title: SUM149_5Gy_24h_B

description:
Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (1, 2) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms.
Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.
Cell line s149 - 35055


title: P34-T3-Tum

status: Public on Oct 31 2015

type: RNA

city: Muscat

first: Manal

middle: Humaid

last: Al Khanbashi

address: Al Khod

department: Medicine

country: Oman

institute: Sultan Qaboos University

description: Tissue Gene expression from locally advanced breast cancer tissue biopsies

hyb_protocol: Hybridization, washing, and staining were performed according to the standard protocols from Affymetrix.

scan_protocol: Arrays were scanned using the Affymetrix® GeneChip® Scanner 3000.

data_processing: Raw data analyzed in Affymetrix ExpressionConsole using method: RMA-DABG, transformation: log2. ANOVA was run initially contrasting the normal versus the tumor tissue. Then a probe list was generated from these significant results (p<0.05), filtering by differences that have a <-2 or >2 fold change.

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: Cancer breast tissue, after third chemo dose

label_protocol: A total of 500 ng of RNA was labeled using the FlashTagTM Biotin HSR RNA labeling kit from Affymatrix

growth_protocol: These are clinical samples from locally advanced breast cancer cases undergoing neo-adjuvant chemotherapy treatment

extract_protocol: Total RNA was extracted following the manufacturer protcol of  mirVana miRNA isolation kit

treatment_protocol: The first time point are tissue at diagnosis where no treatment was adminstered but the timepoint 2, 3 and 4 are after the conventional neo-adjuvant chemotherapy treatment

tag: diagnosis

value: breast cancer

tag: biopsy

value: Cancer biopsy tissue


title: SUM149_0Gy_C

city: Durham

first: Wei

last: Chen

state: NC

address: 101 Science Drive

department: Center for Genomic and Computational Biology

country: USA

institute: Duke University

description:
Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (1, 2) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms.
Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.
Cell line s149 - 35053

hyb_protocol: Hybridization of samples to Affymetrix GeneChip arrays was performed according to Affymetrix manual instructions . RNA from the cell lines was hybridized to Affymetrix U133A2.0 arrays and processed in the Duke Microarray Core facility. Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.

scan_protocol: Scanning of Affymetrix GeneChip arrays was performed according to the Affmetrix manual instructions

data_processing: The Affymetrix HG U133 A2.0 Gene Chip array interrogates mRNA expression based on 22,000 probe sets corresponding to 14,500 annotated human genes. All statistical analyses were conducted using the R statistical environment and extension packages from CRAN and the Bioconductor project. Gene expression estimates were obtained from Affymetrix arrays using the RMA algorithm. The quality of the resultant microarrays was assessed using R/Bioconductor. To check for sample outliers and batch effects, principal component analysis of the global gene expression was conducted. Batch effects were corrected by scale-shift normalization prior to analysis.

label_protocol: Affymetrix ENZO labeling kit for the cell lines (for the Affymetrix U133A2 arrays).

growth_protocol: In order to identify differences in the radiation response gene expression profiles of specific breast cancer subtypes, we exposed 16 biologically-diverse breast tumor cell lines to 0 or 5GY radiation. Microarray analysis was performed on RNA harvested from those cell lines. Microarray analysis was performed on RNA harvested from those cell lines.  Samples were run in triplicate.  Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (25, 26) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms. Cell lines growth conditions: MCF7, ZR751, MDAMB231, and SUM159 were cultured in Dulbecco's modified Eagle's medium supplemented with 10% fetal bovine serum (Hyclone, SH30071.03) and 1X Antibiotic-Antimycotic (Gibco, 15240-062).   SUM149 cells were grown in Ham's F-12 medium supplemented with 5% fetal bovine serum (Hyclone, SH30071.03), 5ug/ml Insulin (Sigma-Aldrich®, I- 5500), 1ug/ml Hydrocortisone (Sigma-Aldrich®, H-4001) and 1X Antibiotics / Antimycotic (Gibco, 15240-062). T47D cells were grown in MEM-alpha medium (Gibco, 12561) supplemented with 6% of fetal bovine serum (Hyclone, SH30071.03), 12mM Hepes (Gibco15630), 1XMEM NEAA(Gibco 11140), 1mM Sodium Pyruvate (Gibco, 11360), 1ug/ml insulin (Sigma-Aldrich®, I-5500), 1ug/ml Hydrocortisone (Sigma-Aldrich®, H-4001), 12.5ng/ml EGF (Sigma-Aldrich®, E4127) and 1X Antibiotic-Antimycotic (Gibco, 15240-062).   AU565 and HCC1965 cells were grown in RPMI1640 medium supplemented with 10% of fetal bovine serum (Hyclone, SH30071.03), 1XSodium Pyruvate (Gibco 11360-070), 10mM Hepes(Gibco, 15630) and 1X Antibiotic-Antimycotic (Gibco, 15240-062). BT474 and SKBR3 cells were grown in RPMI1640 medium supplemented with 10% of fetal bovine serum (Hyclone, SH30071.03) and 1X Antibiotic-Antimycotic(Gibco, 15240-062).   BT549 were grown in RPMI1640 medium supplemented with 10% of fetal bovine serum (Hyclone, SH30071.03), 1XSodium Pyruvate (Gibco 11360-070), 10mM Hepes(Gibco, 15630), 8ug/ml Insulin(life technology 12585014) and 1X Antibiotic-Antimycotic(Gibco, 15240-062).   CAMA1 cells were grown in MEM (Gibco 11095-080) medium supplemented with 10% of fetal bovine serum (Hyclone, SH30071.03), 1XSodium Pyruvate (Gibco 11360-070), 1XNEAA (Gibco 11140) and 1X Antibiotic-Antimycotic (Gibco, 15240-062).  HBL100 cells were grown in McCoy’s 5a medium (Gibco 16600-082) supplemented with 10% of fetal bovine serum (Hyclone, SH30071.03) and1X Antibiotic-Antimycotic (Gibco, 15240-062).  MCF10A cells were grown in DMEM/F12 (GIBCO 11330-032) medium supplemented with 5% of Horse Serum (Invitrogen #16050-122), 0.5ug/ml of hydrocortisone(Sigma-Aldrich®,H4001), 10ug/ml of  Insulin (life technology 12585014), 20ng/ml of EGF(Sigma-Aldrich® ,  e9644) and 1X Antibiotic-Antimycotic (Gibco, 15240-062).  MCF12A cells were grown in DMEM/F12 (GIBCO11330-032) medium supplemented with 10% of fetal bovine serum (Hyclone, SH30071.03), 1ug/ml of hydrocortisone (Sigma-Aldrich, H-4001), 5ug/ml of Insulin (life technology 12585014) and 1X Antibiotic-Antimycotic (Gibco, 15240-062).  DKAT cells were grown in MEGM (Lonza, CC-3150) medium and 1X Antibiotic-Antimycotic (Gibco, 15240-062).  All cell lines were maintained in a humidified incubator with 5% CO2 atmosphere at 37o C.

extract_protocol: Microarray analysis was performed on RNA harvested from those cell lines.  Samples were run in triplicate. Isolation of RNA. Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.

treatment_protocol: 16 cell lines representing luminal HER2- (MCF7, T47D, ZR751, CAMA-1), luminal-HER2+ (BT474, SKBR3, AU565), HER2+ (HCC1954) and basal (SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, and DKAT) breast cancer cell lines were evaluated for response to a single dose of 5Gy.

tag: cell line

tag: cell type

tag: clinical subtype

value: basal


title: AU565_0Gy_B

description:
Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (1, 2) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms.
Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.
Cell line AU565 - 42911

value: luminal (Her2+)


title: P34-T1-Tum

source_name: Cancer breast tissue, after first chemo dose


title: P34-T4-Tum

source_name: Cancer breast tissue, after forth chemo dose


title: SUM149_5Gy_24h_A

description:
Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (1, 2) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms.
Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.
Cell line s149 - 35054


title: SUM159_5Gy_24h_C

description:
Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (1, 2) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms.
Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.
Cell line s159 - 35050


title: SUM149_0Gy_B

description:
Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (1, 2) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms.
Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.
Cell line s149 - 35052


title: P34-T2-Nor

source_name: Normal breast tissue, after second chemo dose

value: Normal tissue biopsy adjacent to cancer tissue


title: AU565_0Gy_A

description:
Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (1, 2) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms.
Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.
Cell line AU565 - 42909


title: P34-T2-Tum

source_name: Cancer breast tissue, after second chemo dose


title: SUM159_0Gy_B

description:
Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (1, 2) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms.
Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.
Cell line s159 - 35046


title: SUM149_0Gy_A

description:
Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (1, 2) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms.
Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.
Cell line s149 - 35051


title: P34-T3-Nor

source_name: Normal breast tissue, after third chemo dose


title: SUM159_5Gy_24h_B

description:
Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (1, 2) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms.
Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.
Cell line s159 - 35049


title: SUM159_0Gy_A

description:
Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (1, 2) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms.
Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.
Cell line s159 - 35045


title: SUM159_5Gy_24h_A

description:
Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (1, 2) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms.
Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.
Cell line s159 - 35048


title: P08-T1-Nor

source_name: Normal breast tissue, after first chemo dose


title: MDA-MB-231_5Gy_24h_C

description:
Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (1, 2) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms.
Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.
Cell line 231 - 35044


title: P34-T4-Nor

source_name: Normal breast tissue, after forth chemo dose


title: SUM159_0Gy_C

description:
Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (1, 2) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms.
Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.
Cell line s159 - 35047


title: MDA-MB-231_5Gy_24h_A

description:
Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (1, 2) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms.
Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.
Cell line 231 - 35042


title: P34-T1-Nor


title: MDA-MB-231_0Gy_A

description:
Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (1, 2) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms.
Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.
Cell line 231 - 35039


title: P29-T4-Tum


title: MDA-MB-231_0Gy_B

description:
Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (1, 2) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms.
Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.
Cell line 231 - 35040


title: MDA-MB-231_0Gy_C

description:
Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (1, 2) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms.
Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.
Cell line 231 - 35041


title: MDA-MB-231_5Gy_24h_B

description:
Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (1, 2) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms.
Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.
Cell line 231 - 35043


title: MCF7_0Gy_C

description:
Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (1, 2) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms.
Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.
Cell line MCF7 - 35035

value: luminal (Her2-)


title: ZR751_0Gy_C

description:
Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (1, 2) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms.
Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.
Cell line ZR751 - 35029


title: ZR751_5Gy_24h_A

description:
Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (1, 2) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms.
Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.
Cell line ZR751 -35030


title: MCF7_5Gy_24h_B

description:
Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (1, 2) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms.
Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.
Cell line MCF7 - 35037


title: ZR751_5Gy_24h_B

description:
Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (1, 2) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms.
Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.
Cell line ZR751 - 35031


title: P29-T3-Nor

description: Tissue Gene expression from locally advanced breast cancer tissue biopsies


title: P29-T3-Tum


title: MCF7_5Gy_24h_A

description:
Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (1, 2) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms.
Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.
Cell line MCF7 - 35036


title: T47D_5Gy_24h_B

description:
Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (1, 2) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms.
Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.
Cell line T47D - 35025


title: ZR751_0Gy_B

description:
Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (1, 2) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms.
Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.
Cell line ZR751 - 35028


title: ZR751_0Gy_A

description:
Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (1, 2) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms.
Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.
Cell line ZR751 - 35027


title: MCF7_0Gy_A

description:
Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (1, 2) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms.
Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.
Cell line MCF7 - 35033


title: P29-T1-Tum


title: P29-T1-Nor


title: T47D_5Gy_24h_A

description:
Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (1, 2) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms.
Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.
Cell line T47D - 35024


title: MCF7_0Gy_B

description:
Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (1, 2) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms.
Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.
Cell line MCF7 - 35034


title: P29-T2-Nor


title: ZR751_5Gy_24h_C

description:
Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (1, 2) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms.
Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.
Cell line ZR751 - 35032


title: P25-T4-Tum


title: MCF7_5Gy_24h_C

description:
Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (1, 2) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms.
Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.
Cell line MCF7 - 35038


title: T47D_5Gy_24h_C

description:
Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (1, 2) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms.
Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.
Cell line T47D - 35026


title: P29-T2-Tum


title: T47D_0Gy_C

description:
Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (1, 2) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms.
Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.
Cell line T47D - 35023


title: P29-T4-Nor


title: P25-T4-Nor


title: T47D_0Gy_B

description:
Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (1, 2) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms.
Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.
Cell line T47D - 35022


title: T47D_0Gy_A

description:
Breast cancer cell lines displaying gene expression patterns consistent with distinct clinical breast subtypes were selected (1, 2) as follows: Luminal - MCF7, T47D, ZR751, CAMA-1, BT474 (Her2+), SKBR3 (Her2+), AU565 (Her2+); Basal - SUM149, SUM159, MDA-MB-231, MCF10A, MCF12A, BT549, HBL100, HCC1954 (Her2+) and DKAT. These cell lines reflect the heterogeneity of human breast cancer, thereby, providing a valid biological model for study of phenotype specific mechanisms.
Total RNA was collected from approximately 1x10^6 cells in each of the sixteen cell lines.  RNA was isolated from the treated cell lines (5Gy) 24 hours after radiation using the RNeasy Mini Isolation Kit (QIAGEN, Valencia, CA). The same protocol was used for control cell lines but with 0Gy radiation. Samples were run in triplicate.  RNA was hybridized to Affymetrix U133A2 arrays and processed in the Duke Microarray Core facility.
Cell line T47D - 35021


title: P25-T2-Tum


title: HUT78_JAKi_3h_rep1

city: Santander

first: Nerea

last: Martinez

address: Avda Cardenal Herrera Oria

country: Spain

institute: IDIVAL

description: Sample 3

hyb_protocol: Microarray: Human Gene Expression G3 60K (Agilent microarray design ID 028004, P/N G4851A). Hybridization chamber type: SureHyb hybridization chamber (Agilent). Quantity of each labeled extract used: 300 ng. Volume: 50 uL. Temperature (ºC): 65. Duration: 17 hours

scan_protocol: Scanned on an G2505C DNA microarray scanner (Agilent). Images were analysed by Agilent Feature Extraction Software (ver. 11.5), which performed feature quantitation and additive detrend correction. No background subtraction was performed

data_processing: Background correction: normexp; Within arrays normalization: loess;  Between arrays normalization: quantiles

source_name: HUT78 treated with JAKi 3h

label_protocol: Amount of nucleic acid labeled: 100ng. Commercial Two-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labeling) version 6.5 kit by following manufacturer instructions. Agilent manual G4140-90050 of May 2010. Amplification: by RNA polymerases.Briefly, MMLV-RT retrotranscription of sample from a T7 promoter primer is followed by a T7 RNA pol catalysed in vitro transcription reaction in the presence of either Cy3-CTP or Cy5-CTP fluorophores.

growth_protocol: Cells were cultured in RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum and 1% penicillin/streptomycin (Invitrogen Corporation, USA) in a humidified atmosphere at 37°C with 5% CO2

extract_protocol: Total RNA was isolated by Trizol reagent (Invitrogen). RNA quality was checked using total RNA (small fraction chip) with the Agilent 2100 Bioanalyzer (Agilent Technologies) and by 1% agarose electrophoresis, following standard procedures

treatment_protocol: Cells were incubated with INCB018424 (using an IC50 concentration) at two times (30 minutes and 3 hours)

tag: treatment

value: JAKi

tag: time

source_name: Universal Human Reference RNA Stratagene

value: untreated


title: HUT78_control_rep1

description: Sample 1

source_name: HUT78 untreated

value: control


title: P25-T1-Tum


title: P10-T4-Nor


title: P25-T2-Nor


title: P25-T1-Nor


title: HUT78_JAKi_30min_rep1

description: Sample 2

source_name: HUT78 treated with JAKi 30min


title: P10-T4-Tum


title: P10-T2-Tum


title: In vitro_48hr_Control_rep3

city: Oslo

first: Maria

middle: Therese

last: Hultman

address: Gaustadalléen 21

department: Ecotoxicology

country: Norway

institute: NIVA

description: Gene expression after 48hr of in vitro exposed hepatocytes to 30nM EE2

hyb_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B)  using one color scan setting for 1x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

scan_protocol: Agilent Feature Extraction software v10.7

data_processing: The raw data was subjected to normalization, including correction for background signal, flagged for missing and low quality features followed by statistical analysis using GeneSpring GX v12.6 (Agilent technologies).

organism: Oncorhynchus mykiss

source_name: Primary hepatocytes, 48hr, Control, replicate 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.6 ug RNA using the One-Color Low RNA Input Linear Amplification kit (Agilent) trictly according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer in order to fulfill the criterias for amount of incorperated dye in the cRNA sample. One-Color Microarray-Based Gene Expression analysis (Low input Quick Amp Labeling), Version 6.5 May 2010

extract_protocol: RNA was prepared using the Qiagen RNeasy Plus mini kit (Qiagen GmbH, Hilden, Germany) following the manufacturer's recommendations with some modifications. The protocol includes lysis of the hepatocyte cells, and an on-column DNase digestion. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Freshly isolated primary rainbow trout hepatocytes were seeded out in 96-well primaria cell plates (500 000 cells/ml) and incubated in 15 degrees at ambient CO2 for 24hr prior to the EE2 exposure. The hepatocytes were then exposed to 0.03, 0.3, 3 and 30 nM EE2 for 48h.

tag: tissue

value: Hepatocytes

tag: developmental stage

value: Juvenile


title: In vitro_48hr_30nM EE2_rep1

source_name: Primary hepatocytes, 48hr, 30nM EE2, replicate 1


title: In vitro_48hr_30nM EE2_rep3

source_name: Primary hepatocytes, 48hr, 30nM EE2, replicate 3


title: In vitro_48hr_Control_rep1

source_name: Primary hepatocytes, 48hr, Control, replicate 1


title: In vitro_48hr_0.3nM EE2_rep4

description: Gene expression after 48hr of in vitro exposed hepatocytes to 0.3nM EE2

source_name: Primary hepatocytes, 48hr, 0.3nM EE2, replicate 4


title: In vitro_48hr_30nM EE2_rep2

source_name: Primary hepatocytes, 48hr, 30nM EE2, replicate 2


title: P10-T3-Tum

source_name: Cancer breast tissue, after third chemo dose


title: In vitro_48hr_3nM EE2_rep3

description: Gene expression after 48hr of in vitro exposed hepatocytes to 3nM EE2

source_name: Primary hepatocytes, 48hr, 3nM EE2, replicate 3


title: P10-T2-Nor

description: Tissue Gene expression from locally advanced breast cancer tissue biopsies

source_name: Normal breast tissue, after second chemo dose


title: P10-T3-Nor


title: In vitro_48hr_3nM EE2_rep4

source_name: Primary hepatocytes, 48hr, 3nM EE2, replicate 4


title: In vitro_48hr_Control_rep2

source_name: Primary hepatocytes, 48hr, Control, replicate 2


title: In vitro_48hr_0.3nM EE2_rep3

source_name: Primary hepatocytes, 48hr, 0.3nM EE2, replicate 3


title: In vitro_48hr_0.3nM EE2_rep1

source_name: Primary hepatocytes, 48hr, 0.3nM EE2, replicate 1


title: In vitro_48hr_Control_rep4

source_name: Primary hepatocytes, 48hr, Control, replicate 4


title: In vitro_48hr_0.3nM EE2_rep2

source_name: Primary hepatocytes, 48hr, 0.3nM EE2, replicate 2


title: In vitro_48hr_3nM EE2_rep1

source_name: Primary hepatocytes, 48hr, 3nM EE2, replicate 1


title: In vitro_48hr_3nM EE2_rep2

source_name: Primary hepatocytes, 48hr, 3nM EE2, replicate 2


title: P10-T1-Tum

source_name: Cancer breast tissue, after first chemo dose


title: In vitro_48hr_30nM EE2_rep4

source_name: Primary hepatocytes, 48hr, 30nM EE2, replicate 4


title: In vitro_48hr_0.03nM EE2_rep3

description: Gene expression after 48hr of in vitro exposed hepatocytes to 0.03nM EE2

source_name: Primary hepatocytes, 48hr, 0.03nM EE2, replicate 3


title: In vitro_48hr_0.03nM EE2_rep4

source_name: Primary hepatocytes, 48hr, 0.03nM EE2, replicate 4


title: In vitro_48hr_0.03nM EE2_rep2

source_name: Primary hepatocytes, 48hr, 0.03nM EE2, replicate 2


title: P10-T1-Nor

source_name: Normal breast tissue, after first chemo dose


title: In vitro_48hr_0.03nM EE2_rep1

source_name: Primary hepatocytes, 48hr, 0.03nM EE2, replicate 1


title: Pilocytic astrocytoma 3397, Optic tract/hypothalamic

status: Public on Oct 30 2015

city: Gliwice

first: Aleksandra

last: Pfeifer

address: Wybrzeze Armii Krajowej 15

country: Poland

institute: MSC Memorial Cancer Center and Institute of Oncology

hyb_protocol: Washing, staining with streptavidin-phycoerythrin conjugate were performed as recommended by the GeneChip® Expression Analysis Technical Manual 2008.

scan_protocol: Arrays were scanned using GeneChip Scanner 3000 (Affymetrix).

data_processing: Data were pre-processed by GC-Robust Multi-array Average (GC-RMA) procedure in R/Bioconductor environment.

label: biotin

source_name: Pilocytic astrocytoma

label_protocol: For cDNA synthesis 250 ng RNA was used (GeneChip® 3' IVT Expression Kit, Affymetrix) and 6 ul of cDNA were used for cRNA synthesis and biotynilation (GeneChip® 3' IVT Expression Kit, Affymetrix). All reactions were performed according to the GeneChip® Expression Analysis Technical Manual 2008.

extract_protocol: Total RNA was extracted by using commercially available sets (RNeasy Mini Kit, Qiagen) and treated with DNAase (Qiagen). The quantity of RNA was measured using the NanoDrop 1000 (Thermo Scientific). RNA samples quality was analysed using 2000 Bioanalyzer (Agilent Technologies) and after capillary electrophoresis the RNA integrity number (RIN) was generated by the software for each specimen.

value: Pilocytic astrocytoma

value: brain

tag: rin

tag: Sex

value: F

tag: age (years)

tag: region

value: Supratentorial

tag: localization

value: Optic tract/hypothalamic

tag: localization group

tag: extent of resection

value: Partial

tag: radiology

value: Solid

tag: radiological feature

value: Solid or mainly Solid tumor

tag: radiology group

tag: progression

value: Free of progression


title: Pilocytic astrocytoma 3409, Cerebellum

tag: diagnosis

value: M

value: Infratentorial

value: Cerebellum

value: Total

value: Cystic

value: Cystic tumor with enhanced cyst


title: Pilocytic astrocytoma 3398, Cerebral hemisphere

value: Cerebral hemisphere

value: Cystic tumor without enhanced cyst wall

tag: nf-1 clinical manifestation

value: NF


title: Pilocytic astrocytoma 3394, Cerebellum

value: Pilocytic astrocytoma

value: brain


title: Pilocytic astrocytoma 3366, Optic tract/hypothalamic

value: F

value: Supratentorial


title: Pilocytic astrocytoma 3110, Cerebral hemisphere


title: Pilocytic astrocytoma 3108, Cerebellum


title: Pilocytic astrocytoma 3104, Optic tract/hypothalamic

value: Optic tract/hypothalamic


title: Pilocytic astrocytoma 3382, Cerebellum

value: Subtotal

value: Solid


title: Pilocytic astrocytoma 3373, Cerebellum

value: Solid or mainly Solid tumor

value: Free of progression


title: Pilocytic astrocytoma 3097, Cerebral hemisphere

value: M


title: Pilocytic astrocytoma 3399, Cerebellum

value: Infratentorial

value: Cerebellum

value: Solid tumor with central necrosis


title: Pilocytic astrocytoma 3389, Cerebellum

value: Total


title: Pilocytic astrocytoma 3391, Cerebellum

value: Partial


title: Pilocytic astrocytoma 3378, Optic tract/hypothalamic

value: Progression


title: Pilocytic astrocytoma 3375, Cerebellum

value: Cystic


title: Pilocytic astrocytoma 3114, Optic tract/hypothalamic

value: Pilocytic astrocytoma

value: Biopsy


title: Pilocytic astrocytoma 3111, Cerebellum

value: brain

value: Cystic tumor without enhanced cyst wall


title: Pilocytic astrocytoma 3371, Cerebellum


title: Pilocytic astrocytoma 3115, Optic tract/hypothalamic

value: F

value: Supratentorial

value: Optic tract/hypothalamic


title: Pilocytic astrocytoma 3112, Cerebellum

value: Cystic tumor with enhanced cyst


title: Pilocytic astrocytoma 3369, Cerebellum

value: Solid

value: Solid or mainly Solid tumor

value: Free of progression


title: Pilocytic astrocytoma 3109, Cerebellum

value: M

value: Infratentorial

value: Cerebellum


title: Pilocytic astrocytoma 3385, Optic tract/hypothalamic

value: NF


title: Pilocytic astrocytoma 3096, Cerebellum

value: Subtotal

value: Solid tumor with central necrosis


title: Pilocytic astrocytoma 3099, Cerebellum

value: Pilocytic astrocytoma

value: Total

value: Cystic


title: Pilocytic astrocytoma 3098, Cerebellum

value: brain


title: Pilocytic astrocytoma 3101, Cerebellum

value: Cystic tumor without enhanced cyst wall


title: Pilocytic astrocytoma 3100, Cerebral hemisphere

value: Supratentorial

value: Cerebral hemisphere


title: Pilocytic astrocytoma 3094, Optic tract/hypothalamic

value: F

value: Optic tract/hypothalamic

value: Partial

value: Progression


title: Pilocytic astrocytoma 3092, Cerebral hemisphere

value: M

value: Solid

value: Solid or mainly Solid tumor

value: Free of progression


title: Pilocytic astrocytoma 3093, Optic tract/hypothalamic

value: Cystic tumor with enhanced cyst


title: Pilocytic astrocytoma 3095, Cerebellum

value: Infratentorial

value: Cerebellum


title: Pilocytic astrocytoma 3090, Cerebellum

value: Pilocytic astrocytoma

value: Total


title: Slide 344290

city: STOCKHOLM

first: Sulman

last: Shafeeq

address: nobel vag 16

department: MTC

country: Sweden

institute: Karolinska Institutet

description: Sample 2

hyb_protocol: The protocol was performed as described in Kloosterman et al., 2006 and Shafeeq et al., 2011.

scan_protocol: Scanning was done using the GenePix 4200AL laser scanner.

data_processing: Dual-channel array images were analyzed with GenePix 6. Spots were screened visually to identify those of low quality. Slide data were processed with MicroPreP software. Prior to analysis, automatically and manually flagged spots and spots with very low background subtracted signal intensity (5% of the weakest spots [sum of Cy3 and Cy5 net signals]) were filtered out of all data sets. Net signal intensities were calculated by grid-based background subtraction. A grid-based Lowess transformation was performed for slide normalization, negative and empty values were removed, and outliers were removed by the deviation test. Expression ratios of D39 wild-type strain over the galR mutant strain were calculated. Further analysis was performed with a Cyber-T Student T-test for paired data.

organism: Streptococcus pneumoniae D39

source_name: wild type grown in GM17

label_protocol: Total RNA was incubated for 16 h at 42°C in the presence of 400 U Superscript III RNase H reverse transcriptase (Invitrogen), 0.2 mM aminoallyl dUTP (Amersham), 0.5 mM dATP, 0.5 mM dCTP, 0.5 mM dGTP, 0.3 mM dTTP, and 3.2 g random nonamers. The synthesized cDNA was then labeled by coupling either Cy3 or Cy5 to the dUTP aminoallyl reactive group (CyScribe postlabeling kit; Amersham Biosciences) and was purified using a GFX PCR, DNA, and gel band purification kit (Amersham Biosciences).

growth_protocol: Cells were grown in GM17 medium and harvested at OD600 of 0.2.

extract_protocol: RNA was isolated and purified using the High Pure RNA isolation kit (Roche Diagnostics) as described (Kloosterman et al., 2006). Contaminating genomic DNA was removed by treatment with RNase-free DNase I (Roche Diagnostics). RNA was isolated from three replicate cultures.

tag: strain/background

tag: genotype/variation

value: wild type

tag: growth medium

value: M17 medium+ 0.5% glucose (GM17)

source_name: galR mutant grown in GM17

value: galR mutant


title: Pilocytic astrocytoma 3071, Cerebellum

tag: tissue

value: brain

value: Solid tumor with central necrosis


title: Slide 346929

description: Sample 2

source_name: wild type grown in GalM17

growth_protocol: Cells were grown in GalM17 medium and harvested at OD600 of 0.15.

value: M17 medium+ 0.5% galactose (GalM17)

source_name: galR mutant grown in GalM17


title: Slide 344289

description: Sample 1


title: Pilocytic astrocytoma 3083, Optic tract/hypothalamic

tag: rin

value: F

value: Supratentorial

value: Optic tract/hypothalamic

value: Subtotal


title: Pilocytic astrocytoma 3079, Cerebellum

tag: Sex

value: M

value: Solid


title: Pilocytic astrocytoma 3078, Cerebral hemisphere

tag: age (years)

value: Cerebral hemisphere

value: Cystic

value: Cystic tumor without enhanced cyst wall

value: Free of progression


title: Slide 345224

description: Sample 1


title: Pilocytic astrocytoma 3074, Cerebral hemisphere

value: Pilocytic astrocytoma

tag: region

value: Cystic tumor with enhanced cyst


title: 20123852 Spleen Low gain-high intake

city: Clay Center

first: Amanda

middle: K

last: Lindholm-Perrry

state: NE

address: State Spur 18D

department: NEMRU

institute: USMARC

hyb_protocol: Following fragmentation, cRNA was hybridized for 20 hr at 45C on Bovine 1.1ST Array. GeneChips were washed and stained in the Affymetrix GeneAtlas Fluidics Station.

scan_protocol: GeneChips were scanned with the Affymetrix GeneAtlas Imager.

data_processing:
The data were transformed by Affymetrix and analyzed with Affymetrix Expression Console;
affymetrix-algorithm-name = rma-gene-full
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.4.0.38
and Affymetrix Transcriptome Analysis Console using the one-way between-Subject ANOVA (Unpaired) algorithm (Linear Fold Change cutoff of 2 and ANOVA p-value (Condition pair) <0.05).

organism: Bos taurus

source_name: spleen_low gain-high intake

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA.

growth_protocol: Steers were fed a standard concentrate diet for 84 days.

extract_protocol: TriPure Reagent was used to extract total RNA according to manufacturer's instructions, except that a 20 minute centrifugation (rather than 15 min) was used following the addition of chloroform.  RNA pellets were centrifuged through RNeasy Plus Mini Kit columns (Qiagen, Valencia, CA, USA) according to the manufacturer’s instructions to remove genomic DNA.

treatment_protocol: Animals most divergent from the bivariate mean from in each of the four phenotypic Cartesian quadrants for gain x intake were selected and spleen tissue samples were collected. The transcriptomes from 50-100mg of  spleen tissue taken from approximately 3 inches from the free end of the spleen were evaluated by microarray.

tag: age/sex

value: steer

tag: gain and feed intake phenotype

value: Low gain-high intake

value: spleen


title: Pilocytic astrocytoma 3082, Optic tract/hypothalamic

value: brain

tag: localization

tag: localization group

tag: extent of resection

value: Total

value: Solid or mainly Solid tumor


title: [C]

city: Fuzhou,

first: guizhu

last: HONG

state: Fujian

address: No. 1 Huatou Road, Minhou Shangjie

department: Centre of Biomedical Research & Development

country: China

institute: Fujian University of Traditional Chinese Medicine

description: gene expression in sham control

hyb_protocol: Purified and labeled cRNA was hybridized to Rat 4x44K Gene Expression Array (Agilent Technologies), according to the manufacturer’s procedures

scan_protocol: The hybridized arrays were washed, fixed, and scanned using the Agilent DNA Microarray Scanner (Agilent Technologies).Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images.

data_processing: Normalization and subsequent data processing were performed with the GeneSpring GX v12.0 software package (Agilent Technologies). After normalization of the raw data, genes that were detected in all samples were chosen for further data analysis

organism: Rattus norvegicus

source_name: sham brain  3

label_protocol: Total RNA from each sample was amplified linearly and labeled with Cy3-UTP. The labeled cRNAs were purified with an RNeasy Mini Kit (Qiagen). Concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: Ischemic brain was dissected for RNA extraction with an RNeasy Mini Kit, in accordance with the manufacturer’s instructions (Qiagen, Hilden, Germany). RNA concentration and quality were determined by NanoDrop ND-1000 (NanoDrop Technologgies, Wilmington, DE) and RNA gel electrophoresis assays, respectively.

treatment_protocol: MCAO rats were injected intraperitoneally with salidroside (50 mg/kg body weight) or vehicle (saline) once a day for 6 d, commencing 1 h after reperfusion (n=3  /group)

tag: strain

value: Sprague Dawley

tag: gender

value: male


title: Pilocytic astrocytoma 3068, Cerebral hemisphere

tag: diagnosis

value: Supratentorial

tag: radiology

tag: radiological feature

tag: radiology group

tag: progression


title: [B]

description: gene expression in sham control

source_name: sham brain  2

tag: tissue


title: Pilocytic astrocytoma 3073, Cerebellum

tag: rin

value: M

value: Infratentorial

value: Cerebellum

value: Subtotal

value: Progression


title: Pilocytic astrocytoma 3072, Cerebellum

tag: Sex

value: Cystic

value: Cystic tumor without enhanced cyst wall

value: Free of progression


title: Pilocytic astrocytoma 3070, Brainstem

value: Pilocytic astrocytoma

tag: age (years)

value: Brainstem

value: Biopsy

value: Solid


title: 20123636 Spleen Low gain-high intake

value: steer

value: Low gain-high intake

value: spleen


title: 20124211 Spleen Low gain-high intake


title: 20124257 Spleen Low gain-high intake


title: 20123850 Spleen Low gain-low intake

source_name: spleen_low gain-low intake

value: Low gain-low intake


title: Pilocytic astrocytoma 3088, Cerebellum

value: brain

tag: region

value: Total


title: Pilocytic astrocytoma 3067, Cerebellum

value: M

value: Infratentorial

value: Cystic tumor with enhanced cyst


title: Pilocytic astrocytoma 3080, Cerebral hemisphere

value: Supratentorial

value: Cerebral hemisphere

value: Partial

value: Progression


title: 20123661 Spleen Low gain-low intake

tag: age/sex


title: 20123593 Spleen Low gain-low intake

tag: gain and feed intake phenotype


title: 20123915 Spleen Low gain-low intake


title: 59-Pancreatic neuroendocrine tumor

city: Sutton

first: Anguraj

last: Sadanandam

state: Surrey

address: 15 Cotswold Road

department: Molecular Pathology

country: United Kingdom

institute: Institute of Cancer Research (ICR), London

description: Pancreatic neuroendocrine tumor

hyb_protocol: The labeled RNAs were hybridized to Agilent human miRNA microarrays for 20 h at 55°C with rotation.

scan_protocol: After hybridization and washing, the arrays were scanned with an Agilent microarray scanner using high dynamic range settings as specified by the manufacturer.

data_processing: All normalization methods were performed on the Total Gene Signal from Agilent “GeneView” data files in R, an open source statistical scripting language (http://www.r-project.org). Except for VSN, data were log2 transformed after adding a small constant such that the smallest value of the data set was 1 before taking the log. Scaling normalization was performed by dividing each array by its mean signal intensity and then by rescaling to the global mean intensity of all arrays. Quantile normalization was performed using the “normalize.quantiles” function from R package “affy” from the Bioconductor project (http://www.bioconductor.org).

source_name: Pancreatic neuroendocrine tumor

label_protocol: Total RNA (100 ng) was dephosphorylated with calf intestine alkaline phosphatase (GE Healthcare Europe GmbH), denatured with dimethyl sulfoxide, and labeled with pCp-Cy3 using T4 RNA ligase (GE Healthcare Europe GmbH).

extract_protocol: total RNA using Qiagen's miRNeasy kit

value: Pancreatic neuroendocrine tumor


title: [A]

description: gene expression in sham control

source_name: sham brain  1

value: Sprague Dawley

value: male


title: 58-Pancreatic neuroendocrine tumor

description: Pancreatic neuroendocrine tumor


title: 57-Pancreatic neuroendocrine tumor

description: Pancreatic neuroendocrine tumor


title: [5-2]

description: gene expression in brain with vehicle treatment 6d after MCAO

source_name: Ischemic brain 3


title: 20123812 Spleen High gain-low intake

source_name: spleen_high gain-low intake

value: High gain-low intake


title: [5-1]

description: gene expression in brain with Salidroside treatment 6d after MCAO

source_name: Ischemic brain + salidroside2


title: [17-5]

source_name: Ischemic brain + salidroside1


title: 20123591 Spleen High gain-low intake

value: steer


title: [17-1]

source_name: Ischemic brain 2


title: 56-Pancreatic neuroendocrine tumor

description: Pancreatic neuroendocrine tumor


title: 20124206 Spleen High gain-high intake

source_name: spleen_high gain-high intake

value: High gain-high intake


title: 20123891 Spleen High gain-low intake

value: spleen


title: 20123806 Spleen High gain-high intake


title: 20123611 Spleen High gain-low intake


title: [1-1]

source_name: Ischemic brain + salidroside3


title: [1-3]

source_name: Ischemic brain 1


title: 55-Pancreatic neuroendocrine tumor

description: Pancreatic neuroendocrine tumor


title: 53-Pancreatic neuroendocrine tumor

description: Pancreatic neuroendocrine tumor


title: 20123616 Spleen High gain-high intake


title: 52-Pancreatic neuroendocrine tumor

description: Pancreatic neuroendocrine tumor


title: 20123841 Spleen High gain-high intake


title: 51-Pancreatic neuroendocrine tumor

description: Pancreatic neuroendocrine tumor


title: 205-E vs FY4

type: genomic

city: Seattle

first: Maitreya

middle: J.

last: Dunham

state: WA

address: Foege Building, S403B, Box 355065

department: Genome Sciences

institute: University of Washington

description: 205-E vs FY4. Testing evolved ars228D clone for Bonny

hyb_protocol: reference URL : http://dunham.gs.washington.edu/UWAgilentDNA.pdf

scan_protocol: Pixel Size : 5 Scan Date : 2013-03-11 Scan Time : 10:48:29 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505C Scanning software : ChipScan Scanning software version : A.8.3.1

data_processing:
Extraction Software : Agilent Feature Extractor
Extraction Software Version : 10.5.1.1
Datafile type : Agilent result file

molecule: genomic DNA

organism: Saccharomyces cerevisiae

extract_protocol:
Extracted molecule : Genomic DNA
Extraction method : Hoffman-Winston prep http://dunham.gs.washington.edu/UWyeastDNAprep.pdf

tag: strain name

value: FY4 (wt)

value: evolved ars228 clone 205-E


title: 202-22B vs FY4.  Run #2

description: 202-22B. Evolved ars228D clone arrayed for Bonny.

scan_protocol: Pixel Size : 5 Scan Date : 2013-03-15 Scan Time : 10:52:01 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505C Scanning software : ChipScan Scanning software version : A.8.3.1

label_protocol: reference URL : http://dunham.gs.washington.edu/UWAgilentDNA.pdf

value: evolved ars228 clone 202-22B


title: 49-Pancreatic neuroendocrine tumor

description: Pancreatic neuroendocrine tumor


title: 206-A vs FY4

description: 206-A vs FY4. Testing evolved ars228D clone for Bonny

value: evolved ars228 clone 206-A


title: 207-A vs FY4

description: 207-A vs FY4. Testing evolved ars228D clone for Bonny

value: evolved ars228 clone 207-A


title: 110912-evol-YMD1474

scan_protocol: Pixel Size : 5 Scan Date : 2011-09-13 Scan Time : 10:33:54 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505C Scanning software : ChipScan Scanning software version : A.8.3.1

value: evolved ars228 clone YMD1474


title: 201-B vs FY4.  Run #2

description: 201-B vs FY4. Evolved ars228D clone arrayed for Bonny

value: evolved ars228 clone 201-B


title: 48-Pancreatic neuroendocrine tumor

description: Pancreatic neuroendocrine tumor


title: 120201-evol-YMD1476

scan_protocol: Pixel Size : 5 Scan Date : 2012-02-02 Scan Time : 13:49:27 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505C Scanning software : ChipScan Scanning software version : A.8.3.1

value: evolved ars228 clone YMD1476


title: 203-C vs FY4.  Run #2

description: 203-C vs FY4. Evolved ars228D clone arrayed for Bonny.

value: evolved ars228 clone 203-C


title: 110912-evol-YMD1465

value: evolved ars228 clone YMD1465


title: 203-E vs FY4.  Run #2

description: 203-E vs FY4. Evolved ars228D clone arrayed for Bonny.

value: evolved ars228 clone 203-E


title: 110813-YMD1473

description: YMD1473 vs. FY4

scan_protocol: Pixel Size : 5 Scan Date : 2011-08-13 Scan Time : 09:36:53 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505C Scanning software : ChipScan Scanning software version : A.8.3.1

value: evolved ars228 clone YMD1473


title: 110813-evolution-YMD1475

description: YMD1475 vs. FY4

value: evolved ars228 clone YMD1475


title: 110813-YMD1463

description: YMD1463 vs. FY4

value: evolved ars228 clone YMD1463


title: 110906-YMD1464-Evol

scan_protocol: Pixel Size : 5 Scan Date : 2011-09-06 Scan Time : 10:52:53 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505C Scanning software : ChipScan Scanning software version : A.8.3.1

value: evolved ars228 clone YMD1464


title: 47-Pancreatic neuroendocrine tumor

description: Pancreatic neuroendocrine tumor

value: Pancreatic neuroendocrine tumor


title: 207-D vs FY4

description: 207-D vs FY4. Testing evolved ars228D clone for Bonny

value: evolved ars228 clone 207-D


title: 46-Pancreatic neuroendocrine tumor

description: Pancreatic neuroendocrine tumor


title: 43-Pancreatic neuroendocrine tumor

description: Pancreatic neuroendocrine tumor


title: 96_weeks_female_wildtype_replicate_2

city: Cologne

first: Peter

last: Frommolt

address: Joseph-Stelzmannstr. 26

country: Germany

institute: CECAD

description: Gene expression data from female wild type at age of 96 weeks

hyb_protocol: Probes were hybridized to the Affymetrix GeneChip Mouse Gene 1.0 ST Array according to the manufacturer’s instructions

scan_protocol: Chips were scanned with a GeneChip 3,000 6G scanner.

data_processing: Raw data (CEL files) were processed using the robust multi-array average (RMA) algorithm and quantile normalization with the Affymetrix Power Tools, version 1.12.0, and platformspecific library files. Differential gene expression was analyzed using descriptive statistics (fold change) and Student’s T-Test method for pairwise comparisons. Genes were prioritized by statistical evidence. In order to create candidate lists for differential gene expression between conditions, we used all genes regulated at least 1.5-fold where differential expression was significant at level 0.05. Type I error inflation was ignored because the p-values were used to prioritize the list rather than being interpreted in a confirmatory sense.

organism: Mus musculus

source_name: Mus musculus female with wild type genotype at age of  96 weeks

label_protocol: cDNA probes were labelled with Encore Biotin Module (NuGen Technologies, Inc.)

growth_protocol: Mice were bred in mixed FVB/C57BL6 (microarray analysis & histology) background. All experiments were conducted according to institutional and federal guidelines and approved by the IACUC in Bilthoven, NIH/NIA 1PO1 AG 17242. Mice were housed according to the standardized specific pathogen-free conditions in the University of Cologne animal facility.

extract_protocol: Total RNA was extracted and purified using commercial homogenization (Bio 101 FastPrep FP120-120 V, Savant, Midland, MI, USA) and the RNeasy kit (Qiagen, Hilden, Germany).

treatment_protocol: mice were sacrificed at 14 and 96 weeks of age and kidneys extracted

tag: genotype

value: Wild type

value: female

tag: age

value: 96 weeks

value: whole kidney

tag: background strain

value: mixed FVB/C57BL6


title: UV irradiated 3

city: Perth

first: Kim

middle: Warwick

last: Carter

state: Western Australia

address: 100 Roberts Road, Subiaco

country: Australia

institute: Telethon Kids Institute

description: Injection of 2 x 10^6 BM cells from a UV irradiated congenic B6.SJL-Ptprca (CD45.1 alloantigen)

hyb_protocol: Biotinylated cRNA (15 μg) was hybridized to  HG-U133A arrays, which were washed, stained,  and scanned using a GeneArray Scanner (Agilent  Technologies) according to the Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: The oligo package was used to read the Affymetrix CEL files into R and to pre-process the arrays using robust multichip average methodology.  Quality control of the arrays was performed using the arrayQualityMetrics package.  The limma package was used to

source_name: UV-irradiated_CD11c+ Dcs

label_protocol: standard Affymetrix protocol

growth_protocol: Freshly-isolated BM cells were cultured for 5 days in RPMI-1640 (HyClone, GE Health Care Life Sciences, Logan, UT) supplemented with 10% FCS (HyClone)(RPMI-10), 10 ng/ml GM-CSF and 10 ng/ml IL-4 (Peprotech Inc, Rocky Hill, NJ) at a density of 8 x 105 cells/ml in 24 well plates to promote CD11c+ cell differentiation (medium replaced on days 2 and 4). Non-adherent cells were enriched to >95% CD11c+ cells (confirmed by flow cytometry) using anti-CD11c magnetic microbeads (Miltenyi Biotec, Bergisch Gladbach, Germany) and autoMACS-Pro (Miltenyi Biotec) separation.

extract_protocol: Total RNA was extracted from triplicate preparations of BM-differentiated CD11c+ cells using TRIzol (Life Technologies, Victoria, Australia) followed by an RNeasy plus mini kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions. At least 500 ng at 50 ng/ml (evaluated by the absorbance 260/280 ratio using a NanoDrop ND 1000 spectrophotometer, NanoDrop Technologies, Wilmington, DE)

tag: strain

tag: gender

tag: injected with

tag: cell type

value: bone marrow (BM)-differentiated dendritic cells (DC)

tag: cell subtype

value: CD11c+ DCs


title: UV irradiated 1

value: 2 x 10^6 BM cells from a UV irradiated congenic B6.SJL-Ptprca (CD45.1 alloantigen)


title: 96_weeks_female_wildtype_replicate_5


title: 96_weeks_female_wildtype_replicate_4


title: 96_weeks_female_wildtype_replicate_3


title: 39-Pancreatic neuroendocrine tumor

description: Pancreatic neuroendocrine tumor


title: UV irradiated 2


title: 14_weeks_female_wildtype_replicate_1

description: Gene expression data from female wild type at age of 14 weeks

source_name: Mus musculus female with wild type genotype at age of 14 weeks

value: 14 weeks


title: Control 1

description: Injection of 2 x 10^6 BM cells from a naïve congenic B6.SJL-Ptprca

source_name: control_CD11c+ Dcs


title: 38-Pancreatic neuroendocrine tumor

description: Pancreatic neuroendocrine tumor


title: Control 2

value: 2 x 10^6 BM cells from a naïve congenic B6.SJL-Ptprca


title: 14_weeks_female_wildtype_replicate_3


title: 14_weeks_female_wildtype_replicate_2


title: 14_weeks_female_wildtype_replicate_4


title: 44-Pancreatic neuroendocrine tumor

description: Pancreatic neuroendocrine tumor


title: 41-Pancreatic neuroendocrine tumor

description: Pancreatic neuroendocrine tumor


title: 40-Pancreatic neuroendocrine tumor

description: Pancreatic neuroendocrine tumor


title: I-9821-Met

description: Liver Metastases

hyb_protocol: Affymetrix GeneChip Mouse Gene 1.0 ST arrays were hybridized with labeled sense DNA, washed, stained, and scanned according to the protocol described in WT Sense Target Labeling Assay Manual (Version 4; FS450_0007).

scan_protocol: Scanned according to the protocol described in WT Sense Target Labeling Assay Manual (Version 4; FS450_0007)

data_processing: The data were analyzed using aroma.affymetrix

source_name: Liver Metastases

label_protocol: Total RNA were amplified and labeled using the Affymetrix Whole-Transcript (WT) Sense Target Labeling Protocol.

extract_protocol: total RNA was TRIzol-purified (Invitrogen)

value: Liver Metastases

value: RIP1-TAG2 genetically engineered PanNET mouse model


title: I-9822-Met

description: Liver Metastases


title: I-9812-MLP

description: Met-like primary

source_name: Met-like primary

value: Met-like primary


title: II-6413-MLP

description: Met-like primary


title: Control 3


title: III-8024-tumor

description: Islet Tumor

source_name: Islet Tumor

value: Islet Tumor


title: III-8023-MLP

description: Met-like primary


title: 96_weeks_female_wildtype_replicate_1

source_name: Mus musculus female with wild type genotype at age of 96 weeks


title: 35-Pancreatic neuroendocrine tumor

description: Pancreatic neuroendocrine tumor

source_name: Pancreatic neuroendocrine tumor


title: II-648-MLP

description: Met-like primary


title: I-9820-Met

description: Liver Metastases


title: III-8016-MLP

description: Met-like primary


title: 33-Pancreatic neuroendocrine tumor

description: Pancreatic neuroendocrine tumor


title: 37-Pancreatic neuroendocrine tumor

description: Pancreatic neuroendocrine tumor


title: 32-Pancreatic neuroendocrine tumor

description: Pancreatic neuroendocrine tumor


title: 34-Pancreatic neuroendocrine tumor

description: Pancreatic neuroendocrine tumor


title: 30-Pancreatic neuroendocrine tumor

description: Pancreatic neuroendocrine tumor


title: 31-Pancreatic neuroendocrine tumor

description: Pancreatic neuroendocrine tumor


title: 28-Pancreatic neuroendocrine tumor

description: Pancreatic neuroendocrine tumor


title: 27-Pancreatic neuroendocrine tumor

description: Pancreatic neuroendocrine tumor


title: 26-Pancreatic neuroendocrine tumor

description: Pancreatic neuroendocrine tumor


title: 23-Pancreatic neuroendocrine tumor

description: Pancreatic neuroendocrine tumor


title: Angiogenic2006

description: Angiogenic Islet

source_name: Angiogenic Islet

value: Angiogenic Islet


title: II-6415-tumor

description: Islet Tumor


title: Angiogenic2007

description: Angiogenic Islet


title: III-8017-tumor

description: Islet Tumor


title: HyperplasticI-93

description: Hyperplastic Islet

source_name: Hyperplastic Islet

value: Hyperplastic Islet


title: Hyperplastic2006

description: Hyperplastic Islet


title: II-649-tumor

description: Islet Tumor


title: I-9811-tumor

description: Islet Tumor


title: Normal2006

description: Normal Islet

source_name: Normal Islet

value: Normal Islet


title: Normal2007

description: Normal Islet


title: 21-Pancreatic neuroendocrine tumor

description: Pancreatic neuroendocrine tumor

value: Pancreatic neuroendocrine tumor


title: AngiogenicI-93

description: Angiogenic Islet


title: glioma20 [No.7]

city: Beijing

first: Xiaolong

last: Fan

state: Beijing

address: No. 19, XinJieKouWai St., HaiDian District

department: School of Life Sciences

institute: Beijing Normal University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45 °C on Affymetrix Human Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000 7G.

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: GBM IV_surgical specimen

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: not applicable

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Surgical specimen

tag: morphological diagnosis

value: GBM IV

tag: rmpa signature

value: RMPAlow

tag: survival(day)

tag: age at diagnosis (yrs)

value: male

tag: sample type

value: surgical specimen


title: Hyperplastic2007

description: Hyperplastic Islet

tag: tissue


title: glioma21 [No.16]


title: 20-Pancreatic neuroendocrine tumor

description: Pancreatic neuroendocrine tumor


title: E15.5 Wild Type

city: Tsukuba

first: Ahmed

last: Abdellatif

state: Ibaraki

address: 1.1.1. Tennodai, Tsukuba-shi, Ibaraki-ken

department: Anatomy and Embryology

country: Japan

institute: University of Tsukuba

description: Gene expression data from wild type embryos at E15.5 (correspods to period of seconary transition, marked expansion in beta cells  population)

hyb_protocol: The hybridization cocktail (80 μl) containing fragmented and biotin-labelled cDNAs was transferred into Affymetrix GeneChip MoGene-1_0-st-v1 cassettes, which were incubated at 45°C inside a hybridization oven by rotating them at 60 rpm for 17 hours.

scan_protocol: The GeneChip arrays were washed and developed using the Hybridization Wash and Stain Kit in a Fluidics Station 450. Then, the array were scanned using the GeneChip Scanner 3000

data_processing: Normalization and probe set summarization were performed using the Affymetrix expression console software. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: Mouse embryos at E15.5 (Period of secondary transition)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol. cRNAs were used to generate ~8.0 μg of cDNAs.

growth_protocol: Whole pancreata were dissected under the microscope and stored immediately in -80 C

treatment_protocol: Embryos for control and test experiments were properly labelled and stored separately in RNAse free epindorff tubes. All measures were taken to avoid cross contamination or RNA degradation.

value: Whole pancreas

value: Wild Type (Control)

value: ICR


title: glioma16 [No.21]

source_name: anaplastic oligoastrocytoma III_surgical specimen

value: anaplastic oligoastrocytoma III

value: female


title: glioma22 [No.23]

value: RMPAhigh


title: E15.5 MafK Tg

description: Gene expression data from MafK Tg embryos at E15.5 (correspods to period of seconary transition, marked expansion in beta cells population)

value: MafK Tg


title: 22-Pancreatic neuroendocrine tumor

description: Pancreatic neuroendocrine tumor


title: glioma18 [No.22]

source_name: oligoastrocytoma II_surgical specimen

value: oligoastrocytoma II


title: NormalI-93

description: Normal Islet

value: RIP1-TAG2 genetically engineered PanNET mouse model


title: 19-Pancreatic neuroendocrine tumor

description: Pancreatic neuroendocrine tumor


title: glioma14 [No.8]


title: 18-Pancreatic neuroendocrine tumor

description: Pancreatic neuroendocrine tumor


title: glioma17 [No.1]

source_name: astrocytoma II_surgical specimen

value: astrocytoma II


title: glioma12 [No.15]


title: 17-Pancreatic neuroendocrine tumor

description: Pancreatic neuroendocrine tumor


title: 16-Pancreatic neuroendocrine tumor

description: Pancreatic neuroendocrine tumor


title: 15-Pancreatic neuroendocrine tumor

description: Pancreatic neuroendocrine tumor


title: 14-Pancreatic neuroendocrine tumor

description: Pancreatic neuroendocrine tumor


title: 12-Pancreatic neuroendocrine tumor

description: Pancreatic neuroendocrine tumor


title: 13-Pancreatic neuroendocrine tumor

description: Pancreatic neuroendocrine tumor


title: 10-Pancreatic neuroendocrine tumor

description: Pancreatic neuroendocrine tumor


title: 9-Pancreatic neuroendocrine tumor

description: Pancreatic neuroendocrine tumor


title: 8-Pancreatic neuroendocrine tumor

description: Pancreatic neuroendocrine tumor


title: glioma19 [No.18]


title: 7-Pancreatic neuroendocrine tumor

description: Pancreatic neuroendocrine tumor


title: 5-Pancreatic neuroendocrine tumor

description: Pancreatic neuroendocrine tumor


title: 3-Pancreatic neuroendocrine tumor

description: Pancreatic neuroendocrine tumor


title: 6-Pancreatic neuroendocrine tumor

description: Pancreatic neuroendocrine tumor


title: 2-Pancreatic neuroendocrine tumor

description: Pancreatic neuroendocrine tumor


title: 4-Pancreatic neuroendocrine tumor

description: Pancreatic neuroendocrine tumor


title: glioma4 [No.14]


title: glioma10 [No.13]


title: glioma13 [No.12]


title: P33_f_panc_prim_73

description: tissue: pancreatic neuroendocrine tumours

hyb_protocol: Affymetrix GeneChip Human Gene 1.0 ST arrays were hybridized with 11 µg of labeled sense DNA, washed, stained, and scanned according to the protocol described in WT Sense Target Labeling Assay Manual (Version 4; FS450_0007).

data_processing: The data were analyzed using R and Bioconductor

source_name: pancreatic neuroendocrine tumours

label_protocol: 100 ng of total RNA were amplified and labeled using the Affymetrix Whole-Transcript (WT) Sense Target Labeling Protocol without rRNA reduction.

value: pancreatic neuroendocrine tumours


title: glioma15 [No.30]


title: glioma11 [No.19]


title: P22_f_panc_prim_89


title: glioma5 [No.26]


title: P31_m_liv_met_40


title: glioma9 [No.2]


title: P37_m_panc_prim_20


title: P39_f_panc_prim_34


title: P40_m_liver_met_64


title: glioma7 [No.5]


title: P23_f_panc_prim_76


title: glioma6 [No.4]


title: P21_f_lymph_met_70


title: P19_f_panc_prim_51


title: glioma2 [No.11]


title: P25_f_panc_prim_59


title: glioma1 [No.32]


title: P26_f_liver_met_82


title: P30_f_lymph_met_54


title: P35_f_panc_prim_68


title: P20_m_panc_prim_1


title: P39_f_liv_met_35


title: P18_m_panc_prim_17


title: glioma8 [No.3]


title: glioma3 [No.31]

source_name: oligodendrocytoma II_surgical specimen

value: oligodendrocytoma II


title: P13_f_liv_met_80


title: P14_m_panc_prim_52


title: P45_f_panc_prim_81


title: P11_m_panc_prim_12


title: P10_m_panc_prim_87


title: P09_m_liv_met_28


title: P08_m_panc_prim_3


title: P04_m_panc_prim_8


title: P02_m_perit_met_53


title: P09_m_panc_prim_10


title: P07_m_panc_prim_11


title: P01_m_panc_prim_60


title: P03_f_panc_prim_50


title: iSSC_rep2

city: Seoul

first: Boyoun

last: Park

address: 50 Yonsei-ro, Seodaemun-gu

department: Systems biology

country: South Korea

institute: Yonsei University

description: Gene expression data from intermediate state SSC

hyb_protocol: Microarray hybridization was then performed using Affymetrix Mouse Genome 430 2.0 Array.

scan_protocol: GeneChips were scanned using the Affymetrix GCS 3000 7G scanner .

data_processing: The data were analyzed with robust multi-array average (RMA) method using 'affy' bioconductor package.

source_name: Intermediate spermatogonial stem cells

label_protocol: 10ug total RNAs were then amplified and labelled using the Nugen WT Ovation One-Direct RNA Amplification and Nugen FL-Ovation cDNA Biotin Module V2 labelling kits, respectively.

growth_protocol: The enzymatically dissociated testicular cell suspension was plated on 0.1% gelatin-coated dishes (1-1.5 x 10^5 cells/cm2) in serum-free germ stem cell (GS) medium. SSC clumps obtained from early (0-1) and middle (9-10) passages were transferred onto mitomycin-treated mouse embryonic fibroblast (MEF) feeder layers and passaged every 5-6 days. When colonies with a flattened or ES-like shape appeared, they were either continuously cultured in GS medium or transferred into serum-free KSR-mES media.

treatment_protocol: Testicular cell-derived SSCs slowly proliferated and then formed clumplike structures on the somatic cells 2-4 weeks after seeding. Cultured cells were dissociated by trypsinization and re-plated on fresh MEFs every 5-7 days.

value: intermediate spermatogonial stem cells

value: 3-5 day old


title: SSC_rep2

description: Gene expression data from SSC

source_name: Unipotent germ-line stem cells

value: unipotent germ-line spermatogonial stem cells


title: mSSC_rep1

description: Gene expression data from multipotent state SSC

source_name: Multipotent spermatogonial stem cells

value: multipotent spermatogonial stem cells

value: male


title: Blantyre Malaria Project_PID_3093

city: Bronx

first: Johanna

middle: Patricia

last: Daily

state: NY

address: 1301 Morris Park Avenue, Price Center

department: Medicine (Infectious Disease)

institute: Albert Einstein College of Medicine

description: Patients with Cerebral Malaria were enrolled in the Blantyre Malaria project. 3 mL of whole blood in EDTA was collected at admission and added to Tri-reagent BD (Molecular Research Center) and frozen at -80oC

hyb_protocol: Following fragmentation, 5.5ug of sscDNA were hybridized for 17 hours at 45C on GeneChip Human Gene 1.0 ST Array, GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G7

data_processing:
CEL files were analyzed using GenePattern; Robust Multi-Array Average (RMA) procedure was used, and the data was quantile normalized and background corrected. There are 32,322 probes
We collapsed the probes to 24,891 genes and removed unannotated genes

source_name: Human whole blood_Cerebral malaria_3093

label_protocol: Biotinylated sscDNA were prepared according to the standard Ambion and Afymetrix protocols from 5.5ug total sscDNA (The Ambion WT Expression Kit for Affymetrix GeneChip Whole Transcript (WT)

extract_protocol: Tri-reagent extraction of total RNA was performed according to the manufacturer's instructions.

tag: retinopathy

value: Ret+

tag: parasitemia

value: blood


title: iSSC_rep1

value: ICR


title: Blantyre Malaria Project_PID_3096

source_name: Human whole blood_Cerebral malaria_3096

value: Ret-


title: Blantyre Malaria Project_PID_3094

source_name: Human whole blood_Cerebral malaria_3094


title: Blantyre Malaria Project_PID_3091

source_name: Human whole blood_Cerebral malaria_3091


title: SSC_rep1

description: Gene expression data from SSC


title: mSSC_rep2


title: Blantyre Malaria Project_PID_3085

source_name: Human whole blood_Cerebral malaria_3085


title: Blantyre Malaria Project_PID_3086

source_name: Human whole blood_Cerebral malaria_3086


title: Oxydative bisulfite treated  genomic DNA from Control Cerebellum  2

city: hackensack

first: Benjamin

last: Tycko

state: NJ

address: 40 prospect avenue

department: Epigenetics

institute: HUMC

description:
Control  Adult Cerebellum of patient 252 with oxidative bisulfite treatment for 5mC assessment
tb8487_OXBS

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol. To distinguish 5mc from 5hmC in a subset of Down syndrome and control cerebellar cortices, bisulfite converted DNA and oxidative bisulfite converted DNA according to TrueMethylTM6 kit (CEGX) protocol was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip, in parallel.

scan_protocol: Arrays were imaged using Illumina iScan according to manufacturer's specifications (Illumina Inc.).

data_processing:
Genome Studio software
For DS_processed_norm_no_batch_correction_no_filtering_matrix_1: normalized average beta values after background correction and normalization to internal controls (before ComBat batch adjustment and with no filtering)
For DS_processed_norm_batch_corrected_filtered_matrix_2: normalized average beta values after background correction and normalization to internal controls. In addition all probes mapping on the X or Y chromosome were removed along with those probes querying CpGs that overlapped common simple nucleotide polymorphisms (SNPs with minor allele frequency>1% in dbSNP build 138). Poorly performing probes with missing values (AVG_Beta detection p-value>.05) in more than 10% of the samples per subgroup were filtered out. We corrected for batch effect in the filtered probe sets using the ComBat R package including disease status in the adjustment model as an explanatory covariate, separately by tissue and cell type.  ComBat adjustment requires at least 2 samples per batch. For each batch and tissue, probes with non missing values in less than 2 samples from the same subgroup were filtered out. These processed data correspond to the supplementary tables S3-S7 of the published manuscript.
For DS_OXBS_processed_matrix_3: BS values correspond to  normalized average beta values (background correction and normalization to internal controls) after bisulfite treatment and OXBS values correspond to  normalized average beta values after oxidative bisulfite treatment. In the manuscript, probes with detection p-values>0.005 in more than 1 sample were filtered out. These processed data correspond to the supplementary table S8 of the published manuscript.
For DS_raw_signal_matrix_1: unmethylated and methylated signal intensities without background correction and normalization to internal controls
For DS_OXBS_raw_signal_matrix_2: unmethylated and methylated signal intensities without background correction and normalization to internal controls.  BS values correspond to intenstities in bisulifte treated DNA samples, OXBS values correspond to intenstities in oxidative bisulfite treated DNA samples.

label: Cy5 and Cy3

source_name: Oxydative bisulfite treated  Control Cerebellum 2

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA samples were isolated using Phenol-chloroform extraction protocol.

value: Female

tag: developmental stage

value: Adult

value: Cerebellar cortex

value: Whole grey matter

tag: disease state

value: Normal


title: Blantyre Malaria Project_PID_3089

source_name: Human whole blood_Cerebral malaria_3089


title: Oxydative bisulfite treated  genomic DNA from Down syndrome Cerebellum  1

description:
Down syndrome  Adult Cerebellum of patient 311 with oxidative bisulfite treatment for 5mC assessment
tb8489_OXBS

source_name: Oxydative bisulfite treated  Down syndrome Cerebellum 1

value: Male

value: Down syndrome


title: Blantyre Malaria Project_PID_3084

source_name: Human whole blood_Cerebral malaria_3084


title: Blantyre Malaria Project_PID_3083

source_name: Human whole blood_Cerebral malaria_3083


title: 1-Pancreatic neuroendocrine tumor

description: Pancreatic neuroendocrine tumor

source_name: Pancreatic neuroendocrine tumor

value: Pancreatic neuroendocrine tumor


title: Oxydative bisulfite treated genomic DNA from Control Cerebellum  1

description:
Control  Adult Cerebellum of patient 248 with oxidative bisulfite treatment for 5mC assessment
tb8486_OXBS

source_name: Oxydative bisulfite treated  Control Cerebellum 1


title: Bisulfite treated genomic DNA from Down syndrome Cerebellum  3

description:
Down syndrome  Adult Cerebellum of patient 1391 with bisulfite treatment for 5hmC and 5mC assessment
tb8491_BS

source_name: Bisulfite treated Down syndrome Cerebellum 3


title: Bisulfite treated genomic DNA from Control Cerebellum  1

description:
Control  Adult Cerebellum of patient 248 with bisulfite treatment for 5hmC and 5mC assessment
tb8486_BS

source_name: Bisulfite treated  Control Cerebellum 1


title: Blantyre Malaria Project_PID_3080

source_name: Human whole blood_Cerebral malaria_3080


title: Bisulfite treated genomic DNA from Control Cerebellum  3

description:
Control  Adult Cerebellum of patient 255 with bisulfite treatment for 5hmC and 5mC assessment
tb8488_BS

source_name: Bisulfite treated  Control Cerebellum 3


title: Blantyre Malaria Project_PID_3078

source_name: Human whole blood_Cerebral malaria_3078


title: Blantyre Malaria Project_PID_3081

source_name: Human whole blood_Cerebral malaria_3081


title: Bisulfite treated genomic DNA from Down syndrome Cerebellum  2

description:
Down syndrome  Adult Cerebellum of patient 482 with bisulfite treatment for 5hmC and 5mC assessment
tb8490_BS

source_name: Bisulfite treated Down syndrome Cerebellum 2


title: Bisulfite treated genomic DNA from Down syndrome Cerebellum  1

description:
Down syndrome  Adult Cerebellum of patient 311 with bisulfite treatment for 5hmC and 5mC assessment
tb8489_BS

source_name: Bisulfite treated Down syndrome Cerebellum 1


title: Blantyre Malaria Project_PID_3070

source_name: Human whole blood_Cerebral malaria_3070


title: genomic DNA from Control Fetal cerebrum  6

description:
Control Fetal cerebrum of patient 16-BR-125
tb7042

source_name: Control Fetal cerebrum 6

value: Fetus

value: Cerebrum

value: Whole Cerebrum