcribed with Superscript II reverse transcriptase (Invitrogen, Carlsbad, CA) using T7-(dT) 24 primer (Geneset Oligos, La Jolla, CA, USA) containing T7 RNA polymerase promoter. After synthesis of the second cDNA strand, this product was used in an in vitro transcription reaction to generate biotinylated cRNA using a BioArray High Yield RNA Transcript Labeling Kit (Affymetrix, Santa Clara, CA). The biotinylated cRNA was cleaned with the RNAeasy Mini Kit (Qiagen, Valencia, CA).
| | Sample_hyb_protocol | Biotin-labeled cRNA was then fragmented at 94oC for 35 min with 5X fragmentation buffer (200 mM Tris-acetate, pH 8.1, 500 mM potassium acetate, 150 mM magnesium acetate) and then hybridized (10 ug) to Affymetrix (Santa Clara, CA) mouse 430_2 oligonucleotide probe arrays for 16 h at 45oC
| | Sample_scan_protocol | Hybridization fluid was removed and the arrays were washed and stained with streptavidin-phycoerythrin (SAPE), and the signal amplified by anti-streptavidin antibody using Affymetrix Fluidics Station 400. Probe set signals were measured using Agilent GeneArray Scanner (Affymetrix).
| | Sample_data_processing | Affymetrix Microarray Suite version 5.0
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jennifer,,Barb
| | Sample_contact_email | barbj@mail.nih.gov
| | Sample_contact_phone | 3014359232
| | Sample_contact_fax | 3014024544
| | Sample_contact_laboratory | MSCL
| | Sample_contact_department | DCB
| | Sample_contact_institute | NIH
| | Sample_contact_address | 12 South Drive Bldg 12A Room 2001
| | Sample_contact_city | Bethesda
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 20892
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM466nnn/GSM466530/suppl/GSM466530.CEL.gz
| | Sample_series_id | GSE18811
| | Sample_data_row_count | 54675
| | |
|
GSM466531 | GPL570 |
|
292FW21
|
adult choroid from 76 y.o. donor
|
cell type: adult choroid from 76 y.o. donor
|
none
|
| Sample_geo_accession | GSM466531
| | Sample_status | Public on Apr 15 2010
| | Sample_submission_date | Oct 29 2009
| | Sample_last_update_date | Apr 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Fetal RPE were cultured on Primaria® flasks for 6 weeks using MEM-α modified medium with additional supplements. Passages 1-2 were used for all studies. The confluent monolayers used in these experiments have the morphology, pigmentation, polarity, and physiology of native RPE.ARPE-19 spontaneously transformed cell line was cultured using MEM-α modified medium with additional supplements on flasks and inserts to match fetal RPE culturing conditions.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Fetal and adult RPE cells were collected, homogenized in TRIzol reagent (Invitrogen, Carlsbad, CA) and RNA was subsequently purified using an RNeasy Mini kit (Qiagen Inc, Valencia, CA). Double-stranded cDNA was synthesized from 6µg of total RNA using the SuperScript Choice system (Invitrogen, Carlsbad, CA) and the T7-Oligo (dT) promoter primer kit (Affymetrix, Santa Clara, CA). cDNA was purified using Phase Lock Gels (Eppendorf, Westbury, NY). Concentration and quality of RNA samples was determined on the Agilent bioanalyzer (Agilent Technologies, Palo Alto, CA). The integrity of RNA is assessed by looking at 18 & 28s rRNA peaks and though the RIN (RNA integrity number). RNA concentrations were measured using the Nano drop spectrophotometer (Wilmington, DE) and all samples used for the study had 260/280 ratios above 2.0 and 260/230 ratios above 1.7.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Ten micrograms of total RNA was reverse transcribed with Superscript II reverse transcriptase (Invitrogen, Carlsbad, CA) using T7-(dT) 24 primer (Geneset Oligos, La Jolla, CA, USA) containing T7 RNA polymerase promoter. After synthesis of the second cDNA strand, this product was used in an in vitro transcription reaction to generate biotinylated cRNA using a BioArray High Yield RNA Transcript Labeling Kit (Affymetrix, Santa Clara, CA). The biotinylated cRNA was cleaned with the RNAeasy Mini Kit (Qiagen, Valencia, CA).
| | Sample_hyb_protocol | Biotin-labeled cRNA was then fragmented at 94oC for 35 min with 5X fragmentation buffer (200 mM Tris-acetate, pH 8.1, 500 mM potassium acetate, 150 mM magnesium acetate) and then hybridized (10 ug) to Affymetrix (Santa Clara, CA) mouse 430_2 oligonucleotide probe arrays for 16 h at 45oC
| | Sample_scan_protocol | Hybridization fluid was removed and the arrays were washed and stained with streptavidin-phycoerythrin (SAPE), and the signal amplified by anti-streptavidin antibody using Affymetrix Fluidics Station 400. Probe set signals were measured using Agilent GeneArray Scanner (Affymetrix).
| | Sample_data_processing | Affymetrix Microarray Suite version 5.0
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jennifer,,Barb
| | Sample_contact_email | barbj@mail.nih.gov
| | Sample_contact_phone | 3014359232
| | Sample_contact_fax | 3014024544
| | Sample_contact_laboratory | MSCL
| | Sample_contact_department | DCB
| | Sample_contact_institute | NIH
| | Sample_contact_address | 12 South Drive Bldg 12A Room 2001
| | Sample_contact_city | Bethesda
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 20892
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM466nnn/GSM466531/suppl/GSM466531.CEL.gz
| | Sample_series_id | GSE18811
| | Sample_data_row_count | 54675
| | |
|
GSM466532 | GPL570 |
|
292FW22
|
adult native RPE
|
cell type: adult native RPE from 78 y.o. donor
|
Adult native RPE (anRPE) were collected from donors of Caucasian decent and total RNA was extracted right after.
|
| Sample_geo_accession | GSM466532
| | Sample_status | Public on Apr 15 2010
| | Sample_submission_date | Oct 29 2009
| | Sample_last_update_date | Apr 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Fetal RPE were cultured on Primaria® flasks for 6 weeks using MEM-α modified medium with additional supplements. Passages 1-2 were used for all studies. The confluent monolayers used in these experiments have the morphology, pigmentation, polarity, and physiology of native RPE.ARPE-19 spontaneously transformed cell line was cultured using MEM-α modified medium with additional supplements on flasks and inserts to match fetal RPE culturing conditions.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Fetal and adult RPE cells were collected, homogenized in TRIzol reagent (Invitrogen, Carlsbad, CA) and RNA was subsequently purified using an RNeasy Mini kit (Qiagen Inc, Valencia, CA). Double-stranded cDNA was synthesized from 6µg of total RNA using the SuperScript Choice system (Invitrogen, Carlsbad, CA) and the T7-Oligo (dT) promoter primer kit (Affymetrix, Santa Clara, CA). cDNA was purified using Phase Lock Gels (Eppendorf, Westbury, NY). Concentration and quality of RNA samples was determined on the Agilent bioanalyzer (Agilent Technologies, Palo Alto, CA). The integrity of RNA is assessed by looking at 18 & 28s rRNA peaks and though the RIN (RNA integrity number). RNA concentrations were measured using the Nano drop spectrophotometer (Wilmington, DE) and all samples used for the study had 260/280 ratios above 2.0 and 260/230 ratios above 1.7.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Ten micrograms of total RNA was reverse transcribed with Superscript II reverse transcriptase (Invitrogen, Carlsbad, CA) using T7-(dT) 24 primer (Geneset Oligos, La Jolla, CA, USA) containing T7 RNA polymerase promoter. After synthesis of the second cDNA strand, this product was used in an in vitro transcription reaction to generate biotinylated cRNA using a BioArray High Yield RNA Transcript Labeling Kit (Affymetrix, Santa Clara, CA). The biotinylated cRNA was cleaned with the RNAeasy Mini Kit (Qiagen, Valencia, CA).
| | Sample_hyb_protocol | Biotin-labeled cRNA was then fragmented at 94oC for 35 min with 5X fragmentation buffer (200 mM Tris-acetate, pH 8.1, 500 mM potassium acetate, 150 mM magnesium acetate) and then hybridized (10 ug) to Affymetrix (Santa Clara, CA) mouse 430_2 oligonucleotide probe arrays for 16 h at 45oC
| | Sample_scan_protocol | Hybridization fluid was removed and the arrays were washed and stained with streptavidin-phycoerythrin (SAPE), and the signal amplified by anti-streptavidin antibody using Affymetrix Fluidics Station 400. Probe set signals were measured using Agilent GeneArray Scanner (Affymetrix).
| | Sample_data_processing | Affymetrix Microarray Suite version 5.0
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jennifer,,Barb
| | Sample_contact_email | barbj@mail.nih.gov
| | Sample_contact_phone | 3014359232
| | Sample_contact_fax | 3014024544
| | Sample_contact_laboratory | MSCL
| | Sample_contact_department | DCB
| | Sample_contact_institute | NIH
| | Sample_contact_address | 12 South Drive Bldg 12A Room 2001
| | Sample_contact_city | Bethesda
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 20892
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM466nnn/GSM466532/suppl/GSM466532.CEL.gz
| | Sample_series_id | GSE18811
| | Sample_data_row_count | 54675
| | |
|
GSM466533 | GPL570 |
|
292FW23
|
adult native RPE
|
cell type: adult native RPE from 89 y.o. donor
|
Adult native RPE (anRPE) were collected from donors of Caucasian decent and total RNA was extracted right after.
|
| Sample_geo_accession | GSM466533
| | Sample_status | Public on Apr 15 2010
| | Sample_submission_date | Oct 29 2009
| | Sample_last_update_date | Apr 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Fetal RPE were cultured on Primaria® flasks for 6 weeks using MEM-α modified medium with additional supplements. Passages 1-2 were used for all studies. The confluent monolayers used in these experiments have the morphology, pigmentation, polarity, and physiology of native RPE.ARPE-19 spontaneously transformed cell line was cultured using MEM-α modified medium with additional supplements on flasks and inserts to match fetal RPE culturing conditions.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Fetal and adult RPE cells were collected, homogenized in TRIzol reagent (Invitrogen, Carlsbad, CA) and RNA was subsequently purified using an RNeasy Mini kit (Qiagen Inc, Valencia, CA). Double-stranded cDNA was synthesized from 6µg of total RNA using the SuperScript Choice system (Invitrogen, Carlsbad, CA) and the T7-Oligo (dT) promoter primer kit (Affymetrix, Santa Clara, CA). cDNA was purified using Phase Lock Gels (Eppendorf, Westbury, NY). Concentration and quality of RNA samples was determined on the Agilent bioanalyzer (Agilent Technologies, Palo Alto, CA). The integrity of RNA is assessed by looking at 18 & 28s rRNA peaks and though the RIN (RNA integrity number). RNA concentrations were measured using the Nano drop spectrophotometer (Wilmington, DE) and all samples used for the study had 260/280 ratios above 2.0 and 260/230 ratios above 1.7.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Ten micrograms of total RNA was reverse transcribed with Superscript II reverse transcriptase (Invitrogen, Carlsbad, CA) using T7-(dT) 24 primer (Geneset Oligos, La Jolla, CA, USA) containing T7 RNA polymerase promoter. After synthesis of the second cDNA strand, this product was used in an in vitro transcription reaction to generate biotinylated cRNA using a BioArray High Yield RNA Transcript Labeling Kit (Affymetrix, Santa Clara, CA). The biotinylated cRNA was cleaned with the RNAeasy Mini Kit (Qiagen, Valencia, CA).
| | Sample_hyb_protocol | Biotin-labeled cRNA was then fragmented at 94oC for 35 min with 5X fragmentation buffer (200 mM Tris-acetate, pH 8.1, 500 mM potassium acetate, 150 mM magnesium acetate) and then hybridized (10 ug) to Affymetrix (Santa Clara, CA) mouse 430_2 oligonucleotide probe arrays for 16 h at 45oC
| | Sample_scan_protocol | Hybridization fluid was removed and the arrays were washed and stained with streptavidin-phycoerythrin (SAPE), and the signal amplified by anti-streptavidin antibody using Affymetrix Fluidics Station 400. Probe set signals were measured using Agilent GeneArray Scanner (Affymetrix).
| | Sample_data_processing | Affymetrix Microarray Suite version 5.0
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jennifer,,Barb
| | Sample_contact_email | barbj@mail.nih.gov
| | Sample_contact_phone | 3014359232
| | Sample_contact_fax | 3014024544
| | Sample_contact_laboratory | MSCL
| | Sample_contact_department | DCB
| | Sample_contact_institute | NIH
| | Sample_contact_address | 12 South Drive Bldg 12A Room 2001
| | Sample_contact_city | Bethesda
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 20892
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM466nnn/GSM466533/suppl/GSM466533.CEL.gz
| | Sample_series_id | GSE18811
| | Sample_data_row_count | 54675
| | |
|
GSM466534 | GPL570 |
|
292FW24
|
ARPE-19 cell line
|
cell line: ARPE-19
|
ARPE-19 spontaneously transformed cell line was cultured using MEM-α modified medium with additional supplements on flasks and inserts to match fetal RPE culturing conditions.
|
| Sample_geo_accession | GSM466534
| | Sample_status | Public on Apr 15 2010
| | Sample_submission_date | Oct 29 2009
| | Sample_last_update_date | Apr 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Fetal RPE were cultured on Primaria® flasks for 6 weeks using MEM-α modified medium with additional supplements. Passages 1-2 were used for all studies. The confluent monolayers used in these experiments have the morphology, pigmentation, polarity, and physiology of native RPE.ARPE-19 spontaneously transformed cell line was cultured using MEM-α modified medium with additional supplements on flasks and inserts to match fetal RPE culturing conditions.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Fetal and adult RPE cells were collected, homogenized in TRIzol reagent (Invitrogen, Carlsbad, CA) and RNA was subsequently purified using an RNeasy Mini kit (Qiagen Inc, Valencia, CA). Double-stranded cDNA was synthesized from 6µg of total RNA using the SuperScript Choice system (Invitrogen, Carlsbad, CA) and the T7-Oligo (dT) promoter primer kit (Affymetrix, Santa Clara, CA). cDNA was purified using Phase Lock Gels (Eppendorf, Westbury, NY). Concentration and quality of RNA samples was determined on the Agilent bioanalyzer (Agilent Technologies, Palo Alto, CA). The integrity of RNA is assessed by looking at 18 & 28s rRNA peaks and though the RIN (RNA integrity number). RNA concentrations were measured using the Nano drop spectrophotometer (Wilmington, DE) and all samples used for the study had 260/280 ratios above 2.0 and 260/230 ratios above 1.7.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Ten micrograms of total RNA was reverse transcribed with Superscript II reverse transcriptase (Invitrogen, Carlsbad, CA) using T7-(dT) 24 primer (Geneset Oligos, La Jolla, CA, USA) containing T7 RNA polymerase promoter. After synthesis of the second cDNA strand, this product was used in an in vitro transcription reaction to generate biotinylated cRNA using a BioArray High Yield RNA Transcript Labeling Kit (Affymetrix, Santa Clara, CA). The biotinylated cRNA was cleaned with the RNAeasy Mini Kit (Qiagen, Valencia, CA).
| | Sample_hyb_protocol | Biotin-labeled cRNA was then fragmented at 94oC for 35 min with 5X fragmentation buffer (200 mM Tris-acetate, pH 8.1, 500 mM potassium acetate, 150 mM magnesium acetate) and then hybridized (10 ug) to Affymetrix (Santa Clara, CA) mouse 430_2 oligonucleotide probe arrays for 16 h at 45oC
| | Sample_scan_protocol | Hybridization fluid was removed and the arrays were washed and stained with streptavidin-phycoerythrin (SAPE), and the signal amplified by anti-streptavidin antibody using Affymetrix Fluidics Station 400. Probe set signals were measured using Agilent GeneArray Scanner (Affymetrix).
| | Sample_data_processing | Affymetrix Microarray Suite version 5.0
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jennifer,,Barb
| | Sample_contact_email | barbj@mail.nih.gov
| | Sample_contact_phone | 3014359232
| | Sample_contact_fax | 3014024544
| | Sample_contact_laboratory | MSCL
| | Sample_contact_department | DCB
| | Sample_contact_institute | NIH
| | Sample_contact_address | 12 South Drive Bldg 12A Room 2001
| | Sample_contact_city | Bethesda
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 20892
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM466nnn/GSM466534/suppl/GSM466534.CEL.gz
| | Sample_series_id | GSE18811
| | Sample_data_row_count | 54675
| | |
|
GSM466535 | GPL570 |
|
292FW25
|
ARPE-19 cell line
|
cell line: ARPE-19
|
ARPE-19 spontaneously transformed cell line was cultured using MEM-α modified medium with additional supplements on flasks and inserts to match fetal RPE culturing conditions.
|
| Sample_geo_accession | GSM466535
| | Sample_status | Public on Apr 15 2010
| | Sample_submission_date | Oct 29 2009
| | Sample_last_update_date | Apr 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Fetal RPE were cultured on Primaria® flasks for 6 weeks using MEM-α modified medium with additional supplements. Passages 1-2 were used for all studies. The confluent monolayers used in these experiments have the morphology, pigmentation, polarity, and physiology of native RPE.ARPE-19 spontaneously transformed cell line was cultured using MEM-α modified medium with additional supplements on flasks and inserts to match fetal RPE culturing conditions.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Fetal and adult RPE cells were collected, homogenized in TRIzol reagent (Invitrogen, Carlsbad, CA) and RNA was subsequently purified using an RNeasy Mini kit (Qiagen Inc, Valencia, CA). Double-stranded cDNA was synthesized from 6µg of total RNA using the SuperScript Choice system (Invitrogen, Carlsbad, CA) and the T7-Oligo (dT) promoter primer kit (Affymetrix, Santa Clara, CA). cDNA was purified using Phase Lock Gels (Eppendorf, Westbury, NY). Concentration and quality of RNA samples was determined on the Agilent bioanalyzer (Agilent Technologies, Palo Alto, CA). The integrity of RNA is assessed by looking at 18 & 28s rRNA peaks and though the RIN (RNA integrity number). RNA concentrations were measured using the Nano drop spectrophotometer (Wilmington, DE) and all samples used for the study had 260/280 ratios above 2.0 and 260/230 ratios above 1.7.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Ten micrograms of total RNA was reverse transcribed with Superscript II reverse transcriptase (Invitrogen, Carlsbad, CA) using T7-(dT) 24 primer (Geneset Oligos, La Jolla, CA, USA) containing T7 RNA polymerase promoter. After synthesis of the second cDNA strand, this product was used in an in vitro transcription reaction to generate biotinylated cRNA using a BioArray High Yield RNA Transcript Labeling Kit (Affymetrix, Santa Clara, CA). The biotinylated cRNA was cleaned with the RNAeasy Mini Kit (Qiagen, Valencia, CA).
| | Sample_hyb_protocol | Biotin-labeled cRNA was then fragmented at 94oC for 35 min with 5X fragmentation buffer (200 mM Tris-acetate, pH 8.1, 500 mM potassium acetate, 150 mM magnesium acetate) and then hybridized (10 ug) to Affymetrix (Santa Clara, CA) mouse 430_2 oligonucleotide probe arrays for 16 h at 45oC
| | Sample_scan_protocol | Hybridization fluid was removed and the arrays were washed and stained with streptavidin-phycoerythrin (SAPE), and the signal amplified by anti-streptavidin antibody using Affymetrix Fluidics Station 400. Probe set signals were measured using Agilent GeneArray Scanner (Affymetrix).
| | Sample_data_processing | Affymetrix Microarray Suite version 5.0
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jennifer,,Barb
| | Sample_contact_email | barbj@mail.nih.gov
| | Sample_contact_phone | 3014359232
| | Sample_contact_fax | 3014024544
| | Sample_contact_laboratory | MSCL
| | Sample_contact_department | DCB
| | Sample_contact_institute | NIH
| | Sample_contact_address | 12 South Drive Bldg 12A Room 2001
| | Sample_contact_city | Bethesda
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 20892
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM466nnn/GSM466535/suppl/GSM466535.CEL.gz
| | Sample_series_id | GSE18811
| | Sample_data_row_count | 54675
| | |
|
GSM466536 | GPL570 |
|
292FW26
|
ARPE-19 cell line
|
cell line: ARPE-19
|
ARPE-19 spontaneously transformed cell line was cultured using MEM-α modified medium with additional supplements on flasks and inserts to match fetal RPE culturing conditions.
|
| Sample_geo_accession | GSM466536
| | Sample_status | Public on Apr 15 2010
| | Sample_submission_date | Oct 29 2009
| | Sample_last_update_date | Apr 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Fetal RPE were cultured on Primaria® flasks for 6 weeks using MEM-α modified medium with additional supplements. Passages 1-2 were used for all studies. The confluent monolayers used in these experiments have the morphology, pigmentation, polarity, and physiology of native RPE.ARPE-19 spontaneously transformed cell line was cultured using MEM-α modified medium with additional supplements on flasks and inserts to match fetal RPE culturing conditions.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Fetal and adult RPE cells were collected, homogenized in TRIzol reagent (Invitrogen, Carlsbad, CA) and RNA was subsequently purified using an RNeasy Mini kit (Qiagen Inc, Valencia, CA). Double-stranded cDNA was synthesized from 6µg of total RNA using the SuperScript Choice system (Invitrogen, Carlsbad, CA) and the T7-Oligo (dT) promoter primer kit (Affymetrix, Santa Clara, CA). cDNA was purified using Phase Lock Gels (Eppendorf, Westbury, NY). Concentration and quality of RNA samples was determined on the Agilent bioanalyzer (Agilent Technologies, Palo Alto, CA). The integrity of RNA is assessed by looking at 18 & 28s rRNA peaks and though the RIN (RNA integrity number). RNA concentrations were measured using the Nano drop spectrophotometer (Wilmington, DE) and all samples used for the study had 260/280 ratios above 2.0 and 260/230 ratios above 1.7.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Ten micrograms of total RNA was reverse transcribed with Superscript II reverse transcriptase (Invitrogen, Carlsbad, CA) using T7-(dT) 24 primer (Geneset Oligos, La Jolla, CA, USA) containing T7 RNA polymerase promoter. After synthesis of the second cDNA strand, this product was used in an in vitro transcription reaction to generate biotinylated cRNA using a BioArray High Yield RNA Transcript Labeling Kit (Affymetrix, Santa Clara, CA). The biotinylated cRNA was cleaned with the RNAeasy Mini Kit (Qiagen, Valencia, CA).
| | Sample_hyb_protocol | Biotin-labeled cRNA was then fragmented at 94oC for 35 min with 5X fragmentation buffer (200 mM Tris-acetate, pH 8.1, 500 mM potassium acetate, 150 mM magnesium acetate) and then hybridized (10 ug) to Affymetrix (Santa Clara, CA) mouse 430_2 oligonucleotide probe arrays for 16 h at 45oC
| | Sample_scan_protocol | Hybridization fluid was removed and the arrays were washed and stained with streptavidin-phycoerythrin (SAPE), and the signal amplified by anti-streptavidin antibody using Affymetrix Fluidics Station 400. Probe set signals were measured using Agilent GeneArray Scanner (Affymetrix).
| | Sample_data_processing | Affymetrix Microarray Suite version 5.0
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jennifer,,Barb
| | Sample_contact_email | barbj@mail.nih.gov
| | Sample_contact_phone | 3014359232
| | Sample_contact_fax | 3014024544
| | Sample_contact_laboratory | MSCL
| | Sample_contact_department | DCB
| | Sample_contact_institute | NIH
| | Sample_contact_address | 12 South Drive Bldg 12A Room 2001
| | Sample_contact_city | Bethesda
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 20892
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM466nnn/GSM466536/suppl/GSM466536.CEL.gz
| | Sample_series_id | GSE18811
| | Sample_data_row_count | 54675
| | |
|
GSM466537 | GPL570 |
|
292FW27
|
ARPE-19 cell line
|
cell line: ARPE-19
|
ARPE-19 spontaneously transformed cell line was cultured using MEM-α modified medium with additional supplements on flasks and inserts to match fetal RPE culturing conditions.
|
| Sample_geo_accession | GSM466537
| | Sample_status | Public on Apr 15 2010
| | Sample_submission_date | Oct 29 2009
| | Sample_last_update_date | Apr 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Fetal RPE were cultured on Primaria® flasks for 6 weeks using MEM-α modified medium with additional supplements. Passages 1-2 were used for all studies. The confluent monolayers used in these experiments have the morphology, pigmentation, polarity, and physiology of native RPE.ARPE-19 spontaneously transformed cell line was cultured using MEM-α modified medium with additional supplements on flasks and inserts to match fetal RPE culturing conditions.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Fetal and adult RPE cells were collected, homogenized in TRIzol reagent (Invitrogen, Carlsbad, CA) and RNA was subsequently purified using an RNeasy Mini kit (Qiagen Inc, Valencia, CA). Double-stranded cDNA was synthesized from 6µg of total RNA using the SuperScript Choice system (Invitrogen, Carlsbad, CA) and the T7-Oligo (dT) promoter primer kit (Affymetrix, Santa Clara, CA). cDNA was purified using Phase Lock Gels (Eppendorf, Westbury, NY). Concentration and quality of RNA samples was determined on the Agilent bioanalyzer (Agilent Technologies, Palo Alto, CA). The integrity of RNA is assessed by looking at 18 & 28s rRNA peaks and though the RIN (RNA integrity number). RNA concentrations were measured using the Nano drop spectrophotometer (Wilmington, DE) and all samples used for the study had 260/280 ratios above 2.0 and 260/230 ratios above 1.7.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Ten micrograms of total RNA was reverse transcribed with Superscript II reverse transcriptase (Invitrogen, Carlsbad, CA) using T7-(dT) 24 primer (Geneset Oligos, La Jolla, CA, USA) containing T7 RNA polymerase promoter. After synthesis of the second cDNA strand, this product was used in an in vitro transcription reaction to generate biotinylated cRNA using a BioArray High Yield RNA Transcript Labeling Kit (Affymetrix, Santa Clara, CA). The biotinylated cRNA was cleaned with the RNAeasy Mini Kit (Qiagen, Valencia, CA).
| | Sample_hyb_protocol | Biotin-labeled cRNA was then fragmented at 94oC for 35 min with 5X fragmentation buffer (200 mM Tris-acetate, pH 8.1, 500 mM potassium acetate, 150 mM magnesium acetate) and then hybridized (10 ug) to Affymetrix (Santa Clara, CA) mouse 430_2 oligonucleotide probe arrays for 16 h at 45oC
| | Sample_scan_protocol | Hybridization fluid was removed and the arrays were washed and stained with streptavidin-phycoerythrin (SAPE), and the signal amplified by anti-streptavidin antibody using Affymetrix Fluidics Station 400. Probe set signals were measured using Agilent GeneArray Scanner (Affymetrix).
| | Sample_data_processing | Affymetrix Microarray Suite version 5.0
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jennifer,,Barb
| | Sample_contact_email | barbj@mail.nih.gov
| | Sample_contact_phone | 3014359232
| | Sample_contact_fax | 3014024544
| | Sample_contact_laboratory | MSCL
| | Sample_contact_department | DCB
| | Sample_contact_institute | NIH
| | Sample_contact_address | 12 South Drive Bldg 12A Room 2001
| | Sample_contact_city | Bethesda
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 20892
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM466nnn/GSM466537/suppl/GSM466537.CEL.gz
| | Sample_series_id | GSE18811
| | Sample_data_row_count | 54675
| | |
|
GSM466538 | GPL570 |
|
292FW28
|
ARPE-19 cell line
|
cell line: ARPE-19
|
ARPE-19 spontaneously transformed cell line was cultured using MEM-α modified medium with additional supplements on flasks and inserts to match fetal RPE culturing conditions.
|
| Sample_geo_accession | GSM466538
| | Sample_status | Public on Apr 15 2010
| | Sample_submission_date | Oct 29 2009
| | Sample_last_update_date | Apr 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Fetal RPE were cultured on Primaria® flasks for 6 weeks using MEM-α modified medium with additional supplements. Passages 1-2 were used for all studies. The confluent monolayers used in these experiments have the morphology, pigmentation, polarity, and physiology of native RPE.ARPE-19 spontaneously transformed cell line was cultured using MEM-α modified medium with additional supplements on flasks and inserts to match fetal RPE culturing conditions.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Fetal and adult RPE cells were collected, homogenized in TRIzol reagent (Invitrogen, Carlsbad, CA) and RNA was subsequently purified using an RNeasy Mini kit (Qiagen Inc, Valencia, CA). Double-stranded cDNA was synthesized from 6µg of total RNA using the SuperScript Choice system (Invitrogen, Carlsbad, CA) and the T7-Oligo (dT) promoter primer kit (Affymetrix, Santa Clara, CA). cDNA was purified using Phase Lock Gels (Eppendorf, Westbury, NY). Concentration and quality of RNA samples was determined on the Agilent bioanalyzer (Agilent Technologies, Palo Alto, CA). The integrity of RNA is assessed by looking at 18 & 28s rRNA peaks and though the RIN (RNA integrity number). RNA concentrations were measured using the Nano drop spectrophotometer (Wilmington, DE) and all samples used for the study had 260/280 ratios above 2.0 and 260/230 ratios above 1.7.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Ten micrograms of total RNA was reverse transcribed with Superscript II reverse transcriptase (Invitrogen, Carlsbad, CA) using T7-(dT) 24 primer (Geneset Oligos, La Jolla, CA, USA) containing T7 RNA polymerase promoter. After synthesis of the second cDNA strand, this product was used in an in vitro transcription reaction to generate biotinylated cRNA using a BioArray High Yield RNA Transcript Labeling Kit (Affymetrix, Santa Clara, CA). The biotinylated cRNA was cleaned with the RNAeasy Mini Kit (Qiagen, Valencia, CA).
| | Sample_hyb_protocol | Biotin-labeled cRNA was then fragmented at 94oC for 35 min with 5X fragmentation buffer (200 mM Tris-acetate, pH 8.1, 500 mM potassium acetate, 150 mM magnesium acetate) and then hybridized (10 ug) to Affymetrix (Santa Clara, CA) mouse 430_2 oligonucleotide probe arrays for 16 h at 45oC
| | Sample_scan_protocol | Hybridization fluid was removed and the arrays were washed and stained with streptavidin-phycoerythrin (SAPE), and the signal amplified by anti-streptavidin antibody using Affymetrix Fluidics Station 400. Probe set signals were measured using Agilent GeneArray Scanner (Affymetrix).
| | Sample_data_processing | Affymetrix Microarray Suite version 5.0
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jennifer,,Barb
| | Sample_contact_email | barbj@mail.nih.gov
| | Sample_contact_phone | 3014359232
| | Sample_contact_fax | 3014024544
| | Sample_contact_laboratory | MSCL
| | Sample_contact_department | DCB
| | Sample_contact_institute | NIH
| | Sample_contact_address | 12 South Drive Bldg 12A Room 2001
| | Sample_contact_city | Bethesda
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 20892
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM466nnn/GSM466538/suppl/GSM466538.CEL.gz
| | Sample_series_id | GSE18811
| | Sample_data_row_count | 54675
| | |
|
GSM466539 | GPL570 |
|
292FW29
|
ARPE-19 cell line
|
cell line: ARPE-19
|
ARPE-19 spontaneously transformed cell line was cultured using MEM-α modified medium with additional supplements on flasks and inserts to match fetal RPE culturing conditions.
|
| Sample_geo_accession | GSM466539
| | Sample_status | Public on Apr 15 2010
| | Sample_submission_date | Oct 29 2009
| | Sample_last_update_date | Apr 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Fetal RPE were cultured on Primaria® flasks for 6 weeks using MEM-α modified medium with additional supplements. Passages 1-2 were used for all studies. The confluent monolayers used in these experiments have the morphology, pigmentation, polarity, and physiology of native RPE.ARPE-19 spontaneously transformed cell line was cultured using MEM-α modified medium with additional supplements on flasks and inserts to match fetal RPE culturing conditions.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Fetal and adult RPE cells were collected, homogenized in TRIzol reagent (Invitrogen, Carlsbad, CA) and RNA was subsequently purified using an RNeasy Mini kit (Qiagen Inc, Valencia, CA). Double-stranded cDNA was synthesized from 6µg of total RNA using the SuperScript Choice system (Invitrogen, Carlsbad, CA) and the T7-Oligo (dT) promoter primer kit (Affymetrix, Santa Clara, CA). cDNA was purified using Phase Lock Gels (Eppendorf, Westbury, NY). Concentration and quality of RNA samples was determined on the Agilent bioanalyzer (Agilent Technologies, Palo Alto, CA). The integrity of RNA is assessed by looking at 18 & 28s rRNA peaks and though the RIN (RNA integrity number). RNA concentrations were measured using the Nano drop spectrophotometer (Wilmington, DE) and all samples used for the study had 260/280 ratios above 2.0 and 260/230 ratios above 1.7.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Ten micrograms of total RNA was reverse transcribed with Superscript II reverse transcriptase (Invitrogen, Carlsbad, CA) using T7-(dT) 24 primer (Geneset Oligos, La Jolla, CA, USA) containing T7 RNA polymerase promoter. After synthesis of the second cDNA strand, this product was used in an in vitro transcription reaction to generate biotinylated cRNA using a BioArray High Yield RNA Transcript Labeling Kit (Affymetrix, Santa Clara, CA). The biotinylated cRNA was cleaned with the RNAeasy Mini Kit (Qiagen, Valencia, CA).
| | Sample_hyb_protocol | Biotin-labeled cRNA was then fragmented at 94oC for 35 min with 5X fragmentation buffer (200 mM Tris-acetate, pH 8.1, 500 mM potassium acetate, 150 mM magnesium acetate) and then hybridized (10 ug) to Affymetrix (Santa Clara, CA) mouse 430_2 oligonucleotide probe arrays for 16 h at 45oC
| | Sample_scan_protocol | Hybridization fluid was removed and the arrays were washed and stained with streptavidin-phycoerythrin (SAPE), and the signal amplified by anti-streptavidin antibody using Affymetrix Fluidics Station 400. Probe set signals were measured using Agilent GeneArray Scanner (Affymetrix).
| | Sample_data_processing | Affymetrix Microarray Suite version 5.0
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jennifer,,Barb
| | Sample_contact_email | barbj@mail.nih.gov
| | Sample_contact_phone | 3014359232
| | Sample_contact_fax | 3014024544
| | Sample_contact_laboratory | MSCL
| | Sample_contact_department | DCB
| | Sample_contact_institute | NIH
| | Sample_contact_address | 12 South Drive Bldg 12A Room 2001
| | Sample_contact_city | Bethesda
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 20892
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM466nnn/GSM466539/suppl/GSM466539.CEL.gz
| | Sample_series_id | GSE18811
| | Sample_data_row_count | 54675
| | |
|
GSM466540 | GPL570 |
|
292FW3
|
fetal RPE cultures
|
cell type: fetal RPE
gestational age: 16 weeks
|
Fetal RPE were cultured on Primaria® flasks for 6 weeks using MEM-α modified medium with additional supplements. Passages 1-2 were used for all studies. The confluent monolayers used in these experiments have the morphology, pigmentation, polarity, and physiology of native RPE.
|
| Sample_geo_accession | GSM466540
| | Sample_status | Public on Apr 15 2010
| | Sample_submission_date | Oct 29 2009
| | Sample_last_update_date | Apr 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Fetal RPE were cultured on Primaria® flasks for 6 weeks using MEM-α modified medium with additional supplements. Passages 1-2 were used for all studies. The confluent monolayers used in these experiments have the morphology, pigmentation, polarity, and physiology of native RPE.ARPE-19 spontaneously transformed cell line was cultured using MEM-α modified medium with additional supplements on flasks and inserts to match fetal RPE culturing conditions.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Fetal and adult RPE cells were collected, homogenized in TRIzol reagent (Invitrogen, Carlsbad, CA) and RNA was subsequently purified using an RNeasy Mini kit (Qiagen Inc, Valencia, CA). Double-stranded cDNA was synthesized from 6µg of total RNA using the SuperScript Choice system (Invitrogen, Carlsbad, CA) and the T7-Oligo (dT) promoter primer kit (Affymetrix, Santa Clara, CA). cDNA was purified using Phase Lock Gels (Eppendorf, Westbury, NY). Concentration and quality of RNA samples was determined on the Agilent bioanalyzer (Agilent Technologies, Palo Alto, CA). The integrity of RNA is assessed by looking at 18 & 28s rRNA peaks and though the RIN (RNA integrity number). RNA concentrations were measured using the Nano drop spectrophotometer (Wilmington, DE) and all samples used for the study had 260/280 ratios above 2.0 and 260/230 ratios above 1.7.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Ten micrograms of total RNA was reverse transcribed with Superscript II reverse transcriptase (Invitrogen, Carlsbad, CA) using T7-(dT) 24 primer (Geneset Oligos, La Jolla, CA, USA) containing T7 RNA polymerase promoter. After synthesis of the second cDNA strand, this product was used in an in vitro transcription reaction to generate biotinylated cRNA using a BioArray High Yield RNA Transcript Labeling Kit (Affymetrix, Santa Clara, CA). The biotinylated cRNA was cleaned with the RNAeasy Mini Kit (Qiagen, Valencia, CA).
| | Sample_hyb_protocol | Biotin-labeled cRNA was then fragmented at 94oC for 35 min with 5X fragmentation buffer (200 mM Tris-acetate, pH 8.1, 500 mM potassium acetate, 150 mM magnesium acetate) and then hybridized (10 ug) to Affymetrix (Santa Clara, CA) mouse 430_2 oligonucleotide probe arrays for 16 h at 45oC
| | Sample_scan_protocol | Hybridization fluid was removed and the arrays were washed and stained with streptavidin-phycoerythrin (SAPE), and the signal amplified by anti-streptavidin antibody using Affymetrix Fluidics Station 400. Probe set signals were measured using Agilent GeneArray Scanner (Affymetrix).
| | Sample_data_processing | Affymetrix Microarray Suite version 5.0
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jennifer,,Barb
| | Sample_contact_email | barbj@mail.nih.gov
| | Sample_contact_phone | 3014359232
| | Sample_contact_fax | 3014024544
| | Sample_contact_laboratory | MSCL
| | Sample_contact_department | DCB
| | Sample_contact_institute | NIH
| | Sample_contact_address | 12 South Drive Bldg 12A Room 2001
| | Sample_contact_city | Bethesda
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 20892
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM466nnn/GSM466540/suppl/GSM466540.CEL.gz
| | Sample_series_id | GSE18811
| | Sample_data_row_count | 54675
| | |
|
GSM466541 | GPL570 |
|
292FW30
|
ARPE-19 cell line
|
cell line: ARPE-19
|
ARPE-19 spontaneously transformed cell line was cultured using MEM-α modified medium with additional supplements on flasks and inserts to match fetal RPE culturing conditions.
|
| Sample_geo_accession | GSM466541
| | Sample_status | Public on Apr 15 2010
| | Sample_submission_date | Oct 29 2009
| | Sample_last_update_date | Apr 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Fetal RPE were cultured on Primaria® flasks for 6 weeks using MEM-α modified medium with additional supplements. Passages 1-2 were used for all studies. The confluent monolayers used in these experiments have the morphology, pigmentation, polarity, and physiology of native RPE.ARPE-19 spontaneously transformed cell line was cultured using MEM-α modified medium with additional supplements on flasks and inserts to match fetal RPE culturing conditions.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Fetal and adult RPE cells were collected, homogenized in TRIzol reagent (Invitrogen, Carlsbad, CA) and RNA was subsequently purified using an RNeasy Mini kit (Qiagen Inc, Valencia, CA). Double-stranded cDNA was synthesized from 6µg of total RNA using the SuperScript Choice system (Invitrogen, Carlsbad, CA) and the T7-Oligo (dT) promoter primer kit (Affymetrix, Santa Clara, CA). cDNA was purified using Phase Lock Gels (Eppendorf, Westbury, NY). Concentration and quality of RNA samples was determined on the Agilent bioanalyzer (Agilent Technologies, Palo Alto, CA). The integrity of RNA is assessed by looking at 18 & 28s rRNA peaks and though the RIN (RNA integrity number). RNA concentrations were measured using the Nano drop spectrophotometer (Wilmington, DE) and all samples used for the study had 260/280 ratios above 2.0 and 260/230 ratios above 1.7.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Ten micrograms of total RNA was reverse transcribed with Superscript II reverse transcriptase (Invitrogen, Carlsbad, CA) using T7-(dT) 24 primer (Geneset Oligos, La Jolla, CA, USA) containing T7 RNA polymerase promoter. After synthesis of the second cDNA strand, this product was used in an in vitro transcription reaction to generate biotinylated cRNA using a BioArray High Yield RNA Transcript Labeling Kit (Affymetrix, Santa Clara, CA). The biotinylated cRNA was cleaned with the RNAeasy Mini Kit (Qiagen, Valencia, CA).
| | Sample_hyb_protocol | Biotin-labeled cRNA was then fragmented at 94oC for 35 min with 5X fragmentation buffer (200 mM Tris-acetate, pH 8.1, 500 mM potassium acetate, 150 mM magnesium acetate) and then hybridized (10 ug) to Affymetrix (Santa Clara, CA) mouse 430_2 oligonucleotide probe arrays for 16 h at 45oC
| | Sample_scan_protocol | Hybridization fluid was removed and the arrays were washed and stained with streptavidin-phycoerythrin (SAPE), and the signal amplified by anti-streptavidin antibody using Affymetrix Fluidics Station 400. Probe set signals were measured using Agilent GeneArray Scanner (Affymetrix).
| | Sample_data_processing | Affymetrix Microarray Suite version 5.0
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jennifer,,Barb
| | Sample_contact_email | barbj@mail.nih.gov
| | Sample_contact_phone | 3014359232
| | Sample_contact_fax | 3014024544
| | Sample_contact_laboratory | MSCL
| | Sample_contact_department | DCB
| | Sample_contact_institute | NIH
| | Sample_contact_address | 12 South Drive Bldg 12A Room 2001
| | Sample_contact_city | Bethesda
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 20892
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM466nnn/GSM466541/suppl/GSM466541.CEL.gz
| | Sample_series_id | GSE18811
| | Sample_data_row_count | 54675
| | |
|
GSM466542 | GPL570 |
|
292FW31
|
ARPE-19 cell line
|
cell line: ARPE-19
|
ARPE-19 spontaneously transformed cell line was cultured using MEM-α modified medium with additional supplements on flasks and inserts to match fetal RPE culturing conditions.
|
| Sample_geo_accession | GSM466542
| | Sample_status | Public on Apr 15 2010
| | Sample_submission_date | Oct 29 2009
| | Sample_last_update_date | Apr 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Fetal RPE were cultured on Primaria® flasks for 6 weeks using MEM-α modified medium with additional supplements. Passages 1-2 were used for all studies. The confluent monolayers used in these experiments have the morphology, pigmentation, polarity, and physiology of native RPE.ARPE-19 spontaneously transformed cell line was cultured using MEM-α modified medium with additional supplements on flasks and inserts to match fetal RPE culturing conditions.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Fetal and adult RPE cells were collected, homogenized in TRIzol reagent (Invitrogen, Carlsbad, CA) and RNA was subsequently purified using an RNeasy Mini kit (Qiagen Inc, Valencia, CA). Double-stranded cDNA was synthesized from 6µg of total RNA using the SuperScript Choice system (Invitrogen, Carlsbad, CA) and the T7-Oligo (dT) promoter primer kit (Affymetrix, Santa Clara, CA). cDNA was purified using Phase Lock Gels (Eppendorf, Westbury, NY). Concentration and quality of RNA samples was determined on the Agilent bioanalyzer (Agilent Technologies, Palo Alto, CA). The integrity of RNA is assessed by looking at 18 & 28s rRNA peaks and though the RIN (RNA integrity number). RNA concentrations were measured using the Nano drop spectrophotometer (Wilmington, DE) and all samples used for the study had 260/280 ratios above 2.0 and 260/230 ratios above 1.7.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Ten micrograms of total RNA was reverse transcribed with Superscript II reverse transcriptase (Invitrogen, Carlsbad, CA) using T7-(dT) 24 primer (Geneset Oligos, La Jolla, CA, USA) containing T7 RNA polymerase promoter. After synthesis of the second cDNA strand, this product was used in an in vitro transcription reaction to generate biotinylated cRNA using a BioArray High Yield RNA Transcript Labeling Kit (Affymetrix, Santa Clara, CA). The biotinylated cRNA was cleaned with the RNAeasy Mini Kit (Qiagen, Valencia, CA).
| | Sample_hyb_protocol | Biotin-labeled cRNA was then fragmented at 94oC for 35 min with 5X fragmentation buffer (200 mM Tris-acetate, pH 8.1, 500 mM potassium acetate, 150 mM magnesium acetate) and then hybridized (10 ug) to Affymetrix (Santa Clara, CA) mouse 430_2 oligonucleotide probe arrays for 16 h at 45oC
| | Sample_scan_protocol | Hybridization fluid was removed and the arrays were washed and stained with streptavidin-phycoerythrin (SAPE), and the signal amplified by anti-streptavidin antibody using Affymetrix Fluidics Station 400. Probe set signals were measured using Agilent GeneArray Scanner (Affymetrix).
| | Sample_data_processing | Affymetrix Microarray Suite version 5.0
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jennifer,,Barb
| | Sample_contact_email | barbj@mail.nih.gov
| | Sample_contact_phone | 3014359232
| | Sample_contact_fax | 3014024544
| | Sample_contact_laboratory | MSCL
| | Sample_contact_department | DCB
| | Sample_contact_institute | NIH
| | Sample_contact_address | 12 South Drive Bldg 12A Room 2001
| | Sample_contact_city | Bethesda
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 20892
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM466nnn/GSM466542/suppl/GSM466542.CEL.gz
| | Sample_series_id | GSE18811
| | Sample_data_row_count | 54675
| | |
|
GSM466543 | GPL570 |
|
292FW32
|
native fetal RPE
|
cell type: native fetal RPE
gestational age: 16 weeks
|
Fetal eyes were obtained from Advanced Bioscience Resources (Alameda, CA) based on the availability of the aborted fetuses. RPE cells were collected and RNA was extracted (24-48 hours period following the abortion procedure).
|
| Sample_geo_accession | GSM466543
| | Sample_status | Public on Apr 15 2010
| | Sample_submission_date | Oct 29 2009
| | Sample_last_update_date | Apr 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Fetal RPE were cultured on Primaria® flasks for 6 weeks using MEM-α modified medium with additional supplements. Passages 1-2 were used for all studies. The confluent monolayers used in these experiments have the morphology, pigmentation, polarity, and physiology of native RPE.ARPE-19 spontaneously transformed cell line was cultured using MEM-α modified medium with additional supplements on flasks and inserts to match fetal RPE culturing conditions.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Fetal and adult RPE cells were collected, homogenized in TRIzol reagent (Invitrogen, Carlsbad, CA) and RNA was subsequently purified using an RNeasy Mini kit (Qiagen Inc, Valencia, CA). Double-stranded cDNA was synthesized from 6µg of total RNA using the SuperScript Choice system (Invitrogen, Carlsbad, CA) and the T7-Oligo (dT) promoter primer kit (Affymetrix, Santa Clara, CA). cDNA was purified using Phase Lock Gels (Eppendorf, Westbury, NY). Concentration and quality of RNA samples was determined on the Agilent bioanalyzer (Agilent Technologies, Palo Alto, CA). The integrity of RNA is assessed by looking at 18 & 28s rRNA peaks and though the RIN (RNA integrity number). RNA concentrations were measured using the Nano drop spectrophotometer (Wilmington, DE) and all samples used for the study had 260/280 ratios above 2.0 and 260/230 ratios above 1.7.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Ten micrograms of total RNA was reverse transcribed with Superscript II reverse transcriptase (Invitrogen, Carlsbad, CA) using T7-(dT) 24 primer (Geneset Oligos, La Jolla, CA, USA) containing T7 RNA polymerase promoter. After synthesis of the second cDNA strand, this product was used in an in vitro transcription reaction to generate biotinylated cRNA using a BioArray High Yield RNA Transcript Labeling Kit (Affymetrix, Santa Clara, CA). The biotinylated cRNA was cleaned with the RNAeasy Mini Kit (Qiagen, Valencia, CA).
| | Sample_hyb_protocol | Biotin-labeled cRNA was then fragmented at 94oC for 35 min with 5X fragmentation buffer (200 mM Tris-acetate, pH 8.1, 500 mM potassium acetate, 150 mM magnesium acetate) and then hybridized (10 ug) to Affymetrix (Santa Clara, CA) mouse 430_2 oligonucleotide probe arrays for 16 h at 45oC
| | Sample_scan_protocol | Hybridization fluid was removed and the arrays were washed and stained with streptavidin-phycoerythrin (SAPE), and the signal amplified by anti-streptavidin antibody using Affymetrix Fluidics Station 400. Probe set signals were measured using Agilent GeneArray Scanner (Affymetrix).
| | Sample_data_processing | Affymetrix Microarray Suite version 5.0
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jennifer,,Barb
| | Sample_contact_email | barbj@mail.nih.gov
| | Sample_contact_phone | 3014359232
| | Sample_contact_fax | 3014024544
| | Sample_contact_laboratory | MSCL
| | Sample_contact_department | DCB
| | Sample_contact_institute | NIH
| | Sample_contact_address | 12 South Drive Bldg 12A Room 2001
| | Sample_contact_city | Bethesda
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 20892
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM466nnn/GSM466543/suppl/GSM466543.CEL.gz
| | Sample_series_id | GSE18811
| | Sample_data_row_count | 54675
| | |
|
GSM466544 | GPL570 |
|
292FW33
|
native fetal RPE
|
cell type: native fetal RPE
gestational age: 17 weeks
|
Fetal eyes were obtained from Advanced Bioscience Resources (Alameda, CA) based on the availability of the aborted fetuses. RPE cells were collected and RNA was extracted (24-48 hours period following the abortion procedure).
|
| Sample_geo_accession | GSM466544
| | Sample_status | Public on Apr 15 2010
| | Sample_submission_date | Oct 29 2009
| | Sample_last_update_date | Apr 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Fetal RPE were cultured on Primaria® flasks for 6 weeks using MEM-α modified medium with additional supplements. Passages 1-2 were used for all studies. The confluent monolayers used in these experiments have the morphology, pigmentation, polarity, and physiology of native RPE.ARPE-19 spontaneously transformed cell line was cultured using MEM-α modified medium with additional supplements on flasks and inserts to match fetal RPE culturing conditions.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Fetal and adult RPE cells were collected, homogenized in TRIzol reagent (Invitrogen, Carlsbad, CA) and RNA was subsequently purified using an RNeasy Mini kit (Qiagen Inc, Valencia, CA). Double-stranded cDNA was synthesized from 6µg of total RNA using the SuperScript Choice system (Invitrogen, Carlsbad, CA) and the T7-Oligo (dT) promoter primer kit (Affymetrix, Santa Clara, CA). cDNA was purified using Phase Lock Gels (Eppendorf, Westbury, NY). Concentration and quality of RNA samples was determined on the Agilent bioanalyzer (Agilent Technologies, Palo Alto, CA). The integrity of RNA is assessed by looking at 18 & 28s rRNA peaks and though the RIN (RNA integrity number). RNA concentrations were measured using the Nano drop spectrophotometer (Wilmington, DE) and all samples used for the study had 260/280 ratios above 2.0 and 260/230 ratios above 1.7.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Ten micrograms of total RNA was reverse transcribed with Superscript II reverse transcriptase (Invitrogen, Carlsbad, CA) using T7-(dT) 24 primer (Geneset Oligos, La Jolla, CA, USA) containing T7 RNA polymerase promoter. After synthesis of the second cDNA strand, this product was used in an in vitro transcription reaction to generate biotinylated cRNA using a BioArray High Yield RNA Transcript Labeling Kit (Affymetrix, Santa Clara, CA). The biotinylated cRNA was cleaned with the RNAeasy Mini Kit (Qiagen, Valencia, CA).
| | Sample_hyb_protocol | Biotin-labeled cRNA was then fragmented at 94oC for 35 min with 5X fragmentation buffer (200 mM Tris-acetate, pH 8.1, 500 mM potassium acetate, 150 mM magnesium acetate) and then hybridized (10 ug) to Affymetrix (Santa Clara, CA) mouse 430_2 oligonucleotide probe arrays for 16 h at 45oC
| | Sample_scan_protocol | Hybridization fluid was removed and the arrays were washed and stained with streptavidin-phycoerythrin (SAPE), and the signal amplified by anti-streptavidin antibody using Affymetrix Fluidics Station 400. Probe set signals were measured using Agilent GeneArray Scanner (Affymetrix).
| | Sample_data_processing | Affymetrix Microarray Suite version 5.0
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jennifer,,Barb
| | Sample_contact_email | barbj@mail.nih.gov
| | Sample_contact_phone | 3014359232
| | Sample_contact_fax | 3014024544
| | Sample_contact_laboratory | MSCL
| | Sample_contact_department | DCB
| | Sample_contact_institute | NIH
| | Sample_contact_address | 12 South Drive Bldg 12A Room 2001
| | Sample_contact_city | Bethesda
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 20892
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM466nnn/GSM466544/suppl/GSM466544.CEL.gz
| | Sample_series_id | GSE18811
| | Sample_data_row_count | 54675
| | |
|
GSM466545 | GPL570 |
|
292FW34
|
native fetal RPE
|
cell type: native fetal RPE
gestational age: 17 weeks
|
Fetal eyes were obtained from Advanced Bioscience Resources (Alameda, CA) based on the availability of the aborted fetuses. RPE cells were collected and RNA was extracted (24-48 hours period following the abortion procedure).
|
| Sample_geo_accession | GSM466545
| | Sample_status | Public on Apr 15 2010
| | Sample_submission_date | Oct 29 2009
| | Sample_last_update_date | Apr 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Fetal RPE were cultured on Primaria® flasks for 6 weeks using MEM-α modified medium with additional supplements. Passages 1-2 were used for all studies. The confluent monolayers used in these experiments have the morphology, pigmentation, polarity, and physiology of native RPE.ARPE-19 spontaneously transformed cell line was cultured using MEM-α modified medium with additional supplements on flasks and inserts to match fetal RPE culturing conditions.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Fetal and adult RPE cells were collected, homogenized in TRIzol reagent (Invitrogen, Carlsbad, CA) and RNA was subsequently purified using an RNeasy Mini kit (Qiagen Inc, Valencia, CA). Double-stranded cDNA was synthesized from 6µg of total RNA using the SuperScript Choice system (Invitrogen, Carlsbad, CA) and the T7-Oligo (dT) promoter primer kit (Affymetrix, Santa Clara, CA). cDNA was purified using Phase Lock Gels (Eppendorf, Westbury, NY). Concentration and quality of RNA samples was determined on the Agilent bioanalyzer (Agilent Technologies, Palo Alto, CA). The integrity of RNA is assessed by looking at 18 & 28s rRNA peaks and though the RIN (RNA integrity number). RNA concentrations were measured using the Nano drop spectrophotometer (Wilmington, DE) and all samples used for the study had 260/280 ratios above 2.0 and 260/230 ratios above 1.7.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Ten micrograms of total RNA was reverse transcribed with Superscript II reverse transcriptase (Invitrogen, Carlsbad, CA) using T7-(dT) 24 primer (Geneset Oligos, La Jolla, CA, USA) containing T7 RNA polymerase promoter. After synthesis of the second cDNA strand, this product was used in an in vitro transcription reaction to generate biotinylated cRNA using a BioArray High Yield RNA Transcript Labeling Kit (Affymetrix, Santa Clara, CA). The biotinylated cRNA was cleaned with the RNAeasy Mini Kit (Qiagen, Valencia, CA).
| | Sample_hyb_protocol | Biotin-labeled cRNA was then fragmented at 94oC for 35 min with 5X fragmentation buffer (200 mM Tris-acetate, pH 8.1, 500 mM potassium acetate, 150 mM magnesium acetate) and then hybridized (10 ug) to Affymetrix (Santa Clara, CA) mouse 430_2 oligonucleotide probe arrays for 16 h at 45oC
| | Sample_scan_protocol | Hybridization fluid was removed and the arrays were washed and stained with streptavidin-phycoerythrin (SAPE), and the signal amplified by anti-streptavidin antibody using Affymetrix Fluidics Station 400. Probe set signals were measured using Agilent GeneArray Scanner (Affymetrix).
| | Sample_data_processing | Affymetrix Microarray Suite version 5.0
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jennifer,,Barb
| | Sample_contact_email | barbj@mail.nih.gov
| | Sample_contact_phone | 3014359232
| | Sample_contact_fax | 3014024544
| | Sample_contact_laboratory | MSCL
| | Sample_contact_department | DCB
| | Sample_contact_institute | NIH
| | Sample_contact_address | 12 South Drive Bldg 12A Room 2001
| | Sample_contact_city | Bethesda
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 20892
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM466nnn/GSM466545/suppl/GSM466545.CEL.gz
| | Sample_series_id | GSE18811
| | Sample_data_row_count | 54675
| | |
|
GSM466546 | GPL570 |
|
292FW35
|
adult native RPE
|
cell type: adult native RPE from 78 y.o. donor
|
Adult native RPE (anRPE) were collected from donors of Caucasian decent and total RNA was extracted right after.
|
| Sample_geo_accession | GSM466546
| | Sample_status | Public on Apr 15 2010
| | Sample_submission_date | Oct 29 2009
| | Sample_last_update_date | Apr 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Fetal RPE were cultured on Primaria® flasks for 6 weeks using MEM-α modified medium with additional supplements. Passages 1-2 were used for all studies. The confluent monolayers used in these experiments have the morphology, pigmentation, polarity, and physiology of native RPE.ARPE-19 spontaneously transformed cell line was cultured using MEM-α modified medium with additional supplements on flasks and inserts to match fetal RPE culturing conditions.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Fetal and adult RPE cells were collected, homogenized in TRIzol reagent (Invitrogen, Carlsbad, CA) and RNA was subsequently purified using an RNeasy Mini kit (Qiagen Inc, Valencia, CA). Double-stranded cDNA was synthesized from 6µg of total RNA using the SuperScript Choice system (Invitrogen, Carlsbad, CA) and the T7-Oligo (dT) promoter primer kit (Affymetrix, Santa Clara, CA). cDNA was purified using Phase Lock Gels (Eppendorf, Westbury, NY). Concentration and quality of RNA samples was determined on the Agilent bioanalyzer (Agilent Technologies, Palo Alto, CA). The integrity of RNA is assessed by looking at 18 & 28s rRNA peaks and though the RIN (RNA integrity number). RNA concentrations were measured using the Nano drop spectrophotometer (Wilmington, DE) and all samples used for the study had 260/280 ratios above 2.0 and 260/230 ratios above 1.7.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Ten micrograms of total RNA was reverse transcribed with Superscript II reverse transcriptase (Invitrogen, Carlsbad, CA) using T7-(dT) 24 primer (Geneset Oligos, La Jolla, CA, USA) containing T7 RNA polymerase promoter. After synthesis of the second cDNA strand, this product was used in an in vitro transcription reaction to generate biotinylated cRNA using a BioArray High Yield RNA Transcript Labeling Kit (Affymetrix, Santa Clara, CA). The biotinylated cRNA was cleaned with the RNAeasy Mini Kit (Qiagen, Valencia, CA).
| | Sample_hyb_protocol | Biotin-labeled cRNA was then fragmented at 94oC for 35 min with 5X fragmentation buffer (200 mM Tris-acetate, pH 8.1, 500 mM potassium acetate, 150 mM magnesium acetate) and then hybridized (10 ug) to Affymetrix (Santa Clara, CA) mouse 430_2 oligonucleotide probe arrays for 16 h at 45oC
| | Sample_scan_protocol | Hybridization fluid was removed and the arrays were washed and stained with streptavidin-phycoerythrin (SAPE), and the signal amplified by anti-streptavidin antibody using Affymetrix Fluidics Station 400. Probe set signals were measured using Agilent GeneArray Scanner (Affymetrix).
| | Sample_data_processing | Affymetrix Microarray Suite version 5.0
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jennifer,,Barb
| | Sample_contact_email | barbj@mail.nih.gov
| | Sample_contact_phone | 3014359232
| | Sample_contact_fax | 3014024544
| | Sample_contact_laboratory | MSCL
| | Sample_contact_department | DCB
| | Sample_contact_institute | NIH
| | Sample_contact_address | 12 South Drive Bldg 12A Room 2001
| | Sample_contact_city | Bethesda
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 20892
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM466nnn/GSM466546/suppl/GSM466546.CEL.gz
| | Sample_series_id | GSE18811
| | Sample_data_row_count | 54675
| | |
|
GSM466547 | GPL570 |
|
292FW4
|
fetal RPE cultures
|
cell type: fetal RPE
gestational age: 16 weeks
|
Fetal RPE were cultured on Primaria® flasks and assages 1-2 were used for all studies. The confluent monolayers used in these experiments have the morphology, pigmentation, polarity, and physiology of native RPE.
|
| Sample_geo_accession | GSM466547
| | Sample_status | Public on Apr 15 2010
| | Sample_submission_date | Oct 29 2009
| | Sample_last_update_date | Apr 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Fetal RPE were cultured on Primaria® flasks for 6 weeks using MEM-α modified medium with additional supplements. Passages 1-2 were used for all studies. The confluent monolayers used in these experiments have the morphology, pigmentation, polarity, and physiology of native RPE.ARPE-19 spontaneously transformed cell line was cultured using MEM-α modified medium with additional supplements on flasks and inserts to match fetal RPE culturing conditions.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Fetal and adult RPE cells were collected, homogenized in TRIzol reagent (Invitrogen, Carlsbad, CA) and RNA was subsequently purified using an RNeasy Mini kit (Qiagen Inc, Valencia, CA). Double-stranded cDNA was synthesized from 6µg of total RNA using the SuperScript Choice system (Invitrogen, Carlsbad, CA) and the T7-Oligo (dT) promoter primer kit (Affymetrix, Santa Clara, CA). cDNA was purified using Phase Lock Gels (Eppendorf, Westbury, NY). Concentration and quality of RNA samples was determined on the Agilent bioanalyzer (Agilent Technologies, Palo Alto, CA). The integrity of RNA is assessed by looking at 18 & 28s rRNA peaks and though the RIN (RNA integrity number). RNA concentrations were measured using the Nano drop spectrophotometer (Wilmington, DE) and all samples used for the study had 260/280 ratios above 2.0 and 260/230 ratios above 1.7.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Ten micrograms of total RNA was reverse transcribed with Superscript II reverse transcriptase (Invitrogen, Carlsbad, CA) using T7-(dT) 24 primer (Geneset Oligos, La Jolla, CA, USA) containing T7 RNA polymerase promoter. After synthesis of the second cDNA strand, this product was used in an in vitro transcription reaction to generate biotinylated cRNA using a BioArray High Yield RNA Transcript Labeling Kit (Affymetrix, Santa Clara, CA). The biotinylated cRNA was cleaned with the RNAeasy Mini Kit (Qiagen, Valencia, CA).
| | Sample_hyb_protocol | Biotin-labeled cRNA was then fragmented at 94oC for 35 min with 5X fragmentation buffer (200 mM Tris-acetate, pH 8.1, 500 mM potassium acetate, 150 mM magnesium acetate) and then hybridized (10 ug) to Affymetrix (Santa Clara, CA) mouse 430_2 oligonucleotide probe arrays for 16 h at 45oC
| | Sample_scan_protocol | Hybridization fluid was removed and the arrays were washed and stained with streptavidin-phycoerythrin (SAPE), and the signal amplified by anti-streptavidin antibody using Affymetrix Fluidics Station 400. Probe set signals were measured using Agilent GeneArray Scanner (Affymetrix).
| | Sample_data_processing | Affymetrix Microarray Suite version 5.0
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jennifer,,Barb
| | Sample_contact_email | barbj@mail.nih.gov
| | Sample_contact_phone | 3014359232
| | Sample_contact_fax | 3014024544
| | Sample_contact_laboratory | MSCL
| | Sample_contact_department | DCB
| | Sample_contact_institute | NIH
| | Sample_contact_address | 12 South Drive Bldg 12A Room 2001
| | Sample_contact_city | Bethesda
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 20892
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM466nnn/GSM466547/suppl/GSM466547.CEL.gz
| | Sample_series_id | GSE18811
| | Sample_data_row_count | 54675
| | |
|
GSM466548 | GPL570 |
|
292FW7
|
fetal RPE cultures
|
cell type: fetal RPE
gestational age: 16 weeks
|
Fetal RPE were cultured on Primaria® flasks and assages 1-2 were used for all studies. The confluent monolayers used in these experiments have the morphology, pigmentation, polarity, and physiology of native RPE.
|
| Sample_geo_accession | GSM466548
| | Sample_status | Public on Apr 15 2010
| | Sample_submission_date | Oct 29 2009
| | Sample_last_update_date | Apr 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Fetal RPE were cultured on Primaria® flasks for 6 weeks using MEM-α modified medium with additional supplements. Passages 1-2 were used for all studies. The confluent monolayers used in these experiments have the morphology, pigmentation, polarity, and physiology of native RPE.ARPE-19 spontaneously transformed cell line was cultured using MEM-α modified medium with additional supplements on flasks and inserts to match fetal RPE culturing conditions.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Fetal and adult RPE cells were collected, homogenized in TRIzol reagent (Invitrogen, Carlsbad, CA) and RNA was subsequently purified using an RNeasy Mini kit (Qiagen Inc, Valencia, CA). Double-stranded cDNA was synthesized from 6µg of total RNA using the SuperScript Choice system (Invitrogen, Carlsbad, CA) and the T7-Oligo (dT) promoter primer kit (Affymetrix, Santa Clara, CA). cDNA was purified using Phase Lock Gels (Eppendorf, Westbury, NY). Concentration and quality of RNA samples was determined on the Agilent bioanalyzer (Agilent Technologies, Palo Alto, CA). The integrity of RNA is assessed by looking at 18 & 28s rRNA peaks and though the RIN (RNA integrity number). RNA concentrations were measured using the Nano drop spectrophotometer (Wilmington, DE) and all samples used for the study had 260/280 ratios above 2.0 and 260/230 ratios above 1.7.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Ten micrograms of total RNA was reverse transcribed with Superscript II reverse transcriptase (Invitrogen, Carlsbad, CA) using T7-(dT) 24 primer (Geneset Oligos, La Jolla, CA, USA) containing T7 RNA polymerase promoter. After synthesis of the second cDNA strand, this product was used in an in vitro transcription reaction to generate biotinylated cRNA using a BioArray High Yield RNA Transcript Labeling Kit (Affymetrix, Santa Clara, CA). The biotinylated cRNA was cleaned with the RNAeasy Mini Kit (Qiagen, Valencia, CA).
| | Sample_hyb_protocol | Biotin-labeled cRNA was then fragmented at 94oC for 35 min with 5X fragmentation buffer (200 mM Tris-acetate, pH 8.1, 500 mM potassium acetate, 150 mM magnesium acetate) and then hybridized (10 ug) to Affymetrix (Santa Clara, CA) mouse 430_2 oligonucleotide probe arrays for 16 h at 45oC
| | Sample_scan_protocol | Hybridization fluid was removed and the arrays were washed and stained with streptavidin-phycoerythrin (SAPE), and the signal amplified by anti-streptavidin antibody using Affymetrix Fluidics Station 400. Probe set signals were measured using Agilent GeneArray Scanner (Affymetrix).
| | Sample_data_processing | Affymetrix Microarray Suite version 5.0
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jennifer,,Barb
| | Sample_contact_email | barbj@mail.nih.gov
| | Sample_contact_phone | 3014359232
| | Sample_contact_fax | 3014024544
| | Sample_contact_laboratory | MSCL
| | Sample_contact_department | DCB
| | Sample_contact_institute | NIH
| | Sample_contact_address | 12 South Drive Bldg 12A Room 2001
| | Sample_contact_city | Bethesda
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 20892
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM466nnn/GSM466548/suppl/GSM466548.CEL.gz
| | Sample_series_id | GSE18811
| | Sample_data_row_count | 54675
| | |
|
GSM466549 | GPL570 |
|
292FW8
|
fetal RPE cultures
|
cell type: fetal RPE
gestational age: 16 weeks
|
Fetal RPE were cultured on Primaria® flasks and assages 1-2 were used for all studies. The confluent monolayers used in these experiments have the morphology, pigmentation, polarity, and physiology of native RPE.
|
| Sample_geo_accession | GSM466549
| | Sample_status | Public on Apr 15 2010
| | Sample_submission_date | Oct 29 2009
| | Sample_last_update_date | Apr 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Fetal RPE were cultured on Primaria® flasks for 6 weeks using MEM-α modified medium with additional supplements. Passages 1-2 were used for all studies. The confluent monolayers used in these experiments have the morphology, pigmentation, polarity, and physiology of native RPE.ARPE-19 spontaneously transformed cell line was cultured using MEM-α modified medium with additional supplements on flasks and inserts to match fetal RPE culturing conditions.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Fetal and adult RPE cells were collected, homogenized in TRIzol reagent (Invitrogen, Carlsbad, CA) and RNA was subsequently purified using an RNeasy Mini kit (Qiagen Inc, Valencia, CA). Double-stranded cDNA was synthesized from 6µg of total RNA using the SuperScript Choice system (Invitrogen, Carlsbad, CA) and the T7-Oligo (dT) promoter primer kit (Affymetrix, Santa Clara, CA). cDNA was purified using Phase Lock Gels (Eppendorf, Westbury, NY). Concentration and quality of RNA samples was determined on the Agilent bioanalyzer (Agilent Technologies, Palo Alto, CA). The integrity of RNA is assessed by looking at 18 & 28s rRNA peaks and though the RIN (RNA integrity number). RNA concentrations were measured using the Nano drop spectrophotometer (Wilmington, DE) and all samples used for the study had 260/280 ratios above 2.0 and 260/230 ratios above 1.7.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Ten micrograms of total RNA was reverse transcribed with Superscript II reverse transcriptase (Invitrogen, Carlsbad, CA) using T7-(dT) 24 primer (Geneset Oligos, La Jolla, CA, USA) containing T7 RNA polymerase promoter. After synthesis of the second cDNA strand, this product was used in an in vitro transcription reaction to generate biotinylated cRNA using a BioArray High Yield RNA Transcript Labeling Kit (Affymetrix, Santa Clara, CA). The biotinylated cRNA was cleaned with the RNAeasy Mini Kit (Qiagen, Valencia, CA).
| | Sample_hyb_protocol | Biotin-labeled cRNA was then fragmented at 94oC for 35 min with 5X fragmentation buffer (200 mM Tris-acetate, pH 8.1, 500 mM potassium acetate, 150 mM magnesium acetate) and then hybridized (10 ug) to Affymetrix (Santa Clara, CA) mouse 430_2 oligonucleotide probe arrays for 16 h at 45oC
| | Sample_scan_protocol | Hybridization fluid was removed and the arrays were washed and stained with streptavidin-phycoerythrin (SAPE), and the signal amplified by anti-streptavidin antibody using Affymetrix Fluidics Station 400. Probe set signals were measured using Agilent GeneArray Scanner (Affymetrix).
| | Sample_data_processing | Affymetrix Microarray Suite version 5.0
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jennifer,,Barb
| | Sample_contact_email | barbj@mail.nih.gov
| | Sample_contact_phone | 3014359232
| | Sample_contact_fax | 3014024544
| | Sample_contact_laboratory | MSCL
| | Sample_contact_department | DCB
| | Sample_contact_institute | NIH
| | Sample_contact_address | 12 South Drive Bldg 12A Room 2001
| | Sample_contact_city | Bethesda
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 20892
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM466nnn/GSM466549/suppl/GSM466549.CEL.gz
| | Sample_series_id | GSE18811
| | Sample_data_row_count | 54675
| | |
|
GSM466550 | GPL570 |
|
292FW9
|
fetal RPE cultures
|
cell type: fetal RPE
gestational age: 16 weeks
|
Fetal RPE were cultured on Primaria® flasks and assages 1-2 were used for all studies. The confluent monolayers used in these experiments have the morphology, pigmentation, polarity, and physiology of native RPE.
|
| Sample_geo_accession | GSM466550
| | Sample_status | Public on Apr 15 2010
| | Sample_submission_date | Oct 29 2009
| | Sample_last_update_date | Apr 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Fetal RPE were cultured on Primaria® flasks for 6 weeks using MEM-α modified medium with additional supplements. Passages 1-2 were used for all studies. The confluent monolayers used in these experiments have the morphology, pigmentation, polarity, and physiology of native RPE.ARPE-19 spontaneously transformed cell line was cultured using MEM-α modified medium with additional supplements on flasks and inserts to match fetal RPE culturing conditions.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Fetal and adult RPE cells were collected, homogenized in TRIzol reagent (Invitrogen, Carlsbad, CA) and RNA was subsequently purified using an RNeasy Mini kit (Qiagen Inc, Valencia, CA). Double-stranded cDNA was synthesized from 6µg of total RNA using the SuperScript Choice system (Invitrogen, Carlsbad, CA) and the T7-Oligo (dT) promoter primer kit (Affymetrix, Santa Clara, CA). cDNA was purified using Phase Lock Gels (Eppendorf, Westbury, NY). Concentration and quality of RNA samples was determined on the Agilent bioanalyzer (Agilent Technologies, Palo Alto, CA). The integrity of RNA is assessed by looking at 18 & 28s rRNA peaks and though the RIN (RNA integrity number). RNA concentrations were measured using the Nano drop spectrophotometer (Wilmington, DE) and all samples used for the study had 260/280 ratios above 2.0 and 260/230 ratios above 1.7.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Ten micrograms of total RNA was reverse transcribed with Superscript II reverse transcriptase (Invitrogen, Carlsbad, CA) using T7-(dT) 24 primer (Geneset Oligos, La Jolla, CA, USA) containing T7 RNA polymerase promoter. After synthesis of the second cDNA strand, this product was used in an in vitro transcription reaction to generate biotinylated cRNA using a BioArray High Yield RNA Transcript Labeling Kit (Affymetrix, Santa Clara, CA). The biotinylated cRNA was cleaned with the RNAeasy Mini Kit (Qiagen, Valencia, CA).
| | Sample_hyb_protocol | Biotin-labeled cRNA was then fragmented at 94oC for 35 min with 5X fragmentation buffer (200 mM Tris-acetate, pH 8.1, 500 mM potassium acetate, 150 mM magnesium acetate) and then hybridized (10 ug) to Affymetrix (Santa Clara, CA) mouse 430_2 oligonucleotide probe arrays for 16 h at 45oC
| | Sample_scan_protocol | Hybridization fluid was removed and the arrays were washed and stained with streptavidin-phycoerythrin (SAPE), and the signal amplified by anti-streptavidin antibody using Affymetrix Fluidics Station 400. Probe set signals were measured using Agilent GeneArray Scanner (Affymetrix).
| | Sample_data_processing | Affymetrix Microarray Suite version 5.0
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jennifer,,Barb
| | Sample_contact_email | barbj@mail.nih.gov
| | Sample_contact_phone | 3014359232
| | Sample_contact_fax | 3014024544
| | Sample_contact_laboratory | MSCL
| | Sample_contact_department | DCB
| | Sample_contact_institute | NIH
| | Sample_contact_address | 12 South Drive Bldg 12A Room 2001
| | Sample_contact_city | Bethesda
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 20892
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM466nnn/GSM466550/suppl/GSM466550.CEL.gz
| | Sample_series_id | GSE18811
| | Sample_data_row_count | 54675
| | |
|
| |
| |
Make groups for comparisons |
(2 groups will be compared at a time) |
|
| Select GSMs and click on "Add groups" |
Enter the group name here: |
|
|
|
