Search results for the GEO ID: GSE25550  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM628033 | GPL570 |
|
MALT_Lymphoma_LL5_t(11;18)-negative
|
MALT lymphoma
|
tissue: MALT_Lymphoma_LL5_t(11;18)-negative tumor
|
MALT lymphoma LL5
|
| Sample_geo_accession | GSM628033
| | Sample_status | Public on Nov 25 2010
| | Sample_submission_date | Nov 23 2010
| | Sample_last_update_date | Nov 24 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Department of Pathology, University Hospitals K.U.Leuven
| | Sample_treatment_protocol_ch1 | tissue blocs were kept at -80° till use
| | Sample_growth_protocol_ch1 | Fresh frozen tissue blocs were kept at -80° till use. They were transported on dry ice to the cryostat where a number (depending on the size of the bloc) of 20 micron thick sections were cut and put into a labeled, 2.0 ml microcentrifuge tube.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from 20 micron sections of each frozen tissue sample, using the TriZol reagent (Invitrogen, Merelbeke, Belgium) followed by purification using the RNaesy mini kit (Qiagen, Venlo, The Netherlands), according to the manufacturer’s recommendations. RNA quality, integrity and concentration were measured using a nanodrop spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microg total RNA.
| | Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45°C and at 60 rounds/min. The GeneChips were washed and stained in the Affymetrix Fluidics Station 400 and 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 7G.
| | Sample_data_processing | Data were normalized using GC-RMA, using the gcrma package in Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Joke,,Allemeersch
| | Sample_contact_email | joke.allemeersch@vib.be
| | Sample_contact_phone | +32(0)16 37 31 26
| | Sample_contact_department | Nucleomics Core
| | Sample_contact_institute | Flanders Institute for Biotechnology (VIB)
| | Sample_contact_address | Herestraat 49 Box 816
| | Sample_contact_city | Leuven
| | Sample_contact_zip/postal_code | B-3000
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM628nnn/GSM628033/suppl/GSM628033_hyb2176.CEL.gz
| | Sample_series_id | GSE25550
| | Sample_data_row_count | 54675
| | |
|
GSM628034 | GPL570 |
|
MALT_Lymphoma_LL52_t(11;18)-negative
|
MALT lymphoma
|
tissue: MALT_Lymphoma_LL52_t(11;18)-negative tumor
|
MALT lymphoma LL52
|
| Sample_geo_accession | GSM628034
| | Sample_status | Public on Nov 25 2010
| | Sample_submission_date | Nov 23 2010
| | Sample_last_update_date | Nov 24 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Department of Pathology, University Hospitals K.U.Leuven
| | Sample_treatment_protocol_ch1 | tissue blocs were kept at -80° till use
| | Sample_growth_protocol_ch1 | Fresh frozen tissue blocs were kept at -80° till use. They were transported on dry ice to the cryostat where a number (depending on the size of the bloc) of 20 micron thick sections were cut and put into a labeled, 2.0 ml microcentrifuge tube.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from 20 micron sections of each frozen tissue sample, using the TriZol reagent (Invitrogen, Merelbeke, Belgium) followed by purification using the RNaesy mini kit (Qiagen, Venlo, The Netherlands), according to the manufacturer’s recommendations. RNA quality, integrity and concentration were measured using a nanodrop spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microg total RNA.
| | Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45°C and at 60 rounds/min. The GeneChips were washed and stained in the Affymetrix Fluidics Station 400 and 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 7G.
| | Sample_data_processing | Data were normalized using GC-RMA, using the gcrma package in Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Joke,,Allemeersch
| | Sample_contact_email | joke.allemeersch@vib.be
| | Sample_contact_phone | +32(0)16 37 31 26
| | Sample_contact_department | Nucleomics Core
| | Sample_contact_institute | Flanders Institute for Biotechnology (VIB)
| | Sample_contact_address | Herestraat 49 Box 816
| | Sample_contact_city | Leuven
| | Sample_contact_zip/postal_code | B-3000
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM628nnn/GSM628034/suppl/GSM628034_hyb2177.CEL.gz
| | Sample_series_id | GSE25550
| | Sample_data_row_count | 54675
| | |
|
GSM628035 | GPL570 |
|
MALT_Lymphoma_LL27_t(11;18)-positive
|
MALT lymphoma
|
tissue: MALT_Lymphoma_LL27_t(11;18)-positive tumor
|
MALT lymphoma LL27
|
| Sample_geo_accession | GSM628035
| | Sample_status | Public on Nov 25 2010
| | Sample_submission_date | Nov 23 2010
| | Sample_last_update_date | Nov 24 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Department of Pathology, University Hospitals K.U.Leuven
| | Sample_treatment_protocol_ch1 | tissue blocs were kept at -80° till use
| | Sample_growth_protocol_ch1 | Fresh frozen tissue blocs were kept at -80° till use. They were transported on dry ice to the cryostat where a number (depending on the size of the bloc) of 20 micron thick sections were cut and put into a labeled, 2.0 ml microcentrifuge tube.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from 20 micron sections of each frozen tissue sample, using the TriZol reagent (Invitrogen, Merelbeke, Belgium) followed by purification using the RNaesy mini kit (Qiagen, Venlo, The Netherlands), according to the manufacturer’s recommendations. RNA quality, integrity and concentration were measured using a nanodrop spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microg total RNA.
| | Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45°C and at 60 rounds/min. The GeneChips were washed and stained in the Affymetrix Fluidics Station 400 and 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 7G.
| | Sample_data_processing | Data were normalized using GC-RMA, using the gcrma package in Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Joke,,Allemeersch
| | Sample_contact_email | joke.allemeersch@vib.be
| | Sample_contact_phone | +32(0)16 37 31 26
| | Sample_contact_department | Nucleomics Core
| | Sample_contact_institute | Flanders Institute for Biotechnology (VIB)
| | Sample_contact_address | Herestraat 49 Box 816
| | Sample_contact_city | Leuven
| | Sample_contact_zip/postal_code | B-3000
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM628nnn/GSM628035/suppl/GSM628035_hyb2178.CEL.gz
| | Sample_series_id | GSE25550
| | Sample_data_row_count | 54675
| | |
|
GSM628036 | GPL570 |
|
MALT_Lymphoma_LL39_t(11;18)-positive
|
MALT lymphoma
|
tissue: MALT_Lymphoma_LL39_t(11;18)-positive tumor
|
MALT lymphoma LL39
|
| Sample_geo_accession | GSM628036
| | Sample_status | Public on Nov 25 2010
| | Sample_submission_date | Nov 23 2010
| | Sample_last_update_date | Nov 24 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Department of Pathology, University Hospitals K.U.Leuven
| | Sample_treatment_protocol_ch1 | tissue blocs were kept at -80° till use
| | Sample_growth_protocol_ch1 | Fresh frozen tissue blocs were kept at -80° till use. They were transported on dry ice to the cryostat where a number (depending on the size of the bloc) of 20 micron thick sections were cut and put into a labeled, 2.0 ml microcentrifuge tube.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from 20 micron sections of each frozen tissue sample, using the TriZol reagent (Invitrogen, Merelbeke, Belgium) followed by purification using the RNaesy mini kit (Qiagen, Venlo, The Netherlands), according to the manufacturer’s recommendations. RNA quality, integrity and concentration were measured using a nanodrop spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microg total RNA.
| | Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45°C and at 60 rounds/min. The GeneChips were washed and stained in the Affymetrix Fluidics Station 400 and 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 7G.
| | Sample_data_processing | Data were normalized using GC-RMA, using the gcrma package in Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Joke,,Allemeersch
| | Sample_contact_email | joke.allemeersch@vib.be
| | Sample_contact_phone | +32(0)16 37 31 26
| | Sample_contact_department | Nucleomics Core
| | Sample_contact_institute | Flanders Institute for Biotechnology (VIB)
| | Sample_contact_address | Herestraat 49 Box 816
| | Sample_contact_city | Leuven
| | Sample_contact_zip/postal_code | B-3000
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM628nnn/GSM628036/suppl/GSM628036_hyb2179.CEL.gz
| | Sample_series_id | GSE25550
| | Sample_data_row_count | 54675
| | |
|
GSM628037 | GPL570 |
|
MALT_Lymphoma_LL79_t(11;18)-positive
|
MALT lymphoma
|
tissue: MALT_Lymphoma_LL79_t(11;18)-positive tumor
|
MALT lymphoma LL79
|
| Sample_geo_accession | GSM628037
| | Sample_status | Public on Nov 25 2010
| | Sample_submission_date | Nov 23 2010
| | Sample_last_update_date | Nov 24 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Department of Pathology, University Hospitals K.U.Leuven
| | Sample_treatment_protocol_ch1 | tissue blocs were kept at -80° till use
| | Sample_growth_protocol_ch1 | Fresh frozen tissue blocs were kept at -80° till use. They were transported on dry ice to the cryostat where a number (depending on the size of the bloc) of 20 micron thick sections were cut and put into a labeled, 2.0 ml microcentrifuge tube.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from 20 micron sections of each frozen tissue sample, using the TriZol reagent (Invitrogen, Merelbeke, Belgium) followed by purification using the RNaesy mini kit (Qiagen, Venlo, The Netherlands), according to the manufacturer’s recommendations. RNA quality, integrity and concentration were measured using a nanodrop spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microg total RNA.
| | Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45°C and at 60 rounds/min. The GeneChips were washed and stained in the Affymetrix Fluidics Station 400 and 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 7G.
| | Sample_data_processing | Data were normalized using GC-RMA, using the gcrma package in Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Joke,,Allemeersch
| | Sample_contact_email | joke.allemeersch@vib.be
| | Sample_contact_phone | +32(0)16 37 31 26
| | Sample_contact_department | Nucleomics Core
| | Sample_contact_institute | Flanders Institute for Biotechnology (VIB)
| | Sample_contact_address | Herestraat 49 Box 816
| | Sample_contact_city | Leuven
| | Sample_contact_zip/postal_code | B-3000
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM628nnn/GSM628037/suppl/GSM628037_hyb2180.CEL.gz
| | Sample_series_id | GSE25550
| | Sample_data_row_count | 54675
| | |
|
GSM628038 | GPL570 |
|
MALT_Lymphoma_LL29_t(11;18)-positive
|
MALT lymphoma
|
tissue: MALT_Lymphoma_LL29_t(11;18)-positive tumor
|
MALT lymphoma LL29
|
| Sample_geo_accession | GSM628038
| | Sample_status | Public on Nov 25 2010
| | Sample_submission_date | Nov 23 2010
| | Sample_last_update_date | Nov 24 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Department of Pathology, University Hospitals K.U.Leuven
| | Sample_treatment_protocol_ch1 | tissue blocs were kept at -80° till use
| | Sample_growth_protocol_ch1 | Fresh frozen tissue blocs were kept at -80° till use. They were transported on dry ice to the cryostat where a number (depending on the size of the bloc) of 20 micron thick sections were cut and put into a labeled, 2.0 ml microcentrifuge tube.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from 20 micron sections of each frozen tissue sample, using the TriZol reagent (Invitrogen, Merelbeke, Belgium) followed by purification using the RNaesy mini kit (Qiagen, Venlo, The Netherlands), according to the manufacturer’s recommendations. RNA quality, integrity and concentration were measured using a nanodrop spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microg total RNA.
| | Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45°C and at 60 rounds/min. The GeneChips were washed and stained in the Affymetrix Fluidics Station 400 and 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 7G.
| | Sample_data_processing | Data were normalized using GC-RMA, using the gcrma package in Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Joke,,Allemeersch
| | Sample_contact_email | joke.allemeersch@vib.be
| | Sample_contact_phone | +32(0)16 37 31 26
| | Sample_contact_department | Nucleomics Core
| | Sample_contact_institute | Flanders Institute for Biotechnology (VIB)
| | Sample_contact_address | Herestraat 49 Box 816
| | Sample_contact_city | Leuven
| | Sample_contact_zip/postal_code | B-3000
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM628nnn/GSM628038/suppl/GSM628038_hyb2181.CEL.gz
| | Sample_series_id | GSE25550
| | Sample_data_row_count | 54675
| | |
|
GSM628039 | GPL570 |
|
MALT_Lymphoma_LL57_t(11;18)-positive
|
MALT lymphoma
|
tissue: MALT_Lymphoma_LL57_t(11;18)-positive tumor
|
MALT lymphoma LL57
|
| Sample_geo_accession | GSM628039
| | Sample_status | Public on Nov 25 2010
| | Sample_submission_date | Nov 23 2010
| | Sample_last_update_date | Nov 24 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Department of Pathology, University Hospitals K.U.Leuven
| | Sample_treatment_protocol_ch1 | tissue blocs were kept at -80° till use
| | Sample_growth_protocol_ch1 | Fresh frozen tissue blocs were kept at -80° till use. They were transported on dry ice to the cryostat where a number (depending on the size of the bloc) of 20 micron thick sections were cut and put into a labeled, 2.0 ml microcentrifuge tube.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from 20 micron sections of each frozen tissue sample, using the TriZol reagent (Invitrogen, Merelbeke, Belgium) followed by purification using the RNaesy mini kit (Qiagen, Venlo, The Netherlands), according to the manufacturer’s recommendations. RNA quality, integrity and concentration were measured using a nanodrop spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microg total RNA.
| | Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45°C and at 60 rounds/min. The GeneChips were washed and stained in the Affymetrix Fluidics Station 400 and 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 7G.
| | Sample_data_processing | Data were normalized using GC-RMA, using the gcrma package in Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Joke,,Allemeersch
| | Sample_contact_email | joke.allemeersch@vib.be
| | Sample_contact_phone | +32(0)16 37 31 26
| | Sample_contact_department | Nucleomics Core
| | Sample_contact_institute | Flanders Institute for Biotechnology (VIB)
| | Sample_contact_address | Herestraat 49 Box 816
| | Sample_contact_city | Leuven
| | Sample_contact_zip/postal_code | B-3000
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM628nnn/GSM628039/suppl/GSM628039_hyb2182.CEL.gz
| | Sample_series_id | GSE25550
| | Sample_data_row_count | 54675
| | |
|
GSM628040 | GPL570 |
|
MALT_Lymphoma_LL96_t(11;18)-positive
|
MALT lymphoma
|
tissue: MALT_Lymphoma_LL96_t(11;18)-positive tumor
|
MALT lymphoma LL96
|
| Sample_geo_accession | GSM628040
| | Sample_status | Public on Nov 25 2010
| | Sample_submission_date | Nov 23 2010
| | Sample_last_update_date | Nov 24 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Department of Pathology, University Hospitals K.U.Leuven
| | Sample_treatment_protocol_ch1 | tissue blocs were kept at -80° till use
| | Sample_growth_protocol_ch1 | Fresh frozen tissue blocs were kept at -80° till use. They were transported on dry ice to the cryostat where a number (depending on the size of the bloc) of 20 micron thick sections were cut and put into a labeled, 2.0 ml microcentrifuge tube.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from 20 micron sections of each frozen tissue sample, using the TriZol reagent (Invitrogen, Merelbeke, Belgium) followed by purification using the RNaesy mini kit (Qiagen, Venlo, The Netherlands), according to the manufacturer’s recommendations. RNA quality, integrity and concentration were measured using a nanodrop spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microg total RNA.
| | Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45°C and at 60 rounds/min. The GeneChips were washed and stained in the Affymetrix Fluidics Station 400 and 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 7G.
| | Sample_data_processing | Data were normalized using GC-RMA, using the gcrma package in Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Joke,,Allemeersch
| | Sample_contact_email | joke.allemeersch@vib.be
| | Sample_contact_phone | +32(0)16 37 31 26
| | Sample_contact_department | Nucleomics Core
| | Sample_contact_institute | Flanders Institute for Biotechnology (VIB)
| | Sample_contact_address | Herestraat 49 Box 816
| | Sample_contact_city | Leuven
| | Sample_contact_zip/postal_code | B-3000
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM628nnn/GSM628040/suppl/GSM628040_hyb2183.CEL.gz
| | Sample_series_id | GSE25550
| | Sample_data_row_count | 54675
| | |
|
GSM628041 | GPL570 |
|
Spleen_control_MIX
|
mix of normal spleen samples
|
tissue: multiple normal spleens
|
Spleen control (MIX)
|
| Sample_geo_accession | GSM628041
| | Sample_status | Public on Nov 25 2010
| | Sample_submission_date | Nov 23 2010
| | Sample_last_update_date | Nov 24 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Department of Pathology, University Hospitals K.U.Leuven
| | Sample_treatment_protocol_ch1 | tissue blocs were kept at -80° till use
| | Sample_growth_protocol_ch1 | Fresh frozen tissue blocs were kept at -80° till use. They were transported on dry ice to the cryostat where a number (depending on the size of the bloc) of 20 micron thick sections were cut and put into a labeled, 2.0 ml microcentrifuge tube.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from 20 micron sections of each frozen tissue sample, using the TriZol reagent (Invitrogen, Merelbeke, Belgium) followed by purification using the RNaesy mini kit (Qiagen, Venlo, The Netherlands), according to the manufacturer’s recommendations. RNA quality, integrity and concentration were measured using a nanodrop spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microg total RNA.
| | Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45°C and at 60 rounds/min. The GeneChips were washed and stained in the Affymetrix Fluidics Station 400 and 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 7G.
| | Sample_data_processing | Data were normalized using GC-RMA, using the gcrma package in Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Joke,,Allemeersch
| | Sample_contact_email | joke.allemeersch@vib.be
| | Sample_contact_phone | +32(0)16 37 31 26
| | Sample_contact_department | Nucleomics Core
| | Sample_contact_institute | Flanders Institute for Biotechnology (VIB)
| | Sample_contact_address | Herestraat 49 Box 816
| | Sample_contact_city | Leuven
| | Sample_contact_zip/postal_code | B-3000
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM628nnn/GSM628041/suppl/GSM628041_hyb2184.CEL.gz
| | Sample_series_id | GSE25550
| | Sample_data_row_count | 54675
| | |
|
GSM628043 | GPL570 |
|
MALT_Lymphoma_LL38_t(11;18)-negative
|
MALT lymphoma
|
tissue: MALT_Lymphoma_LL38_t(11;18)-negative tumor
|
MALT lymphoma LL38
|
| Sample_geo_accession | GSM628043
| | Sample_status | Public on Nov 25 2010
| | Sample_submission_date | Nov 23 2010
| | Sample_last_update_date | Nov 24 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Department of Pathology, University Hospitals K.U.Leuven
| | Sample_treatment_protocol_ch1 | tissue blocs were kept at -80° till use
| | Sample_growth_protocol_ch1 | Fresh frozen tissue blocs were kept at -80° till use. They were transported on dry ice to the cryostat where a number (depending on the size of the bloc) of 20 micron thick sections were cut and put into a labeled, 2.0 ml microcentrifuge tube.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from 20 micron sections of each frozen tissue sample, using the TriZol reagent (Invitrogen, Merelbeke, Belgium) followed by purification using the RNaesy mini kit (Qiagen, Venlo, The Netherlands), according to the manufacturer’s recommendations. RNA quality, integrity and concentration were measured using a nanodrop spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microg total RNA.
| | Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45°C and at 60 rounds/min. The GeneChips were washed and stained in the Affymetrix Fluidics Station 400 and 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 7G.
| | Sample_data_processing | Data were normalized using GC-RMA, using the gcrma package in Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Joke,,Allemeersch
| | Sample_contact_email | joke.allemeersch@vib.be
| | Sample_contact_phone | +32(0)16 37 31 26
| | Sample_contact_department | Nucleomics Core
| | Sample_contact_institute | Flanders Institute for Biotechnology (VIB)
| | Sample_contact_address | Herestraat 49 Box 816
| | Sample_contact_city | Leuven
| | Sample_contact_zip/postal_code | B-3000
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM628nnn/GSM628043/suppl/GSM628043_hyb3198.CEL.gz
| | Sample_series_id | GSE25550
| | Sample_data_row_count | 54675
| | |
|
GSM628044 | GPL570 |
|
MALT_Lymphoma_LL69_t(11;18)-negative
|
MALT lymphoma
|
tissue: MALT_Lymphoma_LL69_t(11;18)-negative tumor
|
MALT lymphoma LL69
|
| Sample_geo_accession | GSM628044
| | Sample_status | Public on Nov 25 2010
| | Sample_submission_date | Nov 23 2010
| | Sample_last_update_date | Nov 24 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Department of Pathology, University Hospitals K.U.Leuven
| | Sample_treatment_protocol_ch1 | tissue blocs were kept at -80° till use
| | Sample_growth_protocol_ch1 | Fresh frozen tissue blocs were kept at -80° till use. They were transported on dry ice to the cryostat where a number (depending on the size of the bloc) of 20 micron thick sections were cut and put into a labeled, 2.0 ml microcentrifuge tube.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from 20 micron sections of each frozen tissue sample, using the TriZol reagent (Invitrogen, Merelbeke, Belgium) followed by purification using the RNaesy mini kit (Qiagen, Venlo, The Netherlands), according to the manufacturer’s recommendations. RNA quality, integrity and concentration were measured using a nanodrop spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microg total RNA.
| | Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45°C and at 60 rounds/min. The GeneChips were washed and stained in the Affymetrix Fluidics Station 400 and 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 7G.
| | Sample_data_processing | Data were normalized using GC-RMA, using the gcrma package in Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Joke,,Allemeersch
| | Sample_contact_email | joke.allemeersch@vib.be
| | Sample_contact_phone | +32(0)16 37 31 26
| | Sample_contact_department | Nucleomics Core
| | Sample_contact_institute | Flanders Institute for Biotechnology (VIB)
| | Sample_contact_address | Herestraat 49 Box 816
| | Sample_contact_city | Leuven
| | Sample_contact_zip/postal_code | B-3000
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM628nnn/GSM628044/suppl/GSM628044_hyb3199.CEL.gz
| | Sample_series_id | GSE25550
| | Sample_data_row_count | 54675
| | |
|
GSM628045 | GPL570 |
|
MALT_Lymphoma_LL49_t(11;18)-negative
|
MALT lymphoma
|
tissue: MALT_Lymphoma_LL49_t(11;18)-negative tumor
|
MALT lymphoma LL49
|
| Sample_geo_accession | GSM628045
| | Sample_status | Public on Nov 25 2010
| | Sample_submission_date | Nov 23 2010
| | Sample_last_update_date | Nov 24 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Department of Pathology, University Hospitals K.U.Leuven
| | Sample_treatment_protocol_ch1 | tissue blocs were kept at -80° till use
| | Sample_growth_protocol_ch1 | Fresh frozen tissue blocs were kept at -80° till use. They were transported on dry ice to the cryostat where a number (depending on the size of the bloc) of 20 micron thick sections were cut and put into a labeled, 2.0 ml microcentrifuge tube.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from 20 micron sections of each frozen tissue sample, using the TriZol reagent (Invitrogen, Merelbeke, Belgium) followed by purification using the RNaesy mini kit (Qiagen, Venlo, The Netherlands), according to the manufacturer’s recommendations. RNA quality, integrity and concentration were measured using a nanodrop spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microg total RNA.
| | Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45°C and at 60 rounds/min. The GeneChips were washed and stained in the Affymetrix Fluidics Station 400 and 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 7G.
| | Sample_data_processing | Data were normalized using GC-RMA, using the gcrma package in Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Joke,,Allemeersch
| | Sample_contact_email | joke.allemeersch@vib.be
| | Sample_contact_phone | +32(0)16 37 31 26
| | Sample_contact_department | Nucleomics Core
| | Sample_contact_institute | Flanders Institute for Biotechnology (VIB)
| | Sample_contact_address | Herestraat 49 Box 816
| | Sample_contact_city | Leuven
| | Sample_contact_zip/postal_code | B-3000
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM628nnn/GSM628045/suppl/GSM628045_hyb3200.CEL.gz
| | Sample_series_id | GSE25550
| | Sample_data_row_count | 54675
| | |
|
GSM628046 | GPL570 |
|
MALT_Lymphoma_LL65_t(11;18)-negative
|
MALT lymphoma
|
tissue: MALT_Lymphoma_LL65_t(11;18)-negative tumor
|
MALT lymphoma LL65
|
| Sample_geo_accession | GSM628046
| | Sample_status | Public on Nov 25 2010
| | Sample_submission_date | Nov 23 2010
| | Sample_last_update_date | Nov 24 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Department of Pathology, University Hospitals K.U.Leuven
| | Sample_treatment_protocol_ch1 | tissue blocs were kept at -80° till use
| | Sample_growth_protocol_ch1 | Fresh frozen tissue blocs were kept at -80° till use. They were transported on dry ice to the cryostat where a number (depending on the size of the bloc) of 20 micron thick sections were cut and put into a labeled, 2.0 ml microcentrifuge tube.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from 20 micron sections of each frozen tissue sample, using the TriZol reagent (Invitrogen, Merelbeke, Belgium) followed by purification using the RNaesy mini kit (Qiagen, Venlo, The Netherlands), according to the manufacturer’s recommendations. RNA quality, integrity and concentration were measured using a nanodrop spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microg total RNA.
| | Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45°C and at 60 rounds/min. The GeneChips were washed and stained in the Affymetrix Fluidics Station 400 and 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 7G.
| | Sample_data_processing | Data were normalized using GC-RMA, using the gcrma package in Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Joke,,Allemeersch
| | Sample_contact_email | joke.allemeersch@vib.be
| | Sample_contact_phone | +32(0)16 37 31 26
| | Sample_contact_department | Nucleomics Core
| | Sample_contact_institute | Flanders Institute for Biotechnology (VIB)
| | Sample_contact_address | Herestraat 49 Box 816
| | Sample_contact_city | Leuven
| | Sample_contact_zip/postal_code | B-3000
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM628nnn/GSM628046/suppl/GSM628046_hyb3201.CEL.gz
| | Sample_series_id | GSE25550
| | Sample_data_row_count | 54675
| | |
|
GSM628047 | GPL570 |
|
MALT_Lymphoma_LLX1_t(11;18)-negative
|
MALT lymphoma
|
tissue: MALT_Lymphoma_LLX1_t(11;18)-negative tumor
|
MALT lymphoma LLX1
|
| Sample_geo_accession | GSM628047
| | Sample_status | Public on Nov 25 2010
| | Sample_submission_date | Nov 23 2010
| | Sample_last_update_date | Nov 24 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Department of Pathology, University Hospitals K.U.Leuven
| | Sample_treatment_protocol_ch1 | tissue blocs were kept at -80° till use
| | Sample_growth_protocol_ch1 | Fresh frozen tissue blocs were kept at -80° till use. They were transported on dry ice to the cryostat where a number (depending on the size of the bloc) of 20 micron thick sections were cut and put into a labeled, 2.0 ml microcentrifuge tube.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from 20 micron sections of each frozen tissue sample, using the TriZol reagent (Invitrogen, Merelbeke, Belgium) followed by purification using the RNaesy mini kit (Qiagen, Venlo, The Netherlands), according to the manufacturer’s recommendations. RNA quality, integrity and concentration were measured using a nanodrop spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microg total RNA.
| | Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45°C and at 60 rounds/min. The GeneChips were washed and stained in the Affymetrix Fluidics Station 400 and 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 7G.
| | Sample_data_processing | Data were normalized using GC-RMA, using the gcrma package in Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Joke,,Allemeersch
| | Sample_contact_email | joke.allemeersch@vib.be
| | Sample_contact_phone | +32(0)16 37 31 26
| | Sample_contact_department | Nucleomics Core
| | Sample_contact_institute | Flanders Institute for Biotechnology (VIB)
| | Sample_contact_address | Herestraat 49 Box 816
| | Sample_contact_city | Leuven
| | Sample_contact_zip/postal_code | B-3000
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM628nnn/GSM628047/suppl/GSM628047_hyb3202.CEL.gz
| | Sample_series_id | GSE25550
| | Sample_data_row_count | 54675
| | |
|
GSM628048 | GPL570 |
|
Spleen_control_S1
|
normal spleen sample
|
tissue: normal spleen
|
Spleen control S1
|
| Sample_geo_accession | GSM628048
| | Sample_status | Public on Nov 25 2010
| | Sample_submission_date | Nov 23 2010
| | Sample_last_update_date | Nov 24 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Department of Pathology, University Hospitals K.U.Leuven
| | Sample_treatment_protocol_ch1 | tissue blocs were kept at -80° till use
| | Sample_growth_protocol_ch1 | Fresh frozen tissue blocs were kept at -80° till use. They were transported on dry ice to the cryostat where a number (depending on the size of the bloc) of 20 micron thick sections were cut and put into a labeled, 2.0 ml microcentrifuge tube.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from 20 micron sections of each frozen tissue sample, using the TriZol reagent (Invitrogen, Merelbeke, Belgium) followed by purification using the RNaesy mini kit (Qiagen, Venlo, The Netherlands), according to the manufacturer’s recommendations. RNA quality, integrity and concentration were measured using a nanodrop spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microg total RNA.
| | Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45°C and at 60 rounds/min. The GeneChips were washed and stained in the Affymetrix Fluidics Station 400 and 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 7G.
| | Sample_data_processing | Data were normalized using GC-RMA, using the gcrma package in Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Joke,,Allemeersch
| | Sample_contact_email | joke.allemeersch@vib.be
| | Sample_contact_phone | +32(0)16 37 31 26
| | Sample_contact_department | Nucleomics Core
| | Sample_contact_institute | Flanders Institute for Biotechnology (VIB)
| | Sample_contact_address | Herestraat 49 Box 816
| | Sample_contact_city | Leuven
| | Sample_contact_zip/postal_code | B-3000
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM628nnn/GSM628048/suppl/GSM628048_hyb3203.CEL.gz
| | Sample_series_id | GSE25550
| | Sample_data_row_count | 54675
| | |
|
GSM628049 | GPL570 |
|
Spleen_control_S2
|
normal spleen sample
|
tissue: normal spleen
|
Spleen control S2
|
| Sample_geo_accession | GSM628049
| | Sample_status | Public on Nov 25 2010
| | Sample_submission_date | Nov 23 2010
| | Sample_last_update_date | Nov 24 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Department of Pathology, University Hospitals K.U.Leuven
| | Sample_treatment_protocol_ch1 | tissue blocs were kept at -80° till use
| | Sample_growth_protocol_ch1 | Fresh frozen tissue blocs were kept at -80° till use. They were transported on dry ice to the cryostat where a number (depending on the size of the bloc) of 20 micron thick sections were cut and put into a labeled, 2.0 ml microcentrifuge tube.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from 20 micron sections of each frozen tissue sample, using the TriZol reagent (Invitrogen, Merelbeke, Belgium) followed by purification using the RNaesy mini kit (Qiagen, Venlo, The Netherlands), according to the manufacturer’s recommendations. RNA quality, integrity and concentration were measured using a nanodrop spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microg total RNA.
| | Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45°C and at 60 rounds/min. The GeneChips were washed and stained in the Affymetrix Fluidics Station 400 and 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 7G.
| | Sample_data_processing | Data were normalized using GC-RMA, using the gcrma package in Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Joke,,Allemeersch
| | Sample_contact_email | joke.allemeersch@vib.be
| | Sample_contact_phone | +32(0)16 37 31 26
| | Sample_contact_department | Nucleomics Core
| | Sample_contact_institute | Flanders Institute for Biotechnology (VIB)
| | Sample_contact_address | Herestraat 49 Box 816
| | Sample_contact_city | Leuven
| | Sample_contact_zip/postal_code | B-3000
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM628nnn/GSM628049/suppl/GSM628049_hyb3204.CEL.gz
| | Sample_series_id | GSE25550
| | Sample_data_row_count | 54675
| | |
|
GSM628050 | GPL570 |
|
Spleen_control_S3
|
normal spleen sample
|
tissue: normal spleen
|
Spleen control S3
|
| Sample_geo_accession | GSM628050
| | Sample_status | Public on Nov 25 2010
| | Sample_submission_date | Nov 23 2010
| | Sample_last_update_date | Nov 24 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Department of Pathology, University Hospitals K.U.Leuven
| | Sample_treatment_protocol_ch1 | tissue blocs were kept at -80° till use
| | Sample_growth_protocol_ch1 | Fresh frozen tissue blocs were kept at -80° till use. They were transported on dry ice to the cryostat where a number (depending on the size of the bloc) of 20 micron thick sections were cut and put into a labeled, 2.0 ml microcentrifuge tube.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from 20 micron sections of each frozen tissue sample, using the TriZol reagent (Invitrogen, Merelbeke, Belgium) followed by purification using the RNaesy mini kit (Qiagen, Venlo, The Netherlands), according to the manufacturer’s recommendations. RNA quality, integrity and concentration were measured using a nanodrop spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microg total RNA.
| | Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45°C and at 60 rounds/min. The GeneChips were washed and stained in the Affymetrix Fluidics Station 400 and 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 7G.
| | Sample_data_processing | Data were normalized using GC-RMA, using the gcrma package in Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Joke,,Allemeersch
| | Sample_contact_email | joke.allemeersch@vib.be
| | Sample_contact_phone | +32(0)16 37 31 26
| | Sample_contact_department | Nucleomics Core
| | Sample_contact_institute | Flanders Institute for Biotechnology (VIB)
| | Sample_contact_address | Herestraat 49 Box 816
| | Sample_contact_city | Leuven
| | Sample_contact_zip/postal_code | B-3000
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM628nnn/GSM628050/suppl/GSM628050_hyb3205.CEL.gz
| | Sample_series_id | GSE25550
| | Sample_data_row_count | 54675
| | |
|
GSM628051 | GPL570 |
|
Spleen_control_S4
|
normal spleen sample
|
tissue: normal spleen
|
Spleen control S4
|
| Sample_geo_accession | GSM628051
| | Sample_status | Public on Nov 25 2010
| | Sample_submission_date | Nov 23 2010
| | Sample_last_update_date | Nov 24 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Department of Pathology, University Hospitals K.U.Leuven
| | Sample_treatment_protocol_ch1 | tissue blocs were kept at -80° till use
| | Sample_growth_protocol_ch1 | Fresh frozen tissue blocs were kept at -80° till use. They were transported on dry ice to the cryostat where a number (depending on the size of the bloc) of 20 micron thick sections were cut and put into a labeled, 2.0 ml microcentrifuge tube.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from 20 micron sections of each frozen tissue sample, using the TriZol reagent (Invitrogen, Merelbeke, Belgium) followed by purification using the RNaesy mini kit (Qiagen, Venlo, The Netherlands), according to the manufacturer’s recommendations. RNA quality, integrity and concentration were measured using a nanodrop spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microg total RNA.
| | Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45°C and at 60 rounds/min. The GeneChips were washed and stained in the Affymetrix Fluidics Station 400 and 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 7G.
| | Sample_data_processing | Data were normalized using GC-RMA, using the gcrma package in Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Joke,,Allemeersch
| | Sample_contact_email | joke.allemeersch@vib.be
| | Sample_contact_phone | +32(0)16 37 31 26
| | Sample_contact_department | Nucleomics Core
| | Sample_contact_institute | Flanders Institute for Biotechnology (VIB)
| | Sample_contact_address | Herestraat 49 Box 816
| | Sample_contact_city | Leuven
| | Sample_contact_zip/postal_code | B-3000
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM628nnn/GSM628051/suppl/GSM628051_hyb3206.CEL.gz
| | Sample_series_id | GSE25550
| | Sample_data_row_count | 54675
| | |
|
GSM628052 | GPL570 |
|
Spleen_control_S5
|
normal spleen sample
|
tissue: normal spleen
|
Spleen control S5
|
| Sample_geo_accession | GSM628052
| | Sample_status | Public on Nov 25 2010
| | Sample_submission_date | Nov 23 2010
| | Sample_last_update_date | Nov 24 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Department of Pathology, University Hospitals K.U.Leuven
| | Sample_treatment_protocol_ch1 | tissue blocs were kept at -80° till use
| | Sample_growth_protocol_ch1 | Fresh frozen tissue blocs were kept at -80° till use. They were transported on dry ice to the cryostat where a number (depending on the size of the bloc) of 20 micron thick sections were cut and put into a labeled, 2.0 ml microcentrifuge tube.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from 20 micron sections of each frozen tissue sample, using the TriZol reagent (Invitrogen, Merelbeke, Belgium) followed by purification using the RNaesy mini kit (Qiagen, Venlo, The Netherlands), according to the manufacturer’s recommendations. RNA quality, integrity and concentration were measured using a nanodrop spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microg total RNA.
| | Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45°C and at 60 rounds/min. The GeneChips were washed and stained in the Affymetrix Fluidics Station 400 and 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 7G.
| | Sample_data_processing | Data were normalized using GC-RMA, using the gcrma package in Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Joke,,Allemeersch
| | Sample_contact_email | joke.allemeersch@vib.be
| | Sample_contact_phone | +32(0)16 37 31 26
| | Sample_contact_department | Nucleomics Core
| | Sample_contact_institute | Flanders Institute for Biotechnology (VIB)
| | Sample_contact_address | Herestraat 49 Box 816
| | Sample_contact_city | Leuven
| | Sample_contact_zip/postal_code | B-3000
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM628nnn/GSM628052/suppl/GSM628052_hyb3207.CEL.gz
| | Sample_series_id | GSE25550
| | Sample_data_row_count | 54675
| | |
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