Search results for the GEO ID: GSE16910 |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM423940 | GPL570 |
|
Human embryonic stem cells, hES-T3, grown on MEF feeder, biological rep1
|
hES-T3 cells grown on MEF feeder
|
growth conditions: hES-T3 cells grown on MEF feeder
gender: female
cell line: hES-T3
|
The mRNA profilings of T3MF, T3CM and T3BA cells were analyzed using Affymetrix Human Genome U133 plus 2.0 GeneChip according to the Manufacturer¡¦s protocols (Santa Clara, CA, USA, http://www.affymetrix.com).
|
Sample_geo_accession | GSM423940
| Sample_status | Public on Sep 10 2010
| Sample_submission_date | Jun 30 2009
| Sample_last_update_date | Sep 10 2010
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Non
| Sample_growth_protocol_ch1 | Human embryonic stem cell line hES-T3, which is one of the five hES cell lines derived with institutional review board approval from preimplantation embryos donated at IVF clinics in Taiwan, exhibits normal female karyotype (46, XX), and it has been continuously cultured on mitomycin C (10 ug/ml) mitotically inactivated MEF feeder in hES medium under 5% CO2 at 37oC and underwent freezing/thawing processes. The hES culture medium consisted of DMEM/F12 (1:1, GIBCO) supplemented with 20% KSR (Invitrogen), 1% non-essential amino acids, 1 mM L-glutamine, 0.1 mM £]-mercaptoethanol, and 4 ng/ml human basic fibroblast growth factor (bFGF; Life Technologies). Routine passages of hES-T3 cells every 5-7 days were done with collagenase ( type IV, 1 mg/ml, Invitrogen) treatment and mechanical scrape. The hES-T3 cells grown on MEF feeder were designated as T3MF.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions. Total RNAs extracted using TRIZOL reagent were quantified spectrophotometrically. The cDNA synthesis was carried out by using SUPERSCRIPTTM one-step RT-PCR kit (Invitrogen). For the reverse transcription step, the whole 5 ul of the resuspended RNAs were incubated for 60 min at 42oC, then 15 min at 72oC in 50 ul of reaction mixture containing 25 ul of 2x Reaction Mix (Invitrogen) and 1 ul of RT/PLANTINUM Taq Mix (Invitrogen). 28.5 ul of the cDNAs present in the 50 ul RT reaction mixture purified by Microarray Target Purification Kit (Roche Applied Science, Indianapolis, ID, USA, http://www.roche-applies-science.com) were used as templates to amplify cDNA by Microarray Target Amplification Kit. The amplified cDNAs were purified by Microarray Target Purification Kit, and complementary RNAs (cRNAs) were synthesized from 200 ng cDNA with Microarray RNA Target Synthesis Kit (Roche Applied Science).
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 micrograms purified cRNA (Expression Analysis Technical Manual, 2004, Affymetrix, http://www.affymetrix.com).
| Sample_hyb_protocol | Following fragmentation, 10 micrograms of cRNA were hybridized for 16 hr at 45oC on Affymetrix Human Genome U133 plus 2.0 GeneChip. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| Sample_scan_protocol | GeneChips from the hybridization experiments were read by the Affymetrix GeneChip scanner 3000.
| Sample_data_processing | The data were processed by GeneSpring GX software version 7.3.1 GC-RMA preprocessor to use on the CEL files
| Sample_platform_id | GPL570
| Sample_contact_name | Sung-Liang,,Yu
| Sample_contact_email | slyu@ntu.edu.tw
| Sample_contact_phone | 886-2-23958341
| Sample_contact_fax | 886-2-23958341
| Sample_contact_laboratory | Microarray Core Facility
| Sample_contact_department | Clinical Laboratory Sciences and Medical Biotechnology
| Sample_contact_institute | National Taiwan University
| Sample_contact_address | Jen Ai Road Section1
| Sample_contact_city | Taipei
| Sample_contact_zip/postal_code | 100
| Sample_contact_country | Taiwan
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM423nnn/GSM423940/suppl/GSM423940_T3MF_1.CEL.gz
| Sample_series_id | GSE16910
| Sample_data_row_count | 54675
| |
|
GSM423941 | GPL570 |
|
Human embryonic stem cells, hES-T3, grown on MEF feeder, biological rep2
|
hES-T3 cells grown on MEF feeder
|
growth conditions: hES-T3 cells grown on MEF feeder
gender: female
cell line: hES-T3
|
The mRNA profilings of T3MF, T3CM and T3BA cells were analyzed using Affymetrix Human Genome U133 plus 2.0 GeneChip according to the Manufacturer¡¦s protocols (Santa Clara, CA, USA, http://www.affymetrix.com).
|
Sample_geo_accession | GSM423941
| Sample_status | Public on Sep 10 2010
| Sample_submission_date | Jun 30 2009
| Sample_last_update_date | Sep 10 2010
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Non
| Sample_growth_protocol_ch1 | Human embryonic stem cell line hES-T3, which is one of the five hES cell lines derived with institutional review board approval from preimplantation embryos donated at IVF clinics in Taiwan, exhibits normal female karyotype (46, XX), and it has been continuously cultured on mitomycin C (10 ug/ml) mitotically inactivated MEF feeder in hES medium under 5% CO2 at 37oC and underwent freezing/thawing processes. The hES culture medium consisted of DMEM/F12 (1:1, GIBCO) supplemented with 20% KSR (Invitrogen), 1% non-essential amino acids, 1 mM L-glutamine, 0.1 mM £]-mercaptoethanol, and 4 ng/ml human basic fibroblast growth factor (bFGF; Life Technologies). Routine passages of hES-T3 cells every 5-7 days were done with collagenase ( type IV, 1 mg/ml, Invitrogen) treatment and mechanical scrape. The hES-T3 cells grown on MEF feeder were designated as T3MF.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions. Total RNAs extracted using TRIZOL reagent were quantified spectrophotometrically. The cDNA synthesis was carried out by using SUPERSCRIPTTM one-step RT-PCR kit (Invitrogen). For the reverse transcription step, the whole 5 ul of the resuspended RNAs were incubated for 60 min at 42oC, then 15 min at 72oC in 50 ul of reaction mixture containing 25 ul of 2x Reaction Mix (Invitrogen) and 1 ul of RT/PLANTINUM Taq Mix (Invitrogen). 28.5 ul of the cDNAs present in the 50 ul RT reaction mixture purified by Microarray Target Purification Kit (Roche Applied Science, Indianapolis, ID, USA, http://www.roche-applies-science.com) were used as templates to amplify cDNA by Microarray Target Amplification Kit. The amplified cDNAs were purified by Microarray Target Purification Kit, and complementary RNAs (cRNAs) were synthesized from 200 ng cDNA with Microarray RNA Target Synthesis Kit (Roche Applied Science).
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 micrograms purified cRNA (Expression Analysis Technical Manual, 2004, Affymetrix, http://www.affymetrix.com).
| Sample_hyb_protocol | Following fragmentation, 10 micrograms of cRNA were hybridized for 16 hr at 45oC on Affymetrix Human Genome U133 plus 2.0 GeneChip. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| Sample_scan_protocol | GeneChips from the hybridization experiments were read by the Affymetrix GeneChip scanner 3000.
| Sample_data_processing | The data were processed by GeneSpring GX software version 7.3.1 GC-RMA preprocessor to use on the CEL files
| Sample_platform_id | GPL570
| Sample_contact_name | Sung-Liang,,Yu
| Sample_contact_email | slyu@ntu.edu.tw
| Sample_contact_phone | 886-2-23958341
| Sample_contact_fax | 886-2-23958341
| Sample_contact_laboratory | Microarray Core Facility
| Sample_contact_department | Clinical Laboratory Sciences and Medical Biotechnology
| Sample_contact_institute | National Taiwan University
| Sample_contact_address | Jen Ai Road Section1
| Sample_contact_city | Taipei
| Sample_contact_zip/postal_code | 100
| Sample_contact_country | Taiwan
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM423nnn/GSM423941/suppl/GSM423941_T3MF_2.CEL.gz
| Sample_series_id | GSE16910
| Sample_data_row_count | 54675
| |
|
GSM423942 | GPL570 |
|
Human embryonic stem cells, hES-T3, grown on feeder-free Matrigel in MEF-conditioned medium, biological rep1
|
hES-T3 cells grown on feeder-free Matrigel in MEF-conditioned medium
|
growth conditions: hES-T3 cells grown on feeder-free Matrigel in MEF-conditioned medium
gender: female
cell line: hES-T3
|
The mRNA profilings of T3MF, T3CM and T3BA cells were analyzed using Affymetrix Human Genome U133 plus 2.0 GeneChip according to the Manufacturer¡¦s protocols (Santa Clara, CA, USA, http://www.affymetrix.com).
|
Sample_geo_accession | GSM423942
| Sample_status | Public on Sep 10 2010
| Sample_submission_date | Jun 30 2009
| Sample_last_update_date | Sep 10 2010
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Non
| Sample_growth_protocol_ch1 | The MEF cells were cultured in MEF medium overnight, and the mitotically inactivated MEF were maintained in hES medium containing 4 ng/ml bFGF. After 24 h, the MEF-conditioned medium was collected and filtered through 0.2 um membrane (PN4612, Pall Life Sciences) as previously described [Xu et al., 2001]. The culture dish was coated with Matrigel diluted with DMEM/F12 (1:30) overnight at 4oC. The BD MartigelTM (Matrix 354234) is the manufacturer¡¦s Trademark for extracellular matrix extracted from the Engelbreth-Holm-Swarm tumor. The hES-T3 cells grown on feeder-free Martigel-coated dish in MEF-conditioned medium (with additional 4 ng/ml bFGF) were designated as T3CM.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions. Total RNAs extracted using TRIZOL reagent were quantified spectrophotometrically. The cDNA synthesis was carried out by using SUPERSCRIPTTM one-step RT-PCR kit (Invitrogen). For the reverse transcription step, the whole 5 ul of the resuspended RNAs were incubated for 60 min at 42oC, then 15 min at 72oC in 50 ul of reaction mixture containing 25 ul of 2x Reaction Mix (Invitrogen) and 1 ul of RT/PLANTINUM Taq Mix (Invitrogen). 28.5 ul of the cDNAs present in the 50 ul RT reaction mixture purified by Microarray Target Purification Kit (Roche Applied Science, Indianapolis, ID, USA, http://www.roche-applies-science.com) were used as templates to amplify cDNA by Microarray Target Amplification Kit. The amplified cDNAs were purified by Microarray Target Purification Kit, and complementary RNAs (cRNAs) were synthesized from 200 ng cDNA with Microarray RNA Target Synthesis Kit (Roche Applied Science).
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 micrograms purified cRNA (Expression Analysis Technical Manual, 2004, Affymetrix, http://www.affymetrix.com).
| Sample_hyb_protocol | Following fragmentation, 10 micrograms of cRNA were hybridized for 16 hr at 45oC on Affymetrix Human Genome U133 plus 2.0 GeneChip. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| Sample_scan_protocol | GeneChips from the hybridization experiments were read by the Affymetrix GeneChip scanner 3000.
| Sample_data_processing | The data were processed by GeneSpring GX software version 7.3.1 GC-RMA preprocessor to use on the CEL files
| Sample_platform_id | GPL570
| Sample_contact_name | Sung-Liang,,Yu
| Sample_contact_email | slyu@ntu.edu.tw
| Sample_contact_phone | 886-2-23958341
| Sample_contact_fax | 886-2-23958341
| Sample_contact_laboratory | Microarray Core Facility
| Sample_contact_department | Clinical Laboratory Sciences and Medical Biotechnology
| Sample_contact_institute | National Taiwan University
| Sample_contact_address | Jen Ai Road Section1
| Sample_contact_city | Taipei
| Sample_contact_zip/postal_code | 100
| Sample_contact_country | Taiwan
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM423nnn/GSM423942/suppl/GSM423942_T3CM_1.CEL.gz
| Sample_series_id | GSE16910
| Sample_data_row_count | 54675
| |
|
GSM423943 | GPL570 |
|
Human embryonic stem cells, hES-T3, grown on feeder-free Matrigel in MEF-conditioned medium, biological rep2
|
hES-T3 cells grown on feeder-free Matrigel in MEF-conditioned medium
|
growth conditions: hES-T3 cells grown on feeder-free Matrigel in MEF-conditioned medium
gender: female
cell line: hES-T3
|
The mRNA profilings of T3MF, T3CM and T3BA cells were analyzed using Affymetrix Human Genome U133 plus 2.0 GeneChip according to the Manufacturer¡¦s protocols (Santa Clara, CA, USA, http://www.affymetrix.com).
|
Sample_geo_accession | GSM423943
| Sample_status | Public on Sep 10 2010
| Sample_submission_date | Jun 30 2009
| Sample_last_update_date | Sep 10 2010
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Non
| Sample_growth_protocol_ch1 | The MEF cells were cultured in MEF medium overnight, and the mitotically inactivated MEF were maintained in hES medium containing 4 ng/ml bFGF. After 24 h, the MEF-conditioned medium was collected and filtered through 0.2 um membrane (PN4612, Pall Life Sciences) as previously described [Xu et al., 2001]. The culture dish was coated with Matrigel diluted with DMEM/F12 (1:30) overnight at 4oC. The BD MartigelTM (Matrix 354234) is the manufacturer¡¦s Trademark for extracellular matrix extracted from the Engelbreth-Holm-Swarm tumor. The hES-T3 cells grown on feeder-free Martigel-coated dish in MEF-conditioned medium (with additional 4 ng/ml bFGF) were designated as T3CM.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions. Total RNAs extracted using TRIZOL reagent were quantified spectrophotometrically. The cDNA synthesis was carried out by using SUPERSCRIPTTM one-step RT-PCR kit (Invitrogen). For the reverse transcription step, the whole 5 ul of the resuspended RNAs were incubated for 60 min at 42oC, then 15 min at 72oC in 50 ul of reaction mixture containing 25 ul of 2x Reaction Mix (Invitrogen) and 1 ul of RT/PLANTINUM Taq Mix (Invitrogen). 28.5 ul of the cDNAs present in the 50 ul RT reaction mixture purified by Microarray Target Purification Kit (Roche Applied Science, Indianapolis, ID, USA, http://www.roche-applies-science.com) were used as templates to amplify cDNA by Microarray Target Amplification Kit. The amplified cDNAs were purified by Microarray Target Purification Kit, and complementary RNAs (cRNAs) were synthesized from 200 ng cDNA with Microarray RNA Target Synthesis Kit (Roche Applied Science).
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 micrograms purified cRNA (Expression Analysis Technical Manual, 2004, Affymetrix, http://www.affymetrix.com).
| Sample_hyb_protocol | Following fragmentation, 10 micrograms of cRNA were hybridized for 16 hr at 45oC on Affymetrix Human Genome U133 plus 2.0 GeneChip. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| Sample_scan_protocol | GeneChips from the hybridization experiments were read by the Affymetrix GeneChip scanner 3000.
| Sample_data_processing | The data were processed by GeneSpring GX software version 7.3.1 GC-RMA preprocessor to use on the CEL files
| Sample_platform_id | GPL570
| Sample_contact_name | Sung-Liang,,Yu
| Sample_contact_email | slyu@ntu.edu.tw
| Sample_contact_phone | 886-2-23958341
| Sample_contact_fax | 886-2-23958341
| Sample_contact_laboratory | Microarray Core Facility
| Sample_contact_department | Clinical Laboratory Sciences and Medical Biotechnology
| Sample_contact_institute | National Taiwan University
| Sample_contact_address | Jen Ai Road Section1
| Sample_contact_city | Taipei
| Sample_contact_zip/postal_code | 100
| Sample_contact_country | Taiwan
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM423nnn/GSM423943/suppl/GSM423943_T3CM_2.CEL.gz
| Sample_series_id | GSE16910
| Sample_data_row_count | 54675
| |
|
GSM423944 | GPL570 |
|
hES-T3 grown in hES medium (containing 4 ng/ml bFGF) supplemented with 5 ng/ml activin A, biological rep1
|
hES-T3 cells grown in hES medium (containing 4 ng/ml bFGF) supplemented with 5 ng/ml activin A
|
growth conditions: hES-T3 cells grown in hES medium (containing 4 ng/ml bFGF) supplemented with 5 ng/ml activin A
gender: female
cell line: hES-T3
|
The mRNA profilings of T3MF, T3CM and T3BA cells were analyzed using Affymetrix Human Genome U133 plus 2.0 GeneChip according to the Manufacturer¡¦s protocols (Santa Clara, CA, USA, http://www.affymetrix.com).
|
Sample_geo_accession | GSM423944
| Sample_status | Public on Sep 10 2010
| Sample_submission_date | Jun 30 2009
| Sample_last_update_date | Sep 10 2010
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Non
| Sample_growth_protocol_ch1 | The hES-T3 cells were grown on feeder-free Matrigel-coated dish in hES medium (containing 4 ng/ml bFGF) supplemented with 5 ng/ml activin A (human recombinant activin A expressed and derived in CHO cells, R&D systems), and these cells were designated as T3BA. Since activin A was previously reported to be necessary and sufficient for the maintenance of self-renewal and pluripotency of hES cells in long-term feeder- and serum-free culture [Xiao et al. 2006], the hES-T3 cells were also grown on feeder-free Matrigel in hES medium (without bFGF) supplemented with 5, 10 and 25 ng/ml activin A.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions. Total RNAs extracted using TRIZOL reagent were quantified spectrophotometrically. The cDNA synthesis was carried out by using SUPERSCRIPTTM one-step RT-PCR kit (Invitrogen). For the reverse transcription step, the whole 5 ul of the resuspended RNAs were incubated for 60 min at 42oC, then 15 min at 72oC in 50 ul of reaction mixture containing 25 ul of 2x Reaction Mix (Invitrogen) and 1 ul of RT/PLANTINUM Taq Mix (Invitrogen). 28.5 ul of the cDNAs present in the 50 ul RT reaction mixture purified by Microarray Target Purification Kit (Roche Applied Science, Indianapolis, ID, USA, http://www.roche-applies-science.com) were used as templates to amplify cDNA by Microarray Target Amplification Kit. The amplified cDNAs were purified by Microarray Target Purification Kit, and complementary RNAs (cRNAs) were synthesized from 200 ng cDNA with Microarray RNA Target Synthesis Kit (Roche Applied Science).
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 micrograms purified cRNA (Expression Analysis Technical Manual, 2004, Affymetrix, http://www.affymetrix.com).
| Sample_hyb_protocol | Following fragmentation, 10 micrograms of cRNA were hybridized for 16 hr at 45oC on Affymetrix Human Genome U133 plus 2.0 GeneChip. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| Sample_scan_protocol | GeneChips from the hybridization experiments were read by the Affymetrix GeneChip scanner 3000.
| Sample_data_processing | The data were processed by GeneSpring GX software version 7.3.1 GC-RMA preprocessor to use on the CEL files
| Sample_platform_id | GPL570
| Sample_contact_name | Sung-Liang,,Yu
| Sample_contact_email | slyu@ntu.edu.tw
| Sample_contact_phone | 886-2-23958341
| Sample_contact_fax | 886-2-23958341
| Sample_contact_laboratory | Microarray Core Facility
| Sample_contact_department | Clinical Laboratory Sciences and Medical Biotechnology
| Sample_contact_institute | National Taiwan University
| Sample_contact_address | Jen Ai Road Section1
| Sample_contact_city | Taipei
| Sample_contact_zip/postal_code | 100
| Sample_contact_country | Taiwan
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM423nnn/GSM423944/suppl/GSM423944_T3BA_1.CEL.gz
| Sample_series_id | GSE16910
| Sample_data_row_count | 54675
| |
|
GSM423945 | GPL570 |
|
hES-T3 grown in hES medium (containing 4 ng/ml bFGF) supplemented with 5 ng/ml activin A, biological rep2
|
hES-T3 cells grown in hES medium (containing 4 ng/ml bFGF) supplemented with 5 ng/ml activin A
|
growth conditions: hES-T3 cells grown in hES medium (containing 4 ng/ml bFGF) supplemented with 5 ng/ml activin A
gender: female
cell line: hES-T3
|
The mRNA profilings of T3MF, T3CM and T3BA cells were analyzed using Affymetrix Human Genome U133 plus 2.0 GeneChip according to the Manufacturer¡¦s protocols (Santa Clara, CA, USA, http://www.affymetrix.com).
|
Sample_geo_accession | GSM423945
| Sample_status | Public on Sep 10 2010
| Sample_submission_date | Jun 30 2009
| Sample_last_update_date | Sep 10 2010
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Non
| Sample_growth_protocol_ch1 | The hES-T3 cells were grown on feeder-free Matrigel-coated dish in hES medium (containing 4 ng/ml bFGF) supplemented with 5 ng/ml activin A (human recombinant activin A expressed and derived in CHO cells, R&D systems), and these cells were designated as T3BA. Since activin A was previously reported to be necessary and sufficient for the maintenance of self-renewal and pluripotency of hES cells in long-term feeder- and serum-free culture [Xiao et al. 2006], the hES-T3 cells were also grown on feeder-free Matrigel in hES medium (without bFGF) supplemented with 5, 10 and 25 ng/ml activin A.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions. Total RNAs extracted using TRIZOL reagent were quantified spectrophotometrically. The cDNA synthesis was carried out by using SUPERSCRIPTTM one-step RT-PCR kit (Invitrogen). For the reverse transcription step, the whole 5 ul of the resuspended RNAs were incubated for 60 min at 42oC, then 15 min at 72oC in 50 ul of reaction mixture containing 25 ul of 2x Reaction Mix (Invitrogen) and 1 ul of RT/PLANTINUM Taq Mix (Invitrogen). 28.5 ul of the cDNAs present in the 50 ul RT reaction mixture purified by Microarray Target Purification Kit (Roche Applied Science, Indianapolis, ID, USA, http://www.roche-applies-science.com) were used as templates to amplify cDNA by Microarray Target Amplification Kit. The amplified cDNAs were purified by Microarray Target Purification Kit, and complementary RNAs (cRNAs) were synthesized from 200 ng cDNA with Microarray RNA Target Synthesis Kit (Roche Applied Science).
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 micrograms purified cRNA (Expression Analysis Technical Manual, 2004, Affymetrix, http://www.affymetrix.com).
| Sample_hyb_protocol | Following fragmentation, 10 micrograms of cRNA were hybridized for 16 hr at 45oC on Affymetrix Human Genome U133 plus 2.0 GeneChip. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| Sample_scan_protocol | GeneChips from the hybridization experiments were read by the Affymetrix GeneChip scanner 3000.
| Sample_data_processing | The data were processed by GeneSpring GX software version 7.3.1 GC-RMA preprocessor to use on the CEL files
| Sample_platform_id | GPL570
| Sample_contact_name | Sung-Liang,,Yu
| Sample_contact_email | slyu@ntu.edu.tw
| Sample_contact_phone | 886-2-23958341
| Sample_contact_fax | 886-2-23958341
| Sample_contact_laboratory | Microarray Core Facility
| Sample_contact_department | Clinical Laboratory Sciences and Medical Biotechnology
| Sample_contact_institute | National Taiwan University
| Sample_contact_address | Jen Ai Road Section1
| Sample_contact_city | Taipei
| Sample_contact_zip/postal_code | 100
| Sample_contact_country | Taiwan
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM423nnn/GSM423945/suppl/GSM423945_T3BA_2.CEL.gz
| Sample_series_id | GSE16910
| Sample_data_row_count | 54675
| |
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