Search results for the GEO ID: GSE43257  |
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GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM1059537 | GPL570 |
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RPE derived from 253G1 iPSC
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RPE-253G1
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cell type: retinal pigment epithelium (RPE)
tissue: RPE derived from 253G1 iPSC
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Gene expression data from cells
human datasheet
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| Sample_geo_accession | GSM1059537
| | Sample_status | Public on Jan 03 2013
| | Sample_submission_date | Jan 03 2013
| | Sample_last_update_date | Jan 03 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Total RNA from primary RPE and 253G1iPS derived-RPE was isolated with RNAeasy Pus Mini Kit (Quiagen ) in accordance with manufacture’s instruction
| | Sample_growth_protocol_ch1 | (RPE-253G1) Human primary retinal pigment epithelium (RPE, Lonza) was maintained in Retinal Pigment Epithelial Cell Basal Medium (Lonza Biologics, Basel, Switzerland) containing supplements (L-glutamine, GA-1000 and bFGF; Lonza). Human iPS cell (iPSC) line 253G1 [1] [Riken Bio Resource Center (Tsukuba, Japan)] was maintained on feeder cell SNL [2] in human ES cell culture medium and 5 ng/ml bFGF (Peprotech). iPSC was cultured in ReproFF2 (ReproCELL) supplemented with 5 ng/ml bFGF medium. iPSC-derived RPE [3,4] was maintained in RPE maintenance medium [DMEM:F12 (7:3) (Sigma-Aldrich) supplemented with B-27 supplement (Invitrogen), 2 mM L-glutamine (Invitrogen), 0.5 mM SB431542 (Sigma-Aldrich) and 10 ng/ml bFGF (WAKO)] .
| | Sample_growth_protocol_ch1 | In an attempt to establish a robust differentiation protocol for pluripotent stem cells into Retinal Pigment Epithelium (RPE), the differentiation protocol . The detailed method for differentiation to RPE from iPSC was previously described [3,4]. Briefly, iPSC clone was seeded on gelatin-coated plate and cultured in human ES cell culture medium supplemented with 10 μM Y-27632 (TOCRIS Bioscience), 5 μM SB431542 (Sigma-Aldrich) and 3 μM CKI-7 (Sigma-Aldrich). After 24 hours incubation, cells were incubated in 20% KSR human differentiation medium [GMEM (GIBCO), 0.1 mM non-essential amino acids (GIBCO), 1 mM sodium pyruvate (Sigma-Aldrich), and 0.1 mM 2-mercaptoethanol (WAKO) containing of 20% KSR (Invitrogen)]. After 4 days incubation, cells were replaced into 15% KSR human differentiation medium supplemented with Y-275632, SB431542 and CKI-7. After 10 days incubation, cells were cultured with 10% KSR human differentiation medium supplemented with Y-275632, SB431542 and CKI-7. After 18 days incubation, culture medium was replaced with 10% KSR human differentiation medium without supplementation. After 20 days incubation cells were dissociated with the CTK solution and incubated on low cell binding plate (Corning, Corning, NY) in RPE maintenance medium (DMEM:F12 [7:3] supplemented with B-27 supplement [Invitrogen] and 2 mM L-glutamine [Invitrogen]). After 10 days floating incubation, the resulting RPE cells were picked up and seeded on CELLstart (Invitorgen)-coated dishes in RPE growing medium [F-10 supplemented with 10% FBS]. When they reach confluence, medium was replaced to RPE maintenance medium supplemented with 0.5 uM SB431542 and 10 ng/ml bFGF. A cobblestone-like block monolayer cells with black color were RPE and harvested RPE with 0.25 % Trypsin-EDTA for further assessment
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with the RNeasy Mini kit, according to manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared using GeneChip 3’ IVT Express Kit according to manufacturer’s instructions from 250 ng total RNA.
| | Sample_hyb_protocol | Following fragmentation, cRNA were hybridized for 16 hr at 45oC, 60 rpm on Gene Chip Human Genome U133 Plus2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using GeneChip Scanner 3000 7G.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Shin,,Kawamata
| | Sample_contact_department | The Basic Reserch Group for Regenerative Medicine
| | Sample_contact_institute | Foundation for Biomedical and Innovation
| | Sample_contact_address | TRI#308,1-5-4,Minatojima-minamimachi,Chuo-ku
| | Sample_contact_city | Kobe
| | Sample_contact_state | Hyogo
| | Sample_contact_zip/postal_code | 650-0047
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1059nnn/GSM1059537/suppl/GSM1059537_Kawamata_EA1027_02.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1059nnn/GSM1059537/suppl/GSM1059537_Kawamata_EA1027_02_scale.CHP.gz
| | Sample_series_id | GSE43257
| | Sample_data_row_count | 54675
| | |
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GSM1059538 | GPL570 |
|
Primary RPE
|
Primary RPE
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cell type: retinal pigment epithelium (RPE)
tissue: Primary RPE
|
Gene expression data from cells
human datasheet
|
| Sample_geo_accession | GSM1059538
| | Sample_status | Public on Jan 03 2013
| | Sample_submission_date | Jan 03 2013
| | Sample_last_update_date | Jan 03 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Total RNA from primary RPE and 253G1iPS derived-RPE was isolated with RNAeasy Pus Mini Kit (Quiagen ) in accordance with manufacture’s instruction
| | Sample_growth_protocol_ch1 | (RPE-253G1) Human primary retinal pigment epithelium (RPE, Lonza) was maintained in Retinal Pigment Epithelial Cell Basal Medium (Lonza Biologics, Basel, Switzerland) containing supplements (L-glutamine, GA-1000 and bFGF; Lonza). Human iPS cell (iPSC) line 253G1 [1] [Riken Bio Resource Center (Tsukuba, Japan)] was maintained on feeder cell SNL [2] in human ES cell culture medium and 5 ng/ml bFGF (Peprotech). iPSC was cultured in ReproFF2 (ReproCELL) supplemented with 5 ng/ml bFGF medium. iPSC-derived RPE [3,4] was maintained in RPE maintenance medium [DMEM:F12 (7:3) (Sigma-Aldrich) supplemented with B-27 supplement (Invitrogen), 2 mM L-glutamine (Invitrogen), 0.5 mM SB431542 (Sigma-Aldrich) and 10 ng/ml bFGF (WAKO)] .
| | Sample_growth_protocol_ch1 | In an attempt to establish a robust differentiation protocol for pluripotent stem cells into Retinal Pigment Epithelium (RPE), the differentiation protocol . The detailed method for differentiation to RPE from iPSC was previously described [3,4]. Briefly, iPSC clone was seeded on gelatin-coated plate and cultured in human ES cell culture medium supplemented with 10 μM Y-27632 (TOCRIS Bioscience), 5 μM SB431542 (Sigma-Aldrich) and 3 μM CKI-7 (Sigma-Aldrich). After 24 hours incubation, cells were incubated in 20% KSR human differentiation medium [GMEM (GIBCO), 0.1 mM non-essential amino acids (GIBCO), 1 mM sodium pyruvate (Sigma-Aldrich), and 0.1 mM 2-mercaptoethanol (WAKO) containing of 20% KSR (Invitrogen)]. After 4 days incubation, cells were replaced into 15% KSR human differentiation medium supplemented with Y-275632, SB431542 and CKI-7. After 10 days incubation, cells were cultured with 10% KSR human differentiation medium supplemented with Y-275632, SB431542 and CKI-7. After 18 days incubation, culture medium was replaced with 10% KSR human differentiation medium without supplementation. After 20 days incubation cells were dissociated with the CTK solution and incubated on low cell binding plate (Corning, Corning, NY) in RPE maintenance medium (DMEM:F12 [7:3] supplemented with B-27 supplement [Invitrogen] and 2 mM L-glutamine [Invitrogen]). After 10 days floating incubation, the resulting RPE cells were picked up and seeded on CELLstart (Invitorgen)-coated dishes in RPE growing medium [F-10 supplemented with 10% FBS]. When they reach confluence, medium was replaced to RPE maintenance medium supplemented with 0.5 uM SB431542 and 10 ng/ml bFGF. A cobblestone-like block monolayer cells with black color were RPE and harvested RPE with 0.25 % Trypsin-EDTA for further assessment
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with the RNeasy Mini kit, according to manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared using GeneChip 3’ IVT Express Kit according to manufacturer’s instructions from 250 ng total RNA.
| | Sample_hyb_protocol | Following fragmentation, cRNA were hybridized for 16 hr at 45oC, 60 rpm on Gene Chip Human Genome U133 Plus2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using GeneChip Scanner 3000 7G.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Shin,,Kawamata
| | Sample_contact_department | The Basic Reserch Group for Regenerative Medicine
| | Sample_contact_institute | Foundation for Biomedical and Innovation
| | Sample_contact_address | TRI#308,1-5-4,Minatojima-minamimachi,Chuo-ku
| | Sample_contact_city | Kobe
| | Sample_contact_state | Hyogo
| | Sample_contact_zip/postal_code | 650-0047
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1059nnn/GSM1059538/suppl/GSM1059538_Kawamata_EA0976_03.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1059nnn/GSM1059538/suppl/GSM1059538_Kawamata_EA0976_03_scale.CHP.gz
| | Sample_series_id | GSE43257
| | Sample_data_row_count | 54675
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