Search results for the GEO ID: GSE46106  |
(Click on the check boxes provided under "Select for analysis", to initiate grouping) |
(Once the selection is made, click on "Add groups" in "Make groups for comparison", to make a group. Scroll down) |
|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM1123782 | GPL570 |
|
2147TG11_U133plus2
|
Excised tumor
|
tissue: Xenograft
transplant generation: 11
patient.number: 1
ethicity: A
established.from.pre.treatment..i....post.treatment..p..or.metastatic..m.: I
patient.nodal.status: P
lung.metastasis.in.mice: N
er.ihc: N
pr.ihc: N
her2.status: N
pam50.intrinsic.subtype: B
ck19.ihc: P
p53.ihc: N
ck.5.6.ihc: P
egfr.ihc: N
|
|
| Sample_geo_accession | GSM1123782
| | Sample_status | Public on May 30 2013
| | Sample_submission_date | Apr 16 2013
| | Sample_last_update_date | May 30 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor fragments were excised and frozen at -80C prior to RNA extraction
| | Sample_growth_protocol_ch1 | Patient-derived xenografts are grown by transplantation into the epithelium-free mammary fat pad of recipient SCID/Bg mice. Transplantation was performed without intervening culture in vitro or experimental manipulation of any kind
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNeasy mini kit was used for RNA extraction and purification , according to manufacturer's protocols.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix IVT and labeling protocol was used with Enzo IVT labeling reagents followed by Affymetrix cleanup columns, according to manufacturer's protocols
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix genechip scanner protocol
| | Sample_data_processing | data were analyzed in R using the GCRMA R package with defaults
| | Sample_platform_id | GPL570
| | Sample_contact_name | Chad,A.,Shaw
| | Sample_contact_email | cashaw@bcm.edu
| | Sample_contact_phone | 7137988087
| | Sample_contact_laboratory | Shaw
| | Sample_contact_department | Molecular and Human Genetics
| | Sample_contact_institute | BCM
| | Sample_contact_address | 1 Baylor Plaza
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1123nnn/GSM1123782/suppl/GSM1123782_2147TG11_U133plus2.CEL.gz
| | Sample_series_id | GSE46106
| | Sample_data_row_count | 54675
| | |
|
GSM1123783 | GPL570 |
|
2147TG15_U133plus2
|
Excised tumor
|
tissue: Xenograft
transplant generation: 15
patient.number: 1
ethicity: A
established.from.pre.treatment..i....post.treatment..p..or.metastatic..m.: I
patient.nodal.status: P
lung.metastasis.in.mice: N
er.ihc: N
pr.ihc: N
her2.status: N
pam50.intrinsic.subtype: B
ck19.ihc: P
p53.ihc: N
ck.5.6.ihc: P
egfr.ihc: N
|
|
| Sample_geo_accession | GSM1123783
| | Sample_status | Public on May 30 2013
| | Sample_submission_date | Apr 16 2013
| | Sample_last_update_date | May 30 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor fragments were excised and frozen at -80C prior to RNA extraction
| | Sample_growth_protocol_ch1 | Patient-derived xenografts are grown by transplantation into the epithelium-free mammary fat pad of recipient SCID/Bg mice. Transplantation was performed without intervening culture in vitro or experimental manipulation of any kind
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNeasy mini kit was used for RNA extraction and purification , according to manufacturer's protocols.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix IVT and labeling protocol was used with Enzo IVT labeling reagents followed by Affymetrix cleanup columns, according to manufacturer's protocols
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix genechip scanner protocol
| | Sample_data_processing | data were analyzed in R using the GCRMA R package with defaults
| | Sample_platform_id | GPL570
| | Sample_contact_name | Chad,A.,Shaw
| | Sample_contact_email | cashaw@bcm.edu
| | Sample_contact_phone | 7137988087
| | Sample_contact_laboratory | Shaw
| | Sample_contact_department | Molecular and Human Genetics
| | Sample_contact_institute | BCM
| | Sample_contact_address | 1 Baylor Plaza
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1123nnn/GSM1123783/suppl/GSM1123783_2147TG15_U133plus2.CEL.gz
| | Sample_series_id | GSE46106
| | Sample_data_row_count | 54675
| | |
|
GSM1123784 | GPL570 |
|
2147TG1_U133plus2
|
Excised tumor
|
tissue: Xenograft
transplant generation: 1
patient.number: 1
ethicity: A
established.from.pre.treatment..i....post.treatment..p..or.metastatic..m.: I
patient.nodal.status: P
lung.metastasis.in.mice: N
er.ihc: N
pr.ihc: N
her2.status: N
pam50.intrinsic.subtype: B
ck19.ihc: P
p53.ihc: N
ck.5.6.ihc: P
egfr.ihc: N
|
|
| Sample_geo_accession | GSM1123784
| | Sample_status | Public on May 30 2013
| | Sample_submission_date | Apr 16 2013
| | Sample_last_update_date | May 30 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor fragments were excised and frozen at -80C prior to RNA extraction
| | Sample_growth_protocol_ch1 | Patient-derived xenografts are grown by transplantation into the epithelium-free mammary fat pad of recipient SCID/Bg mice. Transplantation was performed without intervening culture in vitro or experimental manipulation of any kind
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNeasy mini kit was used for RNA extraction and purification , according to manufacturer's protocols.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix IVT and labeling protocol was used with Enzo IVT labeling reagents followed by Affymetrix cleanup columns, according to manufacturer's protocols
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix genechip scanner protocol
| | Sample_data_processing | data were analyzed in R using the GCRMA R package with defaults
| | Sample_platform_id | GPL570
| | Sample_contact_name | Chad,A.,Shaw
| | Sample_contact_email | cashaw@bcm.edu
| | Sample_contact_phone | 7137988087
| | Sample_contact_laboratory | Shaw
| | Sample_contact_department | Molecular and Human Genetics
| | Sample_contact_institute | BCM
| | Sample_contact_address | 1 Baylor Plaza
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1123nnn/GSM1123784/suppl/GSM1123784_2147TG1_U133plus2.CEL.gz
| | Sample_series_id | GSE46106
| | Sample_data_row_count | 54675
| | |
|
GSM1123785 | GPL570 |
|
2147TG6_U133plus2
|
Excised tumor
|
tissue: Xenograft
transplant generation: 6
patient.number: 1
ethicity: A
established.from.pre.treatment..i....post.treatment..p..or.metastatic..m.: I
patient.nodal.status: P
lung.metastasis.in.mice: N
er.ihc: N
pr.ihc: N
her2.status: N
pam50.intrinsic.subtype: B
ck19.ihc: P
p53.ihc: N
ck.5.6.ihc: P
egfr.ihc: N
|
|
| Sample_geo_accession | GSM1123785
| | Sample_status | Public on May 30 2013
| | Sample_submission_date | Apr 16 2013
| | Sample_last_update_date | May 30 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor fragments were excised and frozen at -80C prior to RNA extraction
| | Sample_growth_protocol_ch1 | Patient-derived xenografts are grown by transplantation into the epithelium-free mammary fat pad of recipient SCID/Bg mice. Transplantation was performed without intervening culture in vitro or experimental manipulation of any kind
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNeasy mini kit was used for RNA extraction and purification , according to manufacturer's protocols.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix IVT and labeling protocol was used with Enzo IVT labeling reagents followed by Affymetrix cleanup columns, according to manufacturer's protocols
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix genechip scanner protocol
| | Sample_data_processing | data were analyzed in R using the GCRMA R package with defaults
| | Sample_platform_id | GPL570
| | Sample_contact_name | Chad,A.,Shaw
| | Sample_contact_email | cashaw@bcm.edu
| | Sample_contact_phone | 7137988087
| | Sample_contact_laboratory | Shaw
| | Sample_contact_department | Molecular and Human Genetics
| | Sample_contact_institute | BCM
| | Sample_contact_address | 1 Baylor Plaza
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1123nnn/GSM1123785/suppl/GSM1123785_2147TG6_U133plus2.CEL.gz
| | Sample_series_id | GSE46106
| | Sample_data_row_count | 54675
| | |
|
GSM1123786 | GPL570 |
|
2277TG1_U133plus2
|
Excised tumor
|
tissue: Xenograft
transplant generation: 1
patient.number: 1
ethicity: A
established.from.pre.treatment..i....post.treatment..p..or.metastatic..m.: P
patient.nodal.status: P
lung.metastasis.in.mice: N
er.ihc: N
pr.ihc: N
her2.status: N
pam50.intrinsic.subtype: B
ck19.ihc: P
p53.ihc: N
ck.5.6.ihc: P
egfr.ihc: N
|
|
| Sample_geo_accession | GSM1123786
| | Sample_status | Public on May 30 2013
| | Sample_submission_date | Apr 16 2013
| | Sample_last_update_date | May 30 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor fragments were excised and frozen at -80C prior to RNA extraction
| | Sample_growth_protocol_ch1 | Patient-derived xenografts are grown by transplantation into the epithelium-free mammary fat pad of recipient SCID/Bg mice. Transplantation was performed without intervening culture in vitro or experimental manipulation of any kind
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNeasy mini kit was used for RNA extraction and purification , according to manufacturer's protocols.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix IVT and labeling protocol was used with Enzo IVT labeling reagents followed by Affymetrix cleanup columns, according to manufacturer's protocols
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix genechip scanner protocol
| | Sample_data_processing | data were analyzed in R using the GCRMA R package with defaults
| | Sample_platform_id | GPL570
| | Sample_contact_name | Chad,A.,Shaw
| | Sample_contact_email | cashaw@bcm.edu
| | Sample_contact_phone | 7137988087
| | Sample_contact_laboratory | Shaw
| | Sample_contact_department | Molecular and Human Genetics
| | Sample_contact_institute | BCM
| | Sample_contact_address | 1 Baylor Plaza
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1123nnn/GSM1123786/suppl/GSM1123786_2277TG1_U133plus2.CEL.gz
| | Sample_series_id | GSE46106
| | Sample_data_row_count | 54675
| | |
|
GSM1123787 | GPL570 |
|
2277TG9_U133plus2
|
Excised tumor
|
tissue: Xenograft
transplant generation: 9
patient.number: 1
ethicity: A
established.from.pre.treatment..i....post.treatment..p..or.metastatic..m.: P
patient.nodal.status: P
lung.metastasis.in.mice: N
er.ihc: N
pr.ihc: N
her2.status: N
pam50.intrinsic.subtype: B
ck19.ihc: P
p53.ihc: N
ck.5.6.ihc: P
egfr.ihc: N
|
|
| Sample_geo_accession | GSM1123787
| | Sample_status | Public on May 30 2013
| | Sample_submission_date | Apr 16 2013
| | Sample_last_update_date | May 30 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor fragments were excised and frozen at -80C prior to RNA extraction
| | Sample_growth_protocol_ch1 | Patient-derived xenografts are grown by transplantation into the epithelium-free mammary fat pad of recipient SCID/Bg mice. Transplantation was performed without intervening culture in vitro or experimental manipulation of any kind
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNeasy mini kit was used for RNA extraction and purification , according to manufacturer's protocols.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix IVT and labeling protocol was used with Enzo IVT labeling reagents followed by Affymetrix cleanup columns, according to manufacturer's protocols
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix genechip scanner protocol
| | Sample_data_processing | data were analyzed in R using the GCRMA R package with defaults
| | Sample_platform_id | GPL570
| | Sample_contact_name | Chad,A.,Shaw
| | Sample_contact_email | cashaw@bcm.edu
| | Sample_contact_phone | 7137988087
| | Sample_contact_laboratory | Shaw
| | Sample_contact_department | Molecular and Human Genetics
| | Sample_contact_institute | BCM
| | Sample_contact_address | 1 Baylor Plaza
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1123nnn/GSM1123787/suppl/GSM1123787_2277TG9_U133plus2.CEL.gz
| | Sample_series_id | GSE46106
| | Sample_data_row_count | 54675
| | |
|
GSM1123788 | GPL570 |
|
2665TG15_U133plus2
|
Excised tumor
|
tissue: Xenograft
transplant generation: 15
patient.number: 2
ethicity: H
established.from.pre.treatment..i....post.treatment..p..or.metastatic..m.: P
patient.nodal.status: N
lung.metastasis.in.mice: Y
er.ihc: N
pr.ihc: N
her2.status: N
pam50.intrinsic.subtype: B
ck19.ihc: P
p53.ihc: P
ck.5.6.ihc: N
egfr.ihc: P
|
|
| Sample_geo_accession | GSM1123788
| | Sample_status | Public on May 30 2013
| | Sample_submission_date | Apr 16 2013
| | Sample_last_update_date | May 30 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor fragments were excised and frozen at -80C prior to RNA extraction
| | Sample_growth_protocol_ch1 | Patient-derived xenografts are grown by transplantation into the epithelium-free mammary fat pad of recipient SCID/Bg mice. Transplantation was performed without intervening culture in vitro or experimental manipulation of any kind
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNeasy mini kit was used for RNA extraction and purification , according to manufacturer's protocols.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix IVT and labeling protocol was used with Enzo IVT labeling reagents followed by Affymetrix cleanup columns, according to manufacturer's protocols
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix genechip scanner protocol
| | Sample_data_processing | data were analyzed in R using the GCRMA R package with defaults
| | Sample_platform_id | GPL570
| | Sample_contact_name | Chad,A.,Shaw
| | Sample_contact_email | cashaw@bcm.edu
| | Sample_contact_phone | 7137988087
| | Sample_contact_laboratory | Shaw
| | Sample_contact_department | Molecular and Human Genetics
| | Sample_contact_institute | BCM
| | Sample_contact_address | 1 Baylor Plaza
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1123nnn/GSM1123788/suppl/GSM1123788_2665TG15_U133plus2.CEL.gz
| | Sample_series_id | GSE46106
| | Sample_data_row_count | 54675
| | |
|
GSM1123789 | GPL570 |
|
2665TG1_U133plus2
|
Excised tumor
|
tissue: Xenograft
transplant generation: 1
patient.number: 2
ethicity: H
established.from.pre.treatment..i....post.treatment..p..or.metastatic..m.: P
patient.nodal.status: N
lung.metastasis.in.mice: Y
er.ihc: N
pr.ihc: N
her2.status: N
pam50.intrinsic.subtype: B
ck19.ihc: P
p53.ihc: P
ck.5.6.ihc: N
egfr.ihc: P
|
|
| Sample_geo_accession | GSM1123789
| | Sample_status | Public on May 30 2013
| | Sample_submission_date | Apr 16 2013
| | Sample_last_update_date | May 30 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor fragments were excised and frozen at -80C prior to RNA extraction
| | Sample_growth_protocol_ch1 | Patient-derived xenografts are grown by transplantation into the epithelium-free mammary fat pad of recipient SCID/Bg mice. Transplantation was performed without intervening culture in vitro or experimental manipulation of any kind
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNeasy mini kit was used for RNA extraction and purification , according to manufacturer's protocols.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix IVT and labeling protocol was used with Enzo IVT labeling reagents followed by Affymetrix cleanup columns, according to manufacturer's protocols
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix genechip scanner protocol
| | Sample_data_processing | data were analyzed in R using the GCRMA R package with defaults
| | Sample_platform_id | GPL570
| | Sample_contact_name | Chad,A.,Shaw
| | Sample_contact_email | cashaw@bcm.edu
| | Sample_contact_phone | 7137988087
| | Sample_contact_laboratory | Shaw
| | Sample_contact_department | Molecular and Human Genetics
| | Sample_contact_institute | BCM
| | Sample_contact_address | 1 Baylor Plaza
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1123nnn/GSM1123789/suppl/GSM1123789_2665TG1_U133plus2.CEL.gz
| | Sample_series_id | GSE46106
| | Sample_data_row_count | 54675
| | |
|
GSM1123790 | GPL570 |
|
2665TG6_U133plus2
|
Excised tumor
|
tissue: Xenograft
transplant generation: 6
patient.number: 2
ethicity: H
established.from.pre.treatment..i....post.treatment..p..or.metastatic..m.: P
patient.nodal.status: N
lung.metastasis.in.mice: Y
er.ihc: N
pr.ihc: N
her2.status: N
pam50.intrinsic.subtype: B
ck19.ihc: P
p53.ihc: P
ck.5.6.ihc: N
egfr.ihc: P
|
|
| Sample_geo_accession | GSM1123790
| | Sample_status | Public on May 30 2013
| | Sample_submission_date | Apr 16 2013
| | Sample_last_update_date | May 30 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor fragments were excised and frozen at -80C prior to RNA extraction
| | Sample_growth_protocol_ch1 | Patient-derived xenografts are grown by transplantation into the epithelium-free mammary fat pad of recipient SCID/Bg mice. Transplantation was performed without intervening culture in vitro or experimental manipulation of any kind
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNeasy mini kit was used for RNA extraction and purification , according to manufacturer's protocols.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix IVT and labeling protocol was used with Enzo IVT labeling reagents followed by Affymetrix cleanup columns, according to manufacturer's protocols
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix genechip scanner protocol
| | Sample_data_processing | data were analyzed in R using the GCRMA R package with defaults
| | Sample_platform_id | GPL570
| | Sample_contact_name | Chad,A.,Shaw
| | Sample_contact_email | cashaw@bcm.edu
| | Sample_contact_phone | 7137988087
| | Sample_contact_laboratory | Shaw
| | Sample_contact_department | Molecular and Human Genetics
| | Sample_contact_institute | BCM
| | Sample_contact_address | 1 Baylor Plaza
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1123nnn/GSM1123790/suppl/GSM1123790_2665TG6_U133plus2.CEL.gz
| | Sample_series_id | GSE46106
| | Sample_data_row_count | 54675
| | |
|
GSM1123791 | GPL570 |
|
3104TG1_U133plus2
|
Excised tumor
|
tissue: Xenograft
transplant generation: 1
patient.number: 3
ethicity: C
established.from.pre.treatment..i....post.treatment..p..or.metastatic..m.: P
patient.nodal.status: N
lung.metastasis.in.mice: N
er.ihc: N
pr.ihc: N
her2.status: N
pam50.intrinsic.subtype: B
ck19.ihc: P
p53.ihc: P
ck.5.6.ihc: P
egfr.ihc: P
|
|
| Sample_geo_accession | GSM1123791
| | Sample_status | Public on May 30 2013
| | Sample_submission_date | Apr 16 2013
| | Sample_last_update_date | May 30 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor fragments were excised and frozen at -80C prior to RNA extraction
| | Sample_growth_protocol_ch1 | Patient-derived xenografts are grown by transplantation into the epithelium-free mammary fat pad of recipient SCID/Bg mice. Transplantation was performed without intervening culture in vitro or experimental manipulation of any kind
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNeasy mini kit was used for RNA extraction and purification , according to manufacturer's protocols.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix IVT and labeling protocol was used with Enzo IVT labeling reagents followed by Affymetrix cleanup columns, according to manufacturer's protocols
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix genechip scanner protocol
| | Sample_data_processing | data were analyzed in R using the GCRMA R package with defaults
| | Sample_platform_id | GPL570
| | Sample_contact_name | Chad,A.,Shaw
| | Sample_contact_email | cashaw@bcm.edu
| | Sample_contact_phone | 7137988087
| | Sample_contact_laboratory | Shaw
| | Sample_contact_department | Molecular and Human Genetics
| | Sample_contact_institute | BCM
| | Sample_contact_address | 1 Baylor Plaza
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1123nnn/GSM1123791/suppl/GSM1123791_3104TG1_U133plus2.CEL.gz
| | Sample_series_id | GSE46106
| | Sample_data_row_count | 54675
| | |
|
GSM1123792 | GPL570 |
|
3104TG3_U133plus2
|
Excised tumor
|
tissue: Xenograft
transplant generation: 3
patient.number: 3
ethicity: C
established.from.pre.treatment..i....post.treatment..p..or.metastatic..m.: P
patient.nodal.status: N
lung.metastasis.in.mice: N
er.ihc: N
pr.ihc: N
her2.status: N
pam50.intrinsic.subtype: B
ck19.ihc: P
p53.ihc: P
ck.5.6.ihc: P
egfr.ihc: P
|
|
| Sample_geo_accession | GSM1123792
| | Sample_status | Public on May 30 2013
| | Sample_submission_date | Apr 16 2013
| | Sample_last_update_date | May 30 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor fragments were excised and frozen at -80C prior to RNA extraction
| | Sample_growth_protocol_ch1 | Patient-derived xenografts are grown by transplantation into the epithelium-free mammary fat pad of recipient SCID/Bg mice. Transplantation was performed without intervening culture in vitro or experimental manipulation of any kind
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNeasy mini kit was used for RNA extraction and purification , according to manufacturer's protocols.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix IVT and labeling protocol was used with Enzo IVT labeling reagents followed by Affymetrix cleanup columns, according to manufacturer's protocols
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix genechip scanner protocol
| | Sample_data_processing | data were analyzed in R using the GCRMA R package with defaults
| | Sample_platform_id | GPL570
| | Sample_contact_name | Chad,A.,Shaw
| | Sample_contact_email | cashaw@bcm.edu
| | Sample_contact_phone | 7137988087
| | Sample_contact_laboratory | Shaw
| | Sample_contact_department | Molecular and Human Genetics
| | Sample_contact_institute | BCM
| | Sample_contact_address | 1 Baylor Plaza
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1123nnn/GSM1123792/suppl/GSM1123792_3104TG3_U133plus2.CEL.gz
| | Sample_series_id | GSE46106
| | Sample_data_row_count | 54675
| | |
|
GSM1123793 | GPL570 |
|
3107TG1_U133plus2
|
Excised tumor
|
tissue: Xenograft
transplant generation: 1
patient.number: 4
ethicity: C
established.from.pre.treatment..i....post.treatment..p..or.metastatic..m.: P
patient.nodal.status: N
lung.metastasis.in.mice: N
er.ihc: N
pr.ihc: N
her2.status: P
pam50.intrinsic.subtype: B
ck19.ihc: P
p53.ihc: P
ck.5.6.ihc: P
egfr.ihc: P
|
|
| Sample_geo_accession | GSM1123793
| | Sample_status | Public on May 30 2013
| | Sample_submission_date | Apr 16 2013
| | Sample_last_update_date | May 30 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor fragments were excised and frozen at -80C prior to RNA extraction
| | Sample_growth_protocol_ch1 | Patient-derived xenografts are grown by transplantation into the epithelium-free mammary fat pad of recipient SCID/Bg mice. Transplantation was performed without intervening culture in vitro or experimental manipulation of any kind
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNeasy mini kit was used for RNA extraction and purification , according to manufacturer's protocols.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix IVT and labeling protocol was used with Enzo IVT labeling reagents followed by Affymetrix cleanup columns, according to manufacturer's protocols
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix genechip scanner protocol
| | Sample_data_processing | data were analyzed in R using the GCRMA R package with defaults
| | Sample_platform_id | GPL570
| | Sample_contact_name | Chad,A.,Shaw
| | Sample_contact_email | cashaw@bcm.edu
| | Sample_contact_phone | 7137988087
| | Sample_contact_laboratory | Shaw
| | Sample_contact_department | Molecular and Human Genetics
| | Sample_contact_institute | BCM
| | Sample_contact_address | 1 Baylor Plaza
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1123nnn/GSM1123793/suppl/GSM1123793_3107TG1_U133plus2.CEL.gz
| | Sample_series_id | GSE46106
| | Sample_data_row_count | 54675
| | |
|
GSM1123794 | GPL570 |
|
3107TG5_U133plus2
|
Excised tumor
|
tissue: Xenograft
transplant generation: 5
patient.number: 4
ethicity: C
established.from.pre.treatment..i....post.treatment..p..or.metastatic..m.: P
patient.nodal.status: N
lung.metastasis.in.mice: N
er.ihc: N
pr.ihc: N
her2.status: P
pam50.intrinsic.subtype: B
ck19.ihc: P
p53.ihc: P
ck.5.6.ihc: P
egfr.ihc: P
|
|
| Sample_geo_accession | GSM1123794
| | Sample_status | Public on May 30 2013
| | Sample_submission_date | Apr 16 2013
| | Sample_last_update_date | May 30 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor fragments were excised and frozen at -80C prior to RNA extraction
| | Sample_growth_protocol_ch1 | Patient-derived xenografts are grown by transplantation into the epithelium-free mammary fat pad of recipient SCID/Bg mice. Transplantation was performed without intervening culture in vitro or experimental manipulation of any kind
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNeasy mini kit was used for RNA extraction and purification , according to manufacturer's protocols.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix IVT and labeling protocol was used with Enzo IVT labeling reagents followed by Affymetrix cleanup columns, according to manufacturer's protocols
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix genechip scanner protocol
| | Sample_data_processing | data were analyzed in R using the GCRMA R package with defaults
| | Sample_platform_id | GPL570
| | Sample_contact_name | Chad,A.,Shaw
| | Sample_contact_email | cashaw@bcm.edu
| | Sample_contact_phone | 7137988087
| | Sample_contact_laboratory | Shaw
| | Sample_contact_department | Molecular and Human Genetics
| | Sample_contact_institute | BCM
| | Sample_contact_address | 1 Baylor Plaza
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1123nnn/GSM1123794/suppl/GSM1123794_3107TG5_U133plus2.CEL.gz
| | Sample_series_id | GSE46106
| | Sample_data_row_count | 54675
| | |
|
GSM1123795 | GPL570 |
|
3143TG1_U133plus2
|
Excised tumor
|
tissue: Xenograft
transplant generation: 1
patient.number: 4
ethicity: C
established.from.pre.treatment..i....post.treatment..p..or.metastatic..m.: P
patient.nodal.status: N
lung.metastasis.in.mice: N
er.ihc: N
pr.ihc: N
her2.status: P
pam50.intrinsic.subtype: B
ck19.ihc: P
p53.ihc: P
ck.5.6.ihc: P
egfr.ihc: P
|
|
| Sample_geo_accession | GSM1123795
| | Sample_status | Public on May 30 2013
| | Sample_submission_date | Apr 16 2013
| | Sample_last_update_date | May 30 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor fragments were excised and frozen at -80C prior to RNA extraction
| | Sample_growth_protocol_ch1 | Patient-derived xenografts are grown by transplantation into the epithelium-free mammary fat pad of recipient SCID/Bg mice. Transplantation was performed without intervening culture in vitro or experimental manipulation of any kind
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNeasy mini kit was used for RNA extraction and purification , according to manufacturer's protocols.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix IVT and labeling protocol was used with Enzo IVT labeling reagents followed by Affymetrix cleanup columns, according to manufacturer's protocols
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix genechip scanner protocol
| | Sample_data_processing | data were analyzed in R using the GCRMA R package with defaults
| | Sample_platform_id | GPL570
| | Sample_contact_name | Chad,A.,Shaw
| | Sample_contact_email | cashaw@bcm.edu
| | Sample_contact_phone | 7137988087
| | Sample_contact_laboratory | Shaw
| | Sample_contact_department | Molecular and Human Genetics
| | Sample_contact_institute | BCM
| | Sample_contact_address | 1 Baylor Plaza
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1123nnn/GSM1123795/suppl/GSM1123795_3143TG1_U133plus2.CEL.gz
| | Sample_series_id | GSE46106
| | Sample_data_row_count | 54675
| | |
|
GSM1123796 | GPL570 |
|
3143TG5_U133plus2
|
Excised tumor
|
tissue: Xenograft
transplant generation: 5
patient.number: 4
ethicity: C
established.from.pre.treatment..i....post.treatment..p..or.metastatic..m.: P
patient.nodal.status: N
lung.metastasis.in.mice: N
er.ihc: N
pr.ihc: N
her2.status: P
pam50.intrinsic.subtype: B
ck19.ihc: P
p53.ihc: P
ck.5.6.ihc: P
egfr.ihc: P
|
|
| Sample_geo_accession | GSM1123796
| | Sample_status | Public on May 30 2013
| | Sample_submission_date | Apr 16 2013
| | Sample_last_update_date | May 30 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor fragments were excised and frozen at -80C prior to RNA extraction
| | Sample_growth_protocol_ch1 | Patient-derived xenografts are grown by transplantation into the epithelium-free mammary fat pad of recipient SCID/Bg mice. Transplantation was performed without intervening culture in vitro or experimental manipulation of any kind
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNeasy mini kit was used for RNA extraction and purification , according to manufacturer's protocols.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix IVT and labeling protocol was used with Enzo IVT labeling reagents followed by Affymetrix cleanup columns, according to manufacturer's protocols
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix genechip scanner protocol
| | Sample_data_processing | data were analyzed in R using the GCRMA R package with defaults
| | Sample_platform_id | GPL570
| | Sample_contact_name | Chad,A.,Shaw
| | Sample_contact_email | cashaw@bcm.edu
| | Sample_contact_phone | 7137988087
| | Sample_contact_laboratory | Shaw
| | Sample_contact_department | Molecular and Human Genetics
| | Sample_contact_institute | BCM
| | Sample_contact_address | 1 Baylor Plaza
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1123nnn/GSM1123796/suppl/GSM1123796_3143TG5_U133plus2.CEL.gz
| | Sample_series_id | GSE46106
| | Sample_data_row_count | 54675
| | |
|
GSM1123797 | GPL570 |
|
3204TG1_U133plus2
|
Excised tumor
|
tissue: Xenograft
transplant generation: 1
patient.number: 5
ethicity: C
established.from.pre.treatment..i....post.treatment..p..or.metastatic..m.: I
patient.nodal.status: N
lung.metastasis.in.mice: Y
er.ihc: N
pr.ihc: N
her2.status: N
pam50.intrinsic.subtype: B
ck19.ihc: P
p53.ihc: P
ck.5.6.ihc: P
egfr.ihc: P
|
|
| Sample_geo_accession | GSM1123797
| | Sample_status | Public on May 30 2013
| | Sample_submission_date | Apr 16 2013
| | Sample_last_update_date | May 30 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor fragments were excised and frozen at -80C prior to RNA extraction
| | Sample_growth_protocol_ch1 | Patient-derived xenografts are grown by transplantation into the epithelium-free mammary fat pad of recipient SCID/Bg mice. Transplantation was performed without intervening culture in vitro or experimental manipulation of any kind
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNeasy mini kit was used for RNA extraction and purification , according to manufacturer's protocols.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix IVT and labeling protocol was used with Enzo IVT labeling reagents followed by Affymetrix cleanup columns, according to manufacturer's protocols
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix genechip scanner protocol
| | Sample_data_processing | data were analyzed in R using the GCRMA R package with defaults
| | Sample_platform_id | GPL570
| | Sample_contact_name | Chad,A.,Shaw
| | Sample_contact_email | cashaw@bcm.edu
| | Sample_contact_phone | 7137988087
| | Sample_contact_laboratory | Shaw
| | Sample_contact_department | Molecular and Human Genetics
| | Sample_contact_institute | BCM
| | Sample_contact_address | 1 Baylor Plaza
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1123nnn/GSM1123797/suppl/GSM1123797_3204TG1_U133plus2.CEL.gz
| | Sample_series_id | GSE46106
| | Sample_data_row_count | 54675
| | |
|
GSM1123798 | GPL570 |
|
3204TG5_U133plus2
|
Excised tumor
|
tissue: Xenograft
transplant generation: 5
patient.number: 5
ethicity: C
established.from.pre.treatment..i....post.treatment..p..or.metastatic..m.: I
patient.nodal.status: N
lung.metastasis.in.mice: Y
er.ihc: N
pr.ihc: N
her2.status: N
pam50.intrinsic.subtype: B
ck19.ihc: P
p53.ihc: P
ck.5.6.ihc: P
egfr.ihc: P
|
|
| Sample_geo_accession | GSM1123798
| | Sample_status | Public on May 30 2013
| | Sample_submission_date | Apr 16 2013
| | Sample_last_update_date | May 30 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor fragments were excised and frozen at -80C prior to RNA extraction
| | Sample_growth_protocol_ch1 | Patient-derived xenografts are grown by transplantation into the epithelium-free mammary fat pad of recipient SCID/Bg mice. Transplantation was performed without intervening culture in vitro or experimental manipulation of any kind
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNeasy mini kit was used for RNA extraction and purification , according to manufacturer's protocols.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix IVT and labeling protocol was used with Enzo IVT labeling reagents followed by Affymetrix cleanup columns, according to manufacturer's protocols
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix genechip scanner protocol
| | Sample_data_processing | data were analyzed in R using the GCRMA R package with defaults
| | Sample_platform_id | GPL570
| | Sample_contact_name | Chad,A.,Shaw
| | Sample_contact_email | cashaw@bcm.edu
| | Sample_contact_phone | 7137988087
| | Sample_contact_laboratory | Shaw
| | Sample_contact_department | Molecular and Human Genetics
| | Sample_contact_institute | BCM
| | Sample_contact_address | 1 Baylor Plaza
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1123nnn/GSM1123798/suppl/GSM1123798_3204TG5_U133plus2.CEL.gz
| | Sample_series_id | GSE46106
| | Sample_data_row_count | 54675
| | |
|
GSM1123799 | GPL570 |
|
3561TG1_U133plus2
|
Excised tumor
|
tissue: Xenograft
transplant generation: 1
patient.number: 6
ethicity: A
established.from.pre.treatment..i....post.treatment..p..or.metastatic..m.: I
patient.nodal.status: P
lung.metastasis.in.mice: N
er.ihc: N
pr.ihc: N
her2.status: N
pam50.intrinsic.subtype: B
ck19.ihc: P
p53.ihc: N
ck.5.6.ihc: N
egfr.ihc: N
|
|
| Sample_geo_accession | GSM1123799
| | Sample_status | Public on May 30 2013
| | Sample_submission_date | Apr 16 2013
| | Sample_last_update_date | May 30 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor fragments were excised and frozen at -80C prior to RNA extraction
| | Sample_growth_protocol_ch1 | Patient-derived xenografts are grown by transplantation into the epithelium-free mammary fat pad of recipient SCID/Bg mice. Transplantation was performed without intervening culture in vitro or experimental manipulation of any kind
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNeasy mini kit was used for RNA extraction and purification , according to manufacturer's protocols.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix IVT and labeling protocol was used with Enzo IVT labeling reagents followed by Affymetrix cleanup columns, according to manufacturer's protocols
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix genechip scanner protocol
| | Sample_data_processing | data were analyzed in R using the GCRMA R package with defaults
| | Sample_platform_id | GPL570
| | Sample_contact_name | Chad,A.,Shaw
| | Sample_contact_email | cashaw@bcm.edu
| | Sample_contact_phone | 7137988087
| | Sample_contact_laboratory | Shaw
| | Sample_contact_department | Molecular and Human Genetics
| | Sample_contact_institute | BCM
| | Sample_contact_address | 1 Baylor Plaza
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1123nnn/GSM1123799/suppl/GSM1123799_3561TG1_U133plus2.CEL.gz
| | Sample_series_id | GSE46106
| | Sample_data_row_count | 54675
| | |
|
GSM1123800 | GPL570 |
|
3561TG5_U133plus2
|
Excised tumor
|
tissue: Xenograft
transplant generation: 5
patient.number: 6
ethicity: A
established.from.pre.treatment..i....post.treatment..p..or.metastatic..m.: I
patient.nodal.status: P
lung.metastasis.in.mice: N
er.ihc: N
pr.ihc: N
her2.status: N
pam50.intrinsic.subtype: B
ck19.ihc: P
p53.ihc: N
ck.5.6.ihc: N
egfr.ihc: N
|
|
| Sample_geo_accession | GSM1123800
| | Sample_status | Public on May 30 2013
| | Sample_submission_date | Apr 16 2013
| | Sample_last_update_date | May 30 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor fragments were excised and frozen at -80C prior to RNA extraction
| | Sample_growth_protocol_ch1 | Patient-derived xenografts are grown by transplantation into the epithelium-free mammary fat pad of recipient SCID/Bg mice. Transplantation was performed without intervening culture in vitro or experimental manipulation of any kind
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNeasy mini kit was used for RNA extraction and purification , according to manufacturer's protocols.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix IVT and labeling protocol was used with Enzo IVT labeling reagents followed by Affymetrix cleanup columns, according to manufacturer's protocols
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix genechip scanner protocol
| | Sample_data_processing | data were analyzed in R using the GCRMA R package with defaults
| | Sample_platform_id | GPL570
| | Sample_contact_name | Chad,A.,Shaw
| | Sample_contact_email | cashaw@bcm.edu
| | Sample_contact_phone | 7137988087
| | Sample_contact_laboratory | Shaw
| | Sample_contact_department | Molecular and Human Genetics
| | Sample_contact_institute | BCM
| | Sample_contact_address | 1 Baylor Plaza
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1123nnn/GSM1123800/suppl/GSM1123800_3561TG5_U133plus2.CEL.gz
| | Sample_series_id | GSE46106
| | Sample_data_row_count | 54675
| | |
|
GSM1123801 | GPL570 |
|
3611TG1_U133plus2
|
Excised tumor
|
tissue: Xenograft
transplant generation: 1
patient.number: 6
ethicity: A
established.from.pre.treatment..i....post.treatment..p..or.metastatic..m.: P
patient.nodal.status: P
lung.metastasis.in.mice: N
er.ihc: N
pr.ihc: N
her2.status: N
pam50.intrinsic.subtype: B
ck19.ihc: P
p53.ihc: N
ck.5.6.ihc: N
egfr.ihc: N
|
|
| Sample_geo_accession | GSM1123801
| | Sample_status | Public on May 30 2013
| | Sample_submission_date | Apr 16 2013
| | Sample_last_update_date | May 30 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor fragments were excised and frozen at -80C prior to RNA extraction
| | Sample_growth_protocol_ch1 | Patient-derived xenografts are grown by transplantation into the epithelium-free mammary fat pad of recipient SCID/Bg mice. Transplantation was performed without intervening culture in vitro or experimental manipulation of any kind
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNeasy mini kit was used for RNA extraction and purification , according to manufacturer's protocols.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix IVT and labeling protocol was used with Enzo IVT labeling reagents followed by Affymetrix cleanup columns, according to manufacturer's protocols
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix genechip scanner protocol
| | Sample_data_processing | data were analyzed in R using the GCRMA R package with defaults
| | Sample_platform_id | GPL570
| | Sample_contact_name | Chad,A.,Shaw
| | Sample_contact_email | cashaw@bcm.edu
| | Sample_contact_phone | 7137988087
| | Sample_contact_laboratory | Shaw
| | Sample_contact_department | Molecular and Human Genetics
| | Sample_contact_institute | BCM
| | Sample_contact_address | 1 Baylor Plaza
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1123nnn/GSM1123801/suppl/GSM1123801_3611TG1_U133plus2.CEL.gz
| | Sample_series_id | GSE46106
| | Sample_data_row_count | 54675
| | |
|
GSM1123802 | GPL570 |
|
3611TG5_U133plus2
|
Excised tumor
|
tissue: Xenograft
transplant generation: 5
patient.number: 7
ethicity: A
established.from.pre.treatment..i....post.treatment..p..or.metastatic..m.: I
patient.nodal.status: N
lung.metastasis.in.mice: Y
er.ihc: N
pr.ihc: N
her2.status: N
pam50.intrinsic.subtype: B
ck19.ihc: P
p53.ihc: N
ck.5.6.ihc: P
egfr.ihc: P
|
|
| Sample_geo_accession | GSM1123802
| | Sample_status | Public on May 30 2013
| | Sample_submission_date | Apr 16 2013
| | Sample_last_update_date | May 30 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor fragments were excised and frozen at -80C prior to RNA extraction
| | Sample_growth_protocol_ch1 | Patient-derived xenografts are grown by transplantation into the epithelium-free mammary fat pad of recipient SCID/Bg mice. Transplantation was performed without intervening culture in vitro or experimental manipulation of any kind
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNeasy mini kit was used for RNA extraction and purification , according to manufacturer's protocols.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix IVT and labeling protocol was used with Enzo IVT labeling reagents followed by Affymetrix cleanup columns, according to manufacturer's protocols
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix genechip scanner protocol
| | Sample_data_processing | data were analyzed in R using the GCRMA R package with defaults
| | Sample_platform_id | GPL570
| | Sample_contact_name | Chad,A.,Shaw
| | Sample_contact_email | cashaw@bcm.edu
| | Sample_contact_phone | 7137988087
| | Sample_contact_laboratory | Shaw
| | Sample_contact_department | Molecular and Human Genetics
| | Sample_contact_institute | BCM
| | Sample_contact_address | 1 Baylor Plaza
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1123nnn/GSM1123802/suppl/GSM1123802_3611TG5_U133plus2.CEL.gz
| | Sample_series_id | GSE46106
| | Sample_data_row_count | 54675
| | |
|
GSM1123803 | GPL570 |
|
3613TG1_U133plus2
|
Excised tumor
|
tissue: Xenograft
transplant generation: 1
patient.number: 7
ethicity: A
established.from.pre.treatment..i....post.treatment..p..or.metastatic..m.: I
patient.nodal.status: N
lung.metastasis.in.mice: Y
er.ihc: N
pr.ihc: N
her2.status: N
pam50.intrinsic.subtype: B
ck19.ihc: P
p53.ihc: N
ck.5.6.ihc: P
egfr.ihc: P
|
|
| Sample_geo_accession | GSM1123803
| | Sample_status | Public on May 30 2013
| | Sample_submission_date | Apr 16 2013
| | Sample_last_update_date | May 30 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor fragments were excised and frozen at -80C prior to RNA extraction
| | Sample_growth_protocol_ch1 | Patient-derived xenografts are grown by transplantation into the epithelium-free mammary fat pad of recipient SCID/Bg mice. Transplantation was performed without intervening culture in vitro or experimental manipulation of any kind
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNeasy mini kit was used for RNA extraction and purification , according to manufacturer's protocols.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix IVT and labeling protocol was used with Enzo IVT labeling reagents followed by Affymetrix cleanup columns, according to manufacturer's protocols
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix genechip scanner protocol
| | Sample_data_processing | data were analyzed in R using the GCRMA R package with defaults
| | Sample_platform_id | GPL570
| | Sample_contact_name | Chad,A.,Shaw
| | Sample_contact_email | cashaw@bcm.edu
| | Sample_contact_phone | 7137988087
| | Sample_contact_laboratory | Shaw
| | Sample_contact_department | Molecular and Human Genetics
| | Sample_contact_institute | BCM
| | Sample_contact_address | 1 Baylor Plaza
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1123nnn/GSM1123803/suppl/GSM1123803_3613TG1_U133plus2.CEL.gz
| | Sample_series_id | GSE46106
| | Sample_data_row_count | 54675
| | |
|
GSM1123804 | GPL570 |
|
3613TG5_U133plus2
|
Excised tumor
|
tissue: Xenograft
transplant generation: 5
patient.number: 8
ethicity: H
established.from.pre.treatment..i....post.treatment..p..or.metastatic..m.: P
patient.nodal.status: P
lung.metastasis.in.mice: Y
er.ihc: N
pr.ihc: N
her2.status: N
pam50.intrinsic.subtype: B
ck19.ihc: N
p53.ihc: N
ck.5.6.ihc: N
egfr.ihc: N
|
|
| Sample_geo_accession | GSM1123804
| | Sample_status | Public on May 30 2013
| | Sample_submission_date | Apr 16 2013
| | Sample_last_update_date | May 30 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor fragments were excised and frozen at -80C prior to RNA extraction
| | Sample_growth_protocol_ch1 | Patient-derived xenografts are grown by transplantation into the epithelium-free mammary fat pad of recipient SCID/Bg mice. Transplantation was performed without intervening culture in vitro or experimental manipulation of any kind
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNeasy mini kit was used for RNA extraction and purification , according to manufacturer's protocols.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix IVT and labeling protocol was used with Enzo IVT labeling reagents followed by Affymetrix cleanup columns, according to manufacturer's protocols
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix genechip scanner protocol
| | Sample_data_processing | data were analyzed in R using the GCRMA R package with defaults
| | Sample_platform_id | GPL570
| | Sample_contact_name | Chad,A.,Shaw
| | Sample_contact_email | cashaw@bcm.edu
| | Sample_contact_phone | 7137988087
| | Sample_contact_laboratory | Shaw
| | Sample_contact_department | Molecular and Human Genetics
| | Sample_contact_institute | BCM
| | Sample_contact_address | 1 Baylor Plaza
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1123nnn/GSM1123804/suppl/GSM1123804_3613TG5_U133plus2.CEL.gz
| | Sample_series_id | GSE46106
| | Sample_data_row_count | 54675
| | |
|
GSM1123805 | GPL570 |
|
3807TG1_U133plus2
|
Excised tumor
|
tissue: Xenograft
transplant generation: 1
patient.number: 8
ethicity: H
established.from.pre.treatment..i....post.treatment..p..or.metastatic..m.: P
patient.nodal.status: P
lung.metastasis.in.mice: Y
er.ihc: N
pr.ihc: N
her2.status: N
pam50.intrinsic.subtype: B
ck19.ihc: N
p53.ihc: N
ck.5.6.ihc: N
egfr.ihc: N
|
|
| Sample_geo_accession | GSM1123805
| | Sample_status | Public on May 30 2013
| | Sample_submission_date | Apr 16 2013
| | Sample_last_update_date | May 30 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor fragments were excised and frozen at -80C prior to RNA extraction
| | Sample_growth_protocol_ch1 | Patient-derived xenografts are grown by transplantation into the epithelium-free mammary fat pad of recipient SCID/Bg mice. Transplantation was performed without intervening culture in vitro or experimental manipulation of any kind
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNeasy mini kit was used for RNA extraction and purification , according to manufacturer's protocols.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix IVT and labeling protocol was used with Enzo IVT labeling reagents followed by Affymetrix cleanup columns, according to manufacturer's protocols
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix genechip scanner protocol
| | Sample_data_processing | data were analyzed in R using the GCRMA R package with defaults
| | Sample_platform_id | GPL570
| | Sample_contact_name | Chad,A.,Shaw
| | Sample_contact_email | cashaw@bcm.edu
| | Sample_contact_phone | 7137988087
| | Sample_contact_laboratory | Shaw
| | Sample_contact_department | Molecular and Human Genetics
| | Sample_contact_institute | BCM
| | Sample_contact_address | 1 Baylor Plaza
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1123nnn/GSM1123805/suppl/GSM1123805_3807TG1_U133plus2.CEL.gz
| | Sample_series_id | GSE46106
| | Sample_data_row_count | 54675
| | |
|
GSM1123806 | GPL570 |
|
3807TG5_U133plus2
|
Excised tumor
|
tissue: Xenograft
transplant generation: 5
patient.number: 9
ethicity: H
established.from.pre.treatment..i....post.treatment..p..or.metastatic..m.: I
patient.nodal.status: N
lung.metastasis.in.mice: N
er.ihc: N
pr.ihc: N
her2.status: N
pam50.intrinsic.subtype: B
ck19.ihc: N
p53.ihc: N
ck.5.6.ihc: P
egfr.ihc: P
|
|
| Sample_geo_accession | GSM1123806
| | Sample_status | Public on May 30 2013
| | Sample_submission_date | Apr 16 2013
| | Sample_last_update_date | May 30 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor fragments were excised and frozen at -80C prior to RNA extraction
| | Sample_growth_protocol_ch1 | Patient-derived xenografts are grown by transplantation into the epithelium-free mammary fat pad of recipient SCID/Bg mice. Transplantation was performed without intervening culture in vitro or experimental manipulation of any kind
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNeasy mini kit was used for RNA extraction and purification , according to manufacturer's protocols.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix IVT and labeling protocol was used with Enzo IVT labeling reagents followed by Affymetrix cleanup columns, according to manufacturer's protocols
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix genechip scanner protocol
| | Sample_data_processing | data were analyzed in R using the GCRMA R package with defaults
| | Sample_platform_id | GPL570
| | Sample_contact_name | Chad,A.,Shaw
| | Sample_contact_email | cashaw@bcm.edu
| | Sample_contact_phone | 7137988087
| | Sample_contact_laboratory | Shaw
| | Sample_contact_department | Molecular and Human Genetics
| | Sample_contact_institute | BCM
| | Sample_contact_address | 1 Baylor Plaza
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1123nnn/GSM1123806/suppl/GSM1123806_3807TG5_U133plus2.CEL.gz
| | Sample_series_id | GSE46106
| | Sample_data_row_count | 54675
| | |
|
GSM1123807 | GPL570 |
|
3824TG2_U133plus2
|
Excised tumor
|
tissue: Xenograft
transplant generation: 2
patient.number: 9
ethicity: H
established.from.pre.treatment..i....post.treatment..p..or.metastatic..m.: I
patient.nodal.status: N
lung.metastasis.in.mice: N
er.ihc: N
pr.ihc: N
her2.status: N
pam50.intrinsic.subtype: B
ck19.ihc: N
p53.ihc: N
ck.5.6.ihc: P
egfr.ihc: P
|
|
| Sample_geo_accession | GSM1123807
| | Sample_status | Public on May 30 2013
| | Sample_submission_date | Apr 16 2013
| | Sample_last_update_date | May 30 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor fragments were excised and frozen at -80C prior to RNA extraction
| | Sample_growth_protocol_ch1 | Patient-derived xenografts are grown by transplantation into the epithelium-free mammary fat pad of recipient SCID/Bg mice. Transplantation was performed without intervening culture in vitro or experimental manipulation of any kind
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNeasy mini kit was used for RNA extraction and purification , according to manufacturer's protocols.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix IVT and labeling protocol was used with Enzo IVT labeling reagents followed by Affymetrix cleanup columns, according to manufacturer's protocols
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix genechip scanner protocol
| | Sample_data_processing | data were analyzed in R using the GCRMA R package with defaults
| | Sample_platform_id | GPL570
| | Sample_contact_name | Chad,A.,Shaw
| | Sample_contact_email | cashaw@bcm.edu
| | Sample_contact_phone | 7137988087
| | Sample_contact_laboratory | Shaw
| | Sample_contact_department | Molecular and Human Genetics
| | Sample_contact_institute | BCM
| | Sample_contact_address | 1 Baylor Plaza
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1123nnn/GSM1123807/suppl/GSM1123807_3824TG2_U133plus2.CEL.gz
| | Sample_series_id | GSE46106
| | Sample_data_row_count | 54675
| | |
|
GSM1123808 | GPL570 |
|
3887TG1_U133plus2
|
Excised tumor
|
tissue: Xenograft
transplant generation: 1
patient.number: 9
ethicity: H
established.from.pre.treatment..i....post.treatment..p..or.metastatic..m.: P
patient.nodal.status: N
lung.metastasis.in.mice: N
er.ihc: N
pr.ihc: N
her2.status: N
pam50.intrinsic.subtype: B
ck19.ihc: N
p53.ihc: N
ck.5.6.ihc: P
egfr.ihc: P
|
|
| Sample_geo_accession | GSM1123808
| | Sample_status | Public on May 30 2013
| | Sample_submission_date | Apr 16 2013
| | Sample_last_update_date | May 30 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor fragments were excised and frozen at -80C prior to RNA extraction
| | Sample_growth_protocol_ch1 | Patient-derived xenografts are grown by transplantation into the epithelium-free mammary fat pad of recipient SCID/Bg mice. Transplantation was performed without intervening culture in vitro or experimental manipulation of any kind
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNeasy mini kit was used for RNA extraction and purification , according to manufacturer's protocols.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix IVT and labeling protocol was used with Enzo IVT labeling reagents followed by Affymetrix cleanup columns, according to manufacturer's protocols
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix genechip scanner protocol
| | Sample_data_processing | data were analyzed in R using the GCRMA R package with defaults
| | Sample_platform_id | GPL570
| | Sample_contact_name | Chad,A.,Shaw
| | Sample_contact_email | cashaw@bcm.edu
| | Sample_contact_phone | 7137988087
| | Sample_contact_laboratory | Shaw
| | Sample_contact_department | Molecular and Human Genetics
| | Sample_contact_institute | BCM
| | Sample_contact_address | 1 Baylor Plaza
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1123nnn/GSM1123808/suppl/GSM1123808_3887TG1_U133plus2.CEL.gz
| | Sample_series_id | GSE46106
| | Sample_data_row_count | 54675
| | |
|
GSM1123809 | GPL570 |
|
3887TG5_U133plus2
|
Excised tumor
|
tissue: Xenograft
transplant generation: 5
patient.number: 9
ethicity: H
established.from.pre.treatment..i....post.treatment..p..or.metastatic..m.: P
patient.nodal.status: N
lung.metastasis.in.mice: N
er.ihc: N
pr.ihc: N
her2.status: N
pam50.intrinsic.subtype: B
ck19.ihc: N
p53.ihc: N
ck.5.6.ihc: P
egfr.ihc: P
|
|
| Sample_geo_accession | GSM1123809
| | Sample_status | Public on May 30 2013
| | Sample_submission_date | Apr 16 2013
| | Sample_last_update_date | May 30 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor fragments were excised and frozen at -80C prior to RNA extraction
| | Sample_growth_protocol_ch1 | Patient-derived xenografts are grown by transplantation into the epithelium-free mammary fat pad of recipient SCID/Bg mice. Transplantation was performed without intervening culture in vitro or experimental manipulation of any kind
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNeasy mini kit was used for RNA extraction and purification , according to manufacturer's protocols.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix IVT and labeling protocol was used with Enzo IVT labeling reagents followed by Affymetrix cleanup columns, according to manufacturer's protocols
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix genechip scanner protocol
| | Sample_data_processing | data were analyzed in R using the GCRMA R package with defaults
| | Sample_platform_id | GPL570
| | Sample_contact_name | Chad,A.,Shaw
| | Sample_contact_email | cashaw@bcm.edu
| | Sample_contact_phone | 7137988087
| | Sample_contact_laboratory | Shaw
| | Sample_contact_department | Molecular and Human Genetics
| | Sample_contact_institute | BCM
| | Sample_contact_address | 1 Baylor Plaza
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1123nnn/GSM1123809/suppl/GSM1123809_3887TG5_U133plus2.CEL.gz
| | Sample_series_id | GSE46106
| | Sample_data_row_count | 54675
| | |
|
GSM1123810 | GPL570 |
|
3904TG1_U133plus2
|
Excised tumor
|
tissue: Xenograft
transplant generation: 1
patient.number: 10
ethicity: H
established.from.pre.treatment..i....post.treatment..p..or.metastatic..m.: I
patient.nodal.status: N
lung.metastasis.in.mice: Y
er.ihc: N
pr.ihc: N
her2.status: N
pam50.intrinsic.subtype: B
ck19.ihc: P
p53.ihc: P
ck.5.6.ihc: P
egfr.ihc: N
|
|
| Sample_geo_accession | GSM1123810
| | Sample_status | Public on May 30 2013
| | Sample_submission_date | Apr 16 2013
| | Sample_last_update_date | May 30 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor fragments were excised and frozen at -80C prior to RNA extraction
| | Sample_growth_protocol_ch1 | Patient-derived xenografts are grown by transplantation into the epithelium-free mammary fat pad of recipient SCID/Bg mice. Transplantation was performed without intervening culture in vitro or experimental manipulation of any kind
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNeasy mini kit was used for RNA extraction and purification , according to manufacturer's protocols.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix IVT and labeling protocol was used with Enzo IVT labeling reagents followed by Affymetrix cleanup columns, according to manufacturer's protocols
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix genechip scanner protocol
| | Sample_data_processing | data were analyzed in R using the GCRMA R package with defaults
| | Sample_platform_id | GPL570
| | Sample_contact_name | Chad,A.,Shaw
| | Sample_contact_email | cashaw@bcm.edu
| | Sample_contact_phone | 7137988087
| | Sample_contact_laboratory | Shaw
| | Sample_contact_department | Molecular and Human Genetics
| | Sample_contact_institute | BCM
| | Sample_contact_address | 1 Baylor Plaza
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1123nnn/GSM1123810/suppl/GSM1123810_3904TG1_U133plus2.CEL.gz
| | Sample_series_id | GSE46106
| | Sample_data_row_count | 54675
| | |
|
GSM1123811 | GPL570 |
|
3904TG5_U133plus2
|
Excised tumor
|
tissue: Xenograft
transplant generation: 5
patient.number: 10
ethicity: H
established.from.pre.treatment..i....post.treatment..p..or.metastatic..m.: I
patient.nodal.status: N
lung.metastasis.in.mice: Y
er.ihc: N
pr.ihc: N
her2.status: N
pam50.intrinsic.subtype: B
ck19.ihc: P
p53.ihc: P
ck.5.6.ihc: P
egfr.ihc: N
|
|
| Sample_geo_accession | GSM1123811
| | Sample_status | Public on May 30 2013
| | Sample_submission_date | Apr 16 2013
| | Sample_last_update_date | May 30 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor fragments were excised and frozen at -80C prior to RNA extraction
| | Sample_growth_protocol_ch1 | Patient-derived xenografts are grown by transplantation into the epithelium-free mammary fat pad of recipient SCID/Bg mice. Transplantation was performed without intervening culture in vitro or experimental manipulation of any kind
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNeasy mini kit was used for RNA extraction and purification , according to manufacturer's protocols.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix IVT and labeling protocol was used with Enzo IVT labeling reagents followed by Affymetrix cleanup columns, according to manufacturer's protocols
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix genechip scanner protocol
| | Sample_data_processing | data were analyzed in R using the GCRMA R package with defaults
| | Sample_platform_id | GPL570
| | Sample_contact_name | Chad,A.,Shaw
| | Sample_contact_email | cashaw@bcm.edu
| | Sample_contact_phone | 7137988087
| | Sample_contact_laboratory | Shaw
| | Sample_contact_department | Molecular and Human Genetics
| | Sample_contact_institute | BCM
| | Sample_contact_address | 1 Baylor Plaza
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1123nnn/GSM1123811/suppl/GSM1123811_3904TG5_U133plus2.CEL.gz
| | Sample_series_id | GSE46106
| | Sample_data_row_count | 54675
| | |
|
GSM1123812 | GPL570 |
|
3936TG1_U133plus2
|
Excised tumor
|
tissue: Xenograft
transplant generation: 1
patient.number: 11
ethicity: H
established.from.pre.treatment..i....post.treatment..p..or.metastatic..m.: P
patient.nodal.status: N
lung.metastasis.in.mice: N
er.ihc: N
pr.ihc: N
her2.status: N
pam50.intrinsic.subtype: H
ck19.ihc: P
p53.ihc: N
ck.5.6.ihc: N
egfr.ihc: N
|
|
| Sample_geo_accession | GSM1123812
| | Sample_status | Public on May 30 2013
| | Sample_submission_date | Apr 16 2013
| | Sample_last_update_date | May 30 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor fragments were excised and frozen at -80C prior to RNA extraction
| | Sample_growth_protocol_ch1 | Patient-derived xenografts are grown by transplantation into the epithelium-free mammary fat pad of recipient SCID/Bg mice. Transplantation was performed without intervening culture in vitro or experimental manipulation of any kind
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNeasy mini kit was used for RNA extraction and purification , according to manufacturer's protocols.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix IVT and labeling protocol was used with Enzo IVT labeling reagents followed by Affymetrix cleanup columns, according to manufacturer's protocols
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix genechip scanner protocol
| | Sample_data_processing | data were analyzed in R using the GCRMA R package with defaults
| | Sample_platform_id | GPL570
| | Sample_contact_name | Chad,A.,Shaw
| | Sample_contact_email | cashaw@bcm.edu
| | Sample_contact_phone | 7137988087
| | Sample_contact_laboratory | Shaw
| | Sample_contact_department | Molecular and Human Genetics
| | Sample_contact_institute | BCM
| | Sample_contact_address | 1 Baylor Plaza
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1123nnn/GSM1123812/suppl/GSM1123812_3936TG1_U133plus2.CEL.gz
| | Sample_series_id | GSE46106
| | Sample_data_row_count | 54675
| | |
|
GSM1123813 | GPL570 |
|
3936TG5_U133plus2
|
Excised tumor
|
tissue: Xenograft
transplant generation: 5
patient.number: 12
ethicity: H
established.from.pre.treatment..i....post.treatment..p..or.metastatic..m.: I
patient.nodal.status: P
lung.metastasis.in.mice: Y
er.ihc: N
pr.ihc: N
her2.status: P
pam50.intrinsic.subtype: H
ck19.ihc: P
p53.ihc: P
ck.5.6.ihc: N
egfr.ihc: N
|
|
| Sample_geo_accession | GSM1123813
| | Sample_status | Public on May 30 2013
| | Sample_submission_date | Apr 16 2013
| | Sample_last_update_date | May 30 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor fragments were excised and frozen at -80C prior to RNA extraction
| | Sample_growth_protocol_ch1 | Patient-derived xenografts are grown by transplantation into the epithelium-free mammary fat pad of recipient SCID/Bg mice. Transplantation was performed without intervening culture in vitro or experimental manipulation of any kind
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNeasy mini kit was used for RNA extraction and purification , according to manufacturer's protocols.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix IVT and labeling protocol was used with Enzo IVT labeling reagents followed by Affymetrix cleanup columns, according to manufacturer's protocols
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix genechip scanner protocol
| | Sample_data_processing | data were analyzed in R using the GCRMA R package with defaults
| | Sample_platform_id | GPL570
| | Sample_contact_name | Chad,A.,Shaw
| | Sample_contact_email | cashaw@bcm.edu
| | Sample_contact_phone | 7137988087
| | Sample_contact_laboratory | Shaw
| | Sample_contact_department | Molecular and Human Genetics
| | Sample_contact_institute | BCM
| | Sample_contact_address | 1 Baylor Plaza
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1123nnn/GSM1123813/suppl/GSM1123813_3936TG5_U133plus2.CEL.gz
| | Sample_series_id | GSE46106
| | Sample_data_row_count | 54675
| | |
|
GSM1123814 | GPL570 |
|
3963TG1_U133plus2
|
Excised tumor
|
tissue: Xenograft
transplant generation: 1
patient.number: 12
ethicity: H
established.from.pre.treatment..i....post.treatment..p..or.metastatic..m.: I
patient.nodal.status: P
lung.metastasis.in.mice: Y
er.ihc: N
pr.ihc: N
her2.status: P
pam50.intrinsic.subtype: H
ck19.ihc: P
p53.ihc: P
ck.5.6.ihc: N
egfr.ihc: N
|
|
| Sample_geo_accession | GSM1123814
| | Sample_status | Public on May 30 2013
| | Sample_submission_date | Apr 16 2013
| | Sample_last_update_date | May 30 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor fragments were excised and frozen at -80C prior to RNA extraction
| | Sample_growth_protocol_ch1 | Patient-derived xenografts are grown by transplantation into the epithelium-free mammary fat pad of recipient SCID/Bg mice. Transplantation was performed without intervening culture in vitro or experimental manipulation of any kind
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNeasy mini kit was used for RNA extraction and purification , according to manufacturer's protocols.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix IVT and labeling protocol was used with Enzo IVT labeling reagents followed by Affymetrix cleanup columns, according to manufacturer's protocols
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix genechip scanner protocol
| | Sample_data_processing | data were analyzed in R using the GCRMA R package with defaults
| | Sample_platform_id | GPL570
| | Sample_contact_name | Chad,A.,Shaw
| | Sample_contact_email | cashaw@bcm.edu
| | Sample_contact_phone | 7137988087
| | Sample_contact_laboratory | Shaw
| | Sample_contact_department | Molecular and Human Genetics
| | Sample_contact_institute | BCM
| | Sample_contact_address | 1 Baylor Plaza
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1123nnn/GSM1123814/suppl/GSM1123814_3963TG1_U133plus2.CEL.gz
| | Sample_series_id | GSE46106
| | Sample_data_row_count | 54675
| | |
|
GSM1123815 | GPL570 |
|
3963TG5_U133plus2
|
Excised tumor
|
tissue: Xenograft
transplant generation: 5
patient.number: 12
ethicity: H
established.from.pre.treatment..i....post.treatment..p..or.metastatic..m.: P
patient.nodal.status: P
lung.metastasis.in.mice: Y
er.ihc: N
pr.ihc: N
her2.status: P
pam50.intrinsic.subtype: H
ck19.ihc: P
p53.ihc: P
ck.5.6.ihc: N
egfr.ihc: N
|
|
| Sample_geo_accession | GSM1123815
| | Sample_status | Public on May 30 2013
| | Sample_submission_date | Apr 16 2013
| | Sample_last_update_date | May 30 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor fragments were excised and frozen at -80C prior to RNA extraction
| | Sample_growth_protocol_ch1 | Patient-derived xenografts are grown by transplantation into the epithelium-free mammary fat pad of recipient SCID/Bg mice. Transplantation was performed without intervening culture in vitro or experimental manipulation of any kind
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNeasy mini kit was used for RNA extraction and purification , according to manufacturer's protocols.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix IVT and labeling protocol was used with Enzo IVT labeling reagents followed by Affymetrix cleanup columns, according to manufacturer's protocols
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix genechip scanner protocol
| | Sample_data_processing | data were analyzed in R using the GCRMA R package with defaults
| | Sample_platform_id | GPL570
| | Sample_contact_name | Chad,A.,Shaw
| | Sample_contact_email | cashaw@bcm.edu
| | Sample_contact_phone | 7137988087
| | Sample_contact_laboratory | Shaw
| | Sample_contact_department | Molecular and Human Genetics
| | Sample_contact_institute | BCM
| | Sample_contact_address | 1 Baylor Plaza
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1123nnn/GSM1123815/suppl/GSM1123815_3963TG5_U133plus2.CEL.gz
| | Sample_series_id | GSE46106
| | Sample_data_row_count | 54675
| | |
|
GSM1123816 | GPL570 |
|
4013TG1_U133plus2
|
Excised tumor
|
tissue: Xenograft
transplant generation: 1
patient.number: 14
ethicity: C
established.from.pre.treatment..i....post.treatment..p..or.metastatic..m.: I
patient.nodal.status: P
lung.metastasis.in.mice: Y
er.ihc: N
pr.ihc: N
her2.status: N
pam50.intrinsic.subtype: B
ck19.ihc: P
p53.ihc: N
ck.5.6.ihc: P
egfr.ihc: P
|
|
| Sample_geo_accession | GSM1123816
| | Sample_status | Public on May 30 2013
| | Sample_submission_date | Apr 16 2013
| | Sample_last_update_date | May 30 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor fragments were excised and frozen at -80C prior to RNA extraction
| | Sample_growth_protocol_ch1 | Patient-derived xenografts are grown by transplantation into the epithelium-free mammary fat pad of recipient SCID/Bg mice. Transplantation was performed without intervening culture in vitro or experimental manipulation of any kind
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNeasy mini kit was used for RNA extraction and purification , according to manufacturer's protocols.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix IVT and labeling protocol was used with Enzo IVT labeling reagents followed by Affymetrix cleanup columns, according to manufacturer's protocols
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix genechip scanner protocol
| | Sample_data_processing | data were analyzed in R using the GCRMA R package with defaults
| | Sample_platform_id | GPL570
| | Sample_contact_name | Chad,A.,Shaw
| | Sample_contact_email | cashaw@bcm.edu
| | Sample_contact_phone | 7137988087
| | Sample_contact_laboratory | Shaw
| | Sample_contact_department | Molecular and Human Genetics
| | Sample_contact_institute | BCM
| | Sample_contact_address | 1 Baylor Plaza
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1123nnn/GSM1123816/suppl/GSM1123816_4013TG1_U133plus2.CEL.gz
| | Sample_series_id | GSE46106
| | Sample_data_row_count | 54675
| | |
|
GSM1123817 | GPL570 |
|
4169TG2_U133plus2
|
Excised tumor
|
tissue: Xenograft
transplant generation: 2
patient.number: 15
ethicity: H
established.from.pre.treatment..i....post.treatment..p..or.metastatic..m.: I
patient.nodal.status: P
lung.metastasis.in.mice: Y
er.ihc: N
pr.ihc: N
her2.status: N
pam50.intrinsic.subtype: B
ck19.ihc: P
p53.ihc: N
ck.5.6.ihc: P
egfr.ihc: P
|
|
| Sample_geo_accession | GSM1123817
| | Sample_status | Public on May 30 2013
| | Sample_submission_date | Apr 16 2013
| | Sample_last_update_date | May 30 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor fragments were excised and frozen at -80C prior to RNA extraction
| | Sample_growth_protocol_ch1 | Patient-derived xenografts are grown by transplantation into the epithelium-free mammary fat pad of recipient SCID/Bg mice. Transplantation was performed without intervening culture in vitro or experimental manipulation of any kind
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNeasy mini kit was used for RNA extraction and purification , according to manufacturer's protocols.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix IVT and labeling protocol was used with Enzo IVT labeling reagents followed by Affymetrix cleanup columns, according to manufacturer's protocols
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix genechip scanner protocol
| | Sample_data_processing | data were analyzed in R using the GCRMA R package with defaults
| | Sample_platform_id | GPL570
| | Sample_contact_name | Chad,A.,Shaw
| | Sample_contact_email | cashaw@bcm.edu
| | Sample_contact_phone | 7137988087
| | Sample_contact_laboratory | Shaw
| | Sample_contact_department | Molecular and Human Genetics
| | Sample_contact_institute | BCM
| | Sample_contact_address | 1 Baylor Plaza
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1123nnn/GSM1123817/suppl/GSM1123817_4169TG2_U133plus2.CEL.gz
| | Sample_series_id | GSE46106
| | Sample_data_row_count | 54675
| | |
|
GSM1123818 | GPL570 |
|
4175TG1_U133plus2
|
Excised tumor
|
tissue: Xenograft
transplant generation: 1
patient.number: 15
ethicity: H
established.from.pre.treatment..i....post.treatment..p..or.metastatic..m.: P
patient.nodal.status: P
lung.metastasis.in.mice: N
er.ihc: N
pr.ihc: N
her2.status: N
pam50.intrinsic.subtype: B
ck19.ihc: P
p53.ihc: N
ck.5.6.ihc: P
egfr.ihc: P
|
|
| Sample_geo_accession | GSM1123818
| | Sample_status | Public on May 30 2013
| | Sample_submission_date | Apr 16 2013
| | Sample_last_update_date | May 30 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor fragments were excised and frozen at -80C prior to RNA extraction
| | Sample_growth_protocol_ch1 | Patient-derived xenografts are grown by transplantation into the epithelium-free mammary fat pad of recipient SCID/Bg mice. Transplantation was performed without intervening culture in vitro or experimental manipulation of any kind
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNeasy mini kit was used for RNA extraction and purification , according to manufacturer's protocols.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix IVT and labeling protocol was used with Enzo IVT labeling reagents followed by Affymetrix cleanup columns, according to manufacturer's protocols
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix genechip scanner protocol
| | Sample_data_processing | data were analyzed in R using the GCRMA R package with defaults
| | Sample_platform_id | GPL570
| | Sample_contact_name | Chad,A.,Shaw
| | Sample_contact_email | cashaw@bcm.edu
| | Sample_contact_phone | 7137988087
| | Sample_contact_laboratory | Shaw
| | Sample_contact_department | Molecular and Human Genetics
| | Sample_contact_institute | BCM
| | Sample_contact_address | 1 Baylor Plaza
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1123nnn/GSM1123818/suppl/GSM1123818_4175TG1_U133plus2.CEL.gz
| | Sample_series_id | GSE46106
| | Sample_data_row_count | 54675
| | |
|
GSM1123819 | GPL570 |
|
4272TG1_U133plus2
|
Excised tumor
|
tissue: Xenograft
transplant generation: 1
patient.number: 16
ethicity: A
established.from.pre.treatment..i....post.treatment..p..or.metastatic..m.: I
patient.nodal.status: P
lung.metastasis.in.mice: N
er.ihc: N
pr.ihc: N
her2.status: N
pam50.intrinsic.subtype: B
ck19.ihc: P
p53.ihc: N
ck.5.6.ihc: N
egfr.ihc: P
|
|
| Sample_geo_accession | GSM1123819
| | Sample_status | Public on May 30 2013
| | Sample_submission_date | Apr 16 2013
| | Sample_last_update_date | May 30 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor fragments were excised and frozen at -80C prior to RNA extraction
| | Sample_growth_protocol_ch1 | Patient-derived xenografts are grown by transplantation into the epithelium-free mammary fat pad of recipient SCID/Bg mice. Transplantation was performed without intervening culture in vitro or experimental manipulation of any kind
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNeasy mini kit was used for RNA extraction and purification , according to manufacturer's protocols.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix IVT and labeling protocol was used with Enzo IVT labeling reagents followed by Affymetrix cleanup columns, according to manufacturer's protocols
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix genechip scanner protocol
| | Sample_data_processing | data were analyzed in R using the GCRMA R package with defaults
| | Sample_platform_id | GPL570
| | Sample_contact_name | Chad,A.,Shaw
| | Sample_contact_email | cashaw@bcm.edu
| | Sample_contact_phone | 7137988087
| | Sample_contact_laboratory | Shaw
| | Sample_contact_department | Molecular and Human Genetics
| | Sample_contact_institute | BCM
| | Sample_contact_address | 1 Baylor Plaza
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1123nnn/GSM1123819/suppl/GSM1123819_4272TG1_U133plus2.CEL.gz
| | Sample_series_id | GSE46106
| | Sample_data_row_count | 54675
| | |
|
GSM1123820 | GPL570 |
|
4400TG1_U133plus2
|
Excised tumor
|
tissue: Xenograft
transplant generation: 1
patient.number: 17
ethicity: A
established.from.pre.treatment..i....post.treatment..p..or.metastatic..m.: P
patient.nodal.status: P
lung.metastasis.in.mice: N
er.ihc: N
pr.ihc: N
her2.status: N
pam50.intrinsic.subtype: B
ck19.ihc: P
p53.ihc: N
ck.5.6.ihc: N
egfr.ihc: P
|
|
| Sample_geo_accession | GSM1123820
| | Sample_status | Public on May 30 2013
| | Sample_submission_date | Apr 16 2013
| | Sample_last_update_date | May 30 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor fragments were excised and frozen at -80C prior to RNA extraction
| | Sample_growth_protocol_ch1 | Patient-derived xenografts are grown by transplantation into the epithelium-free mammary fat pad of recipient SCID/Bg mice. Transplantation was performed without intervening culture in vitro or experimental manipulation of any kind
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNeasy mini kit was used for RNA extraction and purification , according to manufacturer's protocols.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix IVT and labeling protocol was used with Enzo IVT labeling reagents followed by Affymetrix cleanup columns, according to manufacturer's protocols
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix genechip scanner protocol
| | Sample_data_processing | data were analyzed in R using the GCRMA R package with defaults
| | Sample_platform_id | GPL570
| | Sample_contact_name | Chad,A.,Shaw
| | Sample_contact_email | cashaw@bcm.edu
| | Sample_contact_phone | 7137988087
| | Sample_contact_laboratory | Shaw
| | Sample_contact_department | Molecular and Human Genetics
| | Sample_contact_institute | BCM
| | Sample_contact_address | 1 Baylor Plaza
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1123nnn/GSM1123820/suppl/GSM1123820_4400TG1_U133plus2.CEL.gz
| | Sample_series_id | GSE46106
| | Sample_data_row_count | 54675
| | |
|
GSM1123821 | GPL570 |
|
4400TG5_U133plus2
|
Excised tumor
|
tissue: Xenograft
transplant generation: 5
patient.number: 18
ethicity: H
established.from.pre.treatment..i....post.treatment..p..or.metastatic..m.: P
patient.nodal.status: P
lung.metastasis.in.mice: Y
er.ihc: P
pr.ihc: P
her2.status: P
pam50.intrinsic.subtype: H
ck19.ihc: P
p53.ihc: P
ck.5.6.ihc: N
egfr.ihc: N
|
|
| Sample_geo_accession | GSM1123821
| | Sample_status | Public on May 30 2013
| | Sample_submission_date | Apr 16 2013
| | Sample_last_update_date | May 30 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor fragments were excised and frozen at -80C prior to RNA extraction
| | Sample_growth_protocol_ch1 | Patient-derived xenografts are grown by transplantation into the epithelium-free mammary fat pad of recipient SCID/Bg mice. Transplantation was performed without intervening culture in vitro or experimental manipulation of any kind
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNeasy mini kit was used for RNA extraction and purification , according to manufacturer's protocols.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix IVT and labeling protocol was used with Enzo IVT labeling reagents followed by Affymetrix cleanup columns, according to manufacturer's protocols
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix genechip scanner protocol
| | Sample_data_processing | data were analyzed in R using the GCRMA R package with defaults
| | Sample_platform_id | GPL570
| | Sample_contact_name | Chad,A.,Shaw
| | Sample_contact_email | cashaw@bcm.edu
| | Sample_contact_phone | 7137988087
| | Sample_contact_laboratory | Shaw
| | Sample_contact_department | Molecular and Human Genetics
| | Sample_contact_institute | BCM
| | Sample_contact_address | 1 Baylor Plaza
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1123nnn/GSM1123821/suppl/GSM1123821_4400TG5_U133plus2.CEL.gz
| | Sample_series_id | GSE46106
| | Sample_data_row_count | 54675
| | |
|
GSM1123822 | GPL570 |
|
4664TG1_U133plus2
|
Excised tumor
|
tissue: Xenograft
transplant generation: 1
patient.number: 23
ethicity: H
established.from.pre.treatment..i....post.treatment..p..or.metastatic..m.: M
patient.nodal.status: NR
lung.metastasis.in.mice: Y
er.ihc: N
pr.ihc: N
her2.status: P
pam50.intrinsic.subtype: H
ck19.ihc: P
p53.ihc: P
ck.5.6.ihc: N
egfr.ihc: N
|
|
| Sample_geo_accession | GSM1123822
| | Sample_status | Public on May 30 2013
| | Sample_submission_date | Apr 16 2013
| | Sample_last_update_date | May 30 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor fragments were excised and frozen at -80C prior to RNA extraction
| | Sample_growth_protocol_ch1 | Patient-derived xenografts are grown by transplantation into the epithelium-free mammary fat pad of recipient SCID/Bg mice. Transplantation was performed without intervening culture in vitro or experimental manipulation of any kind
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNeasy mini kit was used for RNA extraction and purification , according to manufacturer's protocols.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix IVT and labeling protocol was used with Enzo IVT labeling reagents followed by Affymetrix cleanup columns, according to manufacturer's protocols
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix genechip scanner protocol
| | Sample_data_processing | data were analyzed in R using the GCRMA R package with defaults
| | Sample_platform_id | GPL570
| | Sample_contact_name | Chad,A.,Shaw
| | Sample_contact_email | cashaw@bcm.edu
| | Sample_contact_phone | 7137988087
| | Sample_contact_laboratory | Shaw
| | Sample_contact_department | Molecular and Human Genetics
| | Sample_contact_institute | BCM
| | Sample_contact_address | 1 Baylor Plaza
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1123nnn/GSM1123822/suppl/GSM1123822_4664TG1_U133plus2.CEL.gz
| | Sample_series_id | GSE46106
| | Sample_data_row_count | 54675
| | |
|
GSM1123823 | GPL570 |
|
4849TG1_U133plus2
|
Excised tumor
|
tissue: Xenograft
transplant generation: 1
patient.number: 23
ethicity: H
established.from.pre.treatment..i....post.treatment..p..or.metastatic..m.: M
patient.nodal.status: NR
lung.metastasis.in.mice: Y
er.ihc: N
pr.ihc: N
her2.status: P
pam50.intrinsic.subtype: H
ck19.ihc: P
p53.ihc: P
ck.5.6.ihc: N
egfr.ihc: N
|
|
| Sample_geo_accession | GSM1123823
| | Sample_status | Public on May 30 2013
| | Sample_submission_date | Apr 16 2013
| | Sample_last_update_date | May 30 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor fragments were excised and frozen at -80C prior to RNA extraction
| | Sample_growth_protocol_ch1 | Patient-derived xenografts are grown by transplantation into the epithelium-free mammary fat pad of recipient SCID/Bg mice. Transplantation was performed without intervening culture in vitro or experimental manipulation of any kind
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNeasy mini kit was used for RNA extraction and purification , according to manufacturer's protocols.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix IVT and labeling protocol was used with Enzo IVT labeling reagents followed by Affymetrix cleanup columns, according to manufacturer's protocols
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix genechip scanner protocol
| | Sample_data_processing | data were analyzed in R using the GCRMA R package with defaults
| | Sample_platform_id | GPL570
| | Sample_contact_name | Chad,A.,Shaw
| | Sample_contact_email | cashaw@bcm.edu
| | Sample_contact_phone | 7137988087
| | Sample_contact_laboratory | Shaw
| | Sample_contact_department | Molecular and Human Genetics
| | Sample_contact_institute | BCM
| | Sample_contact_address | 1 Baylor Plaza
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1123nnn/GSM1123823/suppl/GSM1123823_4849TG1_U133plus2.CEL.gz
| | Sample_series_id | GSE46106
| | Sample_data_row_count | 54675
| | |
|
GSM1123824 | GPL570 |
|
4888TG1_U133plus2
|
Excised tumor
|
tissue: Xenograft
transplant generation: 1
patient.number: 24
ethicity: C
established.from.pre.treatment..i....post.treatment..p..or.metastatic..m.: M
patient.nodal.status: N
lung.metastasis.in.mice: N
er.ihc: N
pr.ihc: N
her2.status: N
pam50.intrinsic.subtype: H
ck19.ihc: P
p53.ihc: N
ck.5.6.ihc: N
egfr.ihc: P
|
|
| Sample_geo_accession | GSM1123824
| | Sample_status | Public on May 30 2013
| | Sample_submission_date | Apr 16 2013
| | Sample_last_update_date | May 30 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor fragments were excised and frozen at -80C prior to RNA extraction
| | Sample_growth_protocol_ch1 | Patient-derived xenografts are grown by transplantation into the epithelium-free mammary fat pad of recipient SCID/Bg mice. Transplantation was performed without intervening culture in vitro or experimental manipulation of any kind
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNeasy mini kit was used for RNA extraction and purification , according to manufacturer's protocols.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix IVT and labeling protocol was used with Enzo IVT labeling reagents followed by Affymetrix cleanup columns, according to manufacturer's protocols
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix genechip scanner protocol
| | Sample_data_processing | data were analyzed in R using the GCRMA R package with defaults
| | Sample_platform_id | GPL570
| | Sample_contact_name | Chad,A.,Shaw
| | Sample_contact_email | cashaw@bcm.edu
| | Sample_contact_phone | 7137988087
| | Sample_contact_laboratory | Shaw
| | Sample_contact_department | Molecular and Human Genetics
| | Sample_contact_institute | BCM
| | Sample_contact_address | 1 Baylor Plaza
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1123nnn/GSM1123824/suppl/GSM1123824_4888TG1_U133plus2.CEL.gz
| | Sample_series_id | GSE46106
| | Sample_data_row_count | 54675
| | |
|
GSM1123825 | GPL570 |
|
4913TG1_U133plus2
|
Excised tumor
|
tissue: Xenograft
transplant generation: 1
patient.number: 24
ethicity: C
established.from.pre.treatment..i....post.treatment..p..or.metastatic..m.: M
patient.nodal.status: N
lung.metastasis.in.mice: N
er.ihc: N
pr.ihc: N
her2.status: N
pam50.intrinsic.subtype: H
ck19.ihc: P
p53.ihc: N
ck.5.6.ihc: N
egfr.ihc: P
|
|
| Sample_geo_accession | GSM1123825
| | Sample_status | Public on May 30 2013
| | Sample_submission_date | Apr 16 2013
| | Sample_last_update_date | May 30 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor fragments were excised and frozen at -80C prior to RNA extraction
| | Sample_growth_protocol_ch1 | Patient-derived xenografts are grown by transplantation into the epithelium-free mammary fat pad of recipient SCID/Bg mice. Transplantation was performed without intervening culture in vitro or experimental manipulation of any kind
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNeasy mini kit was used for RNA extraction and purification , according to manufacturer's protocols.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix IVT and labeling protocol was used with Enzo IVT labeling reagents followed by Affymetrix cleanup columns, according to manufacturer's protocols
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix genechip scanner protocol
| | Sample_data_processing | data were analyzed in R using the GCRMA R package with defaults
| | Sample_platform_id | GPL570
| | Sample_contact_name | Chad,A.,Shaw
| | Sample_contact_email | cashaw@bcm.edu
| | Sample_contact_phone | 7137988087
| | Sample_contact_laboratory | Shaw
| | Sample_contact_department | Molecular and Human Genetics
| | Sample_contact_institute | BCM
| | Sample_contact_address | 1 Baylor Plaza
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1123nnn/GSM1123825/suppl/GSM1123825_4913TG1_U133plus2.CEL.gz
| | Sample_series_id | GSE46106
| | Sample_data_row_count | 54675
| | |
|
| |
| |
Make groups for comparisons |
(2 groups will be compared at a time) |
|
| Select GSMs and click on "Add groups" |
Enter the group name here: |
|
|
|
