Search results for the GEO ID: GSE20966  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM524151 | GPL1352 |
|
beta-cells_non-diabetic condition_donor1
|
human beta-cells_non-diabetic
|
sample id: H13
disease: non-diabetic control
cell type: beta-cells
tissue: pancreas
gender: female
age (years): 67
bmi (body mass index, kg/m2): 39.0
|
Gene expression data from control subjects
|
| Sample_geo_accession | GSM524151
| | Sample_status | Public on Mar 20 2010
| | Sample_submission_date | Mar 19 2010
| | Sample_last_update_date | Mar 19 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Pancreas specimens were obtained, placed in cryomolds, embedded in Tissue-Tek OCT medium, immediately frozen in chilled isopentane, and stored at –80°C, pending sectioning at 8 μm. Frozen pancreatic sections were fixed in 70% ethanol for 30 seconds, rinsed by 5 dips in diethylpyrocarbonate (DEPC)-treated water and dehydrated in 100% ethanol twice for 1 min, and xylene for 4 minutes, the sections were air-dried and laser capture microdissection was performed. The microdissected cells were incubated with 10 μl of guanidine thiocyanate and polyethylene glycol octylphenol ether-based buffer (Buffer RLT, Qiagen), for 30 minutes at 42°C, and the samples stored at -80°C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from each population of laser captured β–cells using phenol-chloroform-isoamyl alcohol and precipitated with sodium acetate and glycogen carrier in isopropanol. After initial recovery and resuspension of the RNA pellet, genomic DNA contamination was removed by incubation with 10 units of DNase I for 2 hours at 37°C, in presence of 10 units of RNase inhibitor. The treatment with DNase I was followed by RNA re-extraction and precipitation. The pellet was resuspended and total RNA was amplified by T7-based linear amplification using T7-oligo-dT-primers. Two rounds of amplification were performed using RiboAmp HS RNA Amplification Kits (Arcturus).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Amplified RNA (1 μg) was converted into double-stranded complementary DNA (cDNA) using the RiboAmp HS RNA Amplification Kit (Arcturus), and biotinylated complementary RNA (cRNA) was generated from cDNA by in vitro transcription reaction using the BioArray High Yield RNA Transcript Labeling Kit (Enzo Diagnostics). RNA products were purified using the MiraColTM Purification Columns (Arcturus).
| | Sample_hyb_protocol | 15ug of biotinylated cRNA was hybridized for 16hr at 45C to the Affymetrix Human X3P array. Following hybridization, arrays were washed and stained on the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | Data were analyzed using DNA-chip Analyzer software (dChip), using the invariant set normalization algorithm.
| | Sample_platform_id | GPL1352
| | Sample_contact_name | Lorella,,Marselli
| | Sample_contact_email | Lorella.Marselli@med.unipi.it
| | Sample_contact_phone | +39 050 995135
| | Sample_contact_fax | +39 050 541521
| | Sample_contact_laboratory | Section on Islet Transplantation and Cell Biology
| | Sample_contact_department | Joslin Diabetes Center and the Department of Medicine
| | Sample_contact_institute | Harvard Medical School
| | Sample_contact_address | One Joslin Place
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02215
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM524nnn/GSM524151/suppl/GSM524151.CEL.gz
| | Sample_series_id | GSE20966
| | Sample_data_row_count | 61295
| | |
|
GSM524152 | GPL1352 |
|
beta-cells_non-diabetic condition_donor2
|
human beta-cells_non-diabetic
|
sample id: H16_2
disease: non-diabetic control
cell type: beta-cells
tissue: pancreas
gender: female
age (years): 65
bmi (body mass index, kg/m2): 34.0
|
Gene expression data from control subjects
|
| Sample_geo_accession | GSM524152
| | Sample_status | Public on Mar 20 2010
| | Sample_submission_date | Mar 19 2010
| | Sample_last_update_date | Mar 19 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Pancreas specimens were obtained, placed in cryomolds, embedded in Tissue-Tek OCT medium, immediately frozen in chilled isopentane, and stored at –80°C, pending sectioning at 8 μm. Frozen pancreatic sections were fixed in 70% ethanol for 30 seconds, rinsed by 5 dips in diethylpyrocarbonate (DEPC)-treated water and dehydrated in 100% ethanol twice for 1 min, and xylene for 4 minutes, the sections were air-dried and laser capture microdissection was performed. The microdissected cells were incubated with 10 μl of guanidine thiocyanate and polyethylene glycol octylphenol ether-based buffer (Buffer RLT, Qiagen), for 30 minutes at 42°C, and the samples stored at -80°C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from each population of laser captured β–cells using phenol-chloroform-isoamyl alcohol and precipitated with sodium acetate and glycogen carrier in isopropanol. After initial recovery and resuspension of the RNA pellet, genomic DNA contamination was removed by incubation with 10 units of DNase I for 2 hours at 37°C, in presence of 10 units of RNase inhibitor. The treatment with DNase I was followed by RNA re-extraction and precipitation. The pellet was resuspended and total RNA was amplified by T7-based linear amplification using T7-oligo-dT-primers. Two rounds of amplification were performed using RiboAmp HS RNA Amplification Kits (Arcturus).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Amplified RNA (1 μg) was converted into double-stranded complementary DNA (cDNA) using the RiboAmp HS RNA Amplification Kit (Arcturus), and biotinylated complementary RNA (cRNA) was generated from cDNA by in vitro transcription reaction using the BioArray High Yield RNA Transcript Labeling Kit (Enzo Diagnostics). RNA products were purified using the MiraColTM Purification Columns (Arcturus).
| | Sample_hyb_protocol | 15ug of biotinylated cRNA was hybridized for 16hr at 45C to the Affymetrix Human X3P array. Following hybridization, arrays were washed and stained on the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | Data were analyzed using DNA-chip Analyzer software (dChip), using the invariant set normalization algorithm.
| | Sample_platform_id | GPL1352
| | Sample_contact_name | Lorella,,Marselli
| | Sample_contact_email | Lorella.Marselli@med.unipi.it
| | Sample_contact_phone | +39 050 995135
| | Sample_contact_fax | +39 050 541521
| | Sample_contact_laboratory | Section on Islet Transplantation and Cell Biology
| | Sample_contact_department | Joslin Diabetes Center and the Department of Medicine
| | Sample_contact_institute | Harvard Medical School
| | Sample_contact_address | One Joslin Place
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02215
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM524nnn/GSM524152/suppl/GSM524152.CEL.gz
| | Sample_series_id | GSE20966
| | Sample_data_row_count | 61295
| | |
|
GSM524153 | GPL1352 |
|
beta-cells_non-diabetic condition_donor3
|
human beta-cells_non-diabetic
|
sample id: H03
disease: non-diabetic control
cell type: beta-cells
tissue: pancreas
gender: female
age (years): 62
bmi (body mass index, kg/m2): 22.4
|
Gene expression data from control subjects
|
| Sample_geo_accession | GSM524153
| | Sample_status | Public on Mar 20 2010
| | Sample_submission_date | Mar 19 2010
| | Sample_last_update_date | Mar 19 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Pancreas specimens were obtained, placed in cryomolds, embedded in Tissue-Tek OCT medium, immediately frozen in chilled isopentane, and stored at –80°C, pending sectioning at 8 μm. Frozen pancreatic sections were fixed in 70% ethanol for 30 seconds, rinsed by 5 dips in diethylpyrocarbonate (DEPC)-treated water and dehydrated in 100% ethanol twice for 1 min, and xylene for 4 minutes, the sections were air-dried and laser capture microdissection was performed. The microdissected cells were incubated with 10 μl of guanidine thiocyanate and polyethylene glycol octylphenol ether-based buffer (Buffer RLT, Qiagen), for 30 minutes at 42°C, and the samples stored at -80°C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from each population of laser captured β–cells using phenol-chloroform-isoamyl alcohol and precipitated with sodium acetate and glycogen carrier in isopropanol. After initial recovery and resuspension of the RNA pellet, genomic DNA contamination was removed by incubation with 10 units of DNase I for 2 hours at 37°C, in presence of 10 units of RNase inhibitor. The treatment with DNase I was followed by RNA re-extraction and precipitation. The pellet was resuspended and total RNA was amplified by T7-based linear amplification using T7-oligo-dT-primers. Two rounds of amplification were performed using RiboAmp HS RNA Amplification Kits (Arcturus).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Amplified RNA (1 μg) was converted into double-stranded complementary DNA (cDNA) using the RiboAmp HS RNA Amplification Kit (Arcturus), and biotinylated complementary RNA (cRNA) was generated from cDNA by in vitro transcription reaction using the BioArray High Yield RNA Transcript Labeling Kit (Enzo Diagnostics). RNA products were purified using the MiraColTM Purification Columns (Arcturus).
| | Sample_hyb_protocol | 15ug of biotinylated cRNA was hybridized for 16hr at 45C to the Affymetrix Human X3P array. Following hybridization, arrays were washed and stained on the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | Data were analyzed using DNA-chip Analyzer software (dChip), using the invariant set normalization algorithm.
| | Sample_platform_id | GPL1352
| | Sample_contact_name | Lorella,,Marselli
| | Sample_contact_email | Lorella.Marselli@med.unipi.it
| | Sample_contact_phone | +39 050 995135
| | Sample_contact_fax | +39 050 541521
| | Sample_contact_laboratory | Section on Islet Transplantation and Cell Biology
| | Sample_contact_department | Joslin Diabetes Center and the Department of Medicine
| | Sample_contact_institute | Harvard Medical School
| | Sample_contact_address | One Joslin Place
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02215
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM524nnn/GSM524153/suppl/GSM524153.CEL.gz
| | Sample_series_id | GSE20966
| | Sample_data_row_count | 61295
| | |
|
GSM524154 | GPL1352 |
|
beta-cells_non-diabetic condition_donor4
|
human beta-cells_non-diabetic
|
sample id: H18
disease: non-diabetic control
cell type: beta-cells
tissue: pancreas
gender: male
age (years): 60
bmi (body mass index, kg/m2): 31.0
|
Gene expression data from control subjects
|
| Sample_geo_accession | GSM524154
| | Sample_status | Public on Mar 20 2010
| | Sample_submission_date | Mar 19 2010
| | Sample_last_update_date | Mar 19 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Pancreas specimens were obtained, placed in cryomolds, embedded in Tissue-Tek OCT medium, immediately frozen in chilled isopentane, and stored at –80°C, pending sectioning at 8 μm. Frozen pancreatic sections were fixed in 70% ethanol for 30 seconds, rinsed by 5 dips in diethylpyrocarbonate (DEPC)-treated water and dehydrated in 100% ethanol twice for 1 min, and xylene for 4 minutes, the sections were air-dried and laser capture microdissection was performed. The microdissected cells were incubated with 10 μl of guanidine thiocyanate and polyethylene glycol octylphenol ether-based buffer (Buffer RLT, Qiagen), for 30 minutes at 42°C, and the samples stored at -80°C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from each population of laser captured β–cells using phenol-chloroform-isoamyl alcohol and precipitated with sodium acetate and glycogen carrier in isopropanol. After initial recovery and resuspension of the RNA pellet, genomic DNA contamination was removed by incubation with 10 units of DNase I for 2 hours at 37°C, in presence of 10 units of RNase inhibitor. The treatment with DNase I was followed by RNA re-extraction and precipitation. The pellet was resuspended and total RNA was amplified by T7-based linear amplification using T7-oligo-dT-primers. Two rounds of amplification were performed using RiboAmp HS RNA Amplification Kits (Arcturus).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Amplified RNA (1 μg) was converted into double-stranded complementary DNA (cDNA) using the RiboAmp HS RNA Amplification Kit (Arcturus), and biotinylated complementary RNA (cRNA) was generated from cDNA by in vitro transcription reaction using the BioArray High Yield RNA Transcript Labeling Kit (Enzo Diagnostics). RNA products were purified using the MiraColTM Purification Columns (Arcturus).
| | Sample_hyb_protocol | 15ug of biotinylated cRNA was hybridized for 16hr at 45C to the Affymetrix Human X3P array. Following hybridization, arrays were washed and stained on the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | Data were analyzed using DNA-chip Analyzer software (dChip), using the invariant set normalization algorithm.
| | Sample_platform_id | GPL1352
| | Sample_contact_name | Lorella,,Marselli
| | Sample_contact_email | Lorella.Marselli@med.unipi.it
| | Sample_contact_phone | +39 050 995135
| | Sample_contact_fax | +39 050 541521
| | Sample_contact_laboratory | Section on Islet Transplantation and Cell Biology
| | Sample_contact_department | Joslin Diabetes Center and the Department of Medicine
| | Sample_contact_institute | Harvard Medical School
| | Sample_contact_address | One Joslin Place
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02215
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM524nnn/GSM524154/suppl/GSM524154.CEL.gz
| | Sample_series_id | GSE20966
| | Sample_data_row_count | 61295
| | |
|
GSM524155 | GPL1352 |
|
beta-cells_non-diabetic condition_donor5
|
human beta-cells_non-diabetic
|
sample id: H6
disease: non-diabetic control
cell type: beta-cells
tissue: pancreas
gender: male
age (years): 59
bmi (body mass index, kg/m2): 36.4
|
Gene expression data from control subjects
|
| Sample_geo_accession | GSM524155
| | Sample_status | Public on Mar 20 2010
| | Sample_submission_date | Mar 19 2010
| | Sample_last_update_date | Mar 19 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Pancreas specimens were obtained, placed in cryomolds, embedded in Tissue-Tek OCT medium, immediately frozen in chilled isopentane, and stored at –80°C, pending sectioning at 8 μm. Frozen pancreatic sections were fixed in 70% ethanol for 30 seconds, rinsed by 5 dips in diethylpyrocarbonate (DEPC)-treated water and dehydrated in 100% ethanol twice for 1 min, and xylene for 4 minutes, the sections were air-dried and laser capture microdissection was performed. The microdissected cells were incubated with 10 μl of guanidine thiocyanate and polyethylene glycol octylphenol ether-based buffer (Buffer RLT, Qiagen), for 30 minutes at 42°C, and the samples stored at -80°C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from each population of laser captured β–cells using phenol-chloroform-isoamyl alcohol and precipitated with sodium acetate and glycogen carrier in isopropanol. After initial recovery and resuspension of the RNA pellet, genomic DNA contamination was removed by incubation with 10 units of DNase I for 2 hours at 37°C, in presence of 10 units of RNase inhibitor. The treatment with DNase I was followed by RNA re-extraction and precipitation. The pellet was resuspended and total RNA was amplified by T7-based linear amplification using T7-oligo-dT-primers. Two rounds of amplification were performed using RiboAmp HS RNA Amplification Kits (Arcturus).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Amplified RNA (1 μg) was converted into double-stranded complementary DNA (cDNA) using the RiboAmp HS RNA Amplification Kit (Arcturus), and biotinylated complementary RNA (cRNA) was generated from cDNA by in vitro transcription reaction using the BioArray High Yield RNA Transcript Labeling Kit (Enzo Diagnostics). RNA products were purified using the MiraColTM Purification Columns (Arcturus).
| | Sample_hyb_protocol | 15ug of biotinylated cRNA was hybridized for 16hr at 45C to the Affymetrix Human X3P array. Following hybridization, arrays were washed and stained on the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | Data were analyzed using DNA-chip Analyzer software (dChip), using the invariant set normalization algorithm.
| | Sample_platform_id | GPL1352
| | Sample_contact_name | Lorella,,Marselli
| | Sample_contact_email | Lorella.Marselli@med.unipi.it
| | Sample_contact_phone | +39 050 995135
| | Sample_contact_fax | +39 050 541521
| | Sample_contact_laboratory | Section on Islet Transplantation and Cell Biology
| | Sample_contact_department | Joslin Diabetes Center and the Department of Medicine
| | Sample_contact_institute | Harvard Medical School
| | Sample_contact_address | One Joslin Place
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02215
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM524nnn/GSM524155/suppl/GSM524155.CEL.gz
| | Sample_series_id | GSE20966
| | Sample_data_row_count | 61295
| | |
|
GSM524156 | GPL1352 |
|
beta-cells_non-diabetic condition_donor6
|
human beta-cells_non-diabetic
|
sample id: H7
disease: non-diabetic control
cell type: beta-cells
tissue: pancreas
gender: male
age (years): 52
bmi (body mass index, kg/m2): 26.0
|
Gene expression data from control subjects
|
| Sample_geo_accession | GSM524156
| | Sample_status | Public on Mar 20 2010
| | Sample_submission_date | Mar 19 2010
| | Sample_last_update_date | Mar 19 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Pancreas specimens were obtained, placed in cryomolds, embedded in Tissue-Tek OCT medium, immediately frozen in chilled isopentane, and stored at –80°C, pending sectioning at 8 μm. Frozen pancreatic sections were fixed in 70% ethanol for 30 seconds, rinsed by 5 dips in diethylpyrocarbonate (DEPC)-treated water and dehydrated in 100% ethanol twice for 1 min, and xylene for 4 minutes, the sections were air-dried and laser capture microdissection was performed. The microdissected cells were incubated with 10 μl of guanidine thiocyanate and polyethylene glycol octylphenol ether-based buffer (Buffer RLT, Qiagen), for 30 minutes at 42°C, and the samples stored at -80°C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from each population of laser captured β–cells using phenol-chloroform-isoamyl alcohol and precipitated with sodium acetate and glycogen carrier in isopropanol. After initial recovery and resuspension of the RNA pellet, genomic DNA contamination was removed by incubation with 10 units of DNase I for 2 hours at 37°C, in presence of 10 units of RNase inhibitor. The treatment with DNase I was followed by RNA re-extraction and precipitation. The pellet was resuspended and total RNA was amplified by T7-based linear amplification using T7-oligo-dT-primers. Two rounds of amplification were performed using RiboAmp HS RNA Amplification Kits (Arcturus).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Amplified RNA (1 μg) was converted into double-stranded complementary DNA (cDNA) using the RiboAmp HS RNA Amplification Kit (Arcturus), and biotinylated complementary RNA (cRNA) was generated from cDNA by in vitro transcription reaction using the BioArray High Yield RNA Transcript Labeling Kit (Enzo Diagnostics). RNA products were purified using the MiraColTM Purification Columns (Arcturus).
| | Sample_hyb_protocol | 15ug of biotinylated cRNA was hybridized for 16hr at 45C to the Affymetrix Human X3P array. Following hybridization, arrays were washed and stained on the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | Data were analyzed using DNA-chip Analyzer software (dChip), using the invariant set normalization algorithm.
| | Sample_platform_id | GPL1352
| | Sample_contact_name | Lorella,,Marselli
| | Sample_contact_email | Lorella.Marselli@med.unipi.it
| | Sample_contact_phone | +39 050 995135
| | Sample_contact_fax | +39 050 541521
| | Sample_contact_laboratory | Section on Islet Transplantation and Cell Biology
| | Sample_contact_department | Joslin Diabetes Center and the Department of Medicine
| | Sample_contact_institute | Harvard Medical School
| | Sample_contact_address | One Joslin Place
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02215
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM524nnn/GSM524156/suppl/GSM524156.CEL.gz
| | Sample_series_id | GSE20966
| | Sample_data_row_count | 61295
| | |
|
GSM524157 | GPL1352 |
|
beta-cells_non-diabetic condition_donor7
|
human beta-cells_non-diabetic
|
sample id: H8
disease: non-diabetic control
cell type: beta-cells
tissue: pancreas
gender: male
age (years): 54
bmi (body mass index, kg/m2): 34.2
|
Gene expression data from control subjects
|
| Sample_geo_accession | GSM524157
| | Sample_status | Public on Mar 20 2010
| | Sample_submission_date | Mar 19 2010
| | Sample_last_update_date | Mar 19 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Pancreas specimens were obtained, placed in cryomolds, embedded in Tissue-Tek OCT medium, immediately frozen in chilled isopentane, and stored at –80°C, pending sectioning at 8 μm. Frozen pancreatic sections were fixed in 70% ethanol for 30 seconds, rinsed by 5 dips in diethylpyrocarbonate (DEPC)-treated water and dehydrated in 100% ethanol twice for 1 min, and xylene for 4 minutes, the sections were air-dried and laser capture microdissection was performed. The microdissected cells were incubated with 10 μl of guanidine thiocyanate and polyethylene glycol octylphenol ether-based buffer (Buffer RLT, Qiagen), for 30 minutes at 42°C, and the samples stored at -80°C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from each population of laser captured β–cells using phenol-chloroform-isoamyl alcohol and precipitated with sodium acetate and glycogen carrier in isopropanol. After initial recovery and resuspension of the RNA pellet, genomic DNA contamination was removed by incubation with 10 units of DNase I for 2 hours at 37°C, in presence of 10 units of RNase inhibitor. The treatment with DNase I was followed by RNA re-extraction and precipitation. The pellet was resuspended and total RNA was amplified by T7-based linear amplification using T7-oligo-dT-primers. Two rounds of amplification were performed using RiboAmp HS RNA Amplification Kits (Arcturus).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Amplified RNA (1 μg) was converted into double-stranded complementary DNA (cDNA) using the RiboAmp HS RNA Amplification Kit (Arcturus), and biotinylated complementary RNA (cRNA) was generated from cDNA by in vitro transcription reaction using the BioArray High Yield RNA Transcript Labeling Kit (Enzo Diagnostics). RNA products were purified using the MiraColTM Purification Columns (Arcturus).
| | Sample_hyb_protocol | 15ug of biotinylated cRNA was hybridized for 16hr at 45C to the Affymetrix Human X3P array. Following hybridization, arrays were washed and stained on the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | Data were analyzed using DNA-chip Analyzer software (dChip), using the invariant set normalization algorithm.
| | Sample_platform_id | GPL1352
| | Sample_contact_name | Lorella,,Marselli
| | Sample_contact_email | Lorella.Marselli@med.unipi.it
| | Sample_contact_phone | +39 050 995135
| | Sample_contact_fax | +39 050 541521
| | Sample_contact_laboratory | Section on Islet Transplantation and Cell Biology
| | Sample_contact_department | Joslin Diabetes Center and the Department of Medicine
| | Sample_contact_institute | Harvard Medical School
| | Sample_contact_address | One Joslin Place
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02215
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM524nnn/GSM524157/suppl/GSM524157.CEL.gz
| | Sample_series_id | GSE20966
| | Sample_data_row_count | 61295
| | |
|
GSM524158 | GPL1352 |
|
beta-cells_non-diabetic condition_donor8
|
human beta-cells_non-diabetic
|
sample id: H14
disease: non-diabetic control
cell type: beta-cells
tissue: pancreas
gender: female
age (years): 64
bmi (body mass index, kg/m2): 27.1
|
Gene expression data from control subjects
|
| Sample_geo_accession | GSM524158
| | Sample_status | Public on Mar 20 2010
| | Sample_submission_date | Mar 19 2010
| | Sample_last_update_date | Mar 19 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Pancreas specimens were obtained, placed in cryomolds, embedded in Tissue-Tek OCT medium, immediately frozen in chilled isopentane, and stored at –80°C, pending sectioning at 8 μm. Frozen pancreatic sections were fixed in 70% ethanol for 30 seconds, rinsed by 5 dips in diethylpyrocarbonate (DEPC)-treated water and dehydrated in 100% ethanol twice for 1 min, and xylene for 4 minutes, the sections were air-dried and laser capture microdissection was performed. The microdissected cells were incubated with 10 μl of guanidine thiocyanate and polyethylene glycol octylphenol ether-based buffer (Buffer RLT, Qiagen), for 30 minutes at 42°C, and the samples stored at -80°C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from each population of laser captured β–cells using phenol-chloroform-isoamyl alcohol and precipitated with sodium acetate and glycogen carrier in isopropanol. After initial recovery and resuspension of the RNA pellet, genomic DNA contamination was removed by incubation with 10 units of DNase I for 2 hours at 37°C, in presence of 10 units of RNase inhibitor. The treatment with DNase I was followed by RNA re-extraction and precipitation. The pellet was resuspended and total RNA was amplified by T7-based linear amplification using T7-oligo-dT-primers. Two rounds of amplification were performed using RiboAmp HS RNA Amplification Kits (Arcturus).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Amplified RNA (1 μg) was converted into double-stranded complementary DNA (cDNA) using the RiboAmp HS RNA Amplification Kit (Arcturus), and biotinylated complementary RNA (cRNA) was generated from cDNA by in vitro transcription reaction using the BioArray High Yield RNA Transcript Labeling Kit (Enzo Diagnostics). RNA products were purified using the MiraColTM Purification Columns (Arcturus).
| | Sample_hyb_protocol | 15ug of biotinylated cRNA was hybridized for 16hr at 45C to the Affymetrix Human X3P array. Following hybridization, arrays were washed and stained on the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | Data were analyzed using DNA-chip Analyzer software (dChip), using the invariant set normalization algorithm.
| | Sample_platform_id | GPL1352
| | Sample_contact_name | Lorella,,Marselli
| | Sample_contact_email | Lorella.Marselli@med.unipi.it
| | Sample_contact_phone | +39 050 995135
| | Sample_contact_fax | +39 050 541521
| | Sample_contact_laboratory | Section on Islet Transplantation and Cell Biology
| | Sample_contact_department | Joslin Diabetes Center and the Department of Medicine
| | Sample_contact_institute | Harvard Medical School
| | Sample_contact_address | One Joslin Place
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02215
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM524nnn/GSM524158/suppl/GSM524158.CEL.gz
| | Sample_series_id | GSE20966
| | Sample_data_row_count | 61295
| | |
|
GSM524159 | GPL1352 |
|
beta-cells_non-diabetic condition_donor9
|
human beta-cells_non-diabetic
|
sample id: H16
disease: non-diabetic control
cell type: beta-cells
tissue: pancreas
gender: male
age (years): 57
bmi (body mass index, kg/m2): 27.7
|
Gene expression data from control subjects
|
| Sample_geo_accession | GSM524159
| | Sample_status | Public on Mar 20 2010
| | Sample_submission_date | Mar 19 2010
| | Sample_last_update_date | Mar 19 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Pancreas specimens were obtained, placed in cryomolds, embedded in Tissue-Tek OCT medium, immediately frozen in chilled isopentane, and stored at –80°C, pending sectioning at 8 μm. Frozen pancreatic sections were fixed in 70% ethanol for 30 seconds, rinsed by 5 dips in diethylpyrocarbonate (DEPC)-treated water and dehydrated in 100% ethanol twice for 1 min, and xylene for 4 minutes, the sections were air-dried and laser capture microdissection was performed. The microdissected cells were incubated with 10 μl of guanidine thiocyanate and polyethylene glycol octylphenol ether-based buffer (Buffer RLT, Qiagen), for 30 minutes at 42°C, and the samples stored at -80°C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from each population of laser captured β–cells using phenol-chloroform-isoamyl alcohol and precipitated with sodium acetate and glycogen carrier in isopropanol. After initial recovery and resuspension of the RNA pellet, genomic DNA contamination was removed by incubation with 10 units of DNase I for 2 hours at 37°C, in presence of 10 units of RNase inhibitor. The treatment with DNase I was followed by RNA re-extraction and precipitation. The pellet was resuspended and total RNA was amplified by T7-based linear amplification using T7-oligo-dT-primers. Two rounds of amplification were performed using RiboAmp HS RNA Amplification Kits (Arcturus).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Amplified RNA (1 μg) was converted into double-stranded complementary DNA (cDNA) using the RiboAmp HS RNA Amplification Kit (Arcturus), and biotinylated complementary RNA (cRNA) was generated from cDNA by in vitro transcription reaction using the BioArray High Yield RNA Transcript Labeling Kit (Enzo Diagnostics). RNA products were purified using the MiraColTM Purification Columns (Arcturus).
| | Sample_hyb_protocol | 15ug of biotinylated cRNA was hybridized for 16hr at 45C to the Affymetrix Human X3P array. Following hybridization, arrays were washed and stained on the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | Data were analyzed using DNA-chip Analyzer software (dChip), using the invariant set normalization algorithm.
| | Sample_platform_id | GPL1352
| | Sample_contact_name | Lorella,,Marselli
| | Sample_contact_email | Lorella.Marselli@med.unipi.it
| | Sample_contact_phone | +39 050 995135
| | Sample_contact_fax | +39 050 541521
| | Sample_contact_laboratory | Section on Islet Transplantation and Cell Biology
| | Sample_contact_department | Joslin Diabetes Center and the Department of Medicine
| | Sample_contact_institute | Harvard Medical School
| | Sample_contact_address | One Joslin Place
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02215
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM524nnn/GSM524159/suppl/GSM524159.CEL.gz
| | Sample_series_id | GSE20966
| | Sample_data_row_count | 61295
| | |
|
GSM524160 | GPL1352 |
|
beta-cells_non-diabetic condition_donor10
|
human beta-cells_non-diabetic
|
sample id: H22
disease: non-diabetic control
cell type: beta-cells
tissue: pancreas
gender: male
age (years): 63
bmi (body mass index, kg/m2): 28.5
|
Gene expression data from control subjects
|
| Sample_geo_accession | GSM524160
| | Sample_status | Public on Mar 20 2010
| | Sample_submission_date | Mar 19 2010
| | Sample_last_update_date | Mar 19 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Pancreas specimens were obtained, placed in cryomolds, embedded in Tissue-Tek OCT medium, immediately frozen in chilled isopentane, and stored at –80°C, pending sectioning at 8 μm. Frozen pancreatic sections were fixed in 70% ethanol for 30 seconds, rinsed by 5 dips in diethylpyrocarbonate (DEPC)-treated water and dehydrated in 100% ethanol twice for 1 min, and xylene for 4 minutes, the sections were air-dried and laser capture microdissection was performed. The microdissected cells were incubated with 10 μl of guanidine thiocyanate and polyethylene glycol octylphenol ether-based buffer (Buffer RLT, Qiagen), for 30 minutes at 42°C, and the samples stored at -80°C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from each population of laser captured β–cells using phenol-chloroform-isoamyl alcohol and precipitated with sodium acetate and glycogen carrier in isopropanol. After initial recovery and resuspension of the RNA pellet, genomic DNA contamination was removed by incubation with 10 units of DNase I for 2 hours at 37°C, in presence of 10 units of RNase inhibitor. The treatment with DNase I was followed by RNA re-extraction and precipitation. The pellet was resuspended and total RNA was amplified by T7-based linear amplification using T7-oligo-dT-primers. Two rounds of amplification were performed using RiboAmp HS RNA Amplification Kits (Arcturus).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Amplified RNA (1 μg) was converted into double-stranded complementary DNA (cDNA) using the RiboAmp HS RNA Amplification Kit (Arcturus), and biotinylated complementary RNA (cRNA) was generated from cDNA by in vitro transcription reaction using the BioArray High Yield RNA Transcript Labeling Kit (Enzo Diagnostics). RNA products were purified using the MiraColTM Purification Columns (Arcturus).
| | Sample_hyb_protocol | 15ug of biotinylated cRNA was hybridized for 16hr at 45C to the Affymetrix Human X3P array. Following hybridization, arrays were washed and stained on the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | Data were analyzed using DNA-chip Analyzer software (dChip), using the invariant set normalization algorithm.
| | Sample_platform_id | GPL1352
| | Sample_contact_name | Lorella,,Marselli
| | Sample_contact_email | Lorella.Marselli@med.unipi.it
| | Sample_contact_phone | +39 050 995135
| | Sample_contact_fax | +39 050 541521
| | Sample_contact_laboratory | Section on Islet Transplantation and Cell Biology
| | Sample_contact_department | Joslin Diabetes Center and the Department of Medicine
| | Sample_contact_institute | Harvard Medical School
| | Sample_contact_address | One Joslin Place
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02215
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM524nnn/GSM524160/suppl/GSM524160.CEL.gz
| | Sample_series_id | GSE20966
| | Sample_data_row_count | 61295
| | |
|
GSM524161 | GPL1352 |
|
beta-cells_diabetic condition_donor1
|
human beta-cells_diabetic
|
sample id: D2
disease: type 2 diabetes
cell type: beta-cells
tissue: pancreas
gender: male
age (years): 74
bmi (body mass index, kg/m2): 26.0
|
Gene expression data from type 2 diabetic subjects
|
| Sample_geo_accession | GSM524161
| | Sample_status | Public on Mar 20 2010
| | Sample_submission_date | Mar 19 2010
| | Sample_last_update_date | Mar 19 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Pancreas specimens were obtained, placed in cryomolds, embedded in Tissue-Tek OCT medium, immediately frozen in chilled isopentane, and stored at –80°C, pending sectioning at 8 μm. Frozen pancreatic sections were fixed in 70% ethanol for 30 seconds, rinsed by 5 dips in diethylpyrocarbonate (DEPC)-treated water and dehydrated in 100% ethanol twice for 1 min, and xylene for 4 minutes, the sections were air-dried and laser capture microdissection was performed. The microdissected cells were incubated with 10 μl of guanidine thiocyanate and polyethylene glycol octylphenol ether-based buffer (Buffer RLT, Qiagen), for 30 minutes at 42°C, and the samples stored at -80°C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from each population of laser captured β–cells using phenol-chloroform-isoamyl alcohol and precipitated with sodium acetate and glycogen carrier in isopropanol. After initial recovery and resuspension of the RNA pellet, genomic DNA contamination was removed by incubation with 10 units of DNase I for 2 hours at 37°C, in presence of 10 units of RNase inhibitor. The treatment with DNase I was followed by RNA re-extraction and precipitation. The pellet was resuspended and total RNA was amplified by T7-based linear amplification using T7-oligo-dT-primers. Two rounds of amplification were performed using RiboAmp HS RNA Amplification Kits (Arcturus).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Amplified RNA (1 μg) was converted into double-stranded complementary DNA (cDNA) using the RiboAmp HS RNA Amplification Kit (Arcturus), and biotinylated complementary RNA (cRNA) was generated from cDNA by in vitro transcription reaction using the BioArray High Yield RNA Transcript Labeling Kit (Enzo Diagnostics). RNA products were purified using the MiraColTM Purification Columns (Arcturus).
| | Sample_hyb_protocol | 15ug of biotinylated cRNA was hybridized for 16hr at 45C to the Affymetrix Human X3P array. Following hybridization, arrays were washed and stained on the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | Data were analyzed using DNA-chip Analyzer software (dChip), using the invariant set normalization algorithm.
| | Sample_platform_id | GPL1352
| | Sample_contact_name | Lorella,,Marselli
| | Sample_contact_email | Lorella.Marselli@med.unipi.it
| | Sample_contact_phone | +39 050 995135
| | Sample_contact_fax | +39 050 541521
| | Sample_contact_laboratory | Section on Islet Transplantation and Cell Biology
| | Sample_contact_department | Joslin Diabetes Center and the Department of Medicine
| | Sample_contact_institute | Harvard Medical School
| | Sample_contact_address | One Joslin Place
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02215
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM524nnn/GSM524161/suppl/GSM524161.CEL.gz
| | Sample_series_id | GSE20966
| | Sample_data_row_count | 61295
| | |
|
GSM524162 | GPL1352 |
|
beta-cells_diabetic condition_donor2
|
human beta-cells_diabetic
|
sample id: D3
disease: type 2 diabetes
cell type: beta-cells
tissue: pancreas
gender: female
age (years): 68
bmi (body mass index, kg/m2): 29.4
|
Gene expression data from type 2 diabetic subjects
|
| Sample_geo_accession | GSM524162
| | Sample_status | Public on Mar 20 2010
| | Sample_submission_date | Mar 19 2010
| | Sample_last_update_date | Mar 19 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Pancreas specimens were obtained, placed in cryomolds, embedded in Tissue-Tek OCT medium, immediately frozen in chilled isopentane, and stored at –80°C, pending sectioning at 8 μm. Frozen pancreatic sections were fixed in 70% ethanol for 30 seconds, rinsed by 5 dips in diethylpyrocarbonate (DEPC)-treated water and dehydrated in 100% ethanol twice for 1 min, and xylene for 4 minutes, the sections were air-dried and laser capture microdissection was performed. The microdissected cells were incubated with 10 μl of guanidine thiocyanate and polyethylene glycol octylphenol ether-based buffer (Buffer RLT, Qiagen), for 30 minutes at 42°C, and the samples stored at -80°C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from each population of laser captured β–cells using phenol-chloroform-isoamyl alcohol and precipitated with sodium acetate and glycogen carrier in isopropanol. After initial recovery and resuspension of the RNA pellet, genomic DNA contamination was removed by incubation with 10 units of DNase I for 2 hours at 37°C, in presence of 10 units of RNase inhibitor. The treatment with DNase I was followed by RNA re-extraction and precipitation. The pellet was resuspended and total RNA was amplified by T7-based linear amplification using T7-oligo-dT-primers. Two rounds of amplification were performed using RiboAmp HS RNA Amplification Kits (Arcturus).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Amplified RNA (1 μg) was converted into double-stranded complementary DNA (cDNA) using the RiboAmp HS RNA Amplification Kit (Arcturus), and biotinylated complementary RNA (cRNA) was generated from cDNA by in vitro transcription reaction using the BioArray High Yield RNA Transcript Labeling Kit (Enzo Diagnostics). RNA products were purified using the MiraColTM Purification Columns (Arcturus).
| | Sample_hyb_protocol | 15ug of biotinylated cRNA was hybridized for 16hr at 45C to the Affymetrix Human X3P array. Following hybridization, arrays were washed and stained on the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | Data were analyzed using DNA-chip Analyzer software (dChip), using the invariant set normalization algorithm.
| | Sample_platform_id | GPL1352
| | Sample_contact_name | Lorella,,Marselli
| | Sample_contact_email | Lorella.Marselli@med.unipi.it
| | Sample_contact_phone | +39 050 995135
| | Sample_contact_fax | +39 050 541521
| | Sample_contact_laboratory | Section on Islet Transplantation and Cell Biology
| | Sample_contact_department | Joslin Diabetes Center and the Department of Medicine
| | Sample_contact_institute | Harvard Medical School
| | Sample_contact_address | One Joslin Place
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02215
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM524nnn/GSM524162/suppl/GSM524162.CEL.gz
| | Sample_series_id | GSE20966
| | Sample_data_row_count | 61295
| | |
|
GSM524163 | GPL1352 |
|
beta-cells_diabetic condition_donor3
|
human beta-cells_diabetic
|
sample id: D1
disease: type 2 diabetes
cell type: beta-cells
tissue: pancreas
gender: male
age (years): 63
bmi (body mass index, kg/m2): 29.4
|
Gene expression data from type 2 diabetic subjects
|
| Sample_geo_accession | GSM524163
| | Sample_status | Public on Mar 20 2010
| | Sample_submission_date | Mar 19 2010
| | Sample_last_update_date | Mar 19 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Pancreas specimens were obtained, placed in cryomolds, embedded in Tissue-Tek OCT medium, immediately frozen in chilled isopentane, and stored at –80°C, pending sectioning at 8 μm. Frozen pancreatic sections were fixed in 70% ethanol for 30 seconds, rinsed by 5 dips in diethylpyrocarbonate (DEPC)-treated water and dehydrated in 100% ethanol twice for 1 min, and xylene for 4 minutes, the sections were air-dried and laser capture microdissection was performed. The microdissected cells were incubated with 10 μl of guanidine thiocyanate and polyethylene glycol octylphenol ether-based buffer (Buffer RLT, Qiagen), for 30 minutes at 42°C, and the samples stored at -80°C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from each population of laser captured β–cells using phenol-chloroform-isoamyl alcohol and precipitated with sodium acetate and glycogen carrier in isopropanol. After initial recovery and resuspension of the RNA pellet, genomic DNA contamination was removed by incubation with 10 units of DNase I for 2 hours at 37°C, in presence of 10 units of RNase inhibitor. The treatment with DNase I was followed by RNA re-extraction and precipitation. The pellet was resuspended and total RNA was amplified by T7-based linear amplification using T7-oligo-dT-primers. Two rounds of amplification were performed using RiboAmp HS RNA Amplification Kits (Arcturus).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Amplified RNA (1 μg) was converted into double-stranded complementary DNA (cDNA) using the RiboAmp HS RNA Amplification Kit (Arcturus), and biotinylated complementary RNA (cRNA) was generated from cDNA by in vitro transcription reaction using the BioArray High Yield RNA Transcript Labeling Kit (Enzo Diagnostics). RNA products were purified using the MiraColTM Purification Columns (Arcturus).
| | Sample_hyb_protocol | 15ug of biotinylated cRNA was hybridized for 16hr at 45C to the Affymetrix Human X3P array. Following hybridization, arrays were washed and stained on the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | Data were analyzed using DNA-chip Analyzer software (dChip), using the invariant set normalization algorithm.
| | Sample_platform_id | GPL1352
| | Sample_contact_name | Lorella,,Marselli
| | Sample_contact_email | Lorella.Marselli@med.unipi.it
| | Sample_contact_phone | +39 050 995135
| | Sample_contact_fax | +39 050 541521
| | Sample_contact_laboratory | Section on Islet Transplantation and Cell Biology
| | Sample_contact_department | Joslin Diabetes Center and the Department of Medicine
| | Sample_contact_institute | Harvard Medical School
| | Sample_contact_address | One Joslin Place
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02215
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM524nnn/GSM524163/suppl/GSM524163.CEL.gz
| | Sample_series_id | GSE20966
| | Sample_data_row_count | 61295
| | |
|
GSM524164 | GPL1352 |
|
beta-cells_diabetic condition_donor4
|
human beta-cells_diabetic
|
sample id: DM2
disease: type 2 diabetes
cell type: beta-cells
tissue: pancreas
gender: male
age (years): 64
bmi (body mass index, kg/m2): NA
|
Gene expression data from type 2 diabetic subjects
|
| Sample_geo_accession | GSM524164
| | Sample_status | Public on Mar 20 2010
| | Sample_submission_date | Mar 19 2010
| | Sample_last_update_date | Mar 19 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Pancreas specimens were obtained, placed in cryomolds, embedded in Tissue-Tek OCT medium, immediately frozen in chilled isopentane, and stored at –80°C, pending sectioning at 8 μm. Frozen pancreatic sections were fixed in 70% ethanol for 30 seconds, rinsed by 5 dips in diethylpyrocarbonate (DEPC)-treated water and dehydrated in 100% ethanol twice for 1 min, and xylene for 4 minutes, the sections were air-dried and laser capture microdissection was performed. The microdissected cells were incubated with 10 μl of guanidine thiocyanate and polyethylene glycol octylphenol ether-based buffer (Buffer RLT, Qiagen), for 30 minutes at 42°C, and the samples stored at -80°C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from each population of laser captured β–cells using phenol-chloroform-isoamyl alcohol and precipitated with sodium acetate and glycogen carrier in isopropanol. After initial recovery and resuspension of the RNA pellet, genomic DNA contamination was removed by incubation with 10 units of DNase I for 2 hours at 37°C, in presence of 10 units of RNase inhibitor. The treatment with DNase I was followed by RNA re-extraction and precipitation. The pellet was resuspended and total RNA was amplified by T7-based linear amplification using T7-oligo-dT-primers. Two rounds of amplification were performed using RiboAmp HS RNA Amplification Kits (Arcturus).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Amplified RNA (1 μg) was converted into double-stranded complementary DNA (cDNA) using the RiboAmp HS RNA Amplification Kit (Arcturus), and biotinylated complementary RNA (cRNA) was generated from cDNA by in vitro transcription reaction using the BioArray High Yield RNA Transcript Labeling Kit (Enzo Diagnostics). RNA products were purified using the MiraColTM Purification Columns (Arcturus).
| | Sample_hyb_protocol | 15ug of biotinylated cRNA was hybridized for 16hr at 45C to the Affymetrix Human X3P array. Following hybridization, arrays were washed and stained on the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | Data were analyzed using DNA-chip Analyzer software (dChip), using the invariant set normalization algorithm.
| | Sample_platform_id | GPL1352
| | Sample_contact_name | Lorella,,Marselli
| | Sample_contact_email | Lorella.Marselli@med.unipi.it
| | Sample_contact_phone | +39 050 995135
| | Sample_contact_fax | +39 050 541521
| | Sample_contact_laboratory | Section on Islet Transplantation and Cell Biology
| | Sample_contact_department | Joslin Diabetes Center and the Department of Medicine
| | Sample_contact_institute | Harvard Medical School
| | Sample_contact_address | One Joslin Place
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02215
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM524nnn/GSM524164/suppl/GSM524164.CEL.gz
| | Sample_series_id | GSE20966
| | Sample_data_row_count | 61295
| | |
|
GSM524165 | GPL1352 |
|
beta-cells_diabetic condition_donor5
|
human beta-cells_diabetic
|
sample id: D6
disease: type 2 diabetes
cell type: beta-cells
tissue: pancreas
gender: female
age (years): 74
bmi (body mass index, kg/m2): 28.6
|
Gene expression data from type 2 diabetic subjects
|
| Sample_geo_accession | GSM524165
| | Sample_status | Public on Mar 20 2010
| | Sample_submission_date | Mar 19 2010
| | Sample_last_update_date | Mar 19 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Pancreas specimens were obtained, placed in cryomolds, embedded in Tissue-Tek OCT medium, immediately frozen in chilled isopentane, and stored at –80°C, pending sectioning at 8 μm. Frozen pancreatic sections were fixed in 70% ethanol for 30 seconds, rinsed by 5 dips in diethylpyrocarbonate (DEPC)-treated water and dehydrated in 100% ethanol twice for 1 min, and xylene for 4 minutes, the sections were air-dried and laser capture microdissection was performed. The microdissected cells were incubated with 10 μl of guanidine thiocyanate and polyethylene glycol octylphenol ether-based buffer (Buffer RLT, Qiagen), for 30 minutes at 42°C, and the samples stored at -80°C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from each population of laser captured β–cells using phenol-chloroform-isoamyl alcohol and precipitated with sodium acetate and glycogen carrier in isopropanol. After initial recovery and resuspension of the RNA pellet, genomic DNA contamination was removed by incubation with 10 units of DNase I for 2 hours at 37°C, in presence of 10 units of RNase inhibitor. The treatment with DNase I was followed by RNA re-extraction and precipitation. The pellet was resuspended and total RNA was amplified by T7-based linear amplification using T7-oligo-dT-primers. Two rounds of amplification were performed using RiboAmp HS RNA Amplification Kits (Arcturus).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Amplified RNA (1 μg) was converted into double-stranded complementary DNA (cDNA) using the RiboAmp HS RNA Amplification Kit (Arcturus), and biotinylated complementary RNA (cRNA) was generated from cDNA by in vitro transcription reaction using the BioArray High Yield RNA Transcript Labeling Kit (Enzo Diagnostics). RNA products were purified using the MiraColTM Purification Columns (Arcturus).
| | Sample_hyb_protocol | 15ug of biotinylated cRNA was hybridized for 16hr at 45C to the Affymetrix Human X3P array. Following hybridization, arrays were washed and stained on the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | Data were analyzed using DNA-chip Analyzer software (dChip), using the invariant set normalization algorithm.
| | Sample_platform_id | GPL1352
| | Sample_contact_name | Lorella,,Marselli
| | Sample_contact_email | Lorella.Marselli@med.unipi.it
| | Sample_contact_phone | +39 050 995135
| | Sample_contact_fax | +39 050 541521
| | Sample_contact_laboratory | Section on Islet Transplantation and Cell Biology
| | Sample_contact_department | Joslin Diabetes Center and the Department of Medicine
| | Sample_contact_institute | Harvard Medical School
| | Sample_contact_address | One Joslin Place
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02215
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM524nnn/GSM524165/suppl/GSM524165.CEL.gz
| | Sample_series_id | GSE20966
| | Sample_data_row_count | 61295
| | |
|
GSM524166 | GPL1352 |
|
beta-cells_diabetic condition_donor6
|
human beta-cells_diabetic
|
sample id: D7
disease: type 2 diabetes
cell type: beta-cells
tissue: pancreas
gender: male
age (years): 69
bmi (body mass index, kg/m2): 33.6
|
Gene expression data from type 2 diabetic subjects
|
| Sample_geo_accession | GSM524166
| | Sample_status | Public on Mar 20 2010
| | Sample_submission_date | Mar 19 2010
| | Sample_last_update_date | Mar 19 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Pancreas specimens were obtained, placed in cryomolds, embedded in Tissue-Tek OCT medium, immediately frozen in chilled isopentane, and stored at –80°C, pending sectioning at 8 μm. Frozen pancreatic sections were fixed in 70% ethanol for 30 seconds, rinsed by 5 dips in diethylpyrocarbonate (DEPC)-treated water and dehydrated in 100% ethanol twice for 1 min, and xylene for 4 minutes, the sections were air-dried and laser capture microdissection was performed. The microdissected cells were incubated with 10 μl of guanidine thiocyanate and polyethylene glycol octylphenol ether-based buffer (Buffer RLT, Qiagen), for 30 minutes at 42°C, and the samples stored at -80°C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from each population of laser captured β–cells using phenol-chloroform-isoamyl alcohol and precipitated with sodium acetate and glycogen carrier in isopropanol. After initial recovery and resuspension of the RNA pellet, genomic DNA contamination was removed by incubation with 10 units of DNase I for 2 hours at 37°C, in presence of 10 units of RNase inhibitor. The treatment with DNase I was followed by RNA re-extraction and precipitation. The pellet was resuspended and total RNA was amplified by T7-based linear amplification using T7-oligo-dT-primers. Two rounds of amplification were performed using RiboAmp HS RNA Amplification Kits (Arcturus).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Amplified RNA (1 μg) was converted into double-stranded complementary DNA (cDNA) using the RiboAmp HS RNA Amplification Kit (Arcturus), and biotinylated complementary RNA (cRNA) was generated from cDNA by in vitro transcription reaction using the BioArray High Yield RNA Transcript Labeling Kit (Enzo Diagnostics). RNA products were purified using the MiraColTM Purification Columns (Arcturus).
| | Sample_hyb_protocol | 15ug of biotinylated cRNA was hybridized for 16hr at 45C to the Affymetrix Human X3P array. Following hybridization, arrays were washed and stained on the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | Data were analyzed using DNA-chip Analyzer software (dChip), using the invariant set normalization algorithm.
| | Sample_platform_id | GPL1352
| | Sample_contact_name | Lorella,,Marselli
| | Sample_contact_email | Lorella.Marselli@med.unipi.it
| | Sample_contact_phone | +39 050 995135
| | Sample_contact_fax | +39 050 541521
| | Sample_contact_laboratory | Section on Islet Transplantation and Cell Biology
| | Sample_contact_department | Joslin Diabetes Center and the Department of Medicine
| | Sample_contact_institute | Harvard Medical School
| | Sample_contact_address | One Joslin Place
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02215
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM524nnn/GSM524166/suppl/GSM524166.CEL.gz
| | Sample_series_id | GSE20966
| | Sample_data_row_count | 61295
| | |
|
GSM524167 | GPL1352 |
|
beta-cells_diabetic condition_donor7
|
human beta-cells_diabetic
|
sample id: D8
disease: type 2 diabetes
cell type: beta-cells
tissue: pancreas
gender: male
age (years): 61
bmi (body mass index, kg/m2): 27.8
|
Gene expression data from type 2 diabetic subjects
|
| Sample_geo_accession | GSM524167
| | Sample_status | Public on Mar 20 2010
| | Sample_submission_date | Mar 19 2010
| | Sample_last_update_date | Mar 19 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Pancreas specimens were obtained, placed in cryomolds, embedded in Tissue-Tek OCT medium, immediately frozen in chilled isopentane, and stored at –80°C, pending sectioning at 8 μm. Frozen pancreatic sections were fixed in 70% ethanol for 30 seconds, rinsed by 5 dips in diethylpyrocarbonate (DEPC)-treated water and dehydrated in 100% ethanol twice for 1 min, and xylene for 4 minutes, the sections were air-dried and laser capture microdissection was performed. The microdissected cells were incubated with 10 μl of guanidine thiocyanate and polyethylene glycol octylphenol ether-based buffer (Buffer RLT, Qiagen), for 30 minutes at 42°C, and the samples stored at -80°C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from each population of laser captured β–cells using phenol-chloroform-isoamyl alcohol and precipitated with sodium acetate and glycogen carrier in isopropanol. After initial recovery and resuspension of the RNA pellet, genomic DNA contamination was removed by incubation with 10 units of DNase I for 2 hours at 37°C, in presence of 10 units of RNase inhibitor. The treatment with DNase I was followed by RNA re-extraction and precipitation. The pellet was resuspended and total RNA was amplified by T7-based linear amplification using T7-oligo-dT-primers. Two rounds of amplification were performed using RiboAmp HS RNA Amplification Kits (Arcturus).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Amplified RNA (1 μg) was converted into double-stranded complementary DNA (cDNA) using the RiboAmp HS RNA Amplification Kit (Arcturus), and biotinylated complementary RNA (cRNA) was generated from cDNA by in vitro transcription reaction using the BioArray High Yield RNA Transcript Labeling Kit (Enzo Diagnostics). RNA products were purified using the MiraColTM Purification Columns (Arcturus).
| | Sample_hyb_protocol | 15ug of biotinylated cRNA was hybridized for 16hr at 45C to the Affymetrix Human X3P array. Following hybridization, arrays were washed and stained on the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | Data were analyzed using DNA-chip Analyzer software (dChip), using the invariant set normalization algorithm.
| | Sample_platform_id | GPL1352
| | Sample_contact_name | Lorella,,Marselli
| | Sample_contact_email | Lorella.Marselli@med.unipi.it
| | Sample_contact_phone | +39 050 995135
| | Sample_contact_fax | +39 050 541521
| | Sample_contact_laboratory | Section on Islet Transplantation and Cell Biology
| | Sample_contact_department | Joslin Diabetes Center and the Department of Medicine
| | Sample_contact_institute | Harvard Medical School
| | Sample_contact_address | One Joslin Place
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02215
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM524nnn/GSM524167/suppl/GSM524167.CEL.gz
| | Sample_series_id | GSE20966
| | Sample_data_row_count | 61295
| | |
|
GSM524168 | GPL1352 |
|
beta-cells_diabetic condition_donor8
|
human beta-cells_diabetic
|
sample id: D9
disease: type 2 diabetes
cell type: beta-cells
tissue: pancreas
gender: male
age (years): 79
bmi (body mass index, kg/m2): 25.9
|
Gene expression data from type 2 diabetic subjects
|
| Sample_geo_accession | GSM524168
| | Sample_status | Public on Mar 20 2010
| | Sample_submission_date | Mar 19 2010
| | Sample_last_update_date | Mar 19 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Pancreas specimens were obtained, placed in cryomolds, embedded in Tissue-Tek OCT medium, immediately frozen in chilled isopentane, and stored at –80°C, pending sectioning at 8 μm. Frozen pancreatic sections were fixed in 70% ethanol for 30 seconds, rinsed by 5 dips in diethylpyrocarbonate (DEPC)-treated water and dehydrated in 100% ethanol twice for 1 min, and xylene for 4 minutes, the sections were air-dried and laser capture microdissection was performed. The microdissected cells were incubated with 10 μl of guanidine thiocyanate and polyethylene glycol octylphenol ether-based buffer (Buffer RLT, Qiagen), for 30 minutes at 42°C, and the samples stored at -80°C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from each population of laser captured β–cells using phenol-chloroform-isoamyl alcohol and precipitated with sodium acetate and glycogen carrier in isopropanol. After initial recovery and resuspension of the RNA pellet, genomic DNA contamination was removed by incubation with 10 units of DNase I for 2 hours at 37°C, in presence of 10 units of RNase inhibitor. The treatment with DNase I was followed by RNA re-extraction and precipitation. The pellet was resuspended and total RNA was amplified by T7-based linear amplification using T7-oligo-dT-primers. Two rounds of amplification were performed using RiboAmp HS RNA Amplification Kits (Arcturus).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Amplified RNA (1 μg) was converted into double-stranded complementary DNA (cDNA) using the RiboAmp HS RNA Amplification Kit (Arcturus), and biotinylated complementary RNA (cRNA) was generated from cDNA by in vitro transcription reaction using the BioArray High Yield RNA Transcript Labeling Kit (Enzo Diagnostics). RNA products were purified using the MiraColTM Purification Columns (Arcturus).
| | Sample_hyb_protocol | 15ug of biotinylated cRNA was hybridized for 16hr at 45C to the Affymetrix Human X3P array. Following hybridization, arrays were washed and stained on the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | Data were analyzed using DNA-chip Analyzer software (dChip), using the invariant set normalization algorithm.
| | Sample_platform_id | GPL1352
| | Sample_contact_name | Lorella,,Marselli
| | Sample_contact_email | Lorella.Marselli@med.unipi.it
| | Sample_contact_phone | +39 050 995135
| | Sample_contact_fax | +39 050 541521
| | Sample_contact_laboratory | Section on Islet Transplantation and Cell Biology
| | Sample_contact_department | Joslin Diabetes Center and the Department of Medicine
| | Sample_contact_institute | Harvard Medical School
| | Sample_contact_address | One Joslin Place
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02215
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM524nnn/GSM524168/suppl/GSM524168.CEL.gz
| | Sample_series_id | GSE20966
| | Sample_data_row_count | 61295
| | |
|
GSM524169 | GPL1352 |
|
beta-cells_diabetic condition_donor9
|
human beta-cells_diabetic
|
sample id: D11
disease: type 2 diabetes
cell type: beta-cells
tissue: pancreas
gender: male
age (years): 56
bmi (body mass index, kg/m2): 31.0
|
Gene expression data from type 2 diabetic subjects
|
| Sample_geo_accession | GSM524169
| | Sample_status | Public on Mar 20 2010
| | Sample_submission_date | Mar 19 2010
| | Sample_last_update_date | Mar 19 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Pancreas specimens were obtained, placed in cryomolds, embedded in Tissue-Tek OCT medium, immediately frozen in chilled isopentane, and stored at –80°C, pending sectioning at 8 μm. Frozen pancreatic sections were fixed in 70% ethanol for 30 seconds, rinsed by 5 dips in diethylpyrocarbonate (DEPC)-treated water and dehydrated in 100% ethanol twice for 1 min, and xylene for 4 minutes, the sections were air-dried and laser capture microdissection was performed. The microdissected cells were incubated with 10 μl of guanidine thiocyanate and polyethylene glycol octylphenol ether-based buffer (Buffer RLT, Qiagen), for 30 minutes at 42°C, and the samples stored at -80°C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from each population of laser captured β–cells using phenol-chloroform-isoamyl alcohol and precipitated with sodium acetate and glycogen carrier in isopropanol. After initial recovery and resuspension of the RNA pellet, genomic DNA contamination was removed by incubation with 10 units of DNase I for 2 hours at 37°C, in presence of 10 units of RNase inhibitor. The treatment with DNase I was followed by RNA re-extraction and precipitation. The pellet was resuspended and total RNA was amplified by T7-based linear amplification using T7-oligo-dT-primers. Two rounds of amplification were performed using RiboAmp HS RNA Amplification Kits (Arcturus).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Amplified RNA (1 μg) was converted into double-stranded complementary DNA (cDNA) using the RiboAmp HS RNA Amplification Kit (Arcturus), and biotinylated complementary RNA (cRNA) was generated from cDNA by in vitro transcription reaction using the BioArray High Yield RNA Transcript Labeling Kit (Enzo Diagnostics). RNA products were purified using the MiraColTM Purification Columns (Arcturus).
| | Sample_hyb_protocol | 15ug of biotinylated cRNA was hybridized for 16hr at 45C to the Affymetrix Human X3P array. Following hybridization, arrays were washed and stained on the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | Data were analyzed using DNA-chip Analyzer software (dChip), using the invariant set normalization algorithm.
| | Sample_platform_id | GPL1352
| | Sample_contact_name | Lorella,,Marselli
| | Sample_contact_email | Lorella.Marselli@med.unipi.it
| | Sample_contact_phone | +39 050 995135
| | Sample_contact_fax | +39 050 541521
| | Sample_contact_laboratory | Section on Islet Transplantation and Cell Biology
| | Sample_contact_department | Joslin Diabetes Center and the Department of Medicine
| | Sample_contact_institute | Harvard Medical School
| | Sample_contact_address | One Joslin Place
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02215
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM524nnn/GSM524169/suppl/GSM524169.CEL.gz
| | Sample_series_id | GSE20966
| | Sample_data_row_count | 61295
| | |
|
GSM524170 | GPL1352 |
|
beta-cells_diabetic condition_donor10
|
human beta-cells_diabetic
|
sample id: D12
disease: type 2 diabetes
cell type: beta-cells
tissue: pancreas
gender: female
age (years): 65
bmi (body mass index, kg/m2): 46.0
|
Gene expression data from type 2 diabetic subjects
|
| Sample_geo_accession | GSM524170
| | Sample_status | Public on Mar 20 2010
| | Sample_submission_date | Mar 19 2010
| | Sample_last_update_date | Mar 19 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Pancreas specimens were obtained, placed in cryomolds, embedded in Tissue-Tek OCT medium, immediately frozen in chilled isopentane, and stored at –80°C, pending sectioning at 8 μm. Frozen pancreatic sections were fixed in 70% ethanol for 30 seconds, rinsed by 5 dips in diethylpyrocarbonate (DEPC)-treated water and dehydrated in 100% ethanol twice for 1 min, and xylene for 4 minutes, the sections were air-dried and laser capture microdissection was performed. The microdissected cells were incubated with 10 μl of guanidine thiocyanate and polyethylene glycol octylphenol ether-based buffer (Buffer RLT, Qiagen), for 30 minutes at 42°C, and the samples stored at -80°C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from each population of laser captured β–cells using phenol-chloroform-isoamyl alcohol and precipitated with sodium acetate and glycogen carrier in isopropanol. After initial recovery and resuspension of the RNA pellet, genomic DNA contamination was removed by incubation with 10 units of DNase I for 2 hours at 37°C, in presence of 10 units of RNase inhibitor. The treatment with DNase I was followed by RNA re-extraction and precipitation. The pellet was resuspended and total RNA was amplified by T7-based linear amplification using T7-oligo-dT-primers. Two rounds of amplification were performed using RiboAmp HS RNA Amplification Kits (Arcturus).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Amplified RNA (1 μg) was converted into double-stranded complementary DNA (cDNA) using the RiboAmp HS RNA Amplification Kit (Arcturus), and biotinylated complementary RNA (cRNA) was generated from cDNA by in vitro transcription reaction using the BioArray High Yield RNA Transcript Labeling Kit (Enzo Diagnostics). RNA products were purified using the MiraColTM Purification Columns (Arcturus).
| | Sample_hyb_protocol | 15ug of biotinylated cRNA was hybridized for 16hr at 45C to the Affymetrix Human X3P array. Following hybridization, arrays were washed and stained on the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | Data were analyzed using DNA-chip Analyzer software (dChip), using the invariant set normalization algorithm.
| | Sample_platform_id | GPL1352
| | Sample_contact_name | Lorella,,Marselli
| | Sample_contact_email | Lorella.Marselli@med.unipi.it
| | Sample_contact_phone | +39 050 995135
| | Sample_contact_fax | +39 050 541521
| | Sample_contact_laboratory | Section on Islet Transplantation and Cell Biology
| | Sample_contact_department | Joslin Diabetes Center and the Department of Medicine
| | Sample_contact_institute | Harvard Medical School
| | Sample_contact_address | One Joslin Place
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02215
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM524nnn/GSM524170/suppl/GSM524170.CEL.gz
| | Sample_series_id | GSE20966
| | Sample_data_row_count | 61295
| | |
|
| |
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