Search results for the GEO ID: GSE44260  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM1081388 | GPL1261 |
|
Navie_rep1
|
Navie
|
cell: B cell
background strain: Balb/c
|
Gene expression data from navie sample
|
| Sample_geo_accession | GSM1081388
| | Sample_status | Public on Mar 06 2013
| | Sample_submission_date | Feb 12 2013
| | Sample_last_update_date | Mar 06 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | For isolation of germinal center B cells, Balb/c background mice carrying IgH transgenic alleles and targeted deletions of the endogenous JH locus (VH186.2-Tg JH KO (B1-8) and V23-Tg JH KO (V23)) were immunized i.p. with 50 ug of NP25- chicken gamma globulin (NP-CGG) precipitated in alum. 14-day later, splenocytes were isolated and stained with fluorescently labeled peanut agglutinin (PNA, Vector Laboratories), anti- λ (goat polyclonal, SouthernBiotech) and anti-CD45R/B220 (RA3-6B2) to identify λ+ PNA+ B220+ cells. Naive B cell controls were isolate from spleens of unimmunized Balb/c mice and cells were purified on a FACSAria cell sorter (Becton Dickinson), as previously described. Live/dead discrimination was accomplished based on forward/side scatter (FSC/SSC) and propidium iodide exclusion.
| | Sample_growth_protocol_ch1 | Cells were kept at 4°C in buffers containing 0.05% sodium azide to minimize alterations in gene expression.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from FACS-sorted B cells using the RNeasy Mini kit with on-column DNase digestion (Qiagen) and 1–4 μg were used to prepare biotinylated cRNA
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | A total of 15 μg of labeled cRNA was chemically fragmented at 94°C for 35 min in a 40 mM Tris-acetate (pH 8.1), 100 mM potassium acetate, 30 mM magnesium acetate buffer, and then hybridized to Affymetrix Mouse 430 2.0 oligonucleotide chips
| | Sample_hyb_protocol | Samples are hybridized to arrays for 16 hours at 45C. The standard array is then washed and stained using the fluidics station and then scanned.
| | Sample_scan_protocol | The images are analyzed using Affymetrix Command Console Viewer and metric analyses are carried out according to the instructions provided by Affymetrix using the Affymetrix Expression Console.
| | Sample_data_processing | Raw microarray data in CEL file format were read in and normalized with the R Bioconductor gcrma package.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Hailong,,Meng
| | Sample_contact_institute | Yale University
| | Sample_contact_address | 300 George Str
| | Sample_contact_city | New Haven
| | Sample_contact_state | CT
| | Sample_contact_zip/postal_code | 06525
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1081nnn/GSM1081388/suppl/GSM1081388_TK_YaleA_430_2.CEL.gz
| | Sample_series_id | GSE44260
| | Sample_data_row_count | 45101
| | |
|
GSM1081389 | GPL1261 |
|
Navie_rep2
|
Navie
|
cell: B cell
background strain: Balb/c
|
Gene expression data from navie sample
|
| Sample_geo_accession | GSM1081389
| | Sample_status | Public on Mar 06 2013
| | Sample_submission_date | Feb 12 2013
| | Sample_last_update_date | Mar 06 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | For isolation of germinal center B cells, Balb/c background mice carrying IgH transgenic alleles and targeted deletions of the endogenous JH locus (VH186.2-Tg JH KO (B1-8) and V23-Tg JH KO (V23)) were immunized i.p. with 50 ug of NP25- chicken gamma globulin (NP-CGG) precipitated in alum. 14-day later, splenocytes were isolated and stained with fluorescently labeled peanut agglutinin (PNA, Vector Laboratories), anti- λ (goat polyclonal, SouthernBiotech) and anti-CD45R/B220 (RA3-6B2) to identify λ+ PNA+ B220+ cells. Naive B cell controls were isolate from spleens of unimmunized Balb/c mice and cells were purified on a FACSAria cell sorter (Becton Dickinson), as previously described. Live/dead discrimination was accomplished based on forward/side scatter (FSC/SSC) and propidium iodide exclusion.
| | Sample_growth_protocol_ch1 | Cells were kept at 4°C in buffers containing 0.05% sodium azide to minimize alterations in gene expression.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from FACS-sorted B cells using the RNeasy Mini kit with on-column DNase digestion (Qiagen) and 1–4 μg were used to prepare biotinylated cRNA
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | A total of 15 μg of labeled cRNA was chemically fragmented at 94°C for 35 min in a 40 mM Tris-acetate (pH 8.1), 100 mM potassium acetate, 30 mM magnesium acetate buffer, and then hybridized to Affymetrix Mouse 430 2.0 oligonucleotide chips
| | Sample_hyb_protocol | Samples are hybridized to arrays for 16 hours at 45C. The standard array is then washed and stained using the fluidics station and then scanned.
| | Sample_scan_protocol | The images are analyzed using Affymetrix Command Console Viewer and metric analyses are carried out according to the instructions provided by Affymetrix using the Affymetrix Expression Console.
| | Sample_data_processing | Raw microarray data in CEL file format were read in and normalized with the R Bioconductor gcrma package.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Hailong,,Meng
| | Sample_contact_institute | Yale University
| | Sample_contact_address | 300 George Str
| | Sample_contact_city | New Haven
| | Sample_contact_state | CT
| | Sample_contact_zip/postal_code | 06525
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1081nnn/GSM1081389/suppl/GSM1081389_TK_YaleB_430_2.CEL.gz
| | Sample_series_id | GSE44260
| | Sample_data_row_count | 45101
| | |
|
GSM1081390 | GPL1261 |
|
Navie_rep3
|
Navie
|
cell: B cell
background strain: Balb/c
|
Gene expression data from navie sample
|
| Sample_geo_accession | GSM1081390
| | Sample_status | Public on Mar 06 2013
| | Sample_submission_date | Feb 12 2013
| | Sample_last_update_date | Mar 06 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | For isolation of germinal center B cells, Balb/c background mice carrying IgH transgenic alleles and targeted deletions of the endogenous JH locus (VH186.2-Tg JH KO (B1-8) and V23-Tg JH KO (V23)) were immunized i.p. with 50 ug of NP25- chicken gamma globulin (NP-CGG) precipitated in alum. 14-day later, splenocytes were isolated and stained with fluorescently labeled peanut agglutinin (PNA, Vector Laboratories), anti- λ (goat polyclonal, SouthernBiotech) and anti-CD45R/B220 (RA3-6B2) to identify λ+ PNA+ B220+ cells. Naive B cell controls were isolate from spleens of unimmunized Balb/c mice and cells were purified on a FACSAria cell sorter (Becton Dickinson), as previously described. Live/dead discrimination was accomplished based on forward/side scatter (FSC/SSC) and propidium iodide exclusion.
| | Sample_growth_protocol_ch1 | Cells were kept at 4°C in buffers containing 0.05% sodium azide to minimize alterations in gene expression.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from FACS-sorted B cells using the RNeasy Mini kit with on-column DNase digestion (Qiagen) and 1–4 μg were used to prepare biotinylated cRNA
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | A total of 15 μg of labeled cRNA was chemically fragmented at 94°C for 35 min in a 40 mM Tris-acetate (pH 8.1), 100 mM potassium acetate, 30 mM magnesium acetate buffer, and then hybridized to Affymetrix Mouse 430 2.0 oligonucleotide chips
| | Sample_hyb_protocol | Samples are hybridized to arrays for 16 hours at 45C. The standard array is then washed and stained using the fluidics station and then scanned.
| | Sample_scan_protocol | The images are analyzed using Affymetrix Command Console Viewer and metric analyses are carried out according to the instructions provided by Affymetrix using the Affymetrix Expression Console.
| | Sample_data_processing | Raw microarray data in CEL file format were read in and normalized with the R Bioconductor gcrma package.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Hailong,,Meng
| | Sample_contact_institute | Yale University
| | Sample_contact_address | 300 George Str
| | Sample_contact_city | New Haven
| | Sample_contact_state | CT
| | Sample_contact_zip/postal_code | 06525
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1081nnn/GSM1081390/suppl/GSM1081390_TK_YaleC_430_2.CEL.gz
| | Sample_series_id | GSE44260
| | Sample_data_row_count | 45101
| | |
|
GSM1081391 | GPL1261 |
|
Navie_rep4
|
Navie
|
cell: B cell
background strain: Balb/c
|
Gene expression data from navie sample
|
| Sample_geo_accession | GSM1081391
| | Sample_status | Public on Mar 06 2013
| | Sample_submission_date | Feb 12 2013
| | Sample_last_update_date | Mar 06 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | For isolation of germinal center B cells, Balb/c background mice carrying IgH transgenic alleles and targeted deletions of the endogenous JH locus (VH186.2-Tg JH KO (B1-8) and V23-Tg JH KO (V23)) were immunized i.p. with 50 ug of NP25- chicken gamma globulin (NP-CGG) precipitated in alum. 14-day later, splenocytes were isolated and stained with fluorescently labeled peanut agglutinin (PNA, Vector Laboratories), anti- λ (goat polyclonal, SouthernBiotech) and anti-CD45R/B220 (RA3-6B2) to identify λ+ PNA+ B220+ cells. Naive B cell controls were isolate from spleens of unimmunized Balb/c mice and cells were purified on a FACSAria cell sorter (Becton Dickinson), as previously described. Live/dead discrimination was accomplished based on forward/side scatter (FSC/SSC) and propidium iodide exclusion.
| | Sample_growth_protocol_ch1 | Cells were kept at 4°C in buffers containing 0.05% sodium azide to minimize alterations in gene expression.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from FACS-sorted B cells using the RNeasy Mini kit with on-column DNase digestion (Qiagen) and 1–4 μg were used to prepare biotinylated cRNA
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | A total of 15 μg of labeled cRNA was chemically fragmented at 94°C for 35 min in a 40 mM Tris-acetate (pH 8.1), 100 mM potassium acetate, 30 mM magnesium acetate buffer, and then hybridized to Affymetrix Mouse 430 2.0 oligonucleotide chips
| | Sample_hyb_protocol | Samples are hybridized to arrays for 16 hours at 45C. The standard array is then washed and stained using the fluidics station and then scanned.
| | Sample_scan_protocol | The images are analyzed using Affymetrix Command Console Viewer and metric analyses are carried out according to the instructions provided by Affymetrix using the Affymetrix Expression Console.
| | Sample_data_processing | Raw microarray data in CEL file format were read in and normalized with the R Bioconductor gcrma package.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Hailong,,Meng
| | Sample_contact_institute | Yale University
| | Sample_contact_address | 300 George Str
| | Sample_contact_city | New Haven
| | Sample_contact_state | CT
| | Sample_contact_zip/postal_code | 06525
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1081nnn/GSM1081391/suppl/GSM1081391_TK_YaleD_430_2.CEL.gz
| | Sample_series_id | GSE44260
| | Sample_data_row_count | 45101
| | |
|
GSM1081392 | GPL1261 |
|
d14 GC B1-8_rep1
|
d14 GC B1-8
|
cell: B cell
background strain: Balb/c
|
Gene expression data from d14 GC B1-8
|
| Sample_geo_accession | GSM1081392
| | Sample_status | Public on Mar 06 2013
| | Sample_submission_date | Feb 12 2013
| | Sample_last_update_date | Mar 06 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | For isolation of germinal center B cells, Balb/c background mice carrying IgH transgenic alleles and targeted deletions of the endogenous JH locus (VH186.2-Tg JH KO (B1-8) and V23-Tg JH KO (V23)) were immunized i.p. with 50 ug of NP25- chicken gamma globulin (NP-CGG) precipitated in alum. 14-day later, splenocytes were isolated and stained with fluorescently labeled peanut agglutinin (PNA, Vector Laboratories), anti- λ (goat polyclonal, SouthernBiotech) and anti-CD45R/B220 (RA3-6B2) to identify λ+ PNA+ B220+ cells. Naive B cell controls were isolate from spleens of unimmunized Balb/c mice and cells were purified on a FACSAria cell sorter (Becton Dickinson), as previously described. Live/dead discrimination was accomplished based on forward/side scatter (FSC/SSC) and propidium iodide exclusion.
| | Sample_growth_protocol_ch1 | Cells were kept at 4°C in buffers containing 0.05% sodium azide to minimize alterations in gene expression.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from FACS-sorted B cells using the RNeasy Mini kit with on-column DNase digestion (Qiagen) and 1–4 μg were used to prepare biotinylated cRNA
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | A total of 15 μg of labeled cRNA was chemically fragmented at 94°C for 35 min in a 40 mM Tris-acetate (pH 8.1), 100 mM potassium acetate, 30 mM magnesium acetate buffer, and then hybridized to Affymetrix Mouse 430 2.0 oligonucleotide chips
| | Sample_hyb_protocol | Samples are hybridized to arrays for 16 hours at 45C. The standard array is then washed and stained using the fluidics station and then scanned.
| | Sample_scan_protocol | The images are analyzed using Affymetrix Command Console Viewer and metric analyses are carried out according to the instructions provided by Affymetrix using the Affymetrix Expression Console.
| | Sample_data_processing | Raw microarray data in CEL file format were read in and normalized with the R Bioconductor gcrma package.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Hailong,,Meng
| | Sample_contact_institute | Yale University
| | Sample_contact_address | 300 George Str
| | Sample_contact_city | New Haven
| | Sample_contact_state | CT
| | Sample_contact_zip/postal_code | 06525
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1081nnn/GSM1081392/suppl/GSM1081392_TK_M2_430_2.CEL.gz
| | Sample_series_id | GSE44260
| | Sample_data_row_count | 45101
| | |
|
GSM1081393 | GPL1261 |
|
d14 GC B1-8_rep2
|
d14 GC B1-8
|
cell: B cell
background strain: Balb/c
|
Gene expression data from d14 GC B1-8
|
| Sample_geo_accession | GSM1081393
| | Sample_status | Public on Mar 06 2013
| | Sample_submission_date | Feb 12 2013
| | Sample_last_update_date | Mar 06 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | For isolation of germinal center B cells, Balb/c background mice carrying IgH transgenic alleles and targeted deletions of the endogenous JH locus (VH186.2-Tg JH KO (B1-8) and V23-Tg JH KO (V23)) were immunized i.p. with 50 ug of NP25- chicken gamma globulin (NP-CGG) precipitated in alum. 14-day later, splenocytes were isolated and stained with fluorescently labeled peanut agglutinin (PNA, Vector Laboratories), anti- λ (goat polyclonal, SouthernBiotech) and anti-CD45R/B220 (RA3-6B2) to identify λ+ PNA+ B220+ cells. Naive B cell controls were isolate from spleens of unimmunized Balb/c mice and cells were purified on a FACSAria cell sorter (Becton Dickinson), as previously described. Live/dead discrimination was accomplished based on forward/side scatter (FSC/SSC) and propidium iodide exclusion.
| | Sample_growth_protocol_ch1 | Cells were kept at 4°C in buffers containing 0.05% sodium azide to minimize alterations in gene expression.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from FACS-sorted B cells using the RNeasy Mini kit with on-column DNase digestion (Qiagen) and 1–4 μg were used to prepare biotinylated cRNA
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | A total of 15 μg of labeled cRNA was chemically fragmented at 94°C for 35 min in a 40 mM Tris-acetate (pH 8.1), 100 mM potassium acetate, 30 mM magnesium acetate buffer, and then hybridized to Affymetrix Mouse 430 2.0 oligonucleotide chips
| | Sample_hyb_protocol | Samples are hybridized to arrays for 16 hours at 45C. The standard array is then washed and stained using the fluidics station and then scanned.
| | Sample_scan_protocol | The images are analyzed using Affymetrix Command Console Viewer and metric analyses are carried out according to the instructions provided by Affymetrix using the Affymetrix Expression Console.
| | Sample_data_processing | Raw microarray data in CEL file format were read in and normalized with the R Bioconductor gcrma package.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Hailong,,Meng
| | Sample_contact_institute | Yale University
| | Sample_contact_address | 300 George Str
| | Sample_contact_city | New Haven
| | Sample_contact_state | CT
| | Sample_contact_zip/postal_code | 06525
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1081nnn/GSM1081393/suppl/GSM1081393_TK_M5_430_2.CEL.gz
| | Sample_series_id | GSE44260
| | Sample_data_row_count | 45101
| | |
|
GSM1081394 | GPL1261 |
|
d14 GC B1-8_rep3
|
d14 GC B1-8
|
cell: B cell
background strain: Balb/c
|
Gene expression data from d14 GC B1-8
|
| Sample_geo_accession | GSM1081394
| | Sample_status | Public on Mar 06 2013
| | Sample_submission_date | Feb 12 2013
| | Sample_last_update_date | Mar 06 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | For isolation of germinal center B cells, Balb/c background mice carrying IgH transgenic alleles and targeted deletions of the endogenous JH locus (VH186.2-Tg JH KO (B1-8) and V23-Tg JH KO (V23)) were immunized i.p. with 50 ug of NP25- chicken gamma globulin (NP-CGG) precipitated in alum. 14-day later, splenocytes were isolated and stained with fluorescently labeled peanut agglutinin (PNA, Vector Laboratories), anti- λ (goat polyclonal, SouthernBiotech) and anti-CD45R/B220 (RA3-6B2) to identify λ+ PNA+ B220+ cells. Naive B cell controls were isolate from spleens of unimmunized Balb/c mice and cells were purified on a FACSAria cell sorter (Becton Dickinson), as previously described. Live/dead discrimination was accomplished based on forward/side scatter (FSC/SSC) and propidium iodide exclusion.
| | Sample_growth_protocol_ch1 | Cells were kept at 4°C in buffers containing 0.05% sodium azide to minimize alterations in gene expression.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from FACS-sorted B cells using the RNeasy Mini kit with on-column DNase digestion (Qiagen) and 1–4 μg were used to prepare biotinylated cRNA
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | A total of 15 μg of labeled cRNA was chemically fragmented at 94°C for 35 min in a 40 mM Tris-acetate (pH 8.1), 100 mM potassium acetate, 30 mM magnesium acetate buffer, and then hybridized to Affymetrix Mouse 430 2.0 oligonucleotide chips
| | Sample_hyb_protocol | Samples are hybridized to arrays for 16 hours at 45C. The standard array is then washed and stained using the fluidics station and then scanned.
| | Sample_scan_protocol | The images are analyzed using Affymetrix Command Console Viewer and metric analyses are carried out according to the instructions provided by Affymetrix using the Affymetrix Expression Console.
| | Sample_data_processing | Raw microarray data in CEL file format were read in and normalized with the R Bioconductor gcrma package.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Hailong,,Meng
| | Sample_contact_institute | Yale University
| | Sample_contact_address | 300 George Str
| | Sample_contact_city | New Haven
| | Sample_contact_state | CT
| | Sample_contact_zip/postal_code | 06525
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1081nnn/GSM1081394/suppl/GSM1081394_TK_M9_430_2.CEL.gz
| | Sample_series_id | GSE44260
| | Sample_data_row_count | 45101
| | |
|
GSM1081395 | GPL1261 |
|
d14 GC V23_rep1
|
d14 GC V23
|
cell: B cell
background strain: Balb/c
|
Gene expression data from d14 GC V23
|
| Sample_geo_accession | GSM1081395
| | Sample_status | Public on Mar 06 2013
| | Sample_submission_date | Feb 12 2013
| | Sample_last_update_date | Mar 06 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | For isolation of germinal center B cells, Balb/c background mice carrying IgH transgenic alleles and targeted deletions of the endogenous JH locus (VH186.2-Tg JH KO (B1-8) and V23-Tg JH KO (V23)) were immunized i.p. with 50 ug of NP25- chicken gamma globulin (NP-CGG) precipitated in alum. 14-day later, splenocytes were isolated and stained with fluorescently labeled peanut agglutinin (PNA, Vector Laboratories), anti- λ (goat polyclonal, SouthernBiotech) and anti-CD45R/B220 (RA3-6B2) to identify λ+ PNA+ B220+ cells. Naive B cell controls were isolate from spleens of unimmunized Balb/c mice and cells were purified on a FACSAria cell sorter (Becton Dickinson), as previously described. Live/dead discrimination was accomplished based on forward/side scatter (FSC/SSC) and propidium iodide exclusion.
| | Sample_growth_protocol_ch1 | Cells were kept at 4°C in buffers containing 0.05% sodium azide to minimize alterations in gene expression.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from FACS-sorted B cells using the RNeasy Mini kit with on-column DNase digestion (Qiagen) and 1–4 μg were used to prepare biotinylated cRNA
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | A total of 15 μg of labeled cRNA was chemically fragmented at 94°C for 35 min in a 40 mM Tris-acetate (pH 8.1), 100 mM potassium acetate, 30 mM magnesium acetate buffer, and then hybridized to Affymetrix Mouse 430 2.0 oligonucleotide chips
| | Sample_hyb_protocol | Samples are hybridized to arrays for 16 hours at 45C. The standard array is then washed and stained using the fluidics station and then scanned.
| | Sample_scan_protocol | The images are analyzed using Affymetrix Command Console Viewer and metric analyses are carried out according to the instructions provided by Affymetrix using the Affymetrix Expression Console.
| | Sample_data_processing | Raw microarray data in CEL file format were read in and normalized with the R Bioconductor gcrma package.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Hailong,,Meng
| | Sample_contact_institute | Yale University
| | Sample_contact_address | 300 George Str
| | Sample_contact_city | New Haven
| | Sample_contact_state | CT
| | Sample_contact_zip/postal_code | 06525
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1081nnn/GSM1081395/suppl/GSM1081395_TK_M4_430_2.CEL.gz
| | Sample_series_id | GSE44260
| | Sample_data_row_count | 45101
| | |
|
GSM1081396 | GPL1261 |
|
d14 GC V23_rep2
|
d14 GC V23
|
cell: B cell
background strain: Balb/c
|
Gene expression data from d14 GC V23
|
| Sample_geo_accession | GSM1081396
| | Sample_status | Public on Mar 06 2013
| | Sample_submission_date | Feb 12 2013
| | Sample_last_update_date | Mar 06 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | For isolation of germinal center B cells, Balb/c background mice carrying IgH transgenic alleles and targeted deletions of the endogenous JH locus (VH186.2-Tg JH KO (B1-8) and V23-Tg JH KO (V23)) were immunized i.p. with 50 ug of NP25- chicken gamma globulin (NP-CGG) precipitated in alum. 14-day later, splenocytes were isolated and stained with fluorescently labeled peanut agglutinin (PNA, Vector Laboratories), anti- λ (goat polyclonal, SouthernBiotech) and anti-CD45R/B220 (RA3-6B2) to identify λ+ PNA+ B220+ cells. Naive B cell controls were isolate from spleens of unimmunized Balb/c mice and cells were purified on a FACSAria cell sorter (Becton Dickinson), as previously described. Live/dead discrimination was accomplished based on forward/side scatter (FSC/SSC) and propidium iodide exclusion.
| | Sample_growth_protocol_ch1 | Cells were kept at 4°C in buffers containing 0.05% sodium azide to minimize alterations in gene expression.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from FACS-sorted B cells using the RNeasy Mini kit with on-column DNase digestion (Qiagen) and 1–4 μg were used to prepare biotinylated cRNA
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | A total of 15 μg of labeled cRNA was chemically fragmented at 94°C for 35 min in a 40 mM Tris-acetate (pH 8.1), 100 mM potassium acetate, 30 mM magnesium acetate buffer, and then hybridized to Affymetrix Mouse 430 2.0 oligonucleotide chips
| | Sample_hyb_protocol | Samples are hybridized to arrays for 16 hours at 45C. The standard array is then washed and stained using the fluidics station and then scanned.
| | Sample_scan_protocol | The images are analyzed using Affymetrix Command Console Viewer and metric analyses are carried out according to the instructions provided by Affymetrix using the Affymetrix Expression Console.
| | Sample_data_processing | Raw microarray data in CEL file format were read in and normalized with the R Bioconductor gcrma package.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Hailong,,Meng
| | Sample_contact_institute | Yale University
| | Sample_contact_address | 300 George Str
| | Sample_contact_city | New Haven
| | Sample_contact_state | CT
| | Sample_contact_zip/postal_code | 06525
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1081nnn/GSM1081396/suppl/GSM1081396_TK_M8_430_2.CEL.gz
| | Sample_series_id | GSE44260
| | Sample_data_row_count | 45101
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GSM1081397 | GPL1261 |
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d14 GC V23_rep3
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d14 GC V23
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cell: B cell
background strain: Balb/c
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Gene expression data from d14 GC V23
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| Sample_geo_accession | GSM1081397
| | Sample_status | Public on Mar 06 2013
| | Sample_submission_date | Feb 12 2013
| | Sample_last_update_date | Mar 06 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | For isolation of germinal center B cells, Balb/c background mice carrying IgH transgenic alleles and targeted deletions of the endogenous JH locus (VH186.2-Tg JH KO (B1-8) and V23-Tg JH KO (V23)) were immunized i.p. with 50 ug of NP25- chicken gamma globulin (NP-CGG) precipitated in alum. 14-day later, splenocytes were isolated and stained with fluorescently labeled peanut agglutinin (PNA, Vector Laboratories), anti- λ (goat polyclonal, SouthernBiotech) and anti-CD45R/B220 (RA3-6B2) to identify λ+ PNA+ B220+ cells. Naive B cell controls were isolate from spleens of unimmunized Balb/c mice and cells were purified on a FACSAria cell sorter (Becton Dickinson), as previously described. Live/dead discrimination was accomplished based on forward/side scatter (FSC/SSC) and propidium iodide exclusion.
| | Sample_growth_protocol_ch1 | Cells were kept at 4°C in buffers containing 0.05% sodium azide to minimize alterations in gene expression.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from FACS-sorted B cells using the RNeasy Mini kit with on-column DNase digestion (Qiagen) and 1–4 μg were used to prepare biotinylated cRNA
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | A total of 15 μg of labeled cRNA was chemically fragmented at 94°C for 35 min in a 40 mM Tris-acetate (pH 8.1), 100 mM potassium acetate, 30 mM magnesium acetate buffer, and then hybridized to Affymetrix Mouse 430 2.0 oligonucleotide chips
| | Sample_hyb_protocol | Samples are hybridized to arrays for 16 hours at 45C. The standard array is then washed and stained using the fluidics station and then scanned.
| | Sample_scan_protocol | The images are analyzed using Affymetrix Command Console Viewer and metric analyses are carried out according to the instructions provided by Affymetrix using the Affymetrix Expression Console.
| | Sample_data_processing | Raw microarray data in CEL file format were read in and normalized with the R Bioconductor gcrma package.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Hailong,,Meng
| | Sample_contact_institute | Yale University
| | Sample_contact_address | 300 George Str
| | Sample_contact_city | New Haven
| | Sample_contact_state | CT
| | Sample_contact_zip/postal_code | 06525
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1081nnn/GSM1081397/suppl/GSM1081397_TK_M10_430_2.CEL.gz
| | Sample_series_id | GSE44260
| | Sample_data_row_count | 45101
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