Search results for the GEO ID: GSE34811  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM855708 | GPL1355 |
|
IFNү/IL1-β stimulated non-phagocytosing macrophages (repl 1)
|
Peritoneal macrophages
|
strain: Hsdcpb:WU
weight: 200-224 grams
cell type: peritoneal macrophages
treatment: control, IFNү/IL1-β
|
|
| Sample_geo_accession | GSM855708
| | Sample_status | Public on Aug 20 2012
| | Sample_submission_date | Jan 03 2012
| | Sample_last_update_date | Aug 23 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Macrophages were left untreated or treated with 100 µg/ml of isolated myelin. Following 3 days, both control and myelin-treated macrophages were stimulated with 100 ng/ml IFNү and IL-1β for 9 hours.
| | Sample_growth_protocol_ch1 | Resident peritoneal macrophages were obtained by peritoneal lavage using 10 ml of ice-cold PBS supplemented with 5 mM EDTA. Peritoneal exudate cells were cultured for 2 hours in RPMI 1640 medium. After a 2 hour incubation at 37°C with 5% CO2, non-adherent cells were washed away. Remaining cells were >95% macrophages. Isolated macrophages were seeded in flat-bottem 12-well plates in RPMI 1640 medium supplemented with 50 U/ml streptomycin, 50 U/ml penicillin and 10% FCS at 37°C with 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared using the RNeasy mini kit (Qiagen), according to the manufacturer’s instructions. The RNA concentration and quality was determined with a NanoDrop spectrophotometer.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 11 ug of cRNA was hybridized for 16 hr at 45C on GeneChip Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix Gene Chip Scanner 3000 7G.
| | Sample_data_processing | Bioconductor packages running under the R platform were used to process raw data. Data were processed with RMA method.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Jeroen,Felix Jacobus,Bogie
| | Sample_contact_email | Jeroen.bogie@uhasselt.be
| | Sample_contact_laboratory | Neuro-Immunology
| | Sample_contact_department | Biomedical Research Institute
| | Sample_contact_institute | Hasselt University
| | Sample_contact_address | Agoralaan Building C
| | Sample_contact_city | Diepenbeek
| | Sample_contact_zip/postal_code | B-3590
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM855nnn/GSM855708/suppl/GSM855708_100312_Hasselt-WP5_01_1_MA_Rat230_2_.CEL.gz
| | Sample_series_id | GSE34811
| | Sample_data_row_count | 31099
| | |
|
GSM855709 | GPL1355 |
|
IFNү/IL1-β stimulated non-phagocytosing macrophages (repl 2)
|
Peritoneal macrophages
|
strain: Hsdcpb:WU
weight: 200-224 grams
cell type: peritoneal macrophages
treatment: control, IFNү/IL1-β
|
|
| Sample_geo_accession | GSM855709
| | Sample_status | Public on Aug 20 2012
| | Sample_submission_date | Jan 03 2012
| | Sample_last_update_date | Aug 23 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Macrophages were left untreated or treated with 100 µg/ml of isolated myelin. Following 3 days, both control and myelin-treated macrophages were stimulated with 100 ng/ml IFNү and IL-1β for 9 hours.
| | Sample_growth_protocol_ch1 | Resident peritoneal macrophages were obtained by peritoneal lavage using 10 ml of ice-cold PBS supplemented with 5 mM EDTA. Peritoneal exudate cells were cultured for 2 hours in RPMI 1640 medium. After a 2 hour incubation at 37°C with 5% CO2, non-adherent cells were washed away. Remaining cells were >95% macrophages. Isolated macrophages were seeded in flat-bottem 12-well plates in RPMI 1640 medium supplemented with 50 U/ml streptomycin, 50 U/ml penicillin and 10% FCS at 37°C with 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared using the RNeasy mini kit (Qiagen), according to the manufacturer’s instructions. The RNA concentration and quality was determined with a NanoDrop spectrophotometer.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 11 ug of cRNA was hybridized for 16 hr at 45C on GeneChip Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix Gene Chip Scanner 3000 7G.
| | Sample_data_processing | Bioconductor packages running under the R platform were used to process raw data. Data were processed with RMA method.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Jeroen,Felix Jacobus,Bogie
| | Sample_contact_email | Jeroen.bogie@uhasselt.be
| | Sample_contact_laboratory | Neuro-Immunology
| | Sample_contact_department | Biomedical Research Institute
| | Sample_contact_institute | Hasselt University
| | Sample_contact_address | Agoralaan Building C
| | Sample_contact_city | Diepenbeek
| | Sample_contact_zip/postal_code | B-3590
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM855nnn/GSM855709/suppl/GSM855709_100312_Hasselt-WP5_02_2_MA_Rat230_2_.CEL.gz
| | Sample_series_id | GSE34811
| | Sample_data_row_count | 31099
| | |
|
GSM855710 | GPL1355 |
|
IFNү/IL1-β stimulated non-phagocytosing macrophages (repl 3)
|
Peritoneal macrophages
|
strain: Hsdcpb:WU
weight: 200-224 grams
cell type: peritoneal macrophages
treatment: control, IFNү/IL1-β
|
|
| Sample_geo_accession | GSM855710
| | Sample_status | Public on Aug 20 2012
| | Sample_submission_date | Jan 03 2012
| | Sample_last_update_date | Aug 23 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Macrophages were left untreated or treated with 100 µg/ml of isolated myelin. Following 3 days, both control and myelin-treated macrophages were stimulated with 100 ng/ml IFNү and IL-1β for 9 hours.
| | Sample_growth_protocol_ch1 | Resident peritoneal macrophages were obtained by peritoneal lavage using 10 ml of ice-cold PBS supplemented with 5 mM EDTA. Peritoneal exudate cells were cultured for 2 hours in RPMI 1640 medium. After a 2 hour incubation at 37°C with 5% CO2, non-adherent cells were washed away. Remaining cells were >95% macrophages. Isolated macrophages were seeded in flat-bottem 12-well plates in RPMI 1640 medium supplemented with 50 U/ml streptomycin, 50 U/ml penicillin and 10% FCS at 37°C with 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared using the RNeasy mini kit (Qiagen), according to the manufacturer’s instructions. The RNA concentration and quality was determined with a NanoDrop spectrophotometer.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 11 ug of cRNA was hybridized for 16 hr at 45C on GeneChip Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix Gene Chip Scanner 3000 7G.
| | Sample_data_processing | Bioconductor packages running under the R platform were used to process raw data. Data were processed with RMA method.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Jeroen,Felix Jacobus,Bogie
| | Sample_contact_email | Jeroen.bogie@uhasselt.be
| | Sample_contact_laboratory | Neuro-Immunology
| | Sample_contact_department | Biomedical Research Institute
| | Sample_contact_institute | Hasselt University
| | Sample_contact_address | Agoralaan Building C
| | Sample_contact_city | Diepenbeek
| | Sample_contact_zip/postal_code | B-3590
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM855nnn/GSM855710/suppl/GSM855710_100312_Hasselt-WP5_03_3_MA_Rat230_2_.CEL.gz
| | Sample_series_id | GSE34811
| | Sample_data_row_count | 31099
| | |
|
GSM855711 | GPL1355 |
|
IFNү/IL1-β stimulated non-phagocytosing macrophages (repl 4)
|
Peritoneal macrophages
|
strain: Hsdcpb:WU
weight: 200-224 grams
cell type: peritoneal macrophages
treatment: control, IFNү/IL1-β
|
|
| Sample_geo_accession | GSM855711
| | Sample_status | Public on Aug 20 2012
| | Sample_submission_date | Jan 03 2012
| | Sample_last_update_date | Aug 23 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Macrophages were left untreated or treated with 100 µg/ml of isolated myelin. Following 3 days, both control and myelin-treated macrophages were stimulated with 100 ng/ml IFNү and IL-1β for 9 hours.
| | Sample_growth_protocol_ch1 | Resident peritoneal macrophages were obtained by peritoneal lavage using 10 ml of ice-cold PBS supplemented with 5 mM EDTA. Peritoneal exudate cells were cultured for 2 hours in RPMI 1640 medium. After a 2 hour incubation at 37°C with 5% CO2, non-adherent cells were washed away. Remaining cells were >95% macrophages. Isolated macrophages were seeded in flat-bottem 12-well plates in RPMI 1640 medium supplemented with 50 U/ml streptomycin, 50 U/ml penicillin and 10% FCS at 37°C with 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared using the RNeasy mini kit (Qiagen), according to the manufacturer’s instructions. The RNA concentration and quality was determined with a NanoDrop spectrophotometer.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 11 ug of cRNA was hybridized for 16 hr at 45C on GeneChip Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix Gene Chip Scanner 3000 7G.
| | Sample_data_processing | Bioconductor packages running under the R platform were used to process raw data. Data were processed with RMA method.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Jeroen,Felix Jacobus,Bogie
| | Sample_contact_email | Jeroen.bogie@uhasselt.be
| | Sample_contact_laboratory | Neuro-Immunology
| | Sample_contact_department | Biomedical Research Institute
| | Sample_contact_institute | Hasselt University
| | Sample_contact_address | Agoralaan Building C
| | Sample_contact_city | Diepenbeek
| | Sample_contact_zip/postal_code | B-3590
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM855nnn/GSM855711/suppl/GSM855711_100312_Hasselt-WP5_04_4_MA_Rat230_2_.CEL.gz
| | Sample_series_id | GSE34811
| | Sample_data_row_count | 31099
| | |
|
GSM855712 | GPL1355 |
|
IFNү/IL1-β stimulated non-phagocytosing macrophages (repl 5)
|
Peritoneal macrophages
|
strain: Hsdcpb:WU
weight: 200-224 grams
cell type: peritoneal macrophages
treatment: control, IFNү/IL1-β
|
|
| Sample_geo_accession | GSM855712
| | Sample_status | Public on Aug 20 2012
| | Sample_submission_date | Jan 03 2012
| | Sample_last_update_date | Aug 23 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Macrophages were left untreated or treated with 100 µg/ml of isolated myelin. Following 3 days, both control and myelin-treated macrophages were stimulated with 100 ng/ml IFNү and IL-1β for 9 hours.
| | Sample_growth_protocol_ch1 | Resident peritoneal macrophages were obtained by peritoneal lavage using 10 ml of ice-cold PBS supplemented with 5 mM EDTA. Peritoneal exudate cells were cultured for 2 hours in RPMI 1640 medium. After a 2 hour incubation at 37°C with 5% CO2, non-adherent cells were washed away. Remaining cells were >95% macrophages. Isolated macrophages were seeded in flat-bottem 12-well plates in RPMI 1640 medium supplemented with 50 U/ml streptomycin, 50 U/ml penicillin and 10% FCS at 37°C with 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared using the RNeasy mini kit (Qiagen), according to the manufacturer’s instructions. The RNA concentration and quality was determined with a NanoDrop spectrophotometer.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 11 ug of cRNA was hybridized for 16 hr at 45C on GeneChip Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix Gene Chip Scanner 3000 7G.
| | Sample_data_processing | Bioconductor packages running under the R platform were used to process raw data. Data were processed with RMA method.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Jeroen,Felix Jacobus,Bogie
| | Sample_contact_email | Jeroen.bogie@uhasselt.be
| | Sample_contact_laboratory | Neuro-Immunology
| | Sample_contact_department | Biomedical Research Institute
| | Sample_contact_institute | Hasselt University
| | Sample_contact_address | Agoralaan Building C
| | Sample_contact_city | Diepenbeek
| | Sample_contact_zip/postal_code | B-3590
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM855nnn/GSM855712/suppl/GSM855712_100312_Hasselt-WP5_05_5_MA_Rat230_2_.CEL.gz
| | Sample_series_id | GSE34811
| | Sample_data_row_count | 31099
| | |
|
GSM855713 | GPL1355 |
|
IFNү/IL1-β stimulated myelin-phagocytosing macrophages (repl 1)
|
Peritoneal macrophages
|
strain: Hsdcpb:WU
weight: 200-224 grams
cell type: peritoneal macrophages
treatment: myelin + IFNү/IL1-β
|
|
| Sample_geo_accession | GSM855713
| | Sample_status | Public on Aug 20 2012
| | Sample_submission_date | Jan 03 2012
| | Sample_last_update_date | Aug 23 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Macrophages were left untreated or treated with 100 µg/ml of isolated myelin. Following 3 days, both control and myelin-treated macrophages were stimulated with 100 ng/ml IFNү and IL-1β for 9 hours.
| | Sample_growth_protocol_ch1 | Resident peritoneal macrophages were obtained by peritoneal lavage using 10 ml of ice-cold PBS supplemented with 5 mM EDTA. Peritoneal exudate cells were cultured for 2 hours in RPMI 1640 medium. After a 2 hour incubation at 37°C with 5% CO2, non-adherent cells were washed away. Remaining cells were >95% macrophages. Isolated macrophages were seeded in flat-bottem 12-well plates in RPMI 1640 medium supplemented with 50 U/ml streptomycin, 50 U/ml penicillin and 10% FCS at 37°C with 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared using the RNeasy mini kit (Qiagen), according to the manufacturer’s instructions. The RNA concentration and quality was determined with a NanoDrop spectrophotometer.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 11 ug of cRNA was hybridized for 16 hr at 45C on GeneChip Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix Gene Chip Scanner 3000 7G.
| | Sample_data_processing | Bioconductor packages running under the R platform were used to process raw data. Data were processed with RMA method.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Jeroen,Felix Jacobus,Bogie
| | Sample_contact_email | Jeroen.bogie@uhasselt.be
| | Sample_contact_laboratory | Neuro-Immunology
| | Sample_contact_department | Biomedical Research Institute
| | Sample_contact_institute | Hasselt University
| | Sample_contact_address | Agoralaan Building C
| | Sample_contact_city | Diepenbeek
| | Sample_contact_zip/postal_code | B-3590
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM855nnn/GSM855713/suppl/GSM855713_100312_Hasselt-WP5_06_1_MYEMA_Rat230_2_.CEL.gz
| | Sample_series_id | GSE34811
| | Sample_data_row_count | 31099
| | |
|
GSM855714 | GPL1355 |
|
IFNү/IL1-β stimulated myelin-phagocytosing macrophages (repl 2)
|
Peritoneal macrophages
|
strain: Hsdcpb:WU
weight: 200-224 grams
cell type: peritoneal macrophages
treatment: myelin + IFNү/IL1-β
|
|
| Sample_geo_accession | GSM855714
| | Sample_status | Public on Aug 20 2012
| | Sample_submission_date | Jan 03 2012
| | Sample_last_update_date | Aug 23 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Macrophages were left untreated or treated with 100 µg/ml of isolated myelin. Following 3 days, both control and myelin-treated macrophages were stimulated with 100 ng/ml IFNү and IL-1β for 9 hours.
| | Sample_growth_protocol_ch1 | Resident peritoneal macrophages were obtained by peritoneal lavage using 10 ml of ice-cold PBS supplemented with 5 mM EDTA. Peritoneal exudate cells were cultured for 2 hours in RPMI 1640 medium. After a 2 hour incubation at 37°C with 5% CO2, non-adherent cells were washed away. Remaining cells were >95% macrophages. Isolated macrophages were seeded in flat-bottem 12-well plates in RPMI 1640 medium supplemented with 50 U/ml streptomycin, 50 U/ml penicillin and 10% FCS at 37°C with 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared using the RNeasy mini kit (Qiagen), according to the manufacturer’s instructions. The RNA concentration and quality was determined with a NanoDrop spectrophotometer.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 11 ug of cRNA was hybridized for 16 hr at 45C on GeneChip Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix Gene Chip Scanner 3000 7G.
| | Sample_data_processing | Bioconductor packages running under the R platform were used to process raw data. Data were processed with RMA method.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Jeroen,Felix Jacobus,Bogie
| | Sample_contact_email | Jeroen.bogie@uhasselt.be
| | Sample_contact_laboratory | Neuro-Immunology
| | Sample_contact_department | Biomedical Research Institute
| | Sample_contact_institute | Hasselt University
| | Sample_contact_address | Agoralaan Building C
| | Sample_contact_city | Diepenbeek
| | Sample_contact_zip/postal_code | B-3590
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM855nnn/GSM855714/suppl/GSM855714_100312_Hasselt-WP5_07_2_MYEMA_Rat230_2_.CEL.gz
| | Sample_series_id | GSE34811
| | Sample_data_row_count | 31099
| | |
|
GSM855715 | GPL1355 |
|
IFNү/IL1-β stimulated myelin-phagocytosing macrophages (repl 3)
|
Peritoneal macrophages
|
strain: Hsdcpb:WU
weight: 200-224 grams
cell type: peritoneal macrophages
treatment: myelin + IFNү/IL1-β
|
|
| Sample_geo_accession | GSM855715
| | Sample_status | Public on Aug 20 2012
| | Sample_submission_date | Jan 03 2012
| | Sample_last_update_date | Aug 23 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Macrophages were left untreated or treated with 100 µg/ml of isolated myelin. Following 3 days, both control and myelin-treated macrophages were stimulated with 100 ng/ml IFNү and IL-1β for 9 hours.
| | Sample_growth_protocol_ch1 | Resident peritoneal macrophages were obtained by peritoneal lavage using 10 ml of ice-cold PBS supplemented with 5 mM EDTA. Peritoneal exudate cells were cultured for 2 hours in RPMI 1640 medium. After a 2 hour incubation at 37°C with 5% CO2, non-adherent cells were washed away. Remaining cells were >95% macrophages. Isolated macrophages were seeded in flat-bottem 12-well plates in RPMI 1640 medium supplemented with 50 U/ml streptomycin, 50 U/ml penicillin and 10% FCS at 37°C with 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared using the RNeasy mini kit (Qiagen), according to the manufacturer’s instructions. The RNA concentration and quality was determined with a NanoDrop spectrophotometer.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 11 ug of cRNA was hybridized for 16 hr at 45C on GeneChip Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix Gene Chip Scanner 3000 7G.
| | Sample_data_processing | Bioconductor packages running under the R platform were used to process raw data. Data were processed with RMA method.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Jeroen,Felix Jacobus,Bogie
| | Sample_contact_email | Jeroen.bogie@uhasselt.be
| | Sample_contact_laboratory | Neuro-Immunology
| | Sample_contact_department | Biomedical Research Institute
| | Sample_contact_institute | Hasselt University
| | Sample_contact_address | Agoralaan Building C
| | Sample_contact_city | Diepenbeek
| | Sample_contact_zip/postal_code | B-3590
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM855nnn/GSM855715/suppl/GSM855715_100312_Hasselt-WP5_08_3_MYEMA_Rat230_2_.CEL.gz
| | Sample_series_id | GSE34811
| | Sample_data_row_count | 31099
| | |
|
GSM855716 | GPL1355 |
|
IFNү/IL1-β stimulated myelin-phagocytosing macrophages (repl 4)
|
Peritoneal macrophages
|
strain: Hsdcpb:WU
weight: 200-224 grams
cell type: peritoneal macrophages
treatment: myelin + IFNү/IL1-β
|
|
| Sample_geo_accession | GSM855716
| | Sample_status | Public on Aug 20 2012
| | Sample_submission_date | Jan 03 2012
| | Sample_last_update_date | Aug 23 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Macrophages were left untreated or treated with 100 µg/ml of isolated myelin. Following 3 days, both control and myelin-treated macrophages were stimulated with 100 ng/ml IFNү and IL-1β for 9 hours.
| | Sample_growth_protocol_ch1 | Resident peritoneal macrophages were obtained by peritoneal lavage using 10 ml of ice-cold PBS supplemented with 5 mM EDTA. Peritoneal exudate cells were cultured for 2 hours in RPMI 1640 medium. After a 2 hour incubation at 37°C with 5% CO2, non-adherent cells were washed away. Remaining cells were >95% macrophages. Isolated macrophages were seeded in flat-bottem 12-well plates in RPMI 1640 medium supplemented with 50 U/ml streptomycin, 50 U/ml penicillin and 10% FCS at 37°C with 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared using the RNeasy mini kit (Qiagen), according to the manufacturer’s instructions. The RNA concentration and quality was determined with a NanoDrop spectrophotometer.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 11 ug of cRNA was hybridized for 16 hr at 45C on GeneChip Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix Gene Chip Scanner 3000 7G.
| | Sample_data_processing | Bioconductor packages running under the R platform were used to process raw data. Data were processed with RMA method.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Jeroen,Felix Jacobus,Bogie
| | Sample_contact_email | Jeroen.bogie@uhasselt.be
| | Sample_contact_laboratory | Neuro-Immunology
| | Sample_contact_department | Biomedical Research Institute
| | Sample_contact_institute | Hasselt University
| | Sample_contact_address | Agoralaan Building C
| | Sample_contact_city | Diepenbeek
| | Sample_contact_zip/postal_code | B-3590
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM855nnn/GSM855716/suppl/GSM855716_100312_Hasselt-WP5_09_4_MYEMA_Rat230_2_.CEL.gz
| | Sample_series_id | GSE34811
| | Sample_data_row_count | 31099
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GSM855717 | GPL1355 |
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IFNү/IL1-β stimulated myelin-phagocytosing macrophages (repl 5)
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Peritoneal macrophages
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strain: Hsdcpb:WU
weight: 200-224 grams
cell type: peritoneal macrophages
treatment: myelin + IFNү/IL1-β
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| Sample_geo_accession | GSM855717
| | Sample_status | Public on Aug 20 2012
| | Sample_submission_date | Jan 03 2012
| | Sample_last_update_date | Aug 23 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Macrophages were left untreated or treated with 100 µg/ml of isolated myelin. Following 3 days, both control and myelin-treated macrophages were stimulated with 100 ng/ml IFNү and IL-1β for 9 hours.
| | Sample_growth_protocol_ch1 | Resident peritoneal macrophages were obtained by peritoneal lavage using 10 ml of ice-cold PBS supplemented with 5 mM EDTA. Peritoneal exudate cells were cultured for 2 hours in RPMI 1640 medium. After a 2 hour incubation at 37°C with 5% CO2, non-adherent cells were washed away. Remaining cells were >95% macrophages. Isolated macrophages were seeded in flat-bottem 12-well plates in RPMI 1640 medium supplemented with 50 U/ml streptomycin, 50 U/ml penicillin and 10% FCS at 37°C with 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared using the RNeasy mini kit (Qiagen), according to the manufacturer’s instructions. The RNA concentration and quality was determined with a NanoDrop spectrophotometer.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 11 ug of cRNA was hybridized for 16 hr at 45C on GeneChip Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix Gene Chip Scanner 3000 7G.
| | Sample_data_processing | Bioconductor packages running under the R platform were used to process raw data. Data were processed with RMA method.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Jeroen,Felix Jacobus,Bogie
| | Sample_contact_email | Jeroen.bogie@uhasselt.be
| | Sample_contact_laboratory | Neuro-Immunology
| | Sample_contact_department | Biomedical Research Institute
| | Sample_contact_institute | Hasselt University
| | Sample_contact_address | Agoralaan Building C
| | Sample_contact_city | Diepenbeek
| | Sample_contact_zip/postal_code | B-3590
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM855nnn/GSM855717/suppl/GSM855717_100312_Hasselt-WP5_10_5_MYEMA_Rat230_2_.CEL.gz
| | Sample_series_id | GSE34811
| | Sample_data_row_count | 31099
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