Search results for the GEO ID: GSE17549  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM437494 | GPL570 |
|
CHM_CD14_10
|
peripheral blood of CHM patient
|
cell type: peripheral blood monocytes
disease: choroideremia
|
Strunnikova_10_111308
|
| Sample_geo_accession | GSM437494
| | Sample_status | Public on Jan 27 2010
| | Sample_submission_date | Aug 06 2009
| | Sample_last_update_date | Jan 27 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Peripheral blood samples (36 ml) were collected from CHM males and age-matched male controls, in a tube system containing sodium heparin and Ficoll Hypaque solution. After immediate density gradient centrifugation, mononuclear cells were collected, washed and separated using AutoMacs magnetic sorting to CD14+ and CD14- populations.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Fibroblasts and monocytes 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 94 C 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 g) to Affymetrix (Santa Clara, CA) mouse 430_2 oligonucleotide probe arrays for 16 h at 45 C
| | 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/GSM437nnn/GSM437494/suppl/GSM437494.CEL.gz
| | Sample_series_id | GSE17549
| | Sample_data_row_count | 54675
| | |
|
GSM437495 | GPL570 |
|
CHM_CD14_13
|
peripheral blood of CHM patient
|
cell type: peripheral blood monocytes
disease: choroideremia
|
Strunnikova_13_111308
|
| Sample_geo_accession | GSM437495
| | Sample_status | Public on Jan 27 2010
| | Sample_submission_date | Aug 06 2009
| | Sample_last_update_date | Jan 27 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Peripheral blood samples (36 ml) were collected from CHM males and age-matched male controls, in a tube system containing sodium heparin and Ficoll Hypaque solution. After immediate density gradient centrifugation, mononuclear cells were collected, washed
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Fibroblasts and monocytes 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 94 C 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 g) to Affymetrix (Santa Clara, CA) mouse 430_2 oligonucleotide probe arrays for 16 h at 45 C
| | 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/GSM437nnn/GSM437495/suppl/GSM437495.CEL.gz
| | Sample_series_id | GSE17549
| | Sample_data_row_count | 54675
| | |
|
GSM437496 | GPL570 |
|
CHM_CD14_15
|
peripheral blood of CHM patient
|
cell type: peripheral blood monocytes
disease: choroideremia
|
Strunnikova_15_111308
|
| Sample_geo_accession | GSM437496
| | Sample_status | Public on Jan 27 2010
| | Sample_submission_date | Aug 06 2009
| | Sample_last_update_date | Jan 27 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Peripheral blood samples (36 ml) were collected from CHM males and age-matched male controls, in a tube system containing sodium heparin and Ficoll Hypaque solution. After immediate density gradient centrifugation, mononuclear cells were collected, washed
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Fibroblasts and monocytes 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 94 C 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 g) to Affymetrix (Santa Clara, CA) mouse 430_2 oligonucleotide probe arrays for 16 h at 45 C
| | 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/GSM437nnn/GSM437496/suppl/GSM437496.CEL.gz
| | Sample_series_id | GSE17549
| | Sample_data_row_count | 54675
| | |
|
GSM437497 | GPL570 |
|
CHM_FB_19
|
primary FB cultures from CHM patients
|
cell type: primary fibroblasts cultures
disease: choroideremia
|
Strunnikova_19_111308
|
| Sample_geo_accession | GSM437497
| | Sample_status | Public on Jan 27 2010
| | Sample_submission_date | Aug 06 2009
| | Sample_last_update_date | Jan 27 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Skin biopsy was obtained from CHM affected patients and an age-matched healthy control group and incubated for 10-14 days until fibroblasts started to attach to the plate.Cells at passage 2-7 were used for microarrays.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Fibroblasts and monocytes 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 94 C 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 g) to Affymetrix (Santa Clara, CA) mouse 430_2 oligonucleotide probe arrays for 16 h at 45 C
| | 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/GSM437nnn/GSM437497/suppl/GSM437497.CEL.gz
| | Sample_series_id | GSE17549
| | Sample_data_row_count | 54675
| | |
|
GSM437498 | GPL570 |
|
CHM_FB_21
|
primary FB cultures from CHM patients
|
cell type: primary fibroblasts cultures
disease: choroideremia
|
Strunnikova_21_111308
|
| Sample_geo_accession | GSM437498
| | Sample_status | Public on Jan 27 2010
| | Sample_submission_date | Aug 06 2009
| | Sample_last_update_date | Jan 27 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Skin biopsy was obtained from CHM affected patients and an age-matched healthy control group and incubated for 10-14 days until fibroblasts started to attach to the plate.Cells at passage 2-7 were used for microarrays.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Fibroblasts and monocytes 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 94 C 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 g) to Affymetrix (Santa Clara, CA) mouse 430_2 oligonucleotide probe arrays for 16 h at 45 C
| | 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/GSM437nnn/GSM437498/suppl/GSM437498.CEL.gz
| | Sample_series_id | GSE17549
| | Sample_data_row_count | 54675
| | |
|
GSM437499 | GPL570 |
|
CHM_FB_26
|
primary FB cultures from CHM patients
|
cell type: primary fibroblasts cultures
disease: choroideremia
|
Strunnikova_26_111308
|
| Sample_geo_accession | GSM437499
| | Sample_status | Public on Jan 27 2010
| | Sample_submission_date | Aug 06 2009
| | Sample_last_update_date | Jan 27 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Skin biopsy was obtained from CHM affected patients and an age-matched healthy control group and incubated for 10-14 days until fibroblasts started to attach to the plate.Cells at passage 2-7 were used for microarrays.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Fibroblasts and monocytes 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 94 C 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 g) to Affymetrix (Santa Clara, CA) mouse 430_2 oligonucleotide probe arrays for 16 h at 45 C
| | 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/GSM437nnn/GSM437499/suppl/GSM437499.CEL.gz
| | Sample_series_id | GSE17549
| | Sample_data_row_count | 54675
| | |
|
GSM437500 | GPL570 |
|
CHM_FB_27
|
primary FB cultures from CHM patients
|
cell type: primary fibroblasts cultures
disease: choroideremia
|
Strunnikova_27_111308
|
| Sample_geo_accession | GSM437500
| | Sample_status | Public on Jan 27 2010
| | Sample_submission_date | Aug 06 2009
| | Sample_last_update_date | Jan 27 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Skin biopsy was obtained from CHM affected patients and an age-matched healthy control group and incubated for 10-14 days until fibroblasts started to attach to the plate.Cells at passage 2-7 were used for microarrays.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Fibroblasts and monocytes 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 94 C 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 g) to Affymetrix (Santa Clara, CA) mouse 430_2 oligonucleotide probe arrays for 16 h at 45 C
| | 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/GSM437nnn/GSM437500/suppl/GSM437500.CEL.gz
| | Sample_series_id | GSE17549
| | Sample_data_row_count | 54675
| | |
|
GSM437501 | GPL570 |
|
CHM_CD14_29
|
peripheral blood of CHM patient
|
cell type: peripheral blood monocytes
disease: choroideremia
|
Strunnikova_29_111308
|
| Sample_geo_accession | GSM437501
| | Sample_status | Public on Jan 27 2010
| | Sample_submission_date | Aug 06 2009
| | Sample_last_update_date | Jan 27 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Peripheral blood samples (36 ml) were collected from CHM males and age-matched male controls, in a tube system containing sodium heparin and Ficoll Hypaque solution. After immediate density gradient centrifugation, mononuclear cells were collected, washed
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Fibroblasts and monocytes 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 94 C 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 g) to Affymetrix (Santa Clara, CA) mouse 430_2 oligonucleotide probe arrays for 16 h at 45 C
| | 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/GSM437nnn/GSM437501/suppl/GSM437501.CEL.gz
| | Sample_series_id | GSE17549
| | Sample_data_row_count | 54675
| | |
|
GSM437502 | GPL570 |
|
CHM_CD14_7
|
peripheral blood of CHM patient
|
cell type: peripheral blood monocytes
disease: choroideremia
|
Strunnikova_7_111308
|
| Sample_geo_accession | GSM437502
| | Sample_status | Public on Jan 27 2010
| | Sample_submission_date | Aug 06 2009
| | Sample_last_update_date | Jan 27 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Peripheral blood samples (36 ml) were collected from CHM males and age-matched male controls, in a tube system containing sodium heparin and Ficoll Hypaque solution. After immediate density gradient centrifugation, mononuclear cells were collected, washed
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Fibroblasts and monocytes 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 94 C 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 g) to Affymetrix (Santa Clara, CA) mouse 430_2 oligonucleotide probe arrays for 16 h at 45 C
| | 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/GSM437nnn/GSM437502/suppl/GSM437502.CEL.gz
| | Sample_series_id | GSE17549
| | Sample_data_row_count | 54675
| | |
|
GSM437503 | GPL570 |
|
CHM_CD14_9
|
peripheral blood of CHM patient
|
cell type: peripheral blood monocytes
disease: choroideremia
|
Strunnikova_9_111308
|
| Sample_geo_accession | GSM437503
| | Sample_status | Public on Jan 27 2010
| | Sample_submission_date | Aug 06 2009
| | Sample_last_update_date | Jan 27 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Peripheral blood samples (36 ml) were collected from CHM males and age-matched male controls, in a tube system containing sodium heparin and Ficoll Hypaque solution. After immediate density gradient centrifugation, mononuclear cells were collected, washed
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Fibroblasts and monocytes 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 94 C 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 g) to Affymetrix (Santa Clara, CA) mouse 430_2 oligonucleotide probe arrays for 16 h at 45 C
| | 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/GSM437nnn/GSM437503/suppl/GSM437503.CEL.gz
| | Sample_series_id | GSE17549
| | Sample_data_row_count | 54675
| | |
|
GSM437504 | GPL570 |
|
CONT_CD14_1
|
peripheral blood of control donor
|
cell type: peripheral blood monocytes
disease: normal
|
Strunnikova_1_111308
|
| Sample_geo_accession | GSM437504
| | Sample_status | Public on Jan 27 2010
| | Sample_submission_date | Aug 06 2009
| | Sample_last_update_date | Jan 27 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Peripheral blood samples (36 ml) were collected from CHM males and age-matched male controls, in a tube system containing sodium heparin and Ficoll Hypaque solution. After immediate density gradient centrifugation, mononuclear cells were collected, washed
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Fibroblasts and monocytes 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 94 C 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 g) to Affymetrix (Santa Clara, CA) mouse 430_2 oligonucleotide probe arrays for 16 h at 45 C
| | 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/GSM437nnn/GSM437504/suppl/GSM437504.CEL.gz
| | Sample_series_id | GSE17549
| | Sample_data_row_count | 54675
| | |
|
GSM437505 | GPL570 |
|
CONT_FB_18
|
primary FB cultures from control donor
|
cell type: primary fibroblasts cultures
disease: normal
|
Strunnikova_18_111308
|
| Sample_geo_accession | GSM437505
| | Sample_status | Public on Jan 27 2010
| | Sample_submission_date | Aug 06 2009
| | Sample_last_update_date | Jan 27 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Skin biopsy was obtained from CHM affected patients and an age-matched healthy control group and incubated for 10-14 days until fibroblasts started to attach to the plate.Cells at passage 2-7 were used for microarrays.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Fibroblasts and monocytes 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 94 C 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 g) to Affymetrix (Santa Clara, CA) mouse 430_2 oligonucleotide probe arrays for 16 h at 45 C
| | 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/GSM437nnn/GSM437505/suppl/GSM437505.CEL.gz
| | Sample_series_id | GSE17549
| | Sample_data_row_count | 54675
| | |
|
GSM437506 | GPL570 |
|
CONT_CD14_2
|
peripheral blood of control donor
|
cell type: peripheral blood monocytes
disease: normal
|
Strunnikova_2_111308
|
| Sample_geo_accession | GSM437506
| | Sample_status | Public on Jan 27 2010
| | Sample_submission_date | Aug 06 2009
| | Sample_last_update_date | Jan 27 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Peripheral blood samples (36 ml) were collected from CHM males and age-matched male controls, in a tube system containing sodium heparin and Ficoll Hypaque solution. After immediate density gradient centrifugation, mononuclear cells were collected, washed
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Fibroblasts and monocytes 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 94 C 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 g) to Affymetrix (Santa Clara, CA) mouse 430_2 oligonucleotide probe arrays for 16 h at 45 C
| | 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/GSM437nnn/GSM437506/suppl/GSM437506.CEL.gz
| | Sample_series_id | GSE17549
| | Sample_data_row_count | 54675
| | |
|
GSM437507 | GPL570 |
|
CONT_CD14_3
|
peripheral blood of control donor
|
cell type: peripheral blood monocytes
disease: normal
|
Strunnikova_3_111308
|
| Sample_geo_accession | GSM437507
| | Sample_status | Public on Jan 27 2010
| | Sample_submission_date | Aug 06 2009
| | Sample_last_update_date | Jan 27 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Peripheral blood samples (36 ml) were collected from CHM males and age-matched male controls, in a tube system containing sodium heparin and Ficoll Hypaque solution. After immediate density gradient centrifugation, mononuclear cells were collected, washed
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Fibroblasts and monocytes 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 94 C 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 g) to Affymetrix (Santa Clara, CA) mouse 430_2 oligonucleotide probe arrays for 16 h at 45 C
| | 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/GSM437nnn/GSM437507/suppl/GSM437507.CEL.gz
| | Sample_series_id | GSE17549
| | Sample_data_row_count | 54675
| | |
|
GSM437508 | GPL570 |
|
CONT_CD14_14
|
peripheral blood of control donor
|
cell type: peripheral blood monocytes
disease: normal
|
Strunnikova_14_111308
|
| Sample_geo_accession | GSM437508
| | Sample_status | Public on Jan 27 2010
| | Sample_submission_date | Aug 06 2009
| | Sample_last_update_date | Jan 27 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Peripheral blood samples (36 ml) were collected from CHM males and age-matched male controls, in a tube system containing sodium heparin and Ficoll Hypaque solution. After immediate density gradient centrifugation, mononuclear cells were collected, washed
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Fibroblasts and monocytes 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 94 C 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 g) to Affymetrix (Santa Clara, CA) mouse 430_2 oligonucleotide probe arrays for 16 h at 45 C
| | 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/GSM437nnn/GSM437508/suppl/GSM437508.CEL.gz
| | Sample_series_id | GSE17549
| | Sample_data_row_count | 54675
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