Search results for the GEO ID: GSE45113  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM1096997 | GPL570 |
|
undivided_rep1
|
undivided B cells
|
tissue: peripheral blood
cell type: undivided B cells
cd27: low
divided in vitro: no
|
Un_1
|
| Sample_geo_accession | GSM1096997
| | Sample_status | Public on Mar 13 2013
| | Sample_submission_date | Mar 12 2013
| | Sample_last_update_date | Mar 13 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | CFSE-stained cells were harvested, washed, and counted. The cells were stained with Live/Dead Violet Invitrogen, Carlsbad, CA), washed and stained with anti-CD27-APC-H7 antibody (BD Bioscience, San Diego, CA) on ice. FACS cell sorts were performed on live cells.
| | Sample_growth_protocol_ch1 | Freshly isolated CD27+ IgG enriched human peripheral blood Bc were cultured in the presence of CpG 2006 (10 ng/ml, Oligos, etc., Wilsonville, OR), plus recombinant human cytokines IL-2 (20 IU/ml), IL-10 (50 ng/ml), IL-15 (10 ng/ml) (all from BD Biosciences, San Diego, CA), and recombinant human BAFF (75 ng/ml, Chemicon, Temecula, CA) PC-L medium (IMDM medium, lacromin (50mg/ml, Seracare, Milford, MA), insulin (5mg/ml, Sigma-Aldrich, St. Louis, MO), penicillin/streptomycin (1x, Invitrogen, Carlsbad, CA), gentamicin (15mg/ml, Invitrogen), heat inactivated fetal bovine serum (10% v/v, Invitrogen), normocin (0.1% v/v, Invivogen, San Diego, CA) in round-bottomed 96-well plates (BD Biosciences, San Diego, CA). All cells were cultured at 37 C, 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Immediately after collection, sorted cells were lysed in RLT buffer and passed through a Qiashredder column (both from Qiagen, Germantown, MD) and snap frozen in liquid nitrogen. Samples were stored at -70C until RNA extraction. RNA was extracted using the RNeasy Micro Kit with on-column DNAse as recommended by the manufacturer (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was used to prepare biotinylated cDNA with the WT-Ovation Pico kit as recommended by the kit manufacturer (NuGEN).
| | Sample_hyb_protocol | Biotinylated cDNA was hybridized overnight with Affymetrix U133_Plus_2.0 arrays using conditions recommended by NuGEN. After washing, arrays were stained with SAPE followed by signal enhancement with anti-SAPE antibody as recommended by Affymetrix.
| | Sample_scan_protocol | Phycoerythrin fluorescence was quantified with an Affymetrix scanner, and Affymetrix Command Console software was used to generate cel files from the raw scan data.
| | Sample_data_processing | Cel files were quantile-normalized with the GC-RMA method using the open-source gcrma Bioconductor package (R programming language).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Stephen,,Welle
| | Sample_contact_email | stephen_welle@urmc.rochester.edu
| | Sample_contact_institute | University of Rochester
| | Sample_contact_address | 601 Elmwood Avenue
| | Sample_contact_city | Rochester
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 14642
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1096nnn/GSM1096997/suppl/GSM1096997_01_CpGundiv7D_Zand1_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE45113
| | Sample_data_row_count | 54675
| | |
|
GSM1096998 | GPL570 |
|
CD27_low_rep1
|
CD27_low_proliferating B cells
|
tissue: peripheral blood
cell type: proliferating B cells
cd27: low
divided in vitro: yes
|
CD27Lo_1
|
| Sample_geo_accession | GSM1096998
| | Sample_status | Public on Mar 13 2013
| | Sample_submission_date | Mar 12 2013
| | Sample_last_update_date | Mar 13 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | CFSE-stained cells were harvested, washed, and counted. The cells were stained with Live/Dead Violet Invitrogen, Carlsbad, CA), washed and stained with anti-CD27-APC-H7 antibody (BD Bioscience, San Diego, CA) on ice. FACS cell sorts were performed on live cells.
| | Sample_growth_protocol_ch1 | Freshly isolated CD27+ IgG enriched human peripheral blood Bc were cultured in the presence of CpG 2006 (10 ng/ml, Oligos, etc., Wilsonville, OR), plus recombinant human cytokines IL-2 (20 IU/ml), IL-10 (50 ng/ml), IL-15 (10 ng/ml) (all from BD Biosciences, San Diego, CA), and recombinant human BAFF (75 ng/ml, Chemicon, Temecula, CA) PC-L medium (IMDM medium, lacromin (50mg/ml, Seracare, Milford, MA), insulin (5mg/ml, Sigma-Aldrich, St. Louis, MO), penicillin/streptomycin (1x, Invitrogen, Carlsbad, CA), gentamicin (15mg/ml, Invitrogen), heat inactivated fetal bovine serum (10% v/v, Invitrogen), normocin (0.1% v/v, Invivogen, San Diego, CA) in round-bottomed 96-well plates (BD Biosciences, San Diego, CA). All cells were cultured at 37 C, 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Immediately after collection, sorted cells were lysed in RLT buffer and passed through a Qiashredder column (both from Qiagen, Germantown, MD) and snap frozen in liquid nitrogen. Samples were stored at -70C until RNA extraction. RNA was extracted using the RNeasy Micro Kit with on-column DNAse as recommended by the manufacturer (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was used to prepare biotinylated cDNA with the WT-Ovation Pico kit as recommended by the kit manufacturer (NuGEN).
| | Sample_hyb_protocol | Biotinylated cDNA was hybridized overnight with Affymetrix U133_Plus_2.0 arrays using conditions recommended by NuGEN. After washing, arrays were stained with SAPE followed by signal enhancement with anti-SAPE antibody as recommended by Affymetrix.
| | Sample_scan_protocol | Phycoerythrin fluorescence was quantified with an Affymetrix scanner, and Affymetrix Command Console software was used to generate cel files from the raw scan data.
| | Sample_data_processing | Cel files were quantile-normalized with the GC-RMA method using the open-source gcrma Bioconductor package (R programming language).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Stephen,,Welle
| | Sample_contact_email | stephen_welle@urmc.rochester.edu
| | Sample_contact_institute | University of Rochester
| | Sample_contact_address | 601 Elmwood Avenue
| | Sample_contact_city | Rochester
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 14642
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1096nnn/GSM1096998/suppl/GSM1096998_02_CpGlow7D_Zand1_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE45113
| | Sample_data_row_count | 54675
| | |
|
GSM1096999 | GPL570 |
|
CD27_high_rep1
|
CD27_high_proliferating B cells
|
tissue: peripheral blood
cell type: proliferating B cells
cd27: high
divided in vitro: yes
|
CD27Hi_1
|
| Sample_geo_accession | GSM1096999
| | Sample_status | Public on Mar 13 2013
| | Sample_submission_date | Mar 12 2013
| | Sample_last_update_date | Mar 13 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | CFSE-stained cells were harvested, washed, and counted. The cells were stained with Live/Dead Violet Invitrogen, Carlsbad, CA), washed and stained with anti-CD27-APC-H7 antibody (BD Bioscience, San Diego, CA) on ice. FACS cell sorts were performed on live cells.
| | Sample_growth_protocol_ch1 | Freshly isolated CD27+ IgG enriched human peripheral blood Bc were cultured in the presence of CpG 2006 (10 ng/ml, Oligos, etc., Wilsonville, OR), plus recombinant human cytokines IL-2 (20 IU/ml), IL-10 (50 ng/ml), IL-15 (10 ng/ml) (all from BD Biosciences, San Diego, CA), and recombinant human BAFF (75 ng/ml, Chemicon, Temecula, CA) PC-L medium (IMDM medium, lacromin (50mg/ml, Seracare, Milford, MA), insulin (5mg/ml, Sigma-Aldrich, St. Louis, MO), penicillin/streptomycin (1x, Invitrogen, Carlsbad, CA), gentamicin (15mg/ml, Invitrogen), heat inactivated fetal bovine serum (10% v/v, Invitrogen), normocin (0.1% v/v, Invivogen, San Diego, CA) in round-bottomed 96-well plates (BD Biosciences, San Diego, CA). All cells were cultured at 37 C, 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Immediately after collection, sorted cells were lysed in RLT buffer and passed through a Qiashredder column (both from Qiagen, Germantown, MD) and snap frozen in liquid nitrogen. Samples were stored at -70C until RNA extraction. RNA was extracted using the RNeasy Micro Kit with on-column DNAse as recommended by the manufacturer (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was used to prepare biotinylated cDNA with the WT-Ovation Pico kit as recommended by the kit manufacturer (NuGEN).
| | Sample_hyb_protocol | Biotinylated cDNA was hybridized overnight with Affymetrix U133_Plus_2.0 arrays using conditions recommended by NuGEN. After washing, arrays were stained with SAPE followed by signal enhancement with anti-SAPE antibody as recommended by Affymetrix.
| | Sample_scan_protocol | Phycoerythrin fluorescence was quantified with an Affymetrix scanner, and Affymetrix Command Console software was used to generate cel files from the raw scan data.
| | Sample_data_processing | Cel files were quantile-normalized with the GC-RMA method using the open-source gcrma Bioconductor package (R programming language).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Stephen,,Welle
| | Sample_contact_email | stephen_welle@urmc.rochester.edu
| | Sample_contact_institute | University of Rochester
| | Sample_contact_address | 601 Elmwood Avenue
| | Sample_contact_city | Rochester
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 14642
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1096nnn/GSM1096999/suppl/GSM1096999_03_CpGhi7D_Zand1_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE45113
| | Sample_data_row_count | 54675
| | |
|
GSM1097000 | GPL570 |
|
undivided_rep2
|
undivided B cells
|
tissue: peripheral blood
cell type: undivided B cells
cd27: low
divided in vitro: no
|
Un_2
|
| Sample_geo_accession | GSM1097000
| | Sample_status | Public on Mar 13 2013
| | Sample_submission_date | Mar 12 2013
| | Sample_last_update_date | Mar 13 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | CFSE-stained cells were harvested, washed, and counted. The cells were stained with Live/Dead Violet Invitrogen, Carlsbad, CA), washed and stained with anti-CD27-APC-H7 antibody (BD Bioscience, San Diego, CA) on ice. FACS cell sorts were performed on live cells.
| | Sample_growth_protocol_ch1 | Freshly isolated CD27+ IgG enriched human peripheral blood Bc were cultured in the presence of CpG 2006 (10 ng/ml, Oligos, etc., Wilsonville, OR), plus recombinant human cytokines IL-2 (20 IU/ml), IL-10 (50 ng/ml), IL-15 (10 ng/ml) (all from BD Biosciences, San Diego, CA), and recombinant human BAFF (75 ng/ml, Chemicon, Temecula, CA) PC-L medium (IMDM medium, lacromin (50mg/ml, Seracare, Milford, MA), insulin (5mg/ml, Sigma-Aldrich, St. Louis, MO), penicillin/streptomycin (1x, Invitrogen, Carlsbad, CA), gentamicin (15mg/ml, Invitrogen), heat inactivated fetal bovine serum (10% v/v, Invitrogen), normocin (0.1% v/v, Invivogen, San Diego, CA) in round-bottomed 96-well plates (BD Biosciences, San Diego, CA). All cells were cultured at 37 C, 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Immediately after collection, sorted cells were lysed in RLT buffer and passed through a Qiashredder column (both from Qiagen, Germantown, MD) and snap frozen in liquid nitrogen. Samples were stored at -70C until RNA extraction. RNA was extracted using the RNeasy Micro Kit with on-column DNAse as recommended by the manufacturer (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was used to prepare biotinylated cDNA with the WT-Ovation Pico kit as recommended by the kit manufacturer (NuGEN).
| | Sample_hyb_protocol | Biotinylated cDNA was hybridized overnight with Affymetrix U133_Plus_2.0 arrays using conditions recommended by NuGEN. After washing, arrays were stained with SAPE followed by signal enhancement with anti-SAPE antibody as recommended by Affymetrix.
| | Sample_scan_protocol | Phycoerythrin fluorescence was quantified with an Affymetrix scanner, and Affymetrix Command Console software was used to generate cel files from the raw scan data.
| | Sample_data_processing | Cel files were quantile-normalized with the GC-RMA method using the open-source gcrma Bioconductor package (R programming language).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Stephen,,Welle
| | Sample_contact_email | stephen_welle@urmc.rochester.edu
| | Sample_contact_institute | University of Rochester
| | Sample_contact_address | 601 Elmwood Avenue
| | Sample_contact_city | Rochester
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 14642
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1097nnn/GSM1097000/suppl/GSM1097000_04_CpGundiv8K_Zand1_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE45113
| | Sample_data_row_count | 54675
| | |
|
GSM1097001 | GPL570 |
|
CD27_low_rep2
|
CD27_low_proliferating B cells
|
tissue: peripheral blood
cell type: proliferating B cells
cd27: low
divided in vitro: yes
|
CD27Lo_2
|
| Sample_geo_accession | GSM1097001
| | Sample_status | Public on Mar 13 2013
| | Sample_submission_date | Mar 12 2013
| | Sample_last_update_date | Mar 13 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | CFSE-stained cells were harvested, washed, and counted. The cells were stained with Live/Dead Violet Invitrogen, Carlsbad, CA), washed and stained with anti-CD27-APC-H7 antibody (BD Bioscience, San Diego, CA) on ice. FACS cell sorts were performed on live cells.
| | Sample_growth_protocol_ch1 | Freshly isolated CD27+ IgG enriched human peripheral blood Bc were cultured in the presence of CpG 2006 (10 ng/ml, Oligos, etc., Wilsonville, OR), plus recombinant human cytokines IL-2 (20 IU/ml), IL-10 (50 ng/ml), IL-15 (10 ng/ml) (all from BD Biosciences, San Diego, CA), and recombinant human BAFF (75 ng/ml, Chemicon, Temecula, CA) PC-L medium (IMDM medium, lacromin (50mg/ml, Seracare, Milford, MA), insulin (5mg/ml, Sigma-Aldrich, St. Louis, MO), penicillin/streptomycin (1x, Invitrogen, Carlsbad, CA), gentamicin (15mg/ml, Invitrogen), heat inactivated fetal bovine serum (10% v/v, Invitrogen), normocin (0.1% v/v, Invivogen, San Diego, CA) in round-bottomed 96-well plates (BD Biosciences, San Diego, CA). All cells were cultured at 37 C, 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Immediately after collection, sorted cells were lysed in RLT buffer and passed through a Qiashredder column (both from Qiagen, Germantown, MD) and snap frozen in liquid nitrogen. Samples were stored at -70C until RNA extraction. RNA was extracted using the RNeasy Micro Kit with on-column DNAse as recommended by the manufacturer (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was used to prepare biotinylated cDNA with the WT-Ovation Pico kit as recommended by the kit manufacturer (NuGEN).
| | Sample_hyb_protocol | Biotinylated cDNA was hybridized overnight with Affymetrix U133_Plus_2.0 arrays using conditions recommended by NuGEN. After washing, arrays were stained with SAPE followed by signal enhancement with anti-SAPE antibody as recommended by Affymetrix.
| | Sample_scan_protocol | Phycoerythrin fluorescence was quantified with an Affymetrix scanner, and Affymetrix Command Console software was used to generate cel files from the raw scan data.
| | Sample_data_processing | Cel files were quantile-normalized with the GC-RMA method using the open-source gcrma Bioconductor package (R programming language).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Stephen,,Welle
| | Sample_contact_email | stephen_welle@urmc.rochester.edu
| | Sample_contact_institute | University of Rochester
| | Sample_contact_address | 601 Elmwood Avenue
| | Sample_contact_city | Rochester
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 14642
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1097nnn/GSM1097001/suppl/GSM1097001_05_CpGlow8K_Zand1_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE45113
| | Sample_data_row_count | 54675
| | |
|
GSM1097002 | GPL570 |
|
CD27_high_rep2
|
CD27_high_proliferating B cells
|
tissue: peripheral blood
cell type: proliferating B cells
cd27: high
divided in vitro: yes
|
CD27Hi_2
|
| Sample_geo_accession | GSM1097002
| | Sample_status | Public on Mar 13 2013
| | Sample_submission_date | Mar 12 2013
| | Sample_last_update_date | Mar 13 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | CFSE-stained cells were harvested, washed, and counted. The cells were stained with Live/Dead Violet Invitrogen, Carlsbad, CA), washed and stained with anti-CD27-APC-H7 antibody (BD Bioscience, San Diego, CA) on ice. FACS cell sorts were performed on live cells.
| | Sample_growth_protocol_ch1 | Freshly isolated CD27+ IgG enriched human peripheral blood Bc were cultured in the presence of CpG 2006 (10 ng/ml, Oligos, etc., Wilsonville, OR), plus recombinant human cytokines IL-2 (20 IU/ml), IL-10 (50 ng/ml), IL-15 (10 ng/ml) (all from BD Biosciences, San Diego, CA), and recombinant human BAFF (75 ng/ml, Chemicon, Temecula, CA) PC-L medium (IMDM medium, lacromin (50mg/ml, Seracare, Milford, MA), insulin (5mg/ml, Sigma-Aldrich, St. Louis, MO), penicillin/streptomycin (1x, Invitrogen, Carlsbad, CA), gentamicin (15mg/ml, Invitrogen), heat inactivated fetal bovine serum (10% v/v, Invitrogen), normocin (0.1% v/v, Invivogen, San Diego, CA) in round-bottomed 96-well plates (BD Biosciences, San Diego, CA). All cells were cultured at 37 C, 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Immediately after collection, sorted cells were lysed in RLT buffer and passed through a Qiashredder column (both from Qiagen, Germantown, MD) and snap frozen in liquid nitrogen. Samples were stored at -70C until RNA extraction. RNA was extracted using the RNeasy Micro Kit with on-column DNAse as recommended by the manufacturer (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was used to prepare biotinylated cDNA with the WT-Ovation Pico kit as recommended by the kit manufacturer (NuGEN).
| | Sample_hyb_protocol | Biotinylated cDNA was hybridized overnight with Affymetrix U133_Plus_2.0 arrays using conditions recommended by NuGEN. After washing, arrays were stained with SAPE followed by signal enhancement with anti-SAPE antibody as recommended by Affymetrix.
| | Sample_scan_protocol | Phycoerythrin fluorescence was quantified with an Affymetrix scanner, and Affymetrix Command Console software was used to generate cel files from the raw scan data.
| | Sample_data_processing | Cel files were quantile-normalized with the GC-RMA method using the open-source gcrma Bioconductor package (R programming language).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Stephen,,Welle
| | Sample_contact_email | stephen_welle@urmc.rochester.edu
| | Sample_contact_institute | University of Rochester
| | Sample_contact_address | 601 Elmwood Avenue
| | Sample_contact_city | Rochester
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 14642
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1097nnn/GSM1097002/suppl/GSM1097002_06_CpGhi8K_Zand1_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE45113
| | Sample_data_row_count | 54675
| | |
|
GSM1097003 | GPL570 |
|
undivided_rep3
|
undivided B cells
|
tissue: peripheral blood
cell type: undivided B cells
cd27: low
divided in vitro: no
|
Un_3
|
| Sample_geo_accession | GSM1097003
| | Sample_status | Public on Mar 13 2013
| | Sample_submission_date | Mar 12 2013
| | Sample_last_update_date | Mar 13 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | CFSE-stained cells were harvested, washed, and counted. The cells were stained with Live/Dead Violet Invitrogen, Carlsbad, CA), washed and stained with anti-CD27-APC-H7 antibody (BD Bioscience, San Diego, CA) on ice. FACS cell sorts were performed on live cells.
| | Sample_growth_protocol_ch1 | Freshly isolated CD27+ IgG enriched human peripheral blood Bc were cultured in the presence of CpG 2006 (10 ng/ml, Oligos, etc., Wilsonville, OR), plus recombinant human cytokines IL-2 (20 IU/ml), IL-10 (50 ng/ml), IL-15 (10 ng/ml) (all from BD Biosciences, San Diego, CA), and recombinant human BAFF (75 ng/ml, Chemicon, Temecula, CA) PC-L medium (IMDM medium, lacromin (50mg/ml, Seracare, Milford, MA), insulin (5mg/ml, Sigma-Aldrich, St. Louis, MO), penicillin/streptomycin (1x, Invitrogen, Carlsbad, CA), gentamicin (15mg/ml, Invitrogen), heat inactivated fetal bovine serum (10% v/v, Invitrogen), normocin (0.1% v/v, Invivogen, San Diego, CA) in round-bottomed 96-well plates (BD Biosciences, San Diego, CA). All cells were cultured at 37 C, 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Immediately after collection, sorted cells were lysed in RLT buffer and passed through a Qiashredder column (both from Qiagen, Germantown, MD) and snap frozen in liquid nitrogen. Samples were stored at -70C until RNA extraction. RNA was extracted using the RNeasy Micro Kit with on-column DNAse as recommended by the manufacturer (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was used to prepare biotinylated cDNA with the WT-Ovation Pico kit as recommended by the kit manufacturer (NuGEN).
| | Sample_hyb_protocol | Biotinylated cDNA was hybridized overnight with Affymetrix U133_Plus_2.0 arrays using conditions recommended by NuGEN. After washing, arrays were stained with SAPE followed by signal enhancement with anti-SAPE antibody as recommended by Affymetrix.
| | Sample_scan_protocol | Phycoerythrin fluorescence was quantified with an Affymetrix scanner, and Affymetrix Command Console software was used to generate cel files from the raw scan data.
| | Sample_data_processing | Cel files were quantile-normalized with the GC-RMA method using the open-source gcrma Bioconductor package (R programming language).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Stephen,,Welle
| | Sample_contact_email | stephen_welle@urmc.rochester.edu
| | Sample_contact_institute | University of Rochester
| | Sample_contact_address | 601 Elmwood Avenue
| | Sample_contact_city | Rochester
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 14642
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1097nnn/GSM1097003/suppl/GSM1097003_07_CpGundiv9N_Zand1_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE45113
| | Sample_data_row_count | 54675
| | |
|
GSM1097004 | GPL570 |
|
CD27_low_rep3
|
CD27_low_proliferating B cells
|
tissue: peripheral blood
cell type: proliferating B cells
cd27: low
divided in vitro: yes
|
CD27Lo_3
|
| Sample_geo_accession | GSM1097004
| | Sample_status | Public on Mar 13 2013
| | Sample_submission_date | Mar 12 2013
| | Sample_last_update_date | Mar 13 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | CFSE-stained cells were harvested, washed, and counted. The cells were stained with Live/Dead Violet Invitrogen, Carlsbad, CA), washed and stained with anti-CD27-APC-H7 antibody (BD Bioscience, San Diego, CA) on ice. FACS cell sorts were performed on live cells.
| | Sample_growth_protocol_ch1 | Freshly isolated CD27+ IgG enriched human peripheral blood Bc were cultured in the presence of CpG 2006 (10 ng/ml, Oligos, etc., Wilsonville, OR), plus recombinant human cytokines IL-2 (20 IU/ml), IL-10 (50 ng/ml), IL-15 (10 ng/ml) (all from BD Biosciences, San Diego, CA), and recombinant human BAFF (75 ng/ml, Chemicon, Temecula, CA) PC-L medium (IMDM medium, lacromin (50mg/ml, Seracare, Milford, MA), insulin (5mg/ml, Sigma-Aldrich, St. Louis, MO), penicillin/streptomycin (1x, Invitrogen, Carlsbad, CA), gentamicin (15mg/ml, Invitrogen), heat inactivated fetal bovine serum (10% v/v, Invitrogen), normocin (0.1% v/v, Invivogen, San Diego, CA) in round-bottomed 96-well plates (BD Biosciences, San Diego, CA). All cells were cultured at 37 C, 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Immediately after collection, sorted cells were lysed in RLT buffer and passed through a Qiashredder column (both from Qiagen, Germantown, MD) and snap frozen in liquid nitrogen. Samples were stored at -70C until RNA extraction. RNA was extracted using the RNeasy Micro Kit with on-column DNAse as recommended by the manufacturer (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was used to prepare biotinylated cDNA with the WT-Ovation Pico kit as recommended by the kit manufacturer (NuGEN).
| | Sample_hyb_protocol | Biotinylated cDNA was hybridized overnight with Affymetrix U133_Plus_2.0 arrays using conditions recommended by NuGEN. After washing, arrays were stained with SAPE followed by signal enhancement with anti-SAPE antibody as recommended by Affymetrix.
| | Sample_scan_protocol | Phycoerythrin fluorescence was quantified with an Affymetrix scanner, and Affymetrix Command Console software was used to generate cel files from the raw scan data.
| | Sample_data_processing | Cel files were quantile-normalized with the GC-RMA method using the open-source gcrma Bioconductor package (R programming language).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Stephen,,Welle
| | Sample_contact_email | stephen_welle@urmc.rochester.edu
| | Sample_contact_institute | University of Rochester
| | Sample_contact_address | 601 Elmwood Avenue
| | Sample_contact_city | Rochester
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 14642
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1097nnn/GSM1097004/suppl/GSM1097004_08_CpGlow9N_Zand1_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE45113
| | Sample_data_row_count | 54675
| | |
|
GSM1097005 | GPL570 |
|
CD27_high_rep3
|
CD27_high_proliferating B cells
|
tissue: peripheral blood
cell type: proliferating B cells
cd27: high
divided in vitro: yes
|
CD27Hi_3
|
| Sample_geo_accession | GSM1097005
| | Sample_status | Public on Mar 13 2013
| | Sample_submission_date | Mar 12 2013
| | Sample_last_update_date | Mar 13 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | CFSE-stained cells were harvested, washed, and counted. The cells were stained with Live/Dead Violet Invitrogen, Carlsbad, CA), washed and stained with anti-CD27-APC-H7 antibody (BD Bioscience, San Diego, CA) on ice. FACS cell sorts were performed on live cells.
| | Sample_growth_protocol_ch1 | Freshly isolated CD27+ IgG enriched human peripheral blood Bc were cultured in the presence of CpG 2006 (10 ng/ml, Oligos, etc., Wilsonville, OR), plus recombinant human cytokines IL-2 (20 IU/ml), IL-10 (50 ng/ml), IL-15 (10 ng/ml) (all from BD Biosciences, San Diego, CA), and recombinant human BAFF (75 ng/ml, Chemicon, Temecula, CA) PC-L medium (IMDM medium, lacromin (50mg/ml, Seracare, Milford, MA), insulin (5mg/ml, Sigma-Aldrich, St. Louis, MO), penicillin/streptomycin (1x, Invitrogen, Carlsbad, CA), gentamicin (15mg/ml, Invitrogen), heat inactivated fetal bovine serum (10% v/v, Invitrogen), normocin (0.1% v/v, Invivogen, San Diego, CA) in round-bottomed 96-well plates (BD Biosciences, San Diego, CA). All cells were cultured at 37 C, 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Immediately after collection, sorted cells were lysed in RLT buffer and passed through a Qiashredder column (both from Qiagen, Germantown, MD) and snap frozen in liquid nitrogen. Samples were stored at -70C until RNA extraction. RNA was extracted using the RNeasy Micro Kit with on-column DNAse as recommended by the manufacturer (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was used to prepare biotinylated cDNA with the WT-Ovation Pico kit as recommended by the kit manufacturer (NuGEN).
| | Sample_hyb_protocol | Biotinylated cDNA was hybridized overnight with Affymetrix U133_Plus_2.0 arrays using conditions recommended by NuGEN. After washing, arrays were stained with SAPE followed by signal enhancement with anti-SAPE antibody as recommended by Affymetrix.
| | Sample_scan_protocol | Phycoerythrin fluorescence was quantified with an Affymetrix scanner, and Affymetrix Command Console software was used to generate cel files from the raw scan data.
| | Sample_data_processing | Cel files were quantile-normalized with the GC-RMA method using the open-source gcrma Bioconductor package (R programming language).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Stephen,,Welle
| | Sample_contact_email | stephen_welle@urmc.rochester.edu
| | Sample_contact_institute | University of Rochester
| | Sample_contact_address | 601 Elmwood Avenue
| | Sample_contact_city | Rochester
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 14642
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1097nnn/GSM1097005/suppl/GSM1097005_09_CpGhi9N_Zand1_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE45113
| | Sample_data_row_count | 54675
| | |
|
GSM1097006 | GPL570 |
|
undivided_rep4
|
undivided B cells
|
tissue: peripheral blood
cell type: undivided B cells
cd27: low
divided in vitro: no
|
Un_4
|
| Sample_geo_accession | GSM1097006
| | Sample_status | Public on Mar 13 2013
| | Sample_submission_date | Mar 12 2013
| | Sample_last_update_date | Mar 13 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | CFSE-stained cells were harvested, washed, and counted. The cells were stained with Live/Dead Violet Invitrogen, Carlsbad, CA), washed and stained with anti-CD27-APC-H7 antibody (BD Bioscience, San Diego, CA) on ice. FACS cell sorts were performed on live cells.
| | Sample_growth_protocol_ch1 | Freshly isolated CD27+ IgG enriched human peripheral blood Bc were cultured in the presence of CpG 2006 (10 ng/ml, Oligos, etc., Wilsonville, OR), plus recombinant human cytokines IL-2 (20 IU/ml), IL-10 (50 ng/ml), IL-15 (10 ng/ml) (all from BD Biosciences, San Diego, CA), and recombinant human BAFF (75 ng/ml, Chemicon, Temecula, CA) PC-L medium (IMDM medium, lacromin (50mg/ml, Seracare, Milford, MA), insulin (5mg/ml, Sigma-Aldrich, St. Louis, MO), penicillin/streptomycin (1x, Invitrogen, Carlsbad, CA), gentamicin (15mg/ml, Invitrogen), heat inactivated fetal bovine serum (10% v/v, Invitrogen), normocin (0.1% v/v, Invivogen, San Diego, CA) in round-bottomed 96-well plates (BD Biosciences, San Diego, CA). All cells were cultured at 37 C, 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Immediately after collection, sorted cells were lysed in RLT buffer and passed through a Qiashredder column (both from Qiagen, Germantown, MD) and snap frozen in liquid nitrogen. Samples were stored at -70C until RNA extraction. RNA was extracted using the RNeasy Micro Kit with on-column DNAse as recommended by the manufacturer (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was used to prepare biotinylated cDNA with the WT-Ovation Pico kit as recommended by the kit manufacturer (NuGEN).
| | Sample_hyb_protocol | Biotinylated cDNA was hybridized overnight with Affymetrix U133_Plus_2.0 arrays using conditions recommended by NuGEN. After washing, arrays were stained with SAPE followed by signal enhancement with anti-SAPE antibody as recommended by Affymetrix.
| | Sample_scan_protocol | Phycoerythrin fluorescence was quantified with an Affymetrix scanner, and Affymetrix Command Console software was used to generate cel files from the raw scan data.
| | Sample_data_processing | Cel files were quantile-normalized with the GC-RMA method using the open-source gcrma Bioconductor package (R programming language).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Stephen,,Welle
| | Sample_contact_email | stephen_welle@urmc.rochester.edu
| | Sample_contact_institute | University of Rochester
| | Sample_contact_address | 601 Elmwood Avenue
| | Sample_contact_city | Rochester
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 14642
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1097nnn/GSM1097006/suppl/GSM1097006_10_CpGundiv10X_Zand1_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE45113
| | Sample_data_row_count | 54675
| | |
|
GSM1097007 | GPL570 |
|
CD27_low_rep4
|
CD27_low_proliferating B cells
|
tissue: peripheral blood
cell type: proliferating B cells
cd27: low
divided in vitro: yes
|
CD27Lo_4
|
| Sample_geo_accession | GSM1097007
| | Sample_status | Public on Mar 13 2013
| | Sample_submission_date | Mar 12 2013
| | Sample_last_update_date | Mar 13 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | CFSE-stained cells were harvested, washed, and counted. The cells were stained with Live/Dead Violet Invitrogen, Carlsbad, CA), washed and stained with anti-CD27-APC-H7 antibody (BD Bioscience, San Diego, CA) on ice. FACS cell sorts were performed on live cells.
| | Sample_growth_protocol_ch1 | Freshly isolated CD27+ IgG enriched human peripheral blood Bc were cultured in the presence of CpG 2006 (10 ng/ml, Oligos, etc., Wilsonville, OR), plus recombinant human cytokines IL-2 (20 IU/ml), IL-10 (50 ng/ml), IL-15 (10 ng/ml) (all from BD Biosciences, San Diego, CA), and recombinant human BAFF (75 ng/ml, Chemicon, Temecula, CA) PC-L medium (IMDM medium, lacromin (50mg/ml, Seracare, Milford, MA), insulin (5mg/ml, Sigma-Aldrich, St. Louis, MO), penicillin/streptomycin (1x, Invitrogen, Carlsbad, CA), gentamicin (15mg/ml, Invitrogen), heat inactivated fetal bovine serum (10% v/v, Invitrogen), normocin (0.1% v/v, Invivogen, San Diego, CA) in round-bottomed 96-well plates (BD Biosciences, San Diego, CA). All cells were cultured at 37 C, 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Immediately after collection, sorted cells were lysed in RLT buffer and passed through a Qiashredder column (both from Qiagen, Germantown, MD) and snap frozen in liquid nitrogen. Samples were stored at -70C until RNA extraction. RNA was extracted using the RNeasy Micro Kit with on-column DNAse as recommended by the manufacturer (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was used to prepare biotinylated cDNA with the WT-Ovation Pico kit as recommended by the kit manufacturer (NuGEN).
| | Sample_hyb_protocol | Biotinylated cDNA was hybridized overnight with Affymetrix U133_Plus_2.0 arrays using conditions recommended by NuGEN. After washing, arrays were stained with SAPE followed by signal enhancement with anti-SAPE antibody as recommended by Affymetrix.
| | Sample_scan_protocol | Phycoerythrin fluorescence was quantified with an Affymetrix scanner, and Affymetrix Command Console software was used to generate cel files from the raw scan data.
| | Sample_data_processing | Cel files were quantile-normalized with the GC-RMA method using the open-source gcrma Bioconductor package (R programming language).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Stephen,,Welle
| | Sample_contact_email | stephen_welle@urmc.rochester.edu
| | Sample_contact_institute | University of Rochester
| | Sample_contact_address | 601 Elmwood Avenue
| | Sample_contact_city | Rochester
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 14642
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1097nnn/GSM1097007/suppl/GSM1097007_11_CpGlow10X_Zand1_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE45113
| | Sample_data_row_count | 54675
| | |
|
GSM1097008 | GPL570 |
|
CD27_high_rep4
|
CD27_high_proliferating B cells
|
tissue: peripheral blood
cell type: proliferating B cells
cd27: high
divided in vitro: yes
|
CD27Hi_4
|
| Sample_geo_accession | GSM1097008
| | Sample_status | Public on Mar 13 2013
| | Sample_submission_date | Mar 12 2013
| | Sample_last_update_date | Mar 13 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | CFSE-stained cells were harvested, washed, and counted. The cells were stained with Live/Dead Violet Invitrogen, Carlsbad, CA), washed and stained with anti-CD27-APC-H7 antibody (BD Bioscience, San Diego, CA) on ice. FACS cell sorts were performed on live cells.
| | Sample_growth_protocol_ch1 | Freshly isolated CD27+ IgG enriched human peripheral blood Bc were cultured in the presence of CpG 2006 (10 ng/ml, Oligos, etc., Wilsonville, OR), plus recombinant human cytokines IL-2 (20 IU/ml), IL-10 (50 ng/ml), IL-15 (10 ng/ml) (all from BD Biosciences, San Diego, CA), and recombinant human BAFF (75 ng/ml, Chemicon, Temecula, CA) PC-L medium (IMDM medium, lacromin (50mg/ml, Seracare, Milford, MA), insulin (5mg/ml, Sigma-Aldrich, St. Louis, MO), penicillin/streptomycin (1x, Invitrogen, Carlsbad, CA), gentamicin (15mg/ml, Invitrogen), heat inactivated fetal bovine serum (10% v/v, Invitrogen), normocin (0.1% v/v, Invivogen, San Diego, CA) in round-bottomed 96-well plates (BD Biosciences, San Diego, CA). All cells were cultured at 37 C, 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Immediately after collection, sorted cells were lysed in RLT buffer and passed through a Qiashredder column (both from Qiagen, Germantown, MD) and snap frozen in liquid nitrogen. Samples were stored at -70C until RNA extraction. RNA was extracted using the RNeasy Micro Kit with on-column DNAse as recommended by the manufacturer (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was used to prepare biotinylated cDNA with the WT-Ovation Pico kit as recommended by the kit manufacturer (NuGEN).
| | Sample_hyb_protocol | Biotinylated cDNA was hybridized overnight with Affymetrix U133_Plus_2.0 arrays using conditions recommended by NuGEN. After washing, arrays were stained with SAPE followed by signal enhancement with anti-SAPE antibody as recommended by Affymetrix.
| | Sample_scan_protocol | Phycoerythrin fluorescence was quantified with an Affymetrix scanner, and Affymetrix Command Console software was used to generate cel files from the raw scan data.
| | Sample_data_processing | Cel files were quantile-normalized with the GC-RMA method using the open-source gcrma Bioconductor package (R programming language).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Stephen,,Welle
| | Sample_contact_email | stephen_welle@urmc.rochester.edu
| | Sample_contact_institute | University of Rochester
| | Sample_contact_address | 601 Elmwood Avenue
| | Sample_contact_city | Rochester
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 14642
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1097nnn/GSM1097008/suppl/GSM1097008_12_CpGhi10X_Zand1_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE45113
| | Sample_data_row_count | 54675
| | |
|
GSM1097009 | GPL570 |
|
undivided_rep5
|
undivided B cells
|
tissue: peripheral blood
cell type: undivided B cells
cd27: low
divided in vitro: no
|
Un_5
|
| Sample_geo_accession | GSM1097009
| | Sample_status | Public on Mar 13 2013
| | Sample_submission_date | Mar 12 2013
| | Sample_last_update_date | Mar 13 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | CFSE-stained cells were harvested, washed, and counted. The cells were stained with Live/Dead Violet Invitrogen, Carlsbad, CA), washed and stained with anti-CD27-APC-H7 antibody (BD Bioscience, San Diego, CA) on ice. FACS cell sorts were performed on live cells.
| | Sample_growth_protocol_ch1 | Freshly isolated CD27+ IgG enriched human peripheral blood Bc were cultured in the presence of CpG 2006 (10 ng/ml, Oligos, etc., Wilsonville, OR), plus recombinant human cytokines IL-2 (20 IU/ml), IL-10 (50 ng/ml), IL-15 (10 ng/ml) (all from BD Biosciences, San Diego, CA), and recombinant human BAFF (75 ng/ml, Chemicon, Temecula, CA) PC-L medium (IMDM medium, lacromin (50mg/ml, Seracare, Milford, MA), insulin (5mg/ml, Sigma-Aldrich, St. Louis, MO), penicillin/streptomycin (1x, Invitrogen, Carlsbad, CA), gentamicin (15mg/ml, Invitrogen), heat inactivated fetal bovine serum (10% v/v, Invitrogen), normocin (0.1% v/v, Invivogen, San Diego, CA) in round-bottomed 96-well plates (BD Biosciences, San Diego, CA). All cells were cultured at 37 C, 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Immediately after collection, sorted cells were lysed in RLT buffer and passed through a Qiashredder column (both from Qiagen, Germantown, MD) and snap frozen in liquid nitrogen. Samples were stored at -70C until RNA extraction. RNA was extracted using the RNeasy Micro Kit with on-column DNAse as recommended by the manufacturer (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was used to prepare biotinylated cDNA with the WT-Ovation Pico kit as recommended by the kit manufacturer (NuGEN).
| | Sample_hyb_protocol | Biotinylated cDNA was hybridized overnight with Affymetrix U133_Plus_2.0 arrays using conditions recommended by NuGEN. After washing, arrays were stained with SAPE followed by signal enhancement with anti-SAPE antibody as recommended by Affymetrix.
| | Sample_scan_protocol | Phycoerythrin fluorescence was quantified with an Affymetrix scanner, and Affymetrix Command Console software was used to generate cel files from the raw scan data.
| | Sample_data_processing | Cel files were quantile-normalized with the GC-RMA method using the open-source gcrma Bioconductor package (R programming language).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Stephen,,Welle
| | Sample_contact_email | stephen_welle@urmc.rochester.edu
| | Sample_contact_institute | University of Rochester
| | Sample_contact_address | 601 Elmwood Avenue
| | Sample_contact_city | Rochester
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 14642
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1097nnn/GSM1097009/suppl/GSM1097009_13_CpGundiv11T_Zand1_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE45113
| | Sample_data_row_count | 54675
| | |
|
GSM1097010 | GPL570 |
|
CD27_low_rep5
|
CD27_low_proliferating B cells
|
tissue: peripheral blood
cell type: proliferating B cells
cd27: low
divided in vitro: yes
|
CD27Lo_5
|
| Sample_geo_accession | GSM1097010
| | Sample_status | Public on Mar 13 2013
| | Sample_submission_date | Mar 12 2013
| | Sample_last_update_date | Mar 13 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | CFSE-stained cells were harvested, washed, and counted. The cells were stained with Live/Dead Violet Invitrogen, Carlsbad, CA), washed and stained with anti-CD27-APC-H7 antibody (BD Bioscience, San Diego, CA) on ice. FACS cell sorts were performed on live cells.
| | Sample_growth_protocol_ch1 | Freshly isolated CD27+ IgG enriched human peripheral blood Bc were cultured in the presence of CpG 2006 (10 ng/ml, Oligos, etc., Wilsonville, OR), plus recombinant human cytokines IL-2 (20 IU/ml), IL-10 (50 ng/ml), IL-15 (10 ng/ml) (all from BD Biosciences, San Diego, CA), and recombinant human BAFF (75 ng/ml, Chemicon, Temecula, CA) PC-L medium (IMDM medium, lacromin (50mg/ml, Seracare, Milford, MA), insulin (5mg/ml, Sigma-Aldrich, St. Louis, MO), penicillin/streptomycin (1x, Invitrogen, Carlsbad, CA), gentamicin (15mg/ml, Invitrogen), heat inactivated fetal bovine serum (10% v/v, Invitrogen), normocin (0.1% v/v, Invivogen, San Diego, CA) in round-bottomed 96-well plates (BD Biosciences, San Diego, CA). All cells were cultured at 37 C, 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Immediately after collection, sorted cells were lysed in RLT buffer and passed through a Qiashredder column (both from Qiagen, Germantown, MD) and snap frozen in liquid nitrogen. Samples were stored at -70C until RNA extraction. RNA was extracted using the RNeasy Micro Kit with on-column DNAse as recommended by the manufacturer (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was used to prepare biotinylated cDNA with the WT-Ovation Pico kit as recommended by the kit manufacturer (NuGEN).
| | Sample_hyb_protocol | Biotinylated cDNA was hybridized overnight with Affymetrix U133_Plus_2.0 arrays using conditions recommended by NuGEN. After washing, arrays were stained with SAPE followed by signal enhancement with anti-SAPE antibody as recommended by Affymetrix.
| | Sample_scan_protocol | Phycoerythrin fluorescence was quantified with an Affymetrix scanner, and Affymetrix Command Console software was used to generate cel files from the raw scan data.
| | Sample_data_processing | Cel files were quantile-normalized with the GC-RMA method using the open-source gcrma Bioconductor package (R programming language).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Stephen,,Welle
| | Sample_contact_email | stephen_welle@urmc.rochester.edu
| | Sample_contact_institute | University of Rochester
| | Sample_contact_address | 601 Elmwood Avenue
| | Sample_contact_city | Rochester
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 14642
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1097nnn/GSM1097010/suppl/GSM1097010_14_CpGlow11T_Zand1_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE45113
| | Sample_data_row_count | 54675
| | |
|
GSM1097011 | GPL570 |
|
CD27_high_rep5
|
CD27_high_proliferating B cells
|
tissue: peripheral blood
cell type: proliferating B cells
cd27: high
divided in vitro: yes
|
CD27Hi_5
|
| Sample_geo_accession | GSM1097011
| | Sample_status | Public on Mar 13 2013
| | Sample_submission_date | Mar 12 2013
| | Sample_last_update_date | Mar 13 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | CFSE-stained cells were harvested, washed, and counted. The cells were stained with Live/Dead Violet Invitrogen, Carlsbad, CA), washed and stained with anti-CD27-APC-H7 antibody (BD Bioscience, San Diego, CA) on ice. FACS cell sorts were performed on live cells.
| | Sample_growth_protocol_ch1 | Freshly isolated CD27+ IgG enriched human peripheral blood Bc were cultured in the presence of CpG 2006 (10 ng/ml, Oligos, etc., Wilsonville, OR), plus recombinant human cytokines IL-2 (20 IU/ml), IL-10 (50 ng/ml), IL-15 (10 ng/ml) (all from BD Biosciences, San Diego, CA), and recombinant human BAFF (75 ng/ml, Chemicon, Temecula, CA) PC-L medium (IMDM medium, lacromin (50mg/ml, Seracare, Milford, MA), insulin (5mg/ml, Sigma-Aldrich, St. Louis, MO), penicillin/streptomycin (1x, Invitrogen, Carlsbad, CA), gentamicin (15mg/ml, Invitrogen), heat inactivated fetal bovine serum (10% v/v, Invitrogen), normocin (0.1% v/v, Invivogen, San Diego, CA) in round-bottomed 96-well plates (BD Biosciences, San Diego, CA). All cells were cultured at 37 C, 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Immediately after collection, sorted cells were lysed in RLT buffer and passed through a Qiashredder column (both from Qiagen, Germantown, MD) and snap frozen in liquid nitrogen. Samples were stored at -70C until RNA extraction. RNA was extracted using the RNeasy Micro Kit with on-column DNAse as recommended by the manufacturer (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was used to prepare biotinylated cDNA with the WT-Ovation Pico kit as recommended by the kit manufacturer (NuGEN).
| | Sample_hyb_protocol | Biotinylated cDNA was hybridized overnight with Affymetrix U133_Plus_2.0 arrays using conditions recommended by NuGEN. After washing, arrays were stained with SAPE followed by signal enhancement with anti-SAPE antibody as recommended by Affymetrix.
| | Sample_scan_protocol | Phycoerythrin fluorescence was quantified with an Affymetrix scanner, and Affymetrix Command Console software was used to generate cel files from the raw scan data.
| | Sample_data_processing | Cel files were quantile-normalized with the GC-RMA method using the open-source gcrma Bioconductor package (R programming language).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Stephen,,Welle
| | Sample_contact_email | stephen_welle@urmc.rochester.edu
| | Sample_contact_institute | University of Rochester
| | Sample_contact_address | 601 Elmwood Avenue
| | Sample_contact_city | Rochester
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 14642
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1097nnn/GSM1097011/suppl/GSM1097011_15_CpGhi11T_Zand1_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE45113
| | Sample_data_row_count | 54675
| | |
|
GSM1097012 | GPL570 |
|
undivided_rep6
|
undivided B cells
|
tissue: peripheral blood
cell type: undivided B cells
cd27: low
divided in vitro: no
|
Un_6
|
| Sample_geo_accession | GSM1097012
| | Sample_status | Public on Mar 13 2013
| | Sample_submission_date | Mar 12 2013
| | Sample_last_update_date | Mar 13 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | CFSE-stained cells were harvested, washed, and counted. The cells were stained with Live/Dead Violet Invitrogen, Carlsbad, CA), washed and stained with anti-CD27-APC-H7 antibody (BD Bioscience, San Diego, CA) on ice. FACS cell sorts were performed on live cells.
| | Sample_growth_protocol_ch1 | Freshly isolated CD27+ IgG enriched human peripheral blood Bc were cultured in the presence of CpG 2006 (10 ng/ml, Oligos, etc., Wilsonville, OR), plus recombinant human cytokines IL-2 (20 IU/ml), IL-10 (50 ng/ml), IL-15 (10 ng/ml) (all from BD Biosciences, San Diego, CA), and recombinant human BAFF (75 ng/ml, Chemicon, Temecula, CA) PC-L medium (IMDM medium, lacromin (50mg/ml, Seracare, Milford, MA), insulin (5mg/ml, Sigma-Aldrich, St. Louis, MO), penicillin/streptomycin (1x, Invitrogen, Carlsbad, CA), gentamicin (15mg/ml, Invitrogen), heat inactivated fetal bovine serum (10% v/v, Invitrogen), normocin (0.1% v/v, Invivogen, San Diego, CA) in round-bottomed 96-well plates (BD Biosciences, San Diego, CA). All cells were cultured at 37 C, 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Immediately after collection, sorted cells were lysed in RLT buffer and passed through a Qiashredder column (both from Qiagen, Germantown, MD) and snap frozen in liquid nitrogen. Samples were stored at -70C until RNA extraction. RNA was extracted using the RNeasy Micro Kit with on-column DNAse as recommended by the manufacturer (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was used to prepare biotinylated cDNA with the WT-Ovation Pico kit as recommended by the kit manufacturer (NuGEN).
| | Sample_hyb_protocol | Biotinylated cDNA was hybridized overnight with Affymetrix U133_Plus_2.0 arrays using conditions recommended by NuGEN. After washing, arrays were stained with SAPE followed by signal enhancement with anti-SAPE antibody as recommended by Affymetrix.
| | Sample_scan_protocol | Phycoerythrin fluorescence was quantified with an Affymetrix scanner, and Affymetrix Command Console software was used to generate cel files from the raw scan data.
| | Sample_data_processing | Cel files were quantile-normalized with the GC-RMA method using the open-source gcrma Bioconductor package (R programming language).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Stephen,,Welle
| | Sample_contact_email | stephen_welle@urmc.rochester.edu
| | Sample_contact_institute | University of Rochester
| | Sample_contact_address | 601 Elmwood Avenue
| | Sample_contact_city | Rochester
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 14642
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1097nnn/GSM1097012/suppl/GSM1097012_16_CpGundiv12Z_Zand1_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE45113
| | Sample_data_row_count | 54675
| | |
|
GSM1097013 | GPL570 |
|
CD27_low_rep6
|
CD27_low_proliferating B cells
|
tissue: peripheral blood
cell type: proliferating B cells
cd27: low
divided in vitro: yes
|
CD27Lo_6
|
| Sample_geo_accession | GSM1097013
| | Sample_status | Public on Mar 13 2013
| | Sample_submission_date | Mar 12 2013
| | Sample_last_update_date | Mar 13 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | CFSE-stained cells were harvested, washed, and counted. The cells were stained with Live/Dead Violet Invitrogen, Carlsbad, CA), washed and stained with anti-CD27-APC-H7 antibody (BD Bioscience, San Diego, CA) on ice. FACS cell sorts were performed on live cells.
| | Sample_growth_protocol_ch1 | Freshly isolated CD27+ IgG enriched human peripheral blood Bc were cultured in the presence of CpG 2006 (10 ng/ml, Oligos, etc., Wilsonville, OR), plus recombinant human cytokines IL-2 (20 IU/ml), IL-10 (50 ng/ml), IL-15 (10 ng/ml) (all from BD Biosciences, San Diego, CA), and recombinant human BAFF (75 ng/ml, Chemicon, Temecula, CA) PC-L medium (IMDM medium, lacromin (50mg/ml, Seracare, Milford, MA), insulin (5mg/ml, Sigma-Aldrich, St. Louis, MO), penicillin/streptomycin (1x, Invitrogen, Carlsbad, CA), gentamicin (15mg/ml, Invitrogen), heat inactivated fetal bovine serum (10% v/v, Invitrogen), normocin (0.1% v/v, Invivogen, San Diego, CA) in round-bottomed 96-well plates (BD Biosciences, San Diego, CA). All cells were cultured at 37 C, 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Immediately after collection, sorted cells were lysed in RLT buffer and passed through a Qiashredder column (both from Qiagen, Germantown, MD) and snap frozen in liquid nitrogen. Samples were stored at -70C until RNA extraction. RNA was extracted using the RNeasy Micro Kit with on-column DNAse as recommended by the manufacturer (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was used to prepare biotinylated cDNA with the WT-Ovation Pico kit as recommended by the kit manufacturer (NuGEN).
| | Sample_hyb_protocol | Biotinylated cDNA was hybridized overnight with Affymetrix U133_Plus_2.0 arrays using conditions recommended by NuGEN. After washing, arrays were stained with SAPE followed by signal enhancement with anti-SAPE antibody as recommended by Affymetrix.
| | Sample_scan_protocol | Phycoerythrin fluorescence was quantified with an Affymetrix scanner, and Affymetrix Command Console software was used to generate cel files from the raw scan data.
| | Sample_data_processing | Cel files were quantile-normalized with the GC-RMA method using the open-source gcrma Bioconductor package (R programming language).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Stephen,,Welle
| | Sample_contact_email | stephen_welle@urmc.rochester.edu
| | Sample_contact_institute | University of Rochester
| | Sample_contact_address | 601 Elmwood Avenue
| | Sample_contact_city | Rochester
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 14642
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1097nnn/GSM1097013/suppl/GSM1097013_17_CpGlow12Z_Zand1_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE45113
| | Sample_data_row_count | 54675
| | |
|
GSM1097014 | GPL570 |
|
CD27_high_rep6
|
CD27_high_proliferating B cells
|
tissue: peripheral blood
cell type: proliferating B cells
cd27: high
divided in vitro: yes
|
CD27Hi_6
|
| Sample_geo_accession | GSM1097014
| | Sample_status | Public on Mar 13 2013
| | Sample_submission_date | Mar 12 2013
| | Sample_last_update_date | Mar 13 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | CFSE-stained cells were harvested, washed, and counted. The cells were stained with Live/Dead Violet Invitrogen, Carlsbad, CA), washed and stained with anti-CD27-APC-H7 antibody (BD Bioscience, San Diego, CA) on ice. FACS cell sorts were performed on live cells.
| | Sample_growth_protocol_ch1 | Freshly isolated CD27+ IgG enriched human peripheral blood Bc were cultured in the presence of CpG 2006 (10 ng/ml, Oligos, etc., Wilsonville, OR), plus recombinant human cytokines IL-2 (20 IU/ml), IL-10 (50 ng/ml), IL-15 (10 ng/ml) (all from BD Biosciences, San Diego, CA), and recombinant human BAFF (75 ng/ml, Chemicon, Temecula, CA) PC-L medium (IMDM medium, lacromin (50mg/ml, Seracare, Milford, MA), insulin (5mg/ml, Sigma-Aldrich, St. Louis, MO), penicillin/streptomycin (1x, Invitrogen, Carlsbad, CA), gentamicin (15mg/ml, Invitrogen), heat inactivated fetal bovine serum (10% v/v, Invitrogen), normocin (0.1% v/v, Invivogen, San Diego, CA) in round-bottomed 96-well plates (BD Biosciences, San Diego, CA). All cells were cultured at 37 C, 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Immediately after collection, sorted cells were lysed in RLT buffer and passed through a Qiashredder column (both from Qiagen, Germantown, MD) and snap frozen in liquid nitrogen. Samples were stored at -70C until RNA extraction. RNA was extracted using the RNeasy Micro Kit with on-column DNAse as recommended by the manufacturer (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was used to prepare biotinylated cDNA with the WT-Ovation Pico kit as recommended by the kit manufacturer (NuGEN).
| | Sample_hyb_protocol | Biotinylated cDNA was hybridized overnight with Affymetrix U133_Plus_2.0 arrays using conditions recommended by NuGEN. After washing, arrays were stained with SAPE followed by signal enhancement with anti-SAPE antibody as recommended by Affymetrix.
| | Sample_scan_protocol | Phycoerythrin fluorescence was quantified with an Affymetrix scanner, and Affymetrix Command Console software was used to generate cel files from the raw scan data.
| | Sample_data_processing | Cel files were quantile-normalized with the GC-RMA method using the open-source gcrma Bioconductor package (R programming language).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Stephen,,Welle
| | Sample_contact_email | stephen_welle@urmc.rochester.edu
| | Sample_contact_institute | University of Rochester
| | Sample_contact_address | 601 Elmwood Avenue
| | Sample_contact_city | Rochester
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 14642
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1097nnn/GSM1097014/suppl/GSM1097014_18_CpGhi12Z_Zand1_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE45113
| | Sample_data_row_count | 54675
| | |
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