Search results for the GEO ID: GSE43210  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM1058691 | GPL570 |
|
PBMC_Untreated_donor_1
|
PBMC from donor 1 treatment: Untreated
|
donor: 1
cell type: PBMC
treatment: Untreated
subject: 1
|
Neg_45330
|
| Sample_geo_accession | GSM1058691
| | Sample_status | Public on Jan 31 2013
| | Sample_submission_date | Dec 31 2012
| | Sample_last_update_date | Feb 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using the mirVana RNA isolation kit (Ambion, Inc, Austin, TX, USA) according to manufacturer’s protocol. RNA was quantified using a ND-1000 spectrophotometer (Nanodrop Technology®, Cambridge, UK) and RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent technologies, Santa Clara, CA, USA). The 260/280 ratio were between 1.7 and 2.1 and the RINs (RNA Integrity Numbers) greater than 6 for all samples.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Total RNA (100ng) was transcribed and labeled into amplified RNA (aRNA) using the 3’IVT express kit (Affymetrix Inc., Santa Clara, CA) according to manufacturer’s instruction on a GCAS (Gene Chip Array Station).
| | Sample_hyb_protocol | Fragmented and labeled aRNA was hybridized to the Affymetrix U133 Plus 2.0 chips according to manufacturer’s instructions. Wash and stain protocol FS450_0004.
| | Sample_scan_protocol | GeneChips were scanned using the GC 30007G scanner.
| | Sample_data_processing | Data was normalized in R/Bioconductor using the robust multi-array average (RMA) expression measure. Probesets were annotated using the latest annotation available in Bioconductor and curated using an internal Roche probe inspector tool, which updates gene annotation per probeset based on the latest human genome draft release. As an additional quality measure, probesets were also curated using the tool for sequence specificity; probesets mapping to non-unique locations in the genome were flagged and ignored in subsequent analysis. A total of 26,088 out of 54,675 probesets passed the QC and curation processes, corresponding to 13,464 unique genes.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kai,,Lau
| | Sample_contact_institute | Hoffmann-La Roche
| | Sample_contact_address | 340 Kingsland St
| | Sample_contact_city | Nutley
| | Sample_contact_zip/postal_code | NJ 07110
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1058nnn/GSM1058691/suppl/GSM1058691_CRACi_IC_1_HG_U133_Plus_2.CEL.gz
| | Sample_series_id | GSE43210
| | Sample_data_row_count | 26088
| | |
|
GSM1058692 | GPL570 |
|
PBMC_anti-CD3/CD28_donor_1
|
PBMC from donor 1 treatment: anti-CD3/CD28
|
donor: 1
cell type: PBMC
treatment: anti-CD3/CD28
subject: 1
|
Pos_45330
|
| Sample_geo_accession | GSM1058692
| | Sample_status | Public on Jan 31 2013
| | Sample_submission_date | Dec 31 2012
| | Sample_last_update_date | Feb 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using the mirVana RNA isolation kit (Ambion, Inc, Austin, TX, USA) according to manufacturer’s protocol. RNA was quantified using a ND-1000 spectrophotometer (Nanodrop Technology®, Cambridge, UK) and RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent technologies, Santa Clara, CA, USA). The 260/280 ratio were between 1.7 and 2.1 and the RINs (RNA Integrity Numbers) greater than 6 for all samples.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Total RNA (100ng) was transcribed and labeled into amplified RNA (aRNA) using the 3’IVT express kit (Affymetrix Inc., Santa Clara, CA) according to manufacturer’s instruction on a GCAS (Gene Chip Array Station).
| | Sample_hyb_protocol | Fragmented and labeled aRNA was hybridized to the Affymetrix U133 Plus 2.0 chips according to manufacturer’s instructions. Wash and stain protocol FS450_0004.
| | Sample_scan_protocol | GeneChips were scanned using the GC 30007G scanner.
| | Sample_data_processing | Data was normalized in R/Bioconductor using the robust multi-array average (RMA) expression measure. Probesets were annotated using the latest annotation available in Bioconductor and curated using an internal Roche probe inspector tool, which updates gene annotation per probeset based on the latest human genome draft release. As an additional quality measure, probesets were also curated using the tool for sequence specificity; probesets mapping to non-unique locations in the genome were flagged and ignored in subsequent analysis. A total of 26,088 out of 54,675 probesets passed the QC and curation processes, corresponding to 13,464 unique genes.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kai,,Lau
| | Sample_contact_institute | Hoffmann-La Roche
| | Sample_contact_address | 340 Kingsland St
| | Sample_contact_city | Nutley
| | Sample_contact_zip/postal_code | NJ 07110
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1058nnn/GSM1058692/suppl/GSM1058692_CRACi_IC_2_HG_U133_Plus_2.CEL.gz
| | Sample_series_id | GSE43210
| | Sample_data_row_count | 26088
| | |
|
GSM1058693 | GPL570 |
|
PBMC_CRACi_anti-CD3/CD28_donor_1
|
PBMC from donor 1 treatment: CRACi_anti-CD3/CD28
|
donor: 1
cell type: PBMC
treatment: CRACi_anti-CD3/CD28
subject: 1
|
RO2959_45330
|
| Sample_geo_accession | GSM1058693
| | Sample_status | Public on Jan 31 2013
| | Sample_submission_date | Dec 31 2012
| | Sample_last_update_date | Feb 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using the mirVana RNA isolation kit (Ambion, Inc, Austin, TX, USA) according to manufacturer’s protocol. RNA was quantified using a ND-1000 spectrophotometer (Nanodrop Technology®, Cambridge, UK) and RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent technologies, Santa Clara, CA, USA). The 260/280 ratio were between 1.7 and 2.1 and the RINs (RNA Integrity Numbers) greater than 6 for all samples.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Total RNA (100ng) was transcribed and labeled into amplified RNA (aRNA) using the 3’IVT express kit (Affymetrix Inc., Santa Clara, CA) according to manufacturer’s instruction on a GCAS (Gene Chip Array Station).
| | Sample_hyb_protocol | Fragmented and labeled aRNA was hybridized to the Affymetrix U133 Plus 2.0 chips according to manufacturer’s instructions. Wash and stain protocol FS450_0004.
| | Sample_scan_protocol | GeneChips were scanned using the GC 30007G scanner.
| | Sample_data_processing | Data was normalized in R/Bioconductor using the robust multi-array average (RMA) expression measure. Probesets were annotated using the latest annotation available in Bioconductor and curated using an internal Roche probe inspector tool, which updates gene annotation per probeset based on the latest human genome draft release. As an additional quality measure, probesets were also curated using the tool for sequence specificity; probesets mapping to non-unique locations in the genome were flagged and ignored in subsequent analysis. A total of 26,088 out of 54,675 probesets passed the QC and curation processes, corresponding to 13,464 unique genes.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kai,,Lau
| | Sample_contact_institute | Hoffmann-La Roche
| | Sample_contact_address | 340 Kingsland St
| | Sample_contact_city | Nutley
| | Sample_contact_zip/postal_code | NJ 07110
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1058nnn/GSM1058693/suppl/GSM1058693_CRACi_IC_3_HG_U133_Plus_2.CEL.gz
| | Sample_series_id | GSE43210
| | Sample_data_row_count | 26088
| | |
|
GSM1058694 | GPL570 |
|
PBMC_CsA_anti-CD3/CD28_donor_1
|
PBMC from donor 1 treatment: CsA_anti-CD3/CD28
|
donor: 1
cell type: PBMC
treatment: CsA_anti-CD3/CD28
subject: 1
|
CsA_45330
|
| Sample_geo_accession | GSM1058694
| | Sample_status | Public on Jan 31 2013
| | Sample_submission_date | Dec 31 2012
| | Sample_last_update_date | Feb 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using the mirVana RNA isolation kit (Ambion, Inc, Austin, TX, USA) according to manufacturer’s protocol. RNA was quantified using a ND-1000 spectrophotometer (Nanodrop Technology®, Cambridge, UK) and RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent technologies, Santa Clara, CA, USA). The 260/280 ratio were between 1.7 and 2.1 and the RINs (RNA Integrity Numbers) greater than 6 for all samples.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Total RNA (100ng) was transcribed and labeled into amplified RNA (aRNA) using the 3’IVT express kit (Affymetrix Inc., Santa Clara, CA) according to manufacturer’s instruction on a GCAS (Gene Chip Array Station).
| | Sample_hyb_protocol | Fragmented and labeled aRNA was hybridized to the Affymetrix U133 Plus 2.0 chips according to manufacturer’s instructions. Wash and stain protocol FS450_0004.
| | Sample_scan_protocol | GeneChips were scanned using the GC 30007G scanner.
| | Sample_data_processing | Data was normalized in R/Bioconductor using the robust multi-array average (RMA) expression measure. Probesets were annotated using the latest annotation available in Bioconductor and curated using an internal Roche probe inspector tool, which updates gene annotation per probeset based on the latest human genome draft release. As an additional quality measure, probesets were also curated using the tool for sequence specificity; probesets mapping to non-unique locations in the genome were flagged and ignored in subsequent analysis. A total of 26,088 out of 54,675 probesets passed the QC and curation processes, corresponding to 13,464 unique genes.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kai,,Lau
| | Sample_contact_institute | Hoffmann-La Roche
| | Sample_contact_address | 340 Kingsland St
| | Sample_contact_city | Nutley
| | Sample_contact_zip/postal_code | NJ 07110
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1058nnn/GSM1058694/suppl/GSM1058694_CRACi_IC_8_HG_U133_Plus_2.CEL.gz
| | Sample_series_id | GSE43210
| | Sample_data_row_count | 26088
| | |
|
GSM1058695 | GPL570 |
|
PBMC_FK506_anti-CD3/CD28_donor_1
|
PBMC from donor 1 treatment: FK506_anti-CD3/CD28
|
donor: 1
cell type: PBMC
treatment: FK506_anti-CD3/CD28
subject: 1
|
FK506_45330
|
| Sample_geo_accession | GSM1058695
| | Sample_status | Public on Jan 31 2013
| | Sample_submission_date | Dec 31 2012
| | Sample_last_update_date | Feb 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using the mirVana RNA isolation kit (Ambion, Inc, Austin, TX, USA) according to manufacturer’s protocol. RNA was quantified using a ND-1000 spectrophotometer (Nanodrop Technology®, Cambridge, UK) and RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent technologies, Santa Clara, CA, USA). The 260/280 ratio were between 1.7 and 2.1 and the RINs (RNA Integrity Numbers) greater than 6 for all samples.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Total RNA (100ng) was transcribed and labeled into amplified RNA (aRNA) using the 3’IVT express kit (Affymetrix Inc., Santa Clara, CA) according to manufacturer’s instruction on a GCAS (Gene Chip Array Station).
| | Sample_hyb_protocol | Fragmented and labeled aRNA was hybridized to the Affymetrix U133 Plus 2.0 chips according to manufacturer’s instructions. Wash and stain protocol FS450_0004.
| | Sample_scan_protocol | GeneChips were scanned using the GC 30007G scanner.
| | Sample_data_processing | Data was normalized in R/Bioconductor using the robust multi-array average (RMA) expression measure. Probesets were annotated using the latest annotation available in Bioconductor and curated using an internal Roche probe inspector tool, which updates gene annotation per probeset based on the latest human genome draft release. As an additional quality measure, probesets were also curated using the tool for sequence specificity; probesets mapping to non-unique locations in the genome were flagged and ignored in subsequent analysis. A total of 26,088 out of 54,675 probesets passed the QC and curation processes, corresponding to 13,464 unique genes.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kai,,Lau
| | Sample_contact_institute | Hoffmann-La Roche
| | Sample_contact_address | 340 Kingsland St
| | Sample_contact_city | Nutley
| | Sample_contact_zip/postal_code | NJ 07110
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1058nnn/GSM1058695/suppl/GSM1058695_CRACi_IC_9_HG_U133_Plus_2.CEL.gz
| | Sample_series_id | GSE43210
| | Sample_data_row_count | 26088
| | |
|
GSM1058696 | GPL570 |
|
PBMC_anti-CD3/CD28_donor_2
|
PBMC from donor 2 treatment: anti-CD3/CD28
|
donor: 2
cell type: PBMC
treatment: anti-CD3/CD28
subject: 2
|
Pos_53742
|
| Sample_geo_accession | GSM1058696
| | Sample_status | Public on Jan 31 2013
| | Sample_submission_date | Dec 31 2012
| | Sample_last_update_date | Feb 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using the mirVana RNA isolation kit (Ambion, Inc, Austin, TX, USA) according to manufacturer’s protocol. RNA was quantified using a ND-1000 spectrophotometer (Nanodrop Technology®, Cambridge, UK) and RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent technologies, Santa Clara, CA, USA). The 260/280 ratio were between 1.7 and 2.1 and the RINs (RNA Integrity Numbers) greater than 6 for all samples.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Total RNA (100ng) was transcribed and labeled into amplified RNA (aRNA) using the 3’IVT express kit (Affymetrix Inc., Santa Clara, CA) according to manufacturer’s instruction on a GCAS (Gene Chip Array Station).
| | Sample_hyb_protocol | Fragmented and labeled aRNA was hybridized to the Affymetrix U133 Plus 2.0 chips according to manufacturer’s instructions. Wash and stain protocol FS450_0004.
| | Sample_scan_protocol | GeneChips were scanned using the GC 30007G scanner.
| | Sample_data_processing | Data was normalized in R/Bioconductor using the robust multi-array average (RMA) expression measure. Probesets were annotated using the latest annotation available in Bioconductor and curated using an internal Roche probe inspector tool, which updates gene annotation per probeset based on the latest human genome draft release. As an additional quality measure, probesets were also curated using the tool for sequence specificity; probesets mapping to non-unique locations in the genome were flagged and ignored in subsequent analysis. A total of 26,088 out of 54,675 probesets passed the QC and curation processes, corresponding to 13,464 unique genes.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kai,,Lau
| | Sample_contact_institute | Hoffmann-La Roche
| | Sample_contact_address | 340 Kingsland St
| | Sample_contact_city | Nutley
| | Sample_contact_zip/postal_code | NJ 07110
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1058nnn/GSM1058696/suppl/GSM1058696_CRACi_IC_11_HG_U133_Plus_2.CEL.gz
| | Sample_series_id | GSE43210
| | Sample_data_row_count | 26088
| | |
|
GSM1058697 | GPL570 |
|
PBMC_CRACi_anti-CD3/CD28_donor_2
|
PBMC from donor 2 treatment: CRACi_anti-CD3/CD28
|
donor: 2
cell type: PBMC
treatment: CRACi_anti-CD3/CD28
subject: 2
|
RO2959_53742
|
| Sample_geo_accession | GSM1058697
| | Sample_status | Public on Jan 31 2013
| | Sample_submission_date | Dec 31 2012
| | Sample_last_update_date | Feb 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using the mirVana RNA isolation kit (Ambion, Inc, Austin, TX, USA) according to manufacturer’s protocol. RNA was quantified using a ND-1000 spectrophotometer (Nanodrop Technology®, Cambridge, UK) and RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent technologies, Santa Clara, CA, USA). The 260/280 ratio were between 1.7 and 2.1 and the RINs (RNA Integrity Numbers) greater than 6 for all samples.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Total RNA (100ng) was transcribed and labeled into amplified RNA (aRNA) using the 3’IVT express kit (Affymetrix Inc., Santa Clara, CA) according to manufacturer’s instruction on a GCAS (Gene Chip Array Station).
| | Sample_hyb_protocol | Fragmented and labeled aRNA was hybridized to the Affymetrix U133 Plus 2.0 chips according to manufacturer’s instructions. Wash and stain protocol FS450_0004.
| | Sample_scan_protocol | GeneChips were scanned using the GC 30007G scanner.
| | Sample_data_processing | Data was normalized in R/Bioconductor using the robust multi-array average (RMA) expression measure. Probesets were annotated using the latest annotation available in Bioconductor and curated using an internal Roche probe inspector tool, which updates gene annotation per probeset based on the latest human genome draft release. As an additional quality measure, probesets were also curated using the tool for sequence specificity; probesets mapping to non-unique locations in the genome were flagged and ignored in subsequent analysis. A total of 26,088 out of 54,675 probesets passed the QC and curation processes, corresponding to 13,464 unique genes.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kai,,Lau
| | Sample_contact_institute | Hoffmann-La Roche
| | Sample_contact_address | 340 Kingsland St
| | Sample_contact_city | Nutley
| | Sample_contact_zip/postal_code | NJ 07110
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1058nnn/GSM1058697/suppl/GSM1058697_CRACi_IC_12_HG_U133_Plus_2.CEL.gz
| | Sample_series_id | GSE43210
| | Sample_data_row_count | 26088
| | |
|
GSM1058698 | GPL570 |
|
PBMC_FK506_anti-CD3/CD28_donor_2
|
PBMC from donor 2 treatment: FK506_anti-CD3/CD28
|
donor: 2
cell type: PBMC
treatment: FK506_anti-CD3/CD28
subject: 2
|
FK506_53742
|
| Sample_geo_accession | GSM1058698
| | Sample_status | Public on Jan 31 2013
| | Sample_submission_date | Dec 31 2012
| | Sample_last_update_date | Feb 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using the mirVana RNA isolation kit (Ambion, Inc, Austin, TX, USA) according to manufacturer’s protocol. RNA was quantified using a ND-1000 spectrophotometer (Nanodrop Technology®, Cambridge, UK) and RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent technologies, Santa Clara, CA, USA). The 260/280 ratio were between 1.7 and 2.1 and the RINs (RNA Integrity Numbers) greater than 6 for all samples.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Total RNA (100ng) was transcribed and labeled into amplified RNA (aRNA) using the 3’IVT express kit (Affymetrix Inc., Santa Clara, CA) according to manufacturer’s instruction on a GCAS (Gene Chip Array Station).
| | Sample_hyb_protocol | Fragmented and labeled aRNA was hybridized to the Affymetrix U133 Plus 2.0 chips according to manufacturer’s instructions. Wash and stain protocol FS450_0004.
| | Sample_scan_protocol | GeneChips were scanned using the GC 30007G scanner.
| | Sample_data_processing | Data was normalized in R/Bioconductor using the robust multi-array average (RMA) expression measure. Probesets were annotated using the latest annotation available in Bioconductor and curated using an internal Roche probe inspector tool, which updates gene annotation per probeset based on the latest human genome draft release. As an additional quality measure, probesets were also curated using the tool for sequence specificity; probesets mapping to non-unique locations in the genome were flagged and ignored in subsequent analysis. A total of 26,088 out of 54,675 probesets passed the QC and curation processes, corresponding to 13,464 unique genes.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kai,,Lau
| | Sample_contact_institute | Hoffmann-La Roche
| | Sample_contact_address | 340 Kingsland St
| | Sample_contact_city | Nutley
| | Sample_contact_zip/postal_code | NJ 07110
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1058nnn/GSM1058698/suppl/GSM1058698_CRACi_IC_18_HG_U133_Plus_2.CEL.gz
| | Sample_series_id | GSE43210
| | Sample_data_row_count | 26088
| | |
|
GSM1058699 | GPL570 |
|
PBMC_Untreated_donor_3
|
PBMC from donor 3 treatment: Untreated
|
donor: 3
cell type: PBMC
treatment: Untreated
subject: 3
|
Neg_16928
|
| Sample_geo_accession | GSM1058699
| | Sample_status | Public on Jan 31 2013
| | Sample_submission_date | Dec 31 2012
| | Sample_last_update_date | Feb 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using the mirVana RNA isolation kit (Ambion, Inc, Austin, TX, USA) according to manufacturer’s protocol. RNA was quantified using a ND-1000 spectrophotometer (Nanodrop Technology®, Cambridge, UK) and RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent technologies, Santa Clara, CA, USA). The 260/280 ratio were between 1.7 and 2.1 and the RINs (RNA Integrity Numbers) greater than 6 for all samples.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Total RNA (100ng) was transcribed and labeled into amplified RNA (aRNA) using the 3’IVT express kit (Affymetrix Inc., Santa Clara, CA) according to manufacturer’s instruction on a GCAS (Gene Chip Array Station).
| | Sample_hyb_protocol | Fragmented and labeled aRNA was hybridized to the Affymetrix U133 Plus 2.0 chips according to manufacturer’s instructions. Wash and stain protocol FS450_0004.
| | Sample_scan_protocol | GeneChips were scanned using the GC 30007G scanner.
| | Sample_data_processing | Data was normalized in R/Bioconductor using the robust multi-array average (RMA) expression measure. Probesets were annotated using the latest annotation available in Bioconductor and curated using an internal Roche probe inspector tool, which updates gene annotation per probeset based on the latest human genome draft release. As an additional quality measure, probesets were also curated using the tool for sequence specificity; probesets mapping to non-unique locations in the genome were flagged and ignored in subsequent analysis. A total of 26,088 out of 54,675 probesets passed the QC and curation processes, corresponding to 13,464 unique genes.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kai,,Lau
| | Sample_contact_institute | Hoffmann-La Roche
| | Sample_contact_address | 340 Kingsland St
| | Sample_contact_city | Nutley
| | Sample_contact_zip/postal_code | NJ 07110
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1058nnn/GSM1058699/suppl/GSM1058699_CRACi_IC_19_HG_U133_Plus_2.CEL.gz
| | Sample_series_id | GSE43210
| | Sample_data_row_count | 26088
| | |
|
GSM1058700 | GPL570 |
|
PBMC_anti-CD3/CD28_donor_3
|
PBMC from donor 3 treatment: anti-CD3/CD28
|
donor: 3
cell type: PBMC
treatment: anti-CD3/CD28
subject: 3
|
Pos_16928
|
| Sample_geo_accession | GSM1058700
| | Sample_status | Public on Jan 31 2013
| | Sample_submission_date | Dec 31 2012
| | Sample_last_update_date | Feb 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using the mirVana RNA isolation kit (Ambion, Inc, Austin, TX, USA) according to manufacturer’s protocol. RNA was quantified using a ND-1000 spectrophotometer (Nanodrop Technology®, Cambridge, UK) and RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent technologies, Santa Clara, CA, USA). The 260/280 ratio were between 1.7 and 2.1 and the RINs (RNA Integrity Numbers) greater than 6 for all samples.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Total RNA (100ng) was transcribed and labeled into amplified RNA (aRNA) using the 3’IVT express kit (Affymetrix Inc., Santa Clara, CA) according to manufacturer’s instruction on a GCAS (Gene Chip Array Station).
| | Sample_hyb_protocol | Fragmented and labeled aRNA was hybridized to the Affymetrix U133 Plus 2.0 chips according to manufacturer’s instructions. Wash and stain protocol FS450_0004.
| | Sample_scan_protocol | GeneChips were scanned using the GC 30007G scanner.
| | Sample_data_processing | Data was normalized in R/Bioconductor using the robust multi-array average (RMA) expression measure. Probesets were annotated using the latest annotation available in Bioconductor and curated using an internal Roche probe inspector tool, which updates gene annotation per probeset based on the latest human genome draft release. As an additional quality measure, probesets were also curated using the tool for sequence specificity; probesets mapping to non-unique locations in the genome were flagged and ignored in subsequent analysis. A total of 26,088 out of 54,675 probesets passed the QC and curation processes, corresponding to 13,464 unique genes.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kai,,Lau
| | Sample_contact_institute | Hoffmann-La Roche
| | Sample_contact_address | 340 Kingsland St
| | Sample_contact_city | Nutley
| | Sample_contact_zip/postal_code | NJ 07110
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1058nnn/GSM1058700/suppl/GSM1058700_CRACi_IC_20_HG_U133_Plus_2.CEL.gz
| | Sample_series_id | GSE43210
| | Sample_data_row_count | 26088
| | |
|
GSM1058701 | GPL570 |
|
PBMC_CRACi_anti-CD3/CD28_donor_3
|
PBMC from donor 3 treatment: CRACi_anti-CD3/CD28
|
donor: 3
cell type: PBMC
treatment: CRACi_anti-CD3/CD28
subject: 3
|
RO2959_16928
|
| Sample_geo_accession | GSM1058701
| | Sample_status | Public on Jan 31 2013
| | Sample_submission_date | Dec 31 2012
| | Sample_last_update_date | Feb 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using the mirVana RNA isolation kit (Ambion, Inc, Austin, TX, USA) according to manufacturer’s protocol. RNA was quantified using a ND-1000 spectrophotometer (Nanodrop Technology®, Cambridge, UK) and RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent technologies, Santa Clara, CA, USA). The 260/280 ratio were between 1.7 and 2.1 and the RINs (RNA Integrity Numbers) greater than 6 for all samples.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Total RNA (100ng) was transcribed and labeled into amplified RNA (aRNA) using the 3’IVT express kit (Affymetrix Inc., Santa Clara, CA) according to manufacturer’s instruction on a GCAS (Gene Chip Array Station).
| | Sample_hyb_protocol | Fragmented and labeled aRNA was hybridized to the Affymetrix U133 Plus 2.0 chips according to manufacturer’s instructions. Wash and stain protocol FS450_0004.
| | Sample_scan_protocol | GeneChips were scanned using the GC 30007G scanner.
| | Sample_data_processing | Data was normalized in R/Bioconductor using the robust multi-array average (RMA) expression measure. Probesets were annotated using the latest annotation available in Bioconductor and curated using an internal Roche probe inspector tool, which updates gene annotation per probeset based on the latest human genome draft release. As an additional quality measure, probesets were also curated using the tool for sequence specificity; probesets mapping to non-unique locations in the genome were flagged and ignored in subsequent analysis. A total of 26,088 out of 54,675 probesets passed the QC and curation processes, corresponding to 13,464 unique genes.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kai,,Lau
| | Sample_contact_institute | Hoffmann-La Roche
| | Sample_contact_address | 340 Kingsland St
| | Sample_contact_city | Nutley
| | Sample_contact_zip/postal_code | NJ 07110
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1058nnn/GSM1058701/suppl/GSM1058701_CRACi_IC_21_HG_U133_Plus_2.CEL.gz
| | Sample_series_id | GSE43210
| | Sample_data_row_count | 26088
| | |
|
GSM1058702 | GPL570 |
|
PBMC_CsA_anti-CD3/CD28_donor_3
|
PBMC from donor 3 treatment: CsA_anti-CD3/CD28
|
donor: 3
cell type: PBMC
treatment: CsA_anti-CD3/CD28
subject: 3
|
CsA_16928
|
| Sample_geo_accession | GSM1058702
| | Sample_status | Public on Jan 31 2013
| | Sample_submission_date | Dec 31 2012
| | Sample_last_update_date | Feb 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using the mirVana RNA isolation kit (Ambion, Inc, Austin, TX, USA) according to manufacturer’s protocol. RNA was quantified using a ND-1000 spectrophotometer (Nanodrop Technology®, Cambridge, UK) and RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent technologies, Santa Clara, CA, USA). The 260/280 ratio were between 1.7 and 2.1 and the RINs (RNA Integrity Numbers) greater than 6 for all samples.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Total RNA (100ng) was transcribed and labeled into amplified RNA (aRNA) using the 3’IVT express kit (Affymetrix Inc., Santa Clara, CA) according to manufacturer’s instruction on a GCAS (Gene Chip Array Station).
| | Sample_hyb_protocol | Fragmented and labeled aRNA was hybridized to the Affymetrix U133 Plus 2.0 chips according to manufacturer’s instructions. Wash and stain protocol FS450_0004.
| | Sample_scan_protocol | GeneChips were scanned using the GC 30007G scanner.
| | Sample_data_processing | Data was normalized in R/Bioconductor using the robust multi-array average (RMA) expression measure. Probesets were annotated using the latest annotation available in Bioconductor and curated using an internal Roche probe inspector tool, which updates gene annotation per probeset based on the latest human genome draft release. As an additional quality measure, probesets were also curated using the tool for sequence specificity; probesets mapping to non-unique locations in the genome were flagged and ignored in subsequent analysis. A total of 26,088 out of 54,675 probesets passed the QC and curation processes, corresponding to 13,464 unique genes.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kai,,Lau
| | Sample_contact_institute | Hoffmann-La Roche
| | Sample_contact_address | 340 Kingsland St
| | Sample_contact_city | Nutley
| | Sample_contact_zip/postal_code | NJ 07110
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1058nnn/GSM1058702/suppl/GSM1058702_CRACi_IC_26_HG_U133_Plus_2.CEL.gz
| | Sample_series_id | GSE43210
| | Sample_data_row_count | 26088
| | |
|
GSM1058703 | GPL570 |
|
PBMC_FK506_anti-CD3/CD28_donor_3
|
PBMC from donor 3 treatment: FK506_anti-CD3/CD28
|
donor: 3
cell type: PBMC
treatment: FK506_anti-CD3/CD28
subject: 3
|
FK506_16928
|
| Sample_geo_accession | GSM1058703
| | Sample_status | Public on Jan 31 2013
| | Sample_submission_date | Dec 31 2012
| | Sample_last_update_date | Feb 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using the mirVana RNA isolation kit (Ambion, Inc, Austin, TX, USA) according to manufacturer’s protocol. RNA was quantified using a ND-1000 spectrophotometer (Nanodrop Technology®, Cambridge, UK) and RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent technologies, Santa Clara, CA, USA). The 260/280 ratio were between 1.7 and 2.1 and the RINs (RNA Integrity Numbers) greater than 6 for all samples.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Total RNA (100ng) was transcribed and labeled into amplified RNA (aRNA) using the 3’IVT express kit (Affymetrix Inc., Santa Clara, CA) according to manufacturer’s instruction on a GCAS (Gene Chip Array Station).
| | Sample_hyb_protocol | Fragmented and labeled aRNA was hybridized to the Affymetrix U133 Plus 2.0 chips according to manufacturer’s instructions. Wash and stain protocol FS450_0004.
| | Sample_scan_protocol | GeneChips were scanned using the GC 30007G scanner.
| | Sample_data_processing | Data was normalized in R/Bioconductor using the robust multi-array average (RMA) expression measure. Probesets were annotated using the latest annotation available in Bioconductor and curated using an internal Roche probe inspector tool, which updates gene annotation per probeset based on the latest human genome draft release. As an additional quality measure, probesets were also curated using the tool for sequence specificity; probesets mapping to non-unique locations in the genome were flagged and ignored in subsequent analysis. A total of 26,088 out of 54,675 probesets passed the QC and curation processes, corresponding to 13,464 unique genes.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kai,,Lau
| | Sample_contact_institute | Hoffmann-La Roche
| | Sample_contact_address | 340 Kingsland St
| | Sample_contact_city | Nutley
| | Sample_contact_zip/postal_code | NJ 07110
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1058nnn/GSM1058703/suppl/GSM1058703_CRACi_IC_27_HG_U133_Plus_2.CEL.gz
| | Sample_series_id | GSE43210
| | Sample_data_row_count | 26088
| | |
|
GSM1058704 | GPL570 |
|
PBMC_Untreated_donor_4
|
PBMC from donor 4 treatment: Untreated
|
donor: 4
cell type: PBMC
treatment: Untreated
subject: 4
|
Neg_18188
|
| Sample_geo_accession | GSM1058704
| | Sample_status | Public on Jan 31 2013
| | Sample_submission_date | Dec 31 2012
| | Sample_last_update_date | Feb 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using the mirVana RNA isolation kit (Ambion, Inc, Austin, TX, USA) according to manufacturer’s protocol. RNA was quantified using a ND-1000 spectrophotometer (Nanodrop Technology®, Cambridge, UK) and RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent technologies, Santa Clara, CA, USA). The 260/280 ratio were between 1.7 and 2.1 and the RINs (RNA Integrity Numbers) greater than 6 for all samples.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Total RNA (100ng) was transcribed and labeled into amplified RNA (aRNA) using the 3’IVT express kit (Affymetrix Inc., Santa Clara, CA) according to manufacturer’s instruction on a GCAS (Gene Chip Array Station).
| | Sample_hyb_protocol | Fragmented and labeled aRNA was hybridized to the Affymetrix U133 Plus 2.0 chips according to manufacturer’s instructions. Wash and stain protocol FS450_0004.
| | Sample_scan_protocol | GeneChips were scanned using the GC 30007G scanner.
| | Sample_data_processing | Data was normalized in R/Bioconductor using the robust multi-array average (RMA) expression measure. Probesets were annotated using the latest annotation available in Bioconductor and curated using an internal Roche probe inspector tool, which updates gene annotation per probeset based on the latest human genome draft release. As an additional quality measure, probesets were also curated using the tool for sequence specificity; probesets mapping to non-unique locations in the genome were flagged and ignored in subsequent analysis. A total of 26,088 out of 54,675 probesets passed the QC and curation processes, corresponding to 13,464 unique genes.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kai,,Lau
| | Sample_contact_institute | Hoffmann-La Roche
| | Sample_contact_address | 340 Kingsland St
| | Sample_contact_city | Nutley
| | Sample_contact_zip/postal_code | NJ 07110
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1058nnn/GSM1058704/suppl/GSM1058704_CRACi_IC_28_HG_U133_Plus_2.CEL.gz
| | Sample_series_id | GSE43210
| | Sample_data_row_count | 26088
| | |
|
GSM1058705 | GPL570 |
|
PBMC_anti-CD3/CD28_donor_4
|
PBMC from donor 4 treatment: anti-CD3/CD28
|
donor: 4
cell type: PBMC
treatment: anti-CD3/CD28
subject: 4
|
Pos_18188
|
| Sample_geo_accession | GSM1058705
| | Sample_status | Public on Jan 31 2013
| | Sample_submission_date | Dec 31 2012
| | Sample_last_update_date | Feb 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using the mirVana RNA isolation kit (Ambion, Inc, Austin, TX, USA) according to manufacturer’s protocol. RNA was quantified using a ND-1000 spectrophotometer (Nanodrop Technology®, Cambridge, UK) and RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent technologies, Santa Clara, CA, USA). The 260/280 ratio were between 1.7 and 2.1 and the RINs (RNA Integrity Numbers) greater than 6 for all samples.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Total RNA (100ng) was transcribed and labeled into amplified RNA (aRNA) using the 3’IVT express kit (Affymetrix Inc., Santa Clara, CA) according to manufacturer’s instruction on a GCAS (Gene Chip Array Station).
| | Sample_hyb_protocol | Fragmented and labeled aRNA was hybridized to the Affymetrix U133 Plus 2.0 chips according to manufacturer’s instructions. Wash and stain protocol FS450_0004.
| | Sample_scan_protocol | GeneChips were scanned using the GC 30007G scanner.
| | Sample_data_processing | Data was normalized in R/Bioconductor using the robust multi-array average (RMA) expression measure. Probesets were annotated using the latest annotation available in Bioconductor and curated using an internal Roche probe inspector tool, which updates gene annotation per probeset based on the latest human genome draft release. As an additional quality measure, probesets were also curated using the tool for sequence specificity; probesets mapping to non-unique locations in the genome were flagged and ignored in subsequent analysis. A total of 26,088 out of 54,675 probesets passed the QC and curation processes, corresponding to 13,464 unique genes.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kai,,Lau
| | Sample_contact_institute | Hoffmann-La Roche
| | Sample_contact_address | 340 Kingsland St
| | Sample_contact_city | Nutley
| | Sample_contact_zip/postal_code | NJ 07110
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1058nnn/GSM1058705/suppl/GSM1058705_CRACi_IC_29_HG_U133_Plus_2.CEL.gz
| | Sample_series_id | GSE43210
| | Sample_data_row_count | 26088
| | |
|
GSM1058706 | GPL570 |
|
PBMC_CRACi_anti-CD3/CD28_donor_4
|
PBMC from donor 4 treatment: CRACi_anti-CD3/CD28
|
donor: 4
cell type: PBMC
treatment: CRACi_anti-CD3/CD28
subject: 4
|
RO2959_18188
|
| Sample_geo_accession | GSM1058706
| | Sample_status | Public on Jan 31 2013
| | Sample_submission_date | Dec 31 2012
| | Sample_last_update_date | Feb 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using the mirVana RNA isolation kit (Ambion, Inc, Austin, TX, USA) according to manufacturer’s protocol. RNA was quantified using a ND-1000 spectrophotometer (Nanodrop Technology®, Cambridge, UK) and RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent technologies, Santa Clara, CA, USA). The 260/280 ratio were between 1.7 and 2.1 and the RINs (RNA Integrity Numbers) greater than 6 for all samples.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Total RNA (100ng) was transcribed and labeled into amplified RNA (aRNA) using the 3’IVT express kit (Affymetrix Inc., Santa Clara, CA) according to manufacturer’s instruction on a GCAS (Gene Chip Array Station).
| | Sample_hyb_protocol | Fragmented and labeled aRNA was hybridized to the Affymetrix U133 Plus 2.0 chips according to manufacturer’s instructions. Wash and stain protocol FS450_0004.
| | Sample_scan_protocol | GeneChips were scanned using the GC 30007G scanner.
| | Sample_data_processing | Data was normalized in R/Bioconductor using the robust multi-array average (RMA) expression measure. Probesets were annotated using the latest annotation available in Bioconductor and curated using an internal Roche probe inspector tool, which updates gene annotation per probeset based on the latest human genome draft release. As an additional quality measure, probesets were also curated using the tool for sequence specificity; probesets mapping to non-unique locations in the genome were flagged and ignored in subsequent analysis. A total of 26,088 out of 54,675 probesets passed the QC and curation processes, corresponding to 13,464 unique genes.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kai,,Lau
| | Sample_contact_institute | Hoffmann-La Roche
| | Sample_contact_address | 340 Kingsland St
| | Sample_contact_city | Nutley
| | Sample_contact_zip/postal_code | NJ 07110
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1058nnn/GSM1058706/suppl/GSM1058706_CRACi_IC_30_HG_U133_Plus_2.CEL.gz
| | Sample_series_id | GSE43210
| | Sample_data_row_count | 26088
| | |
|
GSM1058707 | GPL570 |
|
PBMC_CsA_anti-CD3/CD28_donor_4
|
PBMC from donor 4 treatment: CsA_anti-CD3/CD28
|
donor: 4
cell type: PBMC
treatment: CsA_anti-CD3/CD28
subject: 4
|
CsA_18188
|
| Sample_geo_accession | GSM1058707
| | Sample_status | Public on Jan 31 2013
| | Sample_submission_date | Dec 31 2012
| | Sample_last_update_date | Feb 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using the mirVana RNA isolation kit (Ambion, Inc, Austin, TX, USA) according to manufacturer’s protocol. RNA was quantified using a ND-1000 spectrophotometer (Nanodrop Technology®, Cambridge, UK) and RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent technologies, Santa Clara, CA, USA). The 260/280 ratio were between 1.7 and 2.1 and the RINs (RNA Integrity Numbers) greater than 6 for all samples.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Total RNA (100ng) was transcribed and labeled into amplified RNA (aRNA) using the 3’IVT express kit (Affymetrix Inc., Santa Clara, CA) according to manufacturer’s instruction on a GCAS (Gene Chip Array Station).
| | Sample_hyb_protocol | Fragmented and labeled aRNA was hybridized to the Affymetrix U133 Plus 2.0 chips according to manufacturer’s instructions. Wash and stain protocol FS450_0004.
| | Sample_scan_protocol | GeneChips were scanned using the GC 30007G scanner.
| | Sample_data_processing | Data was normalized in R/Bioconductor using the robust multi-array average (RMA) expression measure. Probesets were annotated using the latest annotation available in Bioconductor and curated using an internal Roche probe inspector tool, which updates gene annotation per probeset based on the latest human genome draft release. As an additional quality measure, probesets were also curated using the tool for sequence specificity; probesets mapping to non-unique locations in the genome were flagged and ignored in subsequent analysis. A total of 26,088 out of 54,675 probesets passed the QC and curation processes, corresponding to 13,464 unique genes.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kai,,Lau
| | Sample_contact_institute | Hoffmann-La Roche
| | Sample_contact_address | 340 Kingsland St
| | Sample_contact_city | Nutley
| | Sample_contact_zip/postal_code | NJ 07110
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1058nnn/GSM1058707/suppl/GSM1058707_CRACi_IC_35_HG_U133_Plus_2.CEL.gz
| | Sample_series_id | GSE43210
| | Sample_data_row_count | 26088
| | |
|
GSM1058708 | GPL570 |
|
PBMC_FK506_anti-CD3/CD28_donor_4
|
PBMC from donor 4 treatment: FK506_anti-CD3/CD28
|
donor: 4
cell type: PBMC
treatment: FK506_anti-CD3/CD28
subject: 4
|
FK506_18188
|
| Sample_geo_accession | GSM1058708
| | Sample_status | Public on Jan 31 2013
| | Sample_submission_date | Dec 31 2012
| | Sample_last_update_date | Feb 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using the mirVana RNA isolation kit (Ambion, Inc, Austin, TX, USA) according to manufacturer’s protocol. RNA was quantified using a ND-1000 spectrophotometer (Nanodrop Technology®, Cambridge, UK) and RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent technologies, Santa Clara, CA, USA). The 260/280 ratio were between 1.7 and 2.1 and the RINs (RNA Integrity Numbers) greater than 6 for all samples.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Total RNA (100ng) was transcribed and labeled into amplified RNA (aRNA) using the 3’IVT express kit (Affymetrix Inc., Santa Clara, CA) according to manufacturer’s instruction on a GCAS (Gene Chip Array Station).
| | Sample_hyb_protocol | Fragmented and labeled aRNA was hybridized to the Affymetrix U133 Plus 2.0 chips according to manufacturer’s instructions. Wash and stain protocol FS450_0004.
| | Sample_scan_protocol | GeneChips were scanned using the GC 30007G scanner.
| | Sample_data_processing | Data was normalized in R/Bioconductor using the robust multi-array average (RMA) expression measure. Probesets were annotated using the latest annotation available in Bioconductor and curated using an internal Roche probe inspector tool, which updates gene annotation per probeset based on the latest human genome draft release. As an additional quality measure, probesets were also curated using the tool for sequence specificity; probesets mapping to non-unique locations in the genome were flagged and ignored in subsequent analysis. A total of 26,088 out of 54,675 probesets passed the QC and curation processes, corresponding to 13,464 unique genes.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kai,,Lau
| | Sample_contact_institute | Hoffmann-La Roche
| | Sample_contact_address | 340 Kingsland St
| | Sample_contact_city | Nutley
| | Sample_contact_zip/postal_code | NJ 07110
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1058nnn/GSM1058708/suppl/GSM1058708_CRACi_IC_36_HG_U133_Plus_2.CEL.gz
| | Sample_series_id | GSE43210
| | Sample_data_row_count | 26088
| | |
|
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