title: willm-00090: ALL_230


title: topal-00242: TCGA-04-1342-01A

status: Public on Dec 22 2016

type: RNA

city: Rockville

first: Mervi

last: Heiskanen

state: MD

address: 9609 Medical Center Drive, 1W378

department: CBIIT

country: USA

institute: NCI

hyb_protocol: See mage-tab files linked to series entry for additional details

molecule: total RNA

organism: Homo sapiens

source_name: Primary solid tumor

tag: diseasestate

value: Serous Cystadenocarcinoma

tag: organismpart

value: Ovary

tag: age

tag: Sex

value: Female

tag: individual

tag: diseasestaging

value: IV

tag: external id

tag: tumorgrading


title: willm-00090: ALL_228

scan_protocol: See mage-tab files linked to series entry for additional details

label: biotin

source_name: Pre-treatment leukemia diagnostic sample

tag: agevalue

value: female

value: Peripheral Blood/Bone Marrow

tag: histology

value: B Precursor ALL


title: willm-00090: ALL_226

data_processing: See mage-tab files linked to series entry for additional details

value: Pre-treatment leukemia diagnostic sample

value: male


title: willm-00090: ALL_225

label_protocol: See mage-tab files linked to series entry for additional details


title: topal-00242: TCGA-24-1474-01A

extract_protocol: See mage-tab files linked to series entry for additional details

value: IIIC


title: willm-00090: ALL_238


title: topal-00242: TCGA-13-1506-01A


title: willm-00090: ALL_224


title: willm-00090: ALL_236


title: topal-00242: TCGA-61-1906-01A


title: topal-00242: TCGA-61-1736-01B


title: willm-00090: ALL_222


title: topal-00242: TCGA-13-0720-01A


title: topal-00242: TCGA-61-2613-01A

value: NOT SPECIFIED

value: UNKNOWN


title: willm-00090: ALL_220


title: topal-00242: TCGA-23-1026-01B


title: topal-00242: TCGA-01-0628-11A

source_name: Solid normal tissue

value: many


title: topal-00242: TCGA-24-2020-01A


title: topal-00242: TCGA-29-1688-01A


title: topal-00242: TCGA-13-0891-01A


title: willm-00090: ALL_216


title: topal-00242: TCGA-24-0982-01A


title: willm-00090: ALL_227


title: topal-00242: TCGA-24-2295-01A


title: willm-00090: ALL_215


title: topal-00242: TCGA-29-1781-01A


title: topal-00242: TCGA-24-1466-01A


title: willm-00090: ALL_223


title: willm-00090: ALL_213


title: willm-00090: ALL_212


title: willm-00090: ALL_211


title: willm-00090: ALL_210


title: willm-00090: ALL_221


title: willm-00090: ALL_219


title: topal-00242: TCGA-04-1350-01A


title: willm-00090: ALL_214


title: topal-00242: TCGA-13-1499-01A


title: willm-00090: ALL_218


title: topal-00242: TCGA-61-1730-01A

value: IC


title: willm-00090: ALL_208


title: willm-00090: ALL_205


title: topal-00242: TCGA-23-1021-01B


title: topal-00242: TCGA-04-1347-01A


title: willm-00090: ALL_206


title: willm-00090: ALL_204

value: T-Cell lineage ALL


title: willm-00090: ALL_203


title: topal-00242: TCGA-29-1775-01A


title: willm-00090: ALL_201


title: topal-00242: TCGA-24-1845-01A


title: topal-00242: TCGA-13-1481-01A


title: willm-00090: ALL_202


title: topal-00242: TCGA-24-1842-01A


title: topal-00242: TCGA-61-2612-01A


title: willm-00090: ALL_200


title: topal-00242: TCGA-57-1584-01A


title: willm-00090: ALL_199


title: topal-00242: TCGA-20-1683-01A


title: topal-00242: TCGA-09-1661-01B


title: willm-00090: ALL_207


title: willm-00090: ALL_198


title: topal-00242: TCGA-24-1463-01A


title: topal-00242: TCGA-36-1580-01A


title: willm-00090: ALL_197


title: willm-00090: ALL_196


title: willm-00090: ALL_195


title: topal-00242: TCGA-23-2645-01A


title: topal-00242: TCGA-13-0760-01A


title: willm-00090: ALL_194


title: topal-00242: TCGA-29-1702-01A


title: willm-00090: ALL_193


title: topal-00242: TCGA-13-0900-01B


title: topal-00242: TCGA-24-2261-01A


title: willm-00090: ALL_190


title: topal-00242: TCGA-29-1701-01A


title: topal-00242: TCGA-29-1693-01A


title: willm-00090: ALL_192


title: willm-00090: ALL_188


title: willm-00090: ALL_187


title: topal-00242: TCGA-10-0928-01A


title: willm-00090: ALL_186


title: willm-00090: ALL_191


title: topal-00242: TCGA-04-1338-01A


title: topal-00242: TCGA-04-1648-01A


title: willm-00090: ALL_185


title: willm-00090: ALL_184


title: topal-00242: TCGA-59-2348-01A


title: topal-00242: TCGA-25-1628-01A


title: willm-00090: ALL_183


title: topal-00242: TCGA-04-1530-01A


title: topal-00242: TCGA-61-2000-01A


title: willm-00090: ALL_182


title: willm-00090: ALL_181


title: willm-00090: ALL_209


title: topal-00242: TCGA-31-1946-01A


title: topal-00242: TCGA-29-1764-01A


title: willm-00090: ALL_189


title: topal-00242: TCGA-59-2350-01A


title: topal-00242: TCGA-25-1623-01A


title: willm-00090: ALL_177


title: willm-00090: ALL_176


title: topal-00242: TCGA-57-1586-01A


title: topal-00242: TCGA-13-1410-01A

value: GX


title: willm-00090: ALL_175


title: topal-00242: TCGA-13-0768-01A


title: willm-00090: ALL_173


title: topal-00242: TCGA-13-1488-01A


title: willm-00090: ALL_171


title: willm-00090: ALL_172


title: willm-00090: ALL_174


title: willm-00090: ALL_170


title: topal-00242: TCGA-23-2643-01A


title: topal-00242: TCGA-23-1111-01A


title: topal-00242: TCGA-24-1920-01A


title: willm-00090: ALL_168


title: topal-00242: TCGA-29-2436-01A


title: willm-00090: ALL_169


title: willm-00090: ALL_180


title: topal-00242: TCGA-29-1769-01A


title: topal-00242: TCGA-23-2084-01A


title: topal-00242: TCGA-13-2059-01A


title: willm-00090: ALL_179


title: willm-00090: ALL_167


title: topal-00242: TCGA-29-1707-02A

source_name: Recurrent Solid Tumor

value: IIC


title: willm-00090: ALL_178


title: willm-00090: ALL_166


title: topal-00242: TCGA-29-1707-01A

value: Serous Cystadenocarcinoma


title: willm-00090: ALL_165


title: topal-00242: TCGA-25-1325-01A

value: Ovary


title: topal-00242: TCGA-24-1431-01A

value: Female


title: willm-00090: ALL_164


title: topal-00242: TCGA-13-0725-01A


title: willm-00090: ALL_217


title: willm-00090: ALL_162


title: topal-00242: TCGA-04-1644-01B


title: willm-00090: ALL_163


title: willm-00090: ALL_161


title: topal-00242: TCGA-13-1477-01A

value: IV


title: willm-00090: ALL_160

value: female


title: topal-00242: TCGA-10-0931-01A


title: willm-00090: ALL_159

value: Peripheral Blood/Bone Marrow


title: topal-00242: TCGA-24-1923-01A


title: willm-00090: ALL_158

value: B Precursor ALL


title: willm-00090: ALL_157

value: Pre-treatment leukemia diagnostic sample


title: willm-00090: ALL_155

value: male


title: willm-00090: ALL_154


title: topal-00242: TCGA-36-2551-01A


title: willm-00090: ALL_156


title: topal-00242: TCGA-23-1030-01A

value: IIIC


title: topal-00242: TCGA-61-2095-01A


title: topal-00242: TCGA-23-1120-01A


title: topal-00242: TCGA-30-1869-01A


title: willm-00090: ALL_153


title: willm-00090: ALL_152


title: topal-00242: TCGA-24-1562-01A


title: willm-00090: ALL_149


title: willm-00090: ALL_150


title: willm-00090: ALL_147


title: topal-00242: TCGA-24-1553-01A

value: IIIB


title: willm-00090: ALL_151


title: topal-00242: TCGA-61-2095-02A


title: topal-00242: TCGA-61-2102-01A


title: topal-00242: TCGA-61-1903-01A

value: IB


title: willm-00090: ALL_148


title: willm-00090: ALL_145


title: topal-00242: TCGA-23-1117-01A


title: topal-00242: TCGA-04-1332-01A


title: willm-00090: ALL_146


title: willm-00090: ALL_144


title: willm-00090: ALL_143


title: topal-00242: TCGA-36-2537-01A

value: NOT SPECIFIED

value: UNKNOWN


title: topal-00242: TCGA-13-1482-01A


title: willm-00090: ALL_141


title: willm-00090: ALL_142


title: topal-00242: TCGA-13-0910-01A


title: topal-00242: TCGA-29-1763-01A


title: willm-00090: ALL_140


title: topal-00242: TCGA-42-2588-01A


title: willm-00090: ALL_139


title: topal-00242: TCGA-61-2101-01A


title: topal-00242: TCGA-24-1604-01A


title: topal-00242: TCGA-24-1614-01A


title: willm-00090: ALL_138


title: topal-00242: TCGA-36-2547-01A


title: topal-00242: TCGA-24-1603-01A


title: willm-00090: ALL_137


title: willm-00090: ALL_136


title: topal-00242: TCGA-24-1545-01A


title: topal-00242: TCGA-61-2008-01A


title: topal-00242: TCGA-61-2008-02A


title: willm-00090: ALL_133


title: topal-00242: TCGA-24-2024-01A


title: willm-00090: ALL_135


title: willm-00090: ALL_132


title: topal-00242: TCGA-36-2543-01A


title: willm-00090: ALL_130

value: T-Cell lineage ALL


title: topal-00242: TCGA-24-1549-01A


title: willm-00090: ALL_131


title: willm-00090: ALL_128


title: willm-00090: ALL_127


title: willm-00090: ALL_129


title: topal-00242: TCGA-23-1114-01B


title: topal-00242: TCGA-31-1950-01A


title: topal-00242: TCGA-24-1426-01A


title: topal-00242: TCGA-29-1691-01A


title: willm-00090: ALL_126


title: topal-00242: TCGA-13-0803-01A


title: willm-00090: ALL_125


title: topal-00242: TCGA-25-1631-01A


title: willm-00090: ALL_123


title: willm-00090: ALL_122


title: topal-00242: TCGA-23-1110-01A


title: willm-00090: ALL_134


title: willm-00090: ALL_121


title: topal-00242: TCGA-13-0884-01B


title: topal-00242: TCGA-30-1862-01A


title: topal-00242: TCGA-24-2023-01A

value: IIIA


title: willm-00090: ALL_120


title: topal-00242: TCGA-42-2591-01A


title: willm-00090: ALL_117


title: willm-00090: ALL_119


title: topal-00242: TCGA-20-1684-01A


title: topal-00242: TCGA-09-1665-01B


title: topal-00242: TCGA-24-1843-01A


title: willm-00090: ALL_113


title: willm-00090: ALL_114


title: topal-00242: TCGA-13-2061-01A


title: topal-00242: TCGA-57-1583-01A


title: topal-00242: TCGA-31-1951-01A


title: topal-00242: TCGA-10-0925-01B


title: willm-00090: ALL_115


title: willm-00090: ALL_116


title: willm-00090: ALL_112


title: willm-00090: ALL_124


title: willm-00090: ALL_111


title: topal-00242: TCGA-29-1761-01A


title: willm-00090: ALL_110


title: topal-00242: TCGA-25-1635-01A


title: topal-00242: TCGA-04-1646-01A


title: willm-00090: ALL_109


title: willm-00090: ALL_108


title: topal-00242: TCGA-13-1492-01A


title: topal-00242: TCGA-09-0365-01A


title: topal-00242: TCGA-24-2035-01A


title: willm-00090: ALL_107


title: topal-00242: TCGA-61-1918-01A


title: willm-00090: ALL_106


title: topal-00242: TCGA-13-2066-01A


title: willm-00090: ALL_118


title: willm-00090: ALL_105


title: willm-00090: ALL_104


title: topal-00242: TCGA-61-2003-01A


title: willm-00090: ALL_103


title: topal-00242: TCGA-31-1953-01A


title: topal-00242: TCGA-23-1809-01A

value: IIC


title: topal-00242: TCGA-36-2530-01A


title: willm-00090: ALL_101


title: willm-00090: ALL_102


title: topal-00242: TCGA-61-1915-01A

value: Serous Cystadenocarcinoma


title: willm-00090: ALL_100


title: topal-00242: TCGA-25-1319-01A

value: Ovary


title: willm-00090: ALL_098


title: willm-00090: ALL_099


title: topal-00242: TCGA-61-2097-01A

value: Female


title: topal-00242: TCGA-23-1124-01A


title: topal-00242: TCGA-36-2529-01A


title: topal-00242: TCGA-13-0800-01A


title: willm-00090: ALL_096


title: willm-00090: ALL_097


title: willm-00090: ALL_095


title: topal-00242: TCGA-13-1511-01A

value: IV


title: willm-00090: ALL_094


title: topal-00242: TCGA-01-0638-11A

value: many


title: willm-00090: ALL_093

value: Peripheral Blood/Bone Marrow


title: topal-00242: TCGA-61-1899-01A


title: topal-00242: TCGA-36-1570-01A


title: topal-00242: TCGA-25-1320-01A


title: willm-00090: ALL_092

value: female

value: B Precursor ALL


title: willm-00090: ALL_091

value: Pre-treatment leukemia diagnostic sample

value: male


title: topal-00242: TCGA-24-2280-01A

value: IIIC


title: willm-00090: ALL_090


title: topal-00242: TCGA-29-1785-01A


title: willm-00090: ALL_088


title: willm-00090: ALL_089


title: willm-00090: ALL_086


title: topal-00242: TCGA-13-0792-01A


title: topal-00242: TCGA-09-0366-01A


title: topal-00242: TCGA-25-2399-01A


title: topal-00242: TCGA-25-1634-01A


title: willm-00090: ALL_085


title: willm-00090: ALL_087


title: willm-00090: ALL_084


title: topal-00242: TCGA-23-1029-01B


title: topal-00242: TCGA-59-2363-01A


title: willm-00090: ALL_083


title: topal-00242: TCGA-24-1419-01A


title: willm-00090: ALL_082


title: topal-00242: TCGA-29-1768-01A


title: topal-00242: TCGA-23-2078-01A


title: topal-00242: TCGA-09-1662-01A


title: topal-00242: TCGA-20-0991-01A

value: IIB


title: willm-00090: ALL_080


title: topal-00242: TCGA-29-1703-01A


title: willm-00090: ALL_079


title: topal-00242: TCGA-09-2050-01A

value: IIA


title: willm-00090: ALL_081


title: topal-00242: TCGA-09-1675-01B

value: IC


title: topal-00242: TCGA-61-1917-01A

value: IIIB


title: topal-00242: TCGA-42-2590-01A

value: NOT SPECIFIED

value: UNKNOWN


title: willm-00090: ALL_077


title: topal-00242: TCGA-09-2051-01A

value: Serous Cystadenocarcinoma


title: topal-00242: TCGA-24-2293-01A

value: OMENTUM

value: Ovary


title: willm-00090: ALL_076


title: BT-474_Untreated_DMSO

city: Barcelona

first: Miguel Angel

last: Pujana

address: Gran Via 199

country: Spain

institute: Institut Catala d'Oncologia IDIBELL

description: Gene expression data from untreated (DMSO) BT-474 cells

hyb_protocol: Affymetrix GeneChip Expression Analysis Technical Manual (P/N 702232 Rev 2).

data_processing: The data were analyzed with Partek Genomics Suite using Affymetrix default analysis settings and global scaling as normalization method.

label: Biotin

source_name: BT-474 exposed to DMSO

label_protocol: FL-Ovation cDNA Biotin Module V2 from NuGen Technologies Inc.

growth_protocol: The cells were cultured and maintained in RPMI medium containing 10% FBS and 2 mM glutamine.

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

treatment_protocol: The cells were treated with everolimus (150 nM) or vehicle (DMSO) for 100 days

tag: cell type

value: Breast cancer cell line


title: topal-00242: TCGA-30-1867-01A

value: Female

value: IV

value: GX


title: topal-00242: TCGA-24-1924-01A


title: willm-00090: ALL_075

value: Peripheral Blood/Bone Marrow

value: B Precursor ALL


title: topal-00242: TCGA-13-1496-01A


title: topal-00242: TCGA-36-1568-01A


title: topal-00242: TCGA-24-1470-01A


title: topal-00242: TCGA-23-1023-01R


title: topal-00242: TCGA-59-2355-01A


title: topal-00242: TCGA-23-1023-01A


title: willm-00090: ALL_073

value: Pre-treatment leukemia diagnostic sample

value: female


title: willm-00090: ALL_074


title: willm-00090: ALL_078

value: male


title: willm-00090: ALL_072

value: T-Cell lineage ALL


title: topal-00242: TCGA-25-1316-01A

value: IIIC


title: BT-474_Treated_Everolimus

description: Gene expression data from treated (150 nM everolimus for 100 days) BT-474 cells

scan_protocol: Affymetrix GeneChip Expression Analysis Technical Manual (P/N 702232 Rev 2).

source_name: BT-474 exposed to Everolimus


title: willm-00090: ALL_071


title: HCC1937_Control

hyb_protocol: Affymetrix GeneChip Expression Analysis Technical Manual (P/N 702232 Rev 2)

data_processing: The data were analyzed with Partek Genomics Suite using Affymetrix default analysis settings and global scaling as normalization method

source_name: HCC1937 cell line

label_protocol: FL-Ovation cDNA Biotin Module V2 from NuGen Technologies Inc

growth_protocol: MCF7 and HCC1937 cells were cultured and maintained in RPMI medium containing 10% FBS and 2 mM glutamine.

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

treatment_protocol: MCF7 cells were treated with everolimus (100 nM) and HCC1937 cells were treated with everolimus (150 nM) or vehicle (DMSO) for 120 days.

tag: cell line

tag: cell line orgin

value: Breast cancer

tag: agent

value: vehicle (DMSO)


title: MCF7_120days_everolimus

scan_protocol: Affymetrix GeneChip Expression Analysis Technical Manual (P/N 702232 Rev 2)

source_name: MCF7 cell line treated

value: Everolimus (100 nM)


title: MCF7_Control

source_name: MCF7 cell line


title: topal-00242: TCGA-25-2042-01A

value: Serous Cystadenocarcinoma


title: topal-00242: TCGA-24-2288-01A


title: HCC1937_120days_everolimus

source_name: HCC1937 cell line treated

value: Everolimus (150 nM)


title: topal-00242: TCGA-24-1616-01A

value: Ovary


title: topal-00242: TCGA-13-0901-01B


title: topal-00242: TCGA-13-1407-01A


title: topal-00242: TCGA-23-1123-01A


title: topal-00242: TCGA-04-1654-01A


title: Breast tumor_ Control 1

source_name: Primary breast tumor not treated

growth_protocol: Primary triple-negative breast tumor (from a BRCA1 mutation carrier) orthotopically engrafted in immunocompromised mice was monitored 2 to 3 times per week.

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

treatment_protocol: A daily oral treatment with sirolimus (Rapamune) or control solution (DMSO) was applied (60 days).

value: DMSO

tag: tissue


title: willm-00090: ALL_069


title: Breast tumor_ Sirolimus 2

source_name: Primary breast tumor treated with sirolimus

growth_protocol: Primary breast tumor (from a BRCA mutation carrier) orthotopically implanted in immunocompromised mice was monitored 2 to 3 times per week.

treatment_protocol: A daily oral treatment with sirolimus (Rapamune) or control solution (DMSO) was applied (30 days).

value: Sirolimus


title: Breast tumor_ Control 2


title: topal-00242: TCGA-24-1927-01A

value: Female


title: willm-00090: ALL_070


title: topal-00242: TCGA-24-1556-01A

value: IIB


title: topal-00242: TCGA-24-1422-01A


title: topal-00242: TCGA-31-1959-01A

value: IV


title: topal-00242: TCGA-13-1479-01A

value: NOT SPECIFIED

value: UNKNOWN


title: topal-00242: TCGA-25-1328-01A


title: topal-00242: TCGA-59-2354-01A


title: willm-00090: ALL_067

value: Pre-treatment leukemia diagnostic sample

value: Peripheral Blood/Bone Marrow

value: B Precursor ALL


title: topal-00242: TCGA-29-1770-01A

value: IIIC


title: willm-00090: ALL_065

value: male

value: T-Cell lineage ALL


title: willm-00090: ALL_066

value: female


title: topal-00242: TCGA-24-1930-01A

value: Serous Cystadenocarcinoma


title: willm-00090: ALL_068


title: Breast tumor_ Sirolimus 1

value: Breast cancer


title: topal-00242: TCGA-24-1550-01A

value: Ovary


title: willm-00090: ALL_064


title: willm-00090: ALL_063


title: topal-00242: TCGA-24-2019-01A


title: topal-00242: TCGA-24-2029-01A


title: topal-00242: TCGA-29-1770-02A


title: topal-00242: TCGA-13-2060-01A


title: willm-00090: ALL_062


title: topal-00242: TCGA-04-1336-01A

value: IIIB


title: topal-00242: TCGA-36-2542-01A


title: topal-00242: TCGA-36-2532-01A


title: topal-00242: TCGA-13-0883-01A


title: topal-00242: TCGA-01-0642-11A

value: many


title: topal-00242: TCGA-09-2048-01A

value: Female


title: willm-00090: ALL_060


title: topal-00242: TCGA-61-1914-01A


title: willm-00090: ALL_059


title: topal-00242: TCGA-13-0797-01A


title: Breast tumor_ Control, biological replicate 2

description: Gene expression data from 4T1 cell line

organism: Mus musculus

source_name: 4T1 Tumor cell line DMSO treated

growth_protocol: 4T1 cells were injected subcutaneously in mice and subsequently were treated with RAD001 (5mg/kg) or DMSO solution (placebo).

treatment_protocol: A daily intraperitoneal treatment with Rad001 (5mg/kg) or DMSO solution (placebo) was applied (15 days)

tag: treatment

value: control


title: topal-00242: TCGA-25-2408-01A

value: IV


title: Breast tumor_ RAD001, biological replicate 2

description: Gene expression data from 4T1 cell line

source_name: 4T1 Tumor cell line RAD001 treated


title: topal-00242: TCGA-25-1326-01A


title: willm-00090: ALL_058


title: Breast tumor_ RAD001, biological replicate 3

description: Gene expression data from 4T1 cell line


title: Breast tumor_ Control, biological replicate 4

description: Gene expression data from 4T1 cell line


title: Breast tumor_ RAD001, biological replicate 4

description: Gene expression data from 4T1 cell line


title: Breast tumor_ Control, biological replicate 3

description: Gene expression data from 4T1 cell line


title: topal-00242: TCGA-24-1104-01A


title: Breast tumor_ Control, biological replicate 1

description: Gene expression data from 4T1 cell line


title: Breast tumor_ RAD001, biological replicate 1

description: Gene expression data from 4T1 cell line


title: topal-00242: TCGA-24-2298-01A


title: willm-00090: ALL_056


title: topal-00242: TCGA-13-1485-01A


title: willm-00090: ALL_057


title: willm-00090: ALL_055


title: topal-00242: TCGA-36-1569-01A


title: topal-00242: TCGA-13-1817-01A


title: willm-00090: ALL_054


title: topal-00242: TCGA-13-1817-02A


title: topal-00242: TCGA-25-1315-01A


title: topal-00242: TCGA-61-1910-01A

value: IIC


title: topal-00242: TCGA-20-1685-01A


title: topal-00242: TCGA-24-1428-01A


title: topal-00242: TCGA-30-1857-01A


title: willm-00090: ALL_051


title: topal-00242: TCGA-24-1417-01A


title: willm-00090: ALL_053


title: willm-00090: ALL_052


title: topal-00242: TCGA-42-2587-01A

value: NOT SPECIFIED

value: UNKNOWN


title: topal-00242: TCGA-13-1489-02A


title: topal-00242: TCGA-13-1489-01A


title: topal-00242: TCGA-24-0968-01A


title: willm-00090: ALL_047

value: Pre-treatment leukemia diagnostic sample

value: Peripheral Blood/Bone Marrow


title: willm-00090: ALL_049

value: B Precursor ALL


title: topal-00242: TCGA-04-1331-01A

value: IIIC


title: topal-00242: TCGA-61-2098-01A


title: topal-00242: TCGA-04-1351-01A


title: topal-00242: TCGA-10-0935-01A


title: willm-00090: ALL_045

value: male


title: topal-00242: TCGA-24-1425-01A


title: willm-00090: ALL_046


title: topal-00242: TCGA-20-1686-01A


title: topal-00242: TCGA-09-1659-01B


title: willm-00090: ALL_044


title: topal-00242: TCGA-61-2104-01A


title: Bladder carcinoma tissue_patient 3

city: Chongqing

first: Zhenyu

last: Zhong

address: No. 1 Yixueyuan Road

country: China

institute: Chongqing Medical University

description: N.A.

hyb_protocol: 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned using the Agilent Scanner G2505C.

data_processing: Scanned images were imported into Agilent Feature Extraction software for raw data extraction. Quantile normalization of raw data and subsequent data processing were performed using the R software package.

source_name: Bladder carcinoma tissue

label_protocol: Each sample was amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × Hybridization buffer was added to dilute the labeled cRNA.

extract_protocol: Total RNA was isolated from frozen tissues stored in liquid nitrogen using TRIzol (Invitrogen) according to manufacturer’s recommendations. RNA quantity and quality were determined by OD260 using a NanoDrop ND-1000 spectrophotometer and RNA integrity was assessed by electrophoresis on a denaturing agarose gel.

tag: gender

tag: patient diagnosis

value: bladder cancer


title: Para-carcinoma_patient 2

description: N.A.

source_name: Adjacent normal tissue


title: Bladder carcinoma tissue_patient 4

description: N.A.


title: Para-carcinoma_patient 3

description: N.A.


title: willm-00090: ALL_048

tag: diseasestate

tag: organismpart


title: HCC1937 cells: untreated

type: genomic

hyb_protocol: Purified Cy3 and Cy5 labelled DNA were then combined to prepare the array hybridization mixture. Arrays were then hybridized at 65 C for 40 hours and washed following manufacturer s instructions. Hybridization and washes were performed according to Agilent ChIP-on-chip Analysis protocol version 11.0.

scan_protocol: Scanning was performed on a Roche MS200 scanner

data_processing: Raw data and normalized data were extracted using Agilent Feature Extraction Software

molecule: genomic DNA

source_name: EVI1 CHIP in HCC1937 cell line

label_protocol: Labelling was performed according to Agilent ChIP-on-chip Analysis protocol version 11.0. 2.6?g whole cell   extract DNA (Input) or immunoprecipitated DNA were labeled by incorporation of Cy3 or Cy5 dUTP respectively during Klenow polymerization.

growth_protocol: MCF7 and HCC1937 cells were cultured and maintained in RPMI medium containing 10% FBS and 2 mM glutamine

extract_protocol: Extraction of total DNA was performed according to  manufacturer's instructions

treatment_protocol: MCF7 cells were treated with everolimus (100 nM) and HCC1937 cells were treated with everolimus (150 nM) or vehicle (DMSO) for 120 days

tag: phenotype

value: everolimus sensitive

tag: antibody

source_name: IgG Control chip in HCC1937 cell line


title: Para-carcinoma_patient 4

description: N.A.

tag: age


title: willm-00090: ALL_042

source_name: Pre-treatment leukemia diagnostic sample

tag: Sex


title: topal-00242: TCGA-04-1346-01A

source_name: Primary solid tumor

value: Serous Cystadenocarcinoma

tag: individual

tag: diseasestaging

tag: external id

tag: tumorgrading


title: topal-00242: TCGA-23-1022-01A

value: Ovary


title: willm-00090: ALL_041

tag: agevalue

value: female

tag: histology


title: willm-00090: ALL_043


title: topal-00242: TCGA-61-1919-01A


title: willm-00090: ALL_039

value: T-Cell lineage ALL


title: willm-00090: ALL_040


title: topal-00242: TCGA-13-0887-01A

value: Female


title: willm-00090: ALL_038


title: topal-00242: TCGA-57-1994-01A


title: Para-carcinoma_patient 1

description: N.A.


title: Bladder carcinoma tissue_patient 1

description: N.A.


title: topal-00242: TCGA-24-1551-01A


title: MCF7 cells: everolimus-adapted

source_name: EVI1 CHIP in MCF7 cell line (everolimus-adapted)

tag: cell line

value: everolimus-adapted

source_name: IgG Control chip in MCF7 cell line (everolimus-adapted)


title: topal-00242: TCGA-24-1847-01A

value: IV


title: willm-00090: ALL_037


title: topal-00242: TCGA-29-1697-01A


title: MCF7 cells: untreated

source_name: EVI1 CHIP in MCF7 cell line

source_name: IgG Control chip in MCF7 cell line


title: HCC1937 cells: everolimus-adapted

source_name: EVI1 CHIP in HCC1937 cell line (everolimus-adapted)

source_name: IgG Control chip in HCC1937 cell line (everolimus-adapted)


title: willm-00090: ALL_036


title: willm-00090: ALL_035


title: Bladder carcinoma tissue_patient 2

description: N.A.


title: topal-00242: TCGA-13-0893-01B


title: willm-00090: ALL_034


title: topal-00242: TCGA-13-0724-01A


title: willm-00090: ALL_033


title: topal-00242: TCGA-10-0938-01A


title: topal-00242: TCGA-30-1860-01A


title: topal-00242: TCGA-29-1711-01A


title: willm-00090: ALL_029


title: willm-00090: ALL_030


title: willm-00090: ALL_032


title: willm-00090: ALL_031


title: topal-00242: TCGA-61-2012-01A

value: IIC


title: willm-00090: ALL_028


title: topal-00242: TCGA-23-1032-01A


title: willm-00090: ALL_027


title: topal-00242: TCGA-09-1669-01A

value: IIIA


title: willm-00090: ALL_026


title: topal-00242: TCGA-10-0937-01A


title: topal-00242: TCGA-29-1771-01A


title: willm-00090: ALL_025


title: topal-00242: TCGA-24-1555-01A


title: willm-00090: ALL_024


title: topal-00242: TCGA-25-1627-01A


title: willm-00090: ALL_023


title: willm-00090: ALL_061


title: willm-00090: ALL_022


title: willm-00090: ALL_021


title: topal-00242: TCGA-23-2647-01A

value: NOT SPECIFIED

value: UNKNOWN


title: topal-00242: TCGA-04-1525-01A


title: topal-00242: TCGA-09-2045-01A


title: willm-00090: ALL_050

value: Pre-treatment leukemia diagnostic sample

value: Peripheral Blood/Bone Marrow


title: willm-00090: ALL_020

value: B Precursor ALL


title: topal-00242: TCGA-13-1411-01A

value: IIIC


title: willm-00090: ALL_018


title: ck06HA-8l-2

city: Harbin

first: Dongming

last: Zhao

state: HeilongJiang

address: 678 Haping Road

institute: Harbin Veterinary Research Institute

hyb_protocol: Using Agilents Gene Expression Hybridizatoin kit #4 and Gene Expression wash pack #5, Cy3-labeled cRNA preparations were hybridized with Agilent’s Whole Mouse Genome Microarray Kit, 4×44 K (G4122F) for 17 h at 65°C.

scan_protocol: Immediately after washing, Feature Extraction Software, version 7 (Agilent Technologies) was used for image analysis and data extraction.

data_processing: Per chip and per gene normalization was performed using the LIMMA package in R.

source_name: lung tissue

label_protocol: Using the Quick Amp Labeling Kit, T7 RNA polymerase was used to simultaneously amplify target material and incorporate cyanine 3-labeled CTP to prepare Cy3-labeled cRNA.

growth_protocol: 5 weeks old Balb/c mice were maintained in BSL 3 room for one week adaptation before virus infection

extract_protocol: Total RNA was extracted from lung tissues on day 3 p.i. by using a QIAGEN RNeasy kit. The microarray assay was performed by using a Low RNA Input Linear Amplification Kit (Agilent Technologies, Santa Clara, CA) and Agilent’s Whole Mouse Genome Microarray Kit, 4×44 K (G4122F)

treatment_protocol: Mice were intranasally inoculated with PBS or 106 EID50 of influenza viruses, respectively.

tag: time points

value: day 3 post-infection

tag: strain

value: Balb/c

tag: tissue

value: Lung

tag: inoculum

value: A/chicken/Vietnam-Ca Mau/1180/2006 with HA gene from A/chicken/Vietnam-Bac Lieu/1214/2007 (CK/1214)


title: topal-00242: TCGA-25-2396-01A

tag: diseasestate

value: Serous Cystadenocarcinoma

value: Ovary


title: willm-00090: ALL_019

value: female

tag: organismpart


title: ck06HA-7l-1


title: topal-00242: TCGA-36-2539-01A


title: willm-00090: ALL_016

value: male

value: T-Cell lineage ALL


title: topal-00242: TCGA-29-1705-02A

source_name: Recurrent Solid Tumor

value: Female


title: ck06HA-3l-1


title: ck06-3d-4l-1

value: A/chicken/Vietnam-Ca Mau/1180/2006 (CK/1180) (H5N1)


title: 20mGyM8/ reference male mouse3

city: Rokkasho-mura,Kamikita-gun,

first: Keiji

last: OGURA

state: Aomori

address: Takahoko, Hacchasawa,

department: Department of Radiobiology

country: Japan

institute: Institute for Environmental Science

hyb_protocol: Oligonucleotide Array-Based CGH for Genomic DNA Analysis, protocol version 4.0.8

scan_protocol: Scanned on an Agilent G2565BA scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.1.1).

data_processing: Agilent Genomic Workbench Software (v 7.0.) was used.

extract_protocol: PI-50a (Kurabo Industries LTD.) tissue DNA extraction protocol.

value: tail

source_name: reference male mouse3


title: reference male mouse3/ 20mGyM8

label_protocol: Oligonucleotide Array-Based CGH for Genomic DNA Analysis, protocol version 4.0.8


title: topal-00242: TCGA-29-1705-01A


title: willm-00090: ALL_015


title: ck06-3d-5l-2


title: 20mGyM3/ reference male mouse3


title: 20mGyM4/ reference male mouse3


title: 20mGyM7/ reference male mouse3


title: topal-00242: TCGA-29-1776-01A


title: ck06-3d-3l-1


title: reference male mouse3/ 20mGyM7


title: 20mGyM5/ reference male mouse3


title: topal-00242: TCGA-04-1367-01A


title: willm-00090: ALL_014


title: reference male mouse3/ 20mGyM3


title: reference male mouse3/ 20mGyM2


title: reference male mouse3/ 20mGyM1


title: reference male mouse3/ 20mGyMF


title: reference male mouse3/ 20mGyM5


title: reference male mouse3/ 20mGyM6


title: willm-00090: ALL_013


title: topal-00242: TCGA-23-1122-01A


title: 20mGyM2/ reference male mouse3


title: 20mGyMF/ reference male mouse3


title: willm-00090: ALL_012


title: 20mGyM6/ reference male mouse3


title: control-3d-3l-2

value: PBS


title: topal-00242: TCGA-10-0927-01A


title: 20mGyL8/ reference male mouse3


title: willm-00090: ALL_011

value: Pre-treatment leukemia diagnostic sample


title: topal-00242: TCGA-20-0987-01A


title: reference male mouse3/ 20mGyL8


title: topal-00242: TCGA-24-2290-01A

value: OMENTUM


title: 20mGyM1/ reference male mouse3


title: control-3d-2l-2


title: reference male mouse3/ 20mGyL7


title: topal-00242: TCGA-61-1895-01A

value: IIIB


title: reference male mouse3/ 20mGyMM


title: willm-00090: ALL_010

value: Peripheral Blood/Bone Marrow

value: B Precursor ALL


title: willm-00090: ALL_017


title: willm-00090: ALL_009


title: reference male mouse3/ 20mGyM4


title: topal-00242: TCGA-24-1546-01A

value: IIIC


title: willm-00090: ALL_007


title: 20mGyMM/ reference male mouse3


title: control-3d-1l-1

value: day 3 post-infection

value: Balb/c

value: Lung


title: TW10_OVER#1

city: bethesda

first: abdel

last: elkahloun

address: 50 south dr

institute: nih

description: TCF1 over-expressing P14#1

hyb_protocol: The hybridization cocktail containing the fragmented and labeled cDNAs were hybridized to Affymetrix Human GeneChip 1.0 ST microarrays.  The microarrays were washed and stained in an Affymetrix Fluidics Station using standard Affymetrix protocols.

scan_protocol: Genechips were scanned using an Affymetrix Gene Chip Scanner 3000.

data_processing: Gene expression intensities were calculated using GeneChip Command Console Software (AGCC). .cel files generated by the Affymetrix AGCC program were imported in the Affymetrix Expression Console software and RMA (Robust Multichip Analysis) normalization was performed to generate the .chp files. The .chp files were normalized, log2 transformed, and summarized.

source_name: CD8 T cells

label_protocol: Labeling was performed on a sample-by-sample basis according to manufacturer’s guidelines for use with the Affymetrix Mouse HuGene-1_0-st-v1 GeneChips (Affymetrix, Inc).  Bioanalyzer nanochip (Agilent, Inc) and NanoDrop (ThermoFisher, Inc) were used to validate and quantitate the RNA prior to cRNA synthesis and labeling. 200 ng of total RNA was used for labeling with the Ambion WT Expression Kit (cat#4411974)  and Affymetrix kit (Cat # 900652). After hybridization,  the probe arrays were stained with streptavidin-phycoerythrin solution (Molecular Probes) and enhanced using an antibody solution containing 0.5 mg/mL of biotinylated anti-streptavidin (Vector Laboratories).

extract_protocol: Trizol (Invitrogen) and RNaseazy (Qiagen) kits were used to extract total RNA according to the manufacturer's instructions.

value: CD8 T cells

tag: genotype

value: TCF1 over-expression


title: willm-00090: ALL_008

value: male


title: topal-00242: TCGA-20-0990-01A

value: Serous Cystadenocarcinoma

value: Ovary


title: topal-00242: TCGA-04-1649-01A

value: Female


title: TW11_OVER#2

description: TCF1 over-expressing P14#2


title: willm-00090: ALL_006

value: T-Cell lineage ALL


title: topal-00242: TCGA-25-2409-01A

value: IV


title: willm-00090: ALL_005

value: Pre-treatment leukemia diagnostic sample


title: TW12_OVER#3

description: TCF1 over-expressing P14#3


title: TW09_MIG#3

description: Control P14#3

value: WT


title: topal-00242: TCGA-13-1403-01A


title: 20mGyL7/ reference male mouse3

value: tail


title: willm-00090: ALL_004

value: female

value: Peripheral Blood/Bone Marrow


title: 20mGyL6/ reference male mouse3


title: topal-00242: TCGA-61-2087-01A

value: IC


title: willm-00090: ALL_003

value: B Precursor ALL


title: TW08_MIG#2

description: Control P14#2


title: TW07_MIG#1

description: Control P14#1


title: topal-00242: TCGA-13-1501-01A


title: TW06_YFP-Tims3+#3

description: tetramer+ Tim3highBlimp1high CD8 T cells#3


title: willm-00090: ALL_002


title: reference male mouse3/ 20mGyL6


title: TW05_YFP-Tims3+#2

description: tetramer+ Tim3highBlimp1high CD8 T cells#2


title: willm-00090: ALL_001


title: topal-00242: TCGA-61-1913-01A

value: IIIB


title: 20mGyL5/ reference male mouse3


title: TW04_YFP-Tims3+#1

description: tetramer+ Tim3highBlimp1high CD8 T cells#1


title: topal-00242: TCGA-04-1542-01A


title: reference male mouse3/ 20mGyL5


title: topal-00242: TCGA-09-2044-01B

value: IIB


title: topal-00242: TCGA-24-2271-01A

value: IIIC


title: TW01_YFP-Tims3-#1

description: tetramer+ Tim3lowBlimp1low CD8 T cells#1

value: CD8 T cells


title: topal-00242: TCGA-30-1718-01A


title: TW03_YFP-Tims3-#3

description: tetramer+ Tim3lowBlimp1low CD8 T cells#3


title: TW02_YFP-Tims3-#2

description: tetramer+ Tim3lowBlimp1low CD8 T cells#2


title: Bos taurus_lymphocytes_L32_T2

city: legnaro

first: sara

last: pegolo

address: viale dell'università 16

country: Italy

institute: university of padua

description: Sample of bovine lymphocytes

hyb_protocol: Hybridized according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol

scan_protocol: Array was scanned according to standard Agilent protocol at a resolution of 5 microns modifying default setting to scan the slide twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%)

data_processing: Data processed with FeatureExtraction v9.5 and normalized using cyclic lowess by R 2.11.1 statistical software

label: Cyanine 3

organism: Bos taurus

source_name: Bovine lymphocytes samples collected at the slaughterhouse

label_protocol: Amplified and labeled according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol

extract_protocol: Extracted using the Invitrogen TRIzol reagent and purified according to the QiAgen RNeasy MinElute Cleanup Kit protocol for tissue samples

treatment_protocol: prednisolone 30 mg/head daily per os for 35 days

tag: cell type

value: lymphocytes

tag: time point

tag: treatment

value: PREDNISOLONE


title: TW06_Tcf7 KO3

description: Tcf7 cKO tetramer+ CD8 T cells#3

value: Tcf7loxp/loxp; CD4-Cre


title: Bos taurus_lymphocytes_L30_T2

description: Sample of bovine lymphocytes


title: Bos taurus_lymphocytes_L31_T2

description: Sample of bovine lymphocytes


title: topal-00242: TCGA-13-0912-01A

value: Serous Cystadenocarcinoma

value: Ovary

tag: age

tag: Sex

value: Female

tag: individual


title: 20mGyL4/ reference male mouse3


title: Bos taurus_lymphocytes_L29_T2

description: Sample of bovine lymphocytes


title: TW05_Tcf7 KO2

description: Tcf7 cKO tetramer+ CD8 T cells#2


title: reference male mouse3/ 20mGyL4


title: TW04_Tcf7 KO1

description: Tcf7 cKO tetramer+ CD8 T cells#1


title: TW03_Tcf7 WT3

description: WT tetramer+ CD8 T cells #3


title: Bos taurus_lymphocytes_L28_T2

description: Sample of bovine lymphocytes


title: topal-00242: TCGA-09-1672-01A

tag: diseasestaging

tag: external id

tag: tumorgrading


title: topal-00242: TCGA-04-1341-01A

value: NOT SPECIFIED


title: Bos taurus_lymphocytes_L27_T2

description: Sample of bovine lymphocytes


title: reference male mouse3/ 20mGyL3


title: TW02_Tcf7 WT2

description: WT tetramer+ CD8 T cells #2

value: WT


title: 20mGyL3/ reference male mouse3

value: tail


title: 20mGyL2/ reference male mouse3


title: topal-00242: TCGA-36-2549-01A

value: UNKNOWN


title: topal-00242: TCGA-13-0889-01A

value: IV

value: GX


title: TW01_Tcf7 WT1

description: WT tetramer+ CD8 T cells #1


title: topal-00242: TCGA-61-2109-01A


title: Bos taurus_lymphocytes_L25_T2

description: Sample of bovine lymphocytes


title: reference male mouse3/ 20mGyL2


title: Bos taurus_lymphocytes_L24_T2

description: Sample of bovine lymphocytes

value: CONTROL


title: 20mGyLF/ reference male mouse3


title: reference male mouse3/ 20mGyL1


title: topal-00242: TCGA-13-1509-01A


title: topal-00242: TCGA-01-0633-11A

source_name: Solid normal tissue

value: many


title: topal-00242: TCGA-25-1318-01A


title: 20mGyL1/ reference male mouse3


title: Bos taurus_lymphocytes_L23_T2

description: Sample of bovine lymphocytes


title: topal-00242: TCGA-24-1846-01A


title: Liver Transcriptome from CBDLSH_230613

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

institute: CIBEREHD

description: Liver Transcriptome from CBDLSH_230613

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol using a Gene chip scanner 3000

data_processing: Data processing cel files were normalized with 'rma' function of the Bioconductor environment (v2.9) in R.3.0.0

organism: Rattus norvegicus

source_name: Liver tissue

label_protocol: Standard Affymetrix protocol

extract_protocol: Liver samples were fixed in 10% formalin, embedded in paraffin and sectioned (thickness of 2µm). Slides were stained with hematoxylin and eosin (H&E) and assessed by an expert pathologist (RM).

treatment_protocol: Secondary biliary cirrhosis was induced by common bile duct ligation (CBDL). Briefly, under general anesthesia with midazolam (5mg/kg body weight, i.p., Laboratory Reig Jofre, Barcelona, Spain) and ketamine (100mg/kg body weight, i.p., Imalgene, Barcelona, Spain) the common bile duct was isolated and double ligated with 5-0 silk thread. The first ligature was made below the junction of the hepatic ducts and the second one above the pancreatic ducts. Finally, the portion between the two ligatures was resected. Rats received weekly injections of vitamin K and were studied 4 weeks after the surgery. In the drug treated groups simvastatin was suspended in distilled water and administered by gavage (5mg/kg body weight) once a day from 3 days before the final study. Simvastatin inhibits the HMG-CoA activity in the liver as early as 30 min after oral administration, with a peak of inhibitory activity at one hour. Experiments were performed 1 h after the last dose of the drug.

tag: condition

value: Secondary biliary cirrhosis

value: pre-treated with simvastatin submitted to hemorrhage/resuscitation

tag: treatment group

value: CBDLSH


title: Bos taurus_lymphocytes_L22_T2

description: Sample of bovine lymphocytes

value: lymphocytes


title: Liver Transcriptome from CBDLSH_200613

description: Liver Transcriptome from CBDLSH_200613


title: Bos taurus_lymphocytes_L21_T2

description: Sample of bovine lymphocytes


title: 20mGyJ6/ reference male mouse2

tag: strain

source_name: reference male mouse2


title: 20mGyJ5/ reference male mouse2

tag: tissue


title: Liver Transcriptome from CBDLSH_210613

description: Liver Transcriptome from CBDLSH_210613


title: Bos taurus_lymphocytes_L20_T2

description: Sample of bovine lymphocytes


title: reference male mouse3/ 20mGyLF


title: 20mGyLM/ reference male mouse3


title: topal-00242: TCGA-25-1870-01A

value: IIIC


title: reference male mouse2/ 20mGyJ5


title: reference male mouse2/ 20mGyJ6


title: reference male mouse3/ 20mGyLM


title: topal-00242: TCGA-25-1877-01A


title: Bos taurus_lymphocytes_L18_T2

description: Sample of bovine lymphocytes


title: Bos taurus_lymphocytes_L17_T2

description: Sample of bovine lymphocytes


title: topal-00242: TCGA-04-1360-01A

value: IA


title: Liver Transcriptome from CBDLSH_170613

description: Liver Transcriptome from CBDLSH_170613


title: topal-00242: TCGA-24-1103-01A

value: Serous Cystadenocarcinoma


title: Liver Transcriptome from CBDLSH_130312

description: Liver Transcriptome from CBDLSH_130312


title: topal-00242: TCGA-04-1343-01A

value: Ovary


title: Liver Transcriptome from CBDLSH_120613

description: Liver Transcriptome from CBDLSH_120613


title: Bos taurus_lymphocytes_L31_T1

description: Sample of bovine lymphocytes

value: PREDNISOLONE


title: Bos taurus_lymphocytes_L32_T1

description: Sample of bovine lymphocytes


title: Liver Transcriptome from CBDLSH_110613

description: Liver Transcriptome from CBDLSH_110613


title: topal-00242: TCGA-36-2534-01A

value: NOT SPECIFIED


title: Bos taurus_lymphocytes_L30_T1

description: Sample of bovine lymphocytes


title: Liver Transcriptome from CBDLSH_70212

description: Liver Transcriptome from CBDLSH_70212


title: Bos taurus_lymphocytes_L26_T2

description: Sample of bovine lymphocytes


title: reference male mouse2/ 20mGyJ4


title: 20mGyJ4/ reference male mouse2


title: Bos taurus_lymphocytes_L29_T1

description: Sample of bovine lymphocytes


title: Bos taurus_lymphocytes_L28_T1

description: Sample of bovine lymphocytes


title: topal-00242: TCGA-36-2548-01A


title: Liver Transcriptome from CBDLSS_160613

description: Liver Transcriptome from CBDLSS_160613

value: pre-treated with simvastatin submitted to a sham hemorrhage/resuscitation procedure

value: CBDLSS


title: 20mGyJ3/ reference male mouse2

value: tail


title: Bos taurus_lymphocytes_L27_T1

description: Sample of bovine lymphocytes


title: reference male mouse2/ 20mGyJ3


title: topal-00242: TCGA-30-1866-01A

value: Female

value: IV


title: Liver Transcriptome from CBDLSS_180613

description: Liver Transcriptome from CBDLSS_180613


title: reference male mouse2/ 20mGyJ2


title: topal-00242: TCGA-24-2289-01A


title: Bos taurus_lymphocytes_L26_T1

description: Sample of bovine lymphocytes


title: reference male mouse2/ 20mGyJ1


title: Liver Transcriptome from CBDLSS_130613

description: Liver Transcriptome from CBDLSS_130613


title: Liver Transcriptome from CBDLSS_70612

description: Liver Transcriptome from CBDLSS_70612


title: Bos taurus_lymphocytes_L24_T1

description: Sample of bovine lymphocytes

value: CONTROL


title: 20mGyJ2/ reference male mouse2


title: Liver Transcriptome from CBDLpH_2005

description: Liver Transcriptome from CBDLpH_2005

value: submitted to hemorrhage/resuscitation

value: CBDLpH


title: Bos taurus_lymphocytes_L23_T1

description: Sample of bovine lymphocytes


title: 20mGyJ1/ reference male mouse2


title: reference male mouse2/ 20mGyJF


title: topal-00242: TCGA-13-0793-01A


title: Bos taurus_lymphocytes_L22_T1

description: Sample of bovine lymphocytes


title: topal-00242: TCGA-61-1904-01A


title: 20mGyJF/ reference male mouse2


title: 20mGyJM/ reference male mouse2


title: topal-00242: TCGA-61-1740-01A


title: topal-00242: TCGA-24-2030-01A


title: reference male mouse2/ 20mGyJM


title: topal-00242: TCGA-13-1483-01A


title: Bos taurus_lymphocytes_L21_T1

description: Sample of bovine lymphocytes


title: Liver Transcriptome from CBDLSS_100312

description: Liver Transcriptome from CBDLSS_100312

value: Secondary biliary cirrhosis


title: Bos taurus_lymphocytes_L25_T1

description: Sample of bovine lymphocytes


title: Liver Transcriptome from CBDLpH_1212

description: Liver Transcriptome from CBDLpH_1212


title: topal-00242: TCGA-61-2017-01A


title: topal-00242: TCGA-29-1784-01A


title: Liver Transcriptome from CBDLpH_306

description: Liver Transcriptome from CBDLpH_306


title: Bos taurus_lymphocytes_L20_T1

description: Sample of bovine lymphocytes


title: reference male mouse2/ 20mGyI7


title: Bos taurus_lymphocytes_L18_T1

description: Sample of bovine lymphocytes


title: 20mGyI7/ reference male mouse2


title: topal-00242: TCGA-29-2429-01A

value: UNKNOWN


title: Liver Transcriptome from CBDLpH_1603

description: Liver Transcriptome from CBDLpH_1603


title: topal-00242: TCGA-25-1313-01A


title: Bos taurus_lymphocytes_L17_T1

description: Sample of bovine lymphocytes

value: lymphocytes


title: Liver Transcriptome from CBDLpH_112

description: Liver Transcriptome from CBDLpH_112


title: 20mGyI6/ reference male mouse2


title: Liver Transcriptome from CBDLpS_1804

description: Liver Transcriptome from CBDLpS_1804

value: submitted to a sham hemorrhage/resuscitation procedure

value: CBDLpS


title: reference male mouse2/ 20mGyI6


title: Bos taurus_biceps brachii_P31

description: Bovine biceps brachii samples collected at the slaughterhouse

source_name: Bos tauru_biceps brachii_prednisolone treated

tag: treated with

value: prednisolone 30 mg/head daily per os for 35 days

value: biceps brachii muscle


title: Liver Transcriptome from CBDLpH_1503

description: Liver Transcriptome from CBDLpH_1503


title: reference male mouse2/ 20mGyI5


title: topal-00242: TCGA-24-1416-01A

tag: diseasestate

value: Serous Cystadenocarcinoma

value: Ovary


title: reference male mouse2/ 20mGyI4


title: Liver Transcriptome from CBDLpS_2106

description: Liver Transcriptome from CBDLpS_2106


title: topal-00242: TCGA-23-2641-01A

value: NOT SPECIFIED

tag: organismpart


title: reference male mouse2/ 20mGyI3


title: 20mGyI4/ reference male mouse2


title: Bos taurus_biceps brachii_P30


title: topal-00242: TCGA-09-1666-01A

value: IIIC


title: Liver Transcriptome from CBDLpS_506

description: Liver Transcriptome from CBDLpS_506


title: topal-00242: TCGA-13-0730-01A


title: Liver Transcriptome from CBDLpS_106

description: Liver Transcriptome from CBDLpS_106


title: Bos taurus_biceps brachii_P32


title: 20mGyI3/ reference male mouse2

value: tail


title: topal-00242: TCGA-04-1356-01A

value: Female

value: IIC


title: 20mGyI2/ reference male mouse2


title: topal-00242: TCGA-24-0979-01A

value: IV


title: Bos taurus_biceps brachii_P28


title: Liver Transcriptome from CBDLpS_903

description: Liver Transcriptome from CBDLpS_903


title: topal-00242: TCGA-04-1514-01A

value: IIIA


title: Bos taurus_biceps brachii_P26


title: Liver Transcriptome from CTROLH_1513

description: Liver Transcriptome from CTROLH_1513

value: Control

value: submitted to hemorrhage/resuscitation

value: CTROLH


title: topal-00242: TCGA-61-1733-01A


title: Liver Transcriptome from CTROLH_1013

description: Liver Transcriptome from CTROLH_1013


title: Liver Transcriptome from CTROLH_813

description: Liver Transcriptome from CTROLH_813


title: 20mGyI5/ reference male mouse2


title: Bos taurus_biceps brachii_P29


title: reference male mouse2/ 20mGyI2


title: topal-00242: TCGA-13-0890-01A


title: Liver Transcriptome from CTROLH_913

description: Liver Transcriptome from CTROLH_913


title: Bos taurus_biceps brachii_P25


title: 20mGyI1/ reference male mouse2


title: topal-00242: TCGA-24-2027-01A


title: Liver Transcriptome from CTROLH_513

description: Liver Transcriptome from CTROLH_513


title: reference male mouse2/ 20mGyI1


title: Bos taurus_biceps brachii_P27


title: Bos taurus_testis_P31

description: Bovine testis samples collected at the slaughterhouse

data_processing: Data processed with FeatureExtraction v9.5 and normalized using cyclic lowess by R 2.11.1 statistical software.

source_name: Bos taurus_testis_prednisolone treated

value: testis


title: Liver Transcriptome from CTROLH_113

description: Liver Transcriptome from CTROLH_113


title: topal-00242: TCGA-30-1855-01A

source_name: Primary solid tumor


title: Liver Transcriptome from CTROLS_1713

description: Liver Transcriptome from CTROLS_1713

value: submitted to a sham hemorrhage/resuscitation procedure

value: CTROLS


title: topal-00242: TCGA-04-1353-01A

value: UNKNOWN


title: Bos taurus_testis_P29

value: prednisolone 30 mg/head daily per os for 35 days


title: Bos taurus_testis_P30


title: reference male mouse2/ 20mGyIF


title: topal-00242: TCGA-13-0886-01A

value: Serous Cystadenocarcinoma


title: Liver Transcriptome from CTROLS_1113

description: Liver Transcriptome from CTROLS_1113


title: Bos taurus_testis_P28


title: topal-00242: TCGA-25-2397-01A

value: Ovary


title: Liver Transcriptome from CTROLS_313

description: Liver Transcriptome from CTROLS_313


title: Bos taurus_testis_P26


title: Bos taurus_testis_P32


title: Bos taurus_testis_P27


title: Liver Transcriptome from CTROLS_1613

description: Liver Transcriptome from CTROLS_1613


title: Liver Transcriptome from CTROLS_613

description: Liver Transcriptome from CTROLS_613


title: Bos taurus_testis_P25


title: topal-00242: TCGA-24-1435-01A


title: topal-00242: TCGA-24-1557-01A


title: Bos taurus_testis_C24

source_name: Bos taurus_testis_control

value: none (control)


title: Bos taurus_testis_C23


title: reference male mouse2/ 20mGyH6


title: 20mGyIM/ reference male mouse2


title: topal-00242: TCGA-13-1491-01A

value: IIIC


title: topal-00242: TCGA-13-0807-01B


title: 20mGyH6/ reference male mouse2

value: tail


title: topal-00242: TCGA-13-0920-01A

value: Female


title: Bos taurus_testis_C22


title: 136_Day_7_abi_64

city: Seattle

first: Ilsa

last: Coleman

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center

description: LuCaP 136_Day 7: abi, sample: 64

hyb_protocol: A total of 4.5 µg fragmented biotin-labeled aRNA was hybridized on an HT Human Genome (HG)-U219 96-array plate following the manufacturer's protocol.

scan_protocol: The plate was washed, stained, and scanned with the GeneTitan Instrument following the manufacturer's protocol.

data_processing: Gene expression microarray data were normalized to minimize systematic technical variation using robust multichip average (RMA) and represented in the log2 scale.

source_name: LuCaP 136_Day 7: abi, sample: 64

label_protocol: Biotin-labeled, amplified RNA (aRNA) was synthesized from 200 ng total RNA using the 3′ IVT Express Kit (Affymetrix, Santa Clara, CA). The aRNA was purified using Agencourt RNAClean XP beads (Beckman Coulter Inc., Brea, CA) on the BioMek FX Workstation (Beckman Coulter Inc.). Biotin-labeled aRNA was fragmented using the 3′ IVT Express Kit.

growth_protocol: Animal procedures were carried out in accordance with NIH guidelines and upon University of Washington Institutional Animal Care and Use Committee approval. Four different LuCaP human prostate cancer PDXs (LuCaP 136CR, LuCaP 77CR, LuCaP 96CR, and LuCaP 35CR) were utilized. Intact male CB-17 SCID mice (~6 weeks of age, Charles River Laboratories, San Diego, CA) were implanted subcutaneously with tumor bits of LuCaP 136 or LuCaP 77. Mice were castrated when tumor volume was ≥100 mm3. When tumor regrew to 1.5-fold of the original volume, tumors were referred to as LuCaP 136CR or LuCaP 77CR and were randomized to vehicle (20% HPbCD/0.37N HCl/PBS)  or AA treatment groups (0.5 mmol/kg, Janssen Pharmaceutica, Beerse, Belgium). LuCaP 96CR and LuCaP 35CR are castration-resistant PDXs that are propagated in castrated male mice. Castrated male CB-17 SCID mice were implanted subcutaneously with LuCaP 96CR or LuCaP 35CR tumor bits. When tumor volume ≥ 100 mm3, mice were randomized to vehicle or AA treatment groups (0.5 mmol/kg).

extract_protocol: Frozen pieces of tumor were attached to Optimal Cutting Temperature Compound and 5-µm sections were stained with H&E. Areas of viable tumor cells were identified and macro-dissected for RNA extraction using a standard procedure with RNA STAT 60 (Tel-Test, Friendswood, TX). RNA was then purified using RNeasy Mini kit utilizing the optional DNase digestion in solution prior to purification (Qiagen, Hilden, Germany) for subsequent gene expression analyses.

treatment_protocol: Animals were treated by oral gavage on a weekly schedule of 5 days on 2 days off, tumor volume and body weight were measured twice weekly, and blood samples were drawn weekly for prostate-specific antigen (PSA) measurements using AxSym Total PSA Assay (Abbott Laboratories, Abbott Park, IL). Five animals in each group were sacrificed 7 days after the initiation of treatment (D7) and the rest of the animals were followed and sacrificed until tumors exceeded 1000 mm3 (End of Study, EOS) or sacrificed if animals became compromised. At sacrifice (D7 or EOS), half of the tumor was harvested for paraffin embedding and half was frozen for intratumoral androgen measurement, DNA and RNA extraction.

value: LuCaP 136 PDX tumor

tag: timepoint group

value: Day 7

value: abi


title: 136_Day_7_abi_69

description: LuCaP 136_Day 7: abi, sample: 69

source_name: LuCaP 136_Day 7: abi, sample: 69


title: topal-00242: TCGA-04-1655-01A

value: IIIB


title: 136_Day_7_abi_53

description: LuCaP 136_Day 7: abi, sample: 53

source_name: LuCaP 136_Day 7: abi, sample: 53


title: 20mGyH5/ reference male mouse2


title: Bos taurus_testis_C20


title: Bos taurus_testis_C18


title: reference male mouse2/ 20mGyH5


title: 136_Day_7_control_62

description: LuCaP 136_Day 7: control, sample: 62

source_name: LuCaP 136_Day 7: control, sample: 62

value: control


title: Bos taurus_testis_C17


title: 136_Day_7_control_61

description: LuCaP 136_Day 7: control, sample: 61

source_name: LuCaP 136_Day 7: control, sample: 61


title: 20mGyH3/ reference male mouse2


title: 20mGyH4/ reference male mouse2


title: Treatment Replicate 3

city: University Park

first: Monica

last: Medina

state: PA

address: 218 Mueller Lab

department: Biology

institute: Pennsylvania State University

description: Treatment Replicate 3

hyb_protocol: Prior to hybridization, microarrays were post-processed by 1) ultraviolet crosslinking at 60mJ 30 seconds, 2) a ‘shampoo’ treatment (3x SSC, 0.2% SDS at 65°C 2 minutes), 3) a blocking step by incubating microarrays in 5.5 g of succinic anhydride dissolved in 335 ml 1-methyl-2-pyrrolidinone and 15 ml of sodium borate, and 4) drying by centrifugation. The microarray consists of 10,930 PCR-amplified cDNAs spotted in duplicate on poly-lysine-coated slides yielding a microarray with 21,860 total features and is referenced as Mfaveolata_11k_v1. Spotted cDNAs were chosen from EST libraries partially described by Aranda et al. {Aranda, 2011 #325;,  #47}. Dye-coupled cDNAs were cleaned using the MinElute Cleanup kit (Qiagen) according to manufacturer’s instructions. Each Cy3-labeled treatment was hybridized to the array together with a Cy5-labeled pooled reference sample. Briefly, 12µl of treatment and 12µl of reference were combined with 6µl of hybridization buffer containing 0.25% SDS, 25 mM HEPES, and 3X SSC. Samples were heated to 99°C for 2 min and pipetted into the space between a microarray glass slide and an mSeries Lifterslip (Erie Scientific). Microarrays were hybridized for 14 hours at 63°C and subsequently washed twice in 0.6X SSC and 0.01% SDS followed by a rinse in 0.06X SSC and dried via centrifugation. Slides were immediately scanned using an Axon 4000B scanner.

scan_protocol: After scanning the microarrays, annotation grid files were overlaid and fit for feature extraction of scanned images. GenePix Pro (Molecular Devices) software was used to extract background-subtracted spot intensities that gave rise to 6 GPR files. GPR files were subsequently converted to MEV files using TIGR Express Converter 4.0

data_processing: Microarray data were normalized using TIGR MIDAS 2.21 with printtip-specific LOWESS followed by in-slide replicate analysis. Genes were included in subsequent statistical analyses only if present in two out of three replicates. Differentially expressed genes between uninfected (control) and S. minutum-infected (treatment) polyps were determined via 2-class unpaired SAM analyses and a FDR ≤ 0.05 in MeV software.

organism: Orbicella faveolata

source_name: mf1.05 infected polyps

label_protocol: For each experimental treatment (i.e., 3 control polyps and 3 polyps infected with S. minutum), 3 μg of aRNA were primed with 10μM random pentadecamers for 10 min at 70°C for subsequent cDNA generation (see below). A pooled reference was created by combining 3 µg of aRNA from both experimental treatments and processed accordingly. Reverse transcription was carried out for 2 hours at 50°C using SuperScript III Reverse Transcriptase (Invitrogen) containing a 4:1 ratio of aminoallyl-dUTP to TTP (Ambion). After reverse transcription, RNA was hydrolyzed by adding EDTA and NaOH for a final concentration of 0.1M and 0.2M, respectively, for 15 minutes at 65°C. Following hydrolysis, HEPES was added at a final concentration of 0.5M. Reactions were cleaned using the MinElute Cleanup kit (Qiagen) according to manufacturer’s instructions. cDNAs were labeled with Cy3 and Cy5 fluorescent dyes for sample and reference respectively (GE Healthcare). Briefly, cDNA was added to 4.5 nmol of dye dissolved in 1 M DMSO, and incubated in the dark for two hours.

growth_protocol: Buoyant gamete bundles were collected in plastic jars fixed to the top of each cone-shaped net. Bundles of different colonies were mixed in a cooler with 1 µm filtered seawater (FSW) that was sterilized using ultraviolet light. The egg-sperm solution was mixed gently to break the bundles and increase fertilization rates. After a one-hour incubation, excess sperm was removed with repeatedly washing with FSW until the water was clear. The embryos were initially raised in large plastic coolers (150 liters), containing UV treated FSW and kept at a constant 29ºC. Healthy embryos were then evenly distributed to smaller polypropylene containers (6 liters) at a density of >5 embryos per ml.  Water was changed every other day and kept at a constant 29ºC. Once the embryos developed into the planula stage, they were randomly assigned to the infection treatment (S. minutum) and control (n = 3 replicates per treatment, approximately 1,000 coral larvae per replicate).

extract_protocol: To isolate total RNA from the cotton swabs, microcentrifuge tubes with RNAlater and cotton swab heads were centrifuged for 10 min at 12,000 x g. Swabs were wiped across the interior surfaces of the tubes using tweezers to collect any pelleted coral tissue from the tubes. Swabs were then placed in a mortar containing liquid nitrogen and ground into a powder. The powder was removed with a spatula and placed in a 2 ml screw cap tube. To each tube, 1.5 ml of Qiazol (Qiagen) was added. Samples were then homogenized for 2 min using a Mini Bead-Beater (Biospec) with both 0.1 mm and 0.55 mm silica beads. To each tube, 450 µl of chloroform was added. Tubes were then vortexed for 30 seconds and incubated at RT for 3 min. Each sample was centrifuged at 12,000 g for 15 min at 4°C. From the aqueous layer, 500 μl were transferred to a new tube and RNA was precipitated by adding 500 μl of 100% isopropanol and 5 μl of glycerol (20 ng/μl). To pellet the RNA, tubes were vortexed for 30 s, then incubated at RT for 10 min, then centrifuged for 15 min under the same conditions as above. The isopropanol was removed and RNA pellets were washed twice with 70% EtOH and centrifuged at maximum speed for 5 min at 4°C. The wash and centrifugation step was repeated a second time. RNA pellets were then air-dried for 10 min and resuspended in 50 ul RNase-free water.

treatment_protocol: Cultures of Symbiodinium minutum were grown in ASP-8a media at 12:12 light dark cycle at 150 microeinstein. Planula larvae settled and metamorphosed into sessile polyps seven days after fertilization. For infection (i.e. symbiotic treatment), S. minutum was added to three replicates at an initial concentration of 3 x 105 cells/ml and stable concentrations of S. minutum were ensured by regular reinfection after daily water changes for nine days. The state of infection by S. minutum was confirmed every two days using microscopy by sampling ten polyps and flattening them under a microscope slide.  For the control treatment, the growth media (Asp-8a) without S. minutum was added to another set of three replicates.

tag: sample type

value: mf1.05 infected polyps

source_name: Pooled control and treatment total RNA

value: reference


title: topal-00242: TCGA-25-2398-01A


title: topal-00242: TCGA-24-2026-01A


title: reference male mouse2/ 20mGyIM


title: reference male mouse2/ 20mGyH3


title: reference male mouse2/ 20mGyH4


title: Treatment Replicate 2

description: Treatment Replicate 2


title: 20mGyIF/ reference male mouse2


title: topal-00242: TCGA-30-1887-01A


title: topal-00242: TCGA-04-1516-01A

value: NOT SPECIFIED


title: topal-00242: TCGA-09-0369-01A


title: 136_Day_7_control_56

description: LuCaP 136_Day 7: control, sample: 56

source_name: LuCaP 136_Day 7: control, sample: 56


title: 20mGyH2/ reference male mouse2


title: topal-00242: TCGA-30-1853-01A


title: 136_EOS_abi_70

description: LuCaP 136_EOS: abi, sample: 70

source_name: LuCaP 136_EOS: abi, sample: 70

value: EOS


title: reference male mouse2/ 20mGyH2


title: Bos taurus_testis_C21

value: testis


title: Control Replicate 3

description: Control Replicate 3

source_name: Aposymbiotic polyps

value: Aposymbiotic polyps


title: 136_Day_7_control_54

description: LuCaP 136_Day 7: control, sample: 54

source_name: LuCaP 136_Day 7: control, sample: 54


title: topal-00242: TCGA-25-1317-01A

value: Serous Cystadenocarcinoma


title: Control Replicate 2

description: Control Replicate 2


title: 20mGyHF/ reference male mouse2


title: 136_EOS_abi_67

description: LuCaP 136_EOS: abi, sample: 67

source_name: LuCaP 136_EOS: abi, sample: 67


title: 20mGyHM/ reference male mouse2

source_name: reference male mouse2


title: reference male mouse2/ 20mGyH1


title: 136_EOS_abi_65

description: LuCaP 136_EOS: abi, sample: 65

source_name: LuCaP 136_EOS: abi, sample: 65


title: topal-00242: TCGA-29-1777-01A

value: Ovary


title: 136_Day_7_abi_49

description: LuCaP 136_Day 7: abi, sample: 49

source_name: LuCaP 136_Day 7: abi, sample: 49


title: reference male mouse2/ 20mGyHF


title: Control Replicate 1

description: Control Replicate 1


title: 20mGyH1/ reference male mouse2


title: 136_EOS_abi_55

description: LuCaP 136_EOS: abi, sample: 55

source_name: LuCaP 136_EOS: abi, sample: 55


title: topal-00242: TCGA-13-0903-01A

source_name: Primary solid tumor

value: IV


title: 136_EOS_control_CX_66

description: LuCaP 136_EOS: control CX, sample: 66

source_name: LuCaP 136_EOS: control CX, sample: 66

value: control CX


title: topal-00242: TCGA-61-1722-01A

value: IB


title: 136_EOS_control_CX_63

description: LuCaP 136_EOS: control CX, sample: 63

source_name: LuCaP 136_EOS: control CX, sample: 63


title: reference male mouse2/ 20mGyHM

value: tail


title: topal-00242: TCGA-23-2081-01A

value: Female


title: reference male mouse1/ 20mGyG7

source_name: reference male mouse1


title: 136_EOS_control_CX_59

description: LuCaP 136_EOS: control CX, sample: 59

source_name: LuCaP 136_EOS: control CX, sample: 59

value: LuCaP 136 PDX tumor


title: topal-00242: TCGA-57-1992-01A

value: IC


title: 136_EOS_control_CX_58

description: LuCaP 136_EOS: control CX, sample: 58

source_name: LuCaP 136_EOS: control CX, sample: 58


title: topal-00242: TCGA-59-2352-01A

value: IIIC


title: reference male mouse1/ 20mGyG6


title: Treatment Replicate 1

description: Treatment Replicate 1

source_name: mf1.05 infected polyps


title: 136_EOS_control_CX_50

description: LuCaP 136_EOS: control CX, sample: 50

source_name: LuCaP 136_EOS: control CX, sample: 50


title: 136_EOS_control_CX_52

description: LuCaP 136_EOS: control CX, sample: 52

source_name: LuCaP 136_EOS: control CX, sample: 52


title: topal-00242: TCGA-61-1907-01A


title: topal-00242: TCGA-29-2425-01A


title: topal-00242: TCGA-09-0364-01A

value: IIC


title: 136_EOS_control_60

description: LuCaP 136_EOS: control, sample: 60

source_name: LuCaP 136_EOS: control, sample: 60

value: control


title: 20mGyG5/ reference male mouse1


title: 136_EOS_control_57

description: LuCaP 136_EOS: control, sample: 57

source_name: LuCaP 136_EOS: control, sample: 57


title: 136_EOS_control_68

description: LuCaP 136_EOS: control, sample: 68

source_name: LuCaP 136_EOS: control, sample: 68


title: topal-00242: TCGA-01-0631-11A

source_name: Solid normal tissue

value: UNKNOWN

value: many


title: topal-00242: TCGA-13-1405-01A


title: 136_EOS_control_51

description: LuCaP 136_EOS: control, sample: 51

source_name: LuCaP 136_EOS: control, sample: 51

value: EOS


title: 20mGyG7/ reference male mouse1


title: topal-00242: TCGA-61-2018-01A


title: 96CR_Day_7_abi_47

description: LuCaP 96CR_Day 7: abi, sample: 47

source_name: LuCaP 96CR_Day 7: abi, sample: 47

value: LuCaP 96CR PDX tumor

value: Day 7

value: abi


title: topal-00242: TCGA-13-0906-01A

value: Serous Cystadenocarcinoma

value: Ovary


title: reference male mouse1/ 20mGyG4


title: topal-00242: TCGA-25-1625-01A


title: 96CR_Day_7_abi_35

description: LuCaP 96CR_Day 7: abi, sample: 35

source_name: LuCaP 96CR_Day 7: abi, sample: 35


title: 96CR_Day_7_abi_38

description: LuCaP 96CR_Day 7: abi, sample: 38

source_name: LuCaP 96CR_Day 7: abi, sample: 38


title: topal-00242: TCGA-13-0805-01A

source_name: Primary solid tumor


title: topal-00242: TCGA-24-1544-01A


title: reference male mouse1/ 20mGyG5


title: reference male mouse1/ 20mGyG3


title: 96CR_Day_7_control_48

description: LuCaP 96CR_Day 7: control, sample: 48

source_name: LuCaP 96CR_Day 7: control, sample: 48


title: topal-00242: TCGA-04-1364-01A


title: 20mGyG4/ reference male mouse1


title: 96CR_Day_7_control_42

description: LuCaP 96CR_Day 7: control, sample: 42

source_name: LuCaP 96CR_Day 7: control, sample: 42


title: 20mGyGF/ reference male mouse1

source_name: reference male mouse1


title: 96CR_Day_7_control_37

description: LuCaP 96CR_Day 7: control, sample: 37

source_name: LuCaP 96CR_Day 7: control, sample: 37


title: topal-00242: TCGA-61-2611-02A

source_name: Recurrent Solid Tumor

value: NOT SPECIFIED


title: 20mGyG3/ reference male mouse1


title: reference male mouse1/ 20mGyG1


title: topal-00242: TCGA-61-2111-01A

value: IV


title: topal-00242: TCGA-13-0908-01B


title: 20mGyG1/ reference male mouse1

value: tail


title: topal-00242: TCGA-13-2065-01A


title: 96CR_EOS_abi_46

description: LuCaP 96CR_EOS: abi, sample: 46

source_name: LuCaP 96CR_EOS: abi, sample: 46


title: 96CR_EOS_abi_41

description: LuCaP 96CR_EOS: abi, sample: 41

source_name: LuCaP 96CR_EOS: abi, sample: 41


title: 96CR_Day_7_control_34

description: LuCaP 96CR_Day 7: control, sample: 34

source_name: LuCaP 96CR_Day 7: control, sample: 34


title: topal-00242: TCGA-01-0637-11A


title: reference male mouse1/ 20mGyGM


title: 20mGyGM/ reference male mouse1


title: 20mGyG6/ reference male mouse1


title: 96CR_EOS_abi_39

description: LuCaP 96CR_EOS: abi, sample: 39

source_name: LuCaP 96CR_EOS: abi, sample: 39


title: 96CR_EOS_abi_36

description: LuCaP 96CR_EOS: abi, sample: 36

source_name: LuCaP 96CR_EOS: abi, sample: 36


title: 96CR_Day_7_abi_43

description: LuCaP 96CR_Day 7: abi, sample: 43

source_name: LuCaP 96CR_Day 7: abi, sample: 43


title: topal-00242: TCGA-29-1692-02A

value: Female


title: 96CR_EOS_abi_32

description: LuCaP 96CR_EOS: abi, sample: 32

source_name: LuCaP 96CR_EOS: abi, sample: 32


title: topal-00242: TCGA-29-1692-01B


title: topal-00242: TCGA-61-2113-01A


title: 20mGyG2/ reference male mouse1


title: reference male mouse1/ 20mGyF5


title: topal-00242: TCGA-61-2016-01A


title: 96CR_EOS_control_44

description: LuCaP 96CR_EOS: control, sample: 44

source_name: LuCaP 96CR_EOS: control, sample: 44


title: 20mGyF5/ reference male mouse1


title: topal-00242: TCGA-61-1998-01A


title: reference male mouse1/ 20mGyGF


title: 20mGyF4/ reference male mouse1


title: topal-00242: TCGA-23-1116-01A


title: 96CR_EOS_control_33

description: LuCaP 96CR_EOS: control, sample: 33

source_name: LuCaP 96CR_EOS: control, sample: 33


title: 96CR_EOS_control_45

description: LuCaP 96CR_EOS: control, sample: 45

source_name: LuCaP 96CR_EOS: control, sample: 45


title: reference male mouse1/ 20mGyF4


title: 96CR_EOS_control_40

description: LuCaP 96CR_EOS: control, sample: 40

source_name: LuCaP 96CR_EOS: control, sample: 40


title: topal-00242: TCGA-09-1667-01C

source_name: Primary solid tumor


title: reference male mouse1/ 20mGyF6


title: 20mGyF6/ reference male mouse1


title: topal-00242: TCGA-24-2281-01A

value: IIA


title: reference male mouse1/ 20mGyF3


title: 77_EOS_abi_31

description: LuCaP 77_EOS: abi, sample: 31

source_name: LuCaP 77_EOS: abi, sample: 31

value: LuCaP 77 PDX tumor


title: 77_EOS_abi_30

description: LuCaP 77_EOS: abi, sample: 30

source_name: LuCaP 77_EOS: abi, sample: 30


title: 10-d mEBs rep2

city: Los Angeles

first: Xiaojiang

last: Cui

state: California

address: 8700 Beverly blvd

department: Surgery

institute: Cedars-Sinai medical center

description: Gene expression data from 10d differentiated mEBs

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalization

source_name: 10d differentiated mEBs from iPSCs

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: iPSCs are cultured on a thin layer of Matrigel using mTeSR with its supplements. Medium is changed every day.

extract_protocol: Total RNA was extracted by Rneasy kit (Qiagen)

treatment_protocol: mEBs are generated by culturing iPSCs in a low-attachment dish using MammoCult with its supplements.

value: iPSCs

tag: development stage

value: 10d differentiated mEBs


title: topal-00242: TCGA-57-1585-01A

value: IIIC


title: 10-d mEBs rep1


title: reference male mouse1/ 20mGyF2

source_name: reference male mouse1


title: 77_EOS_abi_26

description: LuCaP 77_EOS: abi, sample: 26

source_name: LuCaP 77_EOS: abi, sample: 26


title: topal-00242: TCGA-09-2049-01D


title: 5-d mEBs rep2

description: Gene expression data from 5d differentiated mEBs

source_name: 5d differentiated mEBs from iPSCs

value: 5d differentiated mEBs


title: topal-00242: TCGA-31-1944-01A


title: 77_EOS_abi_23

description: LuCaP 77_EOS: abi, sample: 23

source_name: LuCaP 77_EOS: abi, sample: 23


title: topal-00242: TCGA-25-2404-01A


title: 5-d mEBs rep1


title: 20mGyF2/ reference male mouse1


title: 77_EOS_abi_22

description: LuCaP 77_EOS: abi, sample: 22

source_name: LuCaP 77_EOS: abi, sample: 22


title: 20mGyF1/ reference male mouse1


title: iPSCs-rep 2

description: Gene expression data from iPSCs

source_name: iPSCs


title: iPSCs-rep 1

description: Gene expression data from iPSCs


title: topal-00242: TCGA-36-2552-01A

value: UNKNOWN


title: 77_EOS_control_CX_27

description: LuCaP 77_EOS: control CX, sample: 27

source_name: LuCaP 77_EOS: control CX, sample: 27

value: EOS

value: control CX


title: topal-00242: TCGA-09-2056-01B


title: 9965280021_I_Grn

city: Cleveland

first: Hoi I

last: Cheong

address: 9500 Euclid Ave

institute: Cleveland Clinic

data_processing: The data were normalised using quantile normalisation with Limma in R

label: Cy 3

label_protocol: not provided.

growth_protocol: Human umbilical cord vein endothelial cells up to passage 6 were used in this experiment.

extract_protocol: RNA was extracted according to manufacturer's protocol in miRNeasy Mini Kit. Only RNA with RIN >7 using BioAnalayzer was used for microarray.

treatment_protocol: Cells were serum-starved for at least 4 hours prior to diluent or propranolol treatment (45 minutes), followed by 24-hour 2% oxygen exposure.

tag: cell type

value: HUVEC

tag: passage

value: =<passage 6


title: reference male mouse1/ 20mGyFF


title: topal-00242: TCGA-04-1369-01A

tag: age

tag: Sex


title: 77_EOS_control_CX_25

description: LuCaP 77_EOS: control CX, sample: 25

source_name: LuCaP 77_EOS: control CX, sample: 25


title: 20mGyFF/ reference male mouse1


title: 77_EOS_control_CX_28

description: LuCaP 77_EOS: control CX, sample: 28

source_name: LuCaP 77_EOS: control CX, sample: 28


title: topal-00242: TCGA-61-2094-01A

value: Serous Cystadenocarcinoma

tag: individual

tag: diseasestaging


title: 77_EOS_control_CX_24

description: LuCaP 77_EOS: control CX, sample: 24

source_name: LuCaP 77_EOS: control CX, sample: 24


title: 9965280021_J_Grn

source_name: PRO


title: 9965280021_G_Grn

source_name: NS


title: 20mGyFM/ reference male mouse1


title: reference male mouse1/ 20mGyF1


title: 20mGyE5/ reference male mouse1


title: topal-00242: TCGA-13-1408-01A

value: Ovary

tag: external id

tag: tumorgrading


title: 9965280021_D_Grn


title: 9965280021_H_Grn


title: reference male mouse1/ 20mGyE5


title: 77_EOS_control_29

description: LuCaP 77_EOS: control, sample: 29

source_name: LuCaP 77_EOS: control, sample: 29

tag: treatment group

value: control


title: 77_EOS_control_CX_17

description: LuCaP 77_EOS: control CX, sample: 17

source_name: LuCaP 77_EOS: control CX, sample: 17


title: 9965280021_C_Grn


title: 20mGyE4/ reference male mouse1

tag: strain


title: reference male mouse1/ 20mGyE4

tag: tissue


title: topal-00242: TCGA-36-2545-01A

source_name: Primary solid tumor

value: NOT SPECIFIED


title: reference male mouse1/ 20mGyFM

value: tail


title: topal-00242: TCGA-24-1852-01A

value: Female


title: 77_EOS_control_21

description: LuCaP 77_EOS: control, sample: 21

source_name: LuCaP 77_EOS: control, sample: 21


title: 77_EOS_control_20

description: LuCaP 77_EOS: control, sample: 20

source_name: LuCaP 77_EOS: control, sample: 20


title: 20mGyF3/ reference male mouse1

source_name: reference male mouse1


title: reference male mouse1/ 20mGyE3


title: 9965280021_B_Grn


title: 20mGyE3/ reference male mouse1


title: 9965280021_A_Grn


title: 35CR_Day_7_abi_15

description: LuCaP 35CR_Day 7: abi, sample: 15

source_name: LuCaP 35CR_Day 7: abi, sample: 15

value: LuCaP 35CR PDX tumor

value: Day 7

value: abi


title: 9965280015_I_Grn


title: topal-00242: TCGA-24-1852-02A

source_name: Recurrent Solid Tumor


title: 9965280015_H_Grn


title: 20mGyE2/ reference male mouse1


title: 9965280015_J_Grn


title: 35CR_Day_7_abi_13

description: LuCaP 35CR_Day 7: abi, sample: 13

source_name: LuCaP 35CR_Day 7: abi, sample: 13


title: 77_EOS_control_19

description: LuCaP 77_EOS: control, sample: 19

source_name: LuCaP 77_EOS: control, sample: 19

value: LuCaP 77 PDX tumor


title: 77_EOS_control_18

description: LuCaP 77_EOS: control, sample: 18

source_name: LuCaP 77_EOS: control, sample: 18


title: 9965280015_D_Grn


title: 9965280015_G_Grn


title: 20mGyEF/ reference male mouse1


title: 35CR_Day_7_abi_5

description: LuCaP 35CR_Day 7: abi, sample: 5

source_name: LuCaP 35CR_Day 7: abi, sample: 5


title: reference male mouse1/ 20mGyE1


title: reference male mouse1/ 20mGyE2


title: 9965280015_C_Grn


title: 35CR_Day_7_control_9

description: LuCaP 35CR_Day 7: control, sample: 9

source_name: LuCaP 35CR_Day 7: control, sample: 9


title: 35CR_Day_7_control_7

description: LuCaP 35CR_Day 7: control, sample: 7

source_name: LuCaP 35CR_Day 7: control, sample: 7


title: reference male mouse1/ 20mGyG2


title: 35CR_Day_7_abi_12

description: LuCaP 35CR_Day 7: abi, sample: 12

source_name: LuCaP 35CR_Day 7: abi, sample: 12


title: 35CR_Day_7_control_1

description: LuCaP 35CR_Day 7: control, sample: 1

source_name: LuCaP 35CR_Day 7: control, sample: 1


title: 20mGyE1/ reference male mouse1


title: 9965280015_A_Grn

source_name: NS


title: 9664921077_H_Grn

description:
D6
The .idat file 9664921077_H_Grn.idat for this sample was not provided.


title: 20mGyEM/ reference male mouse1


title: 35CR_Day_7_control_2

description: LuCaP 35CR_Day 7: control, sample: 2

source_name: LuCaP 35CR_Day 7: control, sample: 2


title: reference male mouse1/ 20mGyEF


title: 20mGyD5/ reference male mouse1


title: 35CR_EOS_abi_16

description: LuCaP 35CR_EOS: abi, sample: 16

source_name: LuCaP 35CR_EOS: abi, sample: 16


title: reference male mouse1/ 20mGyEM


title: 9664921077_E_Grn

description:
D2
The .idat file 9664921077_E_Grn.idat for this sample was not provided.


title: 9664921077_D_Grn

source_name: PRO


title: 9664921077_B_Grn


title: 35CR_EOS_abi_6

description: LuCaP 35CR_EOS: abi, sample: 6

source_name: LuCaP 35CR_EOS: abi, sample: 6


title: reference male mouse1/ 20mGyD5


title: 9664921073_L_Grn


title: 20mGyD4/ reference male mouse1


title: reference male mouse1/ 20mGyD3


title: 9965280015_B_Grn


title: 35CR_EOS_abi_8

description: LuCaP 35CR_EOS: abi, sample: 8

source_name: LuCaP 35CR_EOS: abi, sample: 8


title: reference male mouse1/ 20mGyD4

source_name: reference male mouse1


title: 35CR_EOS_control_11

description: LuCaP 35CR_EOS: control, sample: 11

source_name: LuCaP 35CR_EOS: control, sample: 11


title: 9664921073_J_Grn


title: reference male mouse1/ 20mGyD2


title: 35CR_EOS_control_10

description: LuCaP 35CR_EOS: control, sample: 10

source_name: LuCaP 35CR_EOS: control, sample: 10


title: 20mGyD3/ reference male mouse1


title: 35CR_EOS_control_3

description: LuCaP 35CR_EOS: control, sample: 3

source_name: LuCaP 35CR_EOS: control, sample: 3


title: 20mGyD2/ reference male mouse1


title: reference male mouse1/ 20mGyD1


title: 9664921073_H_Grn


title: 20mGyD1/ reference male mouse1


title: 35CR_EOS_abi_14

description: LuCaP 35CR_EOS: abi, sample: 14

source_name: LuCaP 35CR_EOS: abi, sample: 14


title: reference male mouse1/ 20mGyDF


title: MCF7_siMSI2_1

status: Public on Dec 21 2016

city: Seoul

first: YUNYONG

last: PARK

address: 84 Heukseok-ro

country: South Korea

institute: ChuangAng University

description: siMSI2 in MCF7 Cell

hyb_protocol: Hyb was done at 58 degree for 18 hrs

scan_protocol: HighScan was used

data_processing:
GenomeStudio was used for data processing and quantile normalization method was used.
Log2 value ((normalized), Raw signal intensity (non-normalized).

source_name: siMSI2 in MCF7 Cell

label_protocol: Extracted RNA was amplified and labeled with Amplificatin kit (AMIL1797; Ambion)

growth_protocol: The cells were grown in RPMI1640 media.

extract_protocol: miRvana kit was used for RNA extraction

treatment_protocol: Cells were treated with indicated lenti-viral vector

value: cancer cell


title: MCF7_siMSI2_2

description: siMSI2 in MCF7 Cell


title: MCF7_siMSI2_3

description: siMSI2 in MCF7 Cell


title: MCF7_siCon_3

description: siCon in MCF7 Cell

source_name: siCon in MCF7 Cell


title: MCF7_siCon_2

description: siCon in MCF7 Cell


title: TWNT4_uXBP1

city: Dallas

first: Yujin

last: Hoshida

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

hyb_protocol: Refer to the Illumina BeadArray Assay System Manual.

data_processing: For each probe, replicated measurements (beads) were averaged after removing outliers by GenomeStudio software v.3 (Illumina). Data were then normalized using cubic spline algorithm implemented in GenePattern Illumina normalizer module (www.broadinstitute.org/genepattern) after setting a floor value of 1.

source_name: TWNT4 transduced by uXBP1

growth_protocol: LX2 and TWNT4 cells were cultured in DMEM for 96h.

extract_protocol: RNA was isolated using RNeasy kit (Qiagen) according to manufacturer's protocol.

treatment_protocol: Human hepatic stellate cell lines (LX2 and TWNT4) were lentivirally transduced by either unspliced or spliced XBP1 gene and cultured for 96h.

tag: cell line

value: hepatic stellate cell line

tag: transduction

value: unspliced XBP1 (uXBP1)


title: TWNT4_sXBP1

scan_protocol: Refer to the Illumina BeadArray Assay System Manual.

source_name: TWNT4 transduced by sXBP1

value: spliced XBP1 (sXBP1)


title: MCF7_siCon_1

description: siCon in MCF7 Cell


title: 20mGyC5/ reference male mouse1


title: reference male mouse1/ 20mGyDM


title: LX2_uXBP1

source_name: LX2 transduced by uXBP1

label_protocol: Refer to the Illumina BeadArray Assay System Manual.


title: TWNT4_control

source_name: TWNT4 transduced by control

value: control vector


title: Embryoid body derived from mGriPSC, attached, rep3

city: Darlinghurst

first: Joshua

last: Ho

state: NSW

address: Lowy Packer Building

country: Australia

institute: Victor Chang Cardiac Research Institute

hyb_protocol: Illumina protocol.

scan_protocol: Illumina protocol.

data_processing: lumi R package using the log2 transformation and robust spline normalization.

label: Biotin-Labeled cDNA

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep RNA Amplification Kit (Ambion) for Illumina arrays

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. DNAse treatment was performed according to Qiagen kit instructions. Quality control was performed with Agilent Bioanalyser.

tag: gender

value: female


title: LX2_sXBP1

source_name: LX2 transduced by sXBP1


title: Embryoid body derived from mGriPSC, suspended, rep3


title: 20mGyC4/ reference male mouse1


title: reference male mouse1/ 20mGyC5


title: reference male mouse1/ 20mGyC3


title: Embryoid body derived from mGriPSC, attached, rep1


title: reference male mouse1/ 20mGyC4


title: 20mGyDF/ reference male mouse1


title: Embryoid body derived from mGriPSC, suspended, rep2


title: 9664921073_C_Grn

value: HUVEC

value: =<passage 6


title: Embryoid body derived from mGriPSC, suspended, rep1


title: Embryoid body derived from mESC, suspended, rep2


title: Embryoid body derived from mGriPSC, attached, rep2


title: LX2_control

source_name: LX2 transduced by control


title: 20mGyDM/ reference male mouse1


title: 20mGyC3/ reference male mouse1


title: 20mGyC2/ reference male mouse1


title: P2 ovary rep3

source_name: P2 ovary rep3

value: Postnatal day 2 ovary


title: Embryoid body derived from mESC, attached, rep3


title: P2 ovary rep1

source_name: P2 ovary rep1


title: P2 ovary rep2

source_name: P2 ovary rep2


title: Embryoid body derived from mESC, attached, rep1


title: Adult ovary rep3

source_name: Adult ovary rep3

value: Adult ovary


title: 35CR_EOS_control_4

description: LuCaP 35CR_EOS: control, sample: 4

source_name: LuCaP 35CR_EOS: control, sample: 4

tag: timepoint group

value: EOS

value: control


title: reference male mouse1/ 20mGyC2

source_name: reference male mouse1

value: tail


title: Embryoid body derived from mESC, attached, rep2


title: 20mGyCM/ reference male mouse1


title: Adult ovary rep2

source_name: Adult ovary rep2


title: reference male mouse1/ 20mGyC1


title: Adult ovary rep1

source_name: Adult ovary rep1


title: reference male mouse1/ 20mGyCM


title: 19%_plusFGF2 (S4_H011)

city: Worcester

first: Tanja

last: Dominko

state: MA

address: 100 Institute Rd

department: Biology and Biotechnology

institute: Worcester Polytechnic Institute

hyb_protocol: Cy5-labeled aRNA was hybridized at 50C overnight using the HybBag mixing system with 1x OneArray Hybridization Buffer (Phalanx Biotech), 0.01mg/ml sheared salmon sperm DNA and 0.025mg/ml of labeled target. After hybridization arrays were washed according to OneArray protocol.

scan_protocol: Molecular Dynamics Axon 4100A scanner was used to capture raw intensity signals. Next, data were analyzed using GenePixPro Software and the results were stored in GPR format.

data_processing: R/Bioconductor was used to normalize and filter data. Background corrected data were normalized by adjusting column values to the same median value. Probes that had maximum intensity value across samples lower than 100 were excluded. Intensity values lower than 5 were substituted with 5 to remove negative values. Data were log2 transformed and filtered to leave gene probes with standard deviation above median.

label_protocol: Double-stranded cDNA was prepared from high-quality RNA. Next, amino allyl-modified aRNA was generated by in vitro transcription that included amino-allyl UTP. aRNA was conjugated to Cy5 NHS-ester.

growth_protocol: Adult human dermal fibroblasts (CRL-2352, ATCC) were expanded in 19% oxygen in DMEM/F12 (50:50) with 10% FCIII. At passage 7 they were subjected to four experimental conditions for one week.

extract_protocol: Total RNA was extracted using NucleoSpin RNA kit (Macherey-Nagel) following manufacturer’s instructions.

treatment_protocol: The four experimental conditions included growing adult human dermal fibroblasts in indicated conditions in 2% oxygen, 2% oxygen with addition of 4 ng/ml FGF2, 19% oxygen, and 19% oxygen with addition of 4 ng/ml FGF2 for one week.

value: Adult human dermal fibroblasts

tag: treatment


title: 19%_noFGF2 (S3_H009)

source_name: Adult human dermal fibroblasts (CRL-2352, ATCC)


title: reference male mouse1/ 20mGyCF


title: 19%_plusFGF2 (S4_H010)


title: 19%_plusFGF2 (S4_H012)


title: Lens Crim1 glcr11/+ rep2

description: CIIB

source_name: ocular lens

value: lens

tag: developmetal stage

value: C57BL/6 and C3A.Blia mix

tag: strain source

value: The Jackson Laboratory


title: 19%_noFGF2 (S3_H008)

tag: cell type


title: Lens Crim1 glcr11/glcr11 rep2

description: MIIB


title: 19%_noFGF2 (S3_H007)


title: 20mGyCF/ reference male mouse1


title: 20mGyC1/ reference male mouse1


title: Embryoid body derived from mESC, suspended, rep1


title: 2%_plusFGF2 (S2_H005)


title: 2%_noFGF2 (S1_H003)


title: 2%_plusFGF2 (S2_H006)


title: LEC_bLN_D30_3

city: Parkville

first: Joel

middle: Zhi-Iong

last: Ma

state: Victoria

address: Grattan Street

institute: University of Melbourne

hyb_protocol: Performed using GeneChip® Hybridization, Wash, and Stain Kit (Affymetrix), at Molecular Genomics Core Facility, Peter MacCallum Cancer Centre, Australia.

scan_protocol: Performed using GeneChip Scanner 7G (Affymetrix), at Molecular Genomics Core Facility, Peter MacCallum Cancer Centre, Australia.

data_processing: Probe intensities were background corrected, normalized and summarized at the probe-set level by the RMA algorithm using the aroma.affymetrix package in R.

source_name: brachial lymph nodes, HSV, 30 days p.i.

label_protocol: Performed using Encore Biotin module (Nugen), at Molecular Genomics Core Facility, Peter MacCallum Cancer Centre, Australia.

extract_protocol: Briefly, brachial draining lymph nodes were digested with collagenase D (Roche) and DNase (Sigma), followed by further incubation with Dispase (Roche).

treatment_protocol: HSV infection

value: Brachial draining lymph node

tag: phenotype

value: LEC

tag: infection

value: HSV, 30 days p.i.


title: LEC_bLN_D6_4

source_name: brachial lymph nodes, HSV, 6 days p.i.

tag: Sex

value: HSV, 6 days p.i.


title: LEC_bLN_D6_3


title: Silica-treated transgenic lung Replicate 4

city: Tampere

first: Dario

last: Greco

address: Arvo ylpön Katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University

description:
raw data file: TG_KMK45++_+TG_silica_KMK42++_US23502401_252800516532_S01_GE2_1100_Jul11_2_2.txt
Silica-treated transgenic lung tissue

hyb_protocol: According to Agilent protocol: Two-Color Microarray-Based Gene Expression Analysis, version 6.6, Sep 2012

scan_protocol: Agilent Scanner G2505C, Agilent Scan Control version A.8.5.1

data_processing: Agilent Feature Extraction 11.0.1.1, R v.2.3

source_name: Silica-treated transgenic lung tissue

label_protocol: Agilent Low Input Quick Amp Labeling Kit according to manufacturer's instructions.

extract_protocol: Total lung tissue RNA extracted using Qiagen RNeasy-kit according to manufacturer's instructions including treatment with DNase I. RNA quality was verified using Agilent 2100 Bioanalyzer.

treatment_protocol: Mice were exposed to silicon dioxide (silica) (Sigma, St. Louis, MO, 2.5 mg/50 µl sterile PBS). Two subsequent oropharyngeal aspiration doses were given on days 0 and 3 of the experiment. Mice were sacrificed after two months.

value: lung

tag: genotype

value: Gremlin-1 transgene expression

tag: time

value: 6 months


title: Lens Crim1 glcr11/glcr11 rep1

description: MIIA


title: 2%_noFGF2 (S1_H002)


title: LEC_bLN_D3_3

source_name: brachial lymph nodes, HSV, 3 days p.i.

value: female

value: HSV, 3 days p.i.


title: LEC_bLN_D6_1


title: LEC_bLN_D30_1


title: LEC_bLN_D6_2


title: LEC_bLN_D30_2


title: LEC_bLN_D3_4


title: Transgenic lung Replicate 4

description:
raw data file: TG_silica_KMK61++_+TG_KMK64++_US23502401_252800516532_S01_GE2_1100_Jul11_2_3.txt
Transgenic lung tissue

source_name: Transgenic lung tissue


title: Silica-treated transgenic lung Replicate 2

description:
raw data file: TG_silica_KMK61++_+TG_KMK64++_US23502401_252800516532_S01_GE2_1100_Jul11_2_3.txt
Silica-treated transgenic lung tissue


title: Silica-treated transgenic lung Replicate 3

description:
raw data file: WT_silica_KMK37--_+TG_silica_KMK35++_US23502401_252800516532_S01_GE2_1100_Jul11_2_1.txt
Silica-treated transgenic lung tissue


title: LEC_bLN_D3_1


title: LEC_bLN_Naive_3

source_name: brachial lymph nodes, naïve

value: naïve


title: Silica-treated transgenic lung Replicate 1

description:
raw data file: TG_silica_KMK34++_+WT_silica_KMK29--_US23502401_252800516532_S01_GE2_1100_Jul11_2_4.txt
Silica-treated transgenic lung tissue


title: LEC_bLN_D3_2


title: LEC_bLN_Naive_2


title: Transgenic lung Replicate 3

description:
raw data file: TG_KMK45++_+TG_silica_KMK42++_US23502401_252800516532_S01_GE2_1100_Jul11_2_2.txt
Transgenic lung tissue


title: LEC_bLN_Naive_1


title: 2%_noFGF2 (S1_H001)


title: FRC_bLN_D30_4

value: FRC


title: Silica-treated wild type lung Replicate 4

description:
raw data file: WT_KMK46--_+WT_silica_KMK44--_US23502401_252800516532_S01_GE2_1100_Jul11_1_2.txt
Silica-treated wild type lung tissue

source_name: Silica-treated wild type lung tissue

value: wildtype


title: Silica-treated wild type lung Replicate 3

description:
raw data file: WT_silica_KMK37--_+TG_silica_KMK35++_US23502401_252800516532_S01_GE2_1100_Jul11_2_1.txt
Silica-treated wild type lung tissue


title: FRC_bLN_D30_3


title: Silica-treated wild type lung Replicate 2

description:
raw data file: WT_silica_KMK59--_+WT_KMK62--_US23502401_252800516532_S01_GE2_1100_Jul11_1_3.txt
Silica-treated wild type lung tissue


title: FRC_bLN_D30_2


title: Transgenic lung Replicate 1

description:
raw data file: WT_KMK33--_+TG_KMK30++_US23502401_252800516532_S01_GE2_1100_Jul11_1_1.txt
Transgenic lung tissue


title: FRC_bLN_D30_1


title: FRC_bLN_D6_4


title: FRC_bLN_D6_1


title: Wild type lung Replicate 3

description:
raw data file: WT_silica_KMK59--_+WT_KMK62--_US23502401_252800516532_S01_GE2_1100_Jul11_1_3.txt
Wild type lung tissue

source_name: Wild type lung tissue


title: Silica-treated wild type lung Replicate 1

description:
raw data file: TG_silica_KMK34++_+WT_silica_KMK29--_US23502401_252800516532_S01_GE2_1100_Jul11_2_4.txt
Silica-treated wild type lung tissue


title: FRC_bLN_D6_2


title: Wild type lung Replicate 4

description:
raw data file: TG_KMK48++_+WT_KMK47--_US23502401_252800516532_S01_GE2_1100_Jul11_1_4.txt
Wild type lung tissue


title: FRC_bLN_D3_4


title: Wild type lung Replicate 1

description:
raw data file: WT_KMK33--_+TG_KMK30++_US23502401_252800516532_S01_GE2_1100_Jul11_1_1.txt
Wild type lung tissue


title: FRC_bLN_D3_2


title: FRC_bLN_D6_3


title: Wild type lung Replicate 2

description:
raw data file: WT_KMK46--_+WT_silica_KMK44--_US23502401_252800516532_S01_GE2_1100_Jul11_1_2.txt
Wild type lung tissue


title: FRC_bLN_Naive_5


title: FRC_bLN_D3_1


title: 020+IFNg+TNFa

city: Copenhagen

first: Tina

last: Jehs

address: Blegdamsvej 3

country: Denmark

institute: University of Copenhagen

description: Gene expression data from primary choroidal melanocyte culture (donor 020) stimulated with IFNγ+TNFα

hyb_protocol: Standard protocol, Affymetrix Core center, Rigshospitalet, Copenhagen, Denmark

data_processing: The data was analyzed with the Expression Console

source_name: choroidal melanocytes

label_protocol: Biotinylated cRNA was prepared according to the strandard Affymetrix one-cycle protocol from RNA (Expression Analysis Technical Manual 2001, Affymetrix)

growth_protocol: Choroidal melanocyte were used at an early passage which did not exceed p+4. 100,000 cells were plated into 6-well plates and grown for 14-21 d in FIC medium which is F12 medium (Gibco) supplemented with 10% FCS (Seralab, West Sussex, UK), 2 mM glutamine (Gibco), 20 ng/ml basic fibroblast growth factor (Gibco), 0.1 mM isobutylmethylxanthine (Sigma), 10 ng/ml cholera toxin (Sigma) and 50 µg/ml gentamicin (Gibco). The culture medium was then changed to the serum-free Melanocyte Growth Medium M2 (PromoCell, Heidelberg, Germany) and the cells cultured for another 12-25 d, at which time they became highly pigmented and developed a three-dimensional structure.

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

treatment_protocol: The cells were stimulated for 48 h at 37 °C and 5% CO2 with 1.5 ml of supernatant from activated T-cells and 1.5 ml of fresh M2 medium, or 27 ng/ml IFN-γ and 10 ng/ml recombinant TNF-α (both from R&D Systems, Minneapolis, MN) in a total volume of 3 ml.

tag: donor

value: choroidal melanocytes


title: 2%_plusFGF2 (S2_H004)

value: Adult human dermal fibroblasts


title: FRC_bLN_D3_3


title: 020+T cell supern.

description: Gene expression data from primary choroidal melanocyte culture (donor 020) stimulated with supernatant from activated T cells

scan_protocol: Standard protocol, Affymetrix Core center, Rigshospitalet, Copenhagen, Denmark


title: Embryoid body derived from mESC, suspended, rep3


title: Lens Crim1 glcr11/+ rep1

description: CIIA

value: lens


title: 020 unstimulated

description: Gene expression data from primary choroidal melanocyte culture (donor 020) unstimulated


title: 019+IFNg+TNFa

description: Gene expression data from primary choroidal melanocyte culture (donor 019) stimulated with IFNγ+TNFα


title: FRC_bLN_Naive_1


title: FRC_bLN_Naive_4


title: FRC_bLN_Naive_3


title: BEC_bLN_D30_3

value: BEC


title: FRC_bLN_Naive_2


title: BEC_bLN_D6_4


title: 014+T cell supern.

description: Gene expression data from primary choroidal melanocyte culture (donor 014) stimulated with supernatant from activated T cells


title: 016+IFNg+TNFa

description: Gene expression data from primary choroidal melanocyte culture (donor 016) stimulated with IFNγ+TNFα


title: 019 unstimulated

description: Gene expression data from primary choroidal melanocyte culture (donor 019) unstimulated


title: 015+T cell supern.

description: Gene expression data from primary choroidal melanocyte culture (donor 015) stimulated with supernatant from activated T cells


title: BEC_bLN_D6_3


title: 014+IFNg+TNFa

description: Gene expression data from primary choroidal melanocyte culture (donor 014) stimulated with IFNγ+TNFα


title: BEC_bLN_D30_2


title: BEC_bLN_D30_1


title: 014 unstimulated

description: Gene expression data from primary choroidal melanocyte culture (donor 014) unstimulated


title: 016 unstimulated

description: Gene expression data from primary choroidal melanocyte culture (donor 016) unstimulated


title: 016+T cell supern.

description: Gene expression data from primary choroidal melanocyte culture (donor 016) stimulated with supernatant from activated T cells


title: 015 unstimulated

description: Gene expression data from primary choroidal melanocyte culture (donor 015) unstimulated


title: 019+T cell supern.

description: Gene expression data from primary choroidal melanocyte culture (donor 019) stimulated with supernatant from activated T cells


title: BEC_bLN_D6_2


title: 007+T cell supern.

description: Gene expression data from primary choroidal melanocyte culture (donor 007) stimulated with supernatant from activated T cells


title: Transgenic lung Replicate 2

description:
raw data file: TG_KMK48++_+WT_KMK47--_US23502401_252800516532_S01_GE2_1100_Jul11_1_4.txt
Transgenic lung tissue


title: 007+IFNg+TNFa

description: Gene expression data from primary choroidal melanocyte culture (donor 007) stimulated with IFNγ+TNFα


title: BEC_bLN_D6_1


title: BEC_bLN_D3_4


title: BEC_bLN_D3_1