title: laird-00224: TCGA-13-1412-01A-01D-0460-05


title: laird-00224: TCGA-30-1853-01A-02D-0652-05

status: Public on Nov 21 2015

type: genomic

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

label: biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: Primary solid_tumor

tag: diseasestate

value: Serous Cystadenocarcinoma

tag: organismpart

value: Ovary

tag: diseasestaging

value: IIIC

tag: individual

tag: Sex

value: FEMALE

tag: age

tag: external id

tag: tumorgrading


title: laird-00051: Brain_TCGA-02-0104

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

source_name: Brain

value: GLIOBLASTOMA MULTIFORME

value: Brain

tag: pathologic status

value: NOT SPECIFIED

tag: histologic diagnosis

tag: tissue anatomic site


title: laird-00224: TCGA-29-1763-01A-02D-0563-05

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

value: IIC

tag: clinical diagnosis


title: laird-00224: TCGA-20-0987-01A-02D-0432-05

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


title: laird-00224: TCGA-30-1855-01A-01D-0581-05

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


title: laird-00051: Cell_TCGA-07-0227

source_name: cell

value: cell


title: laird-00224: TCGA-24-2035-01A-01D-0667-05


title: laird-00051: Brain_TCGA-08-0348

value: MALIGNANT

value: OCCIPITAL LOBE


title: laird-00051: Brain_TCGA-06-0177

value: TEMPORAL LOBE


title: laird-00224: TCGA-24-1418-01A-01D-0475-05


title: laird-00224: TCGA-25-1634-01A-01D-0536-05


title: laird-00224: TCGA-59-2352-01A-01D-0708-05


title: laird-00051: Brain_TCGA-06-0645


title: laird-00051: Brain_TCGA-06-0176

value: FRONTAL LOBE


title: laird-00224: TCGA-23-1120-01A-02D-0432-05


title: laird-00051: Brain_TCGA-08-0521

value: PARIETAL LOBE


title: laird-00224: TCGA-24-1463-01A-01D-0475-05


title: laird-00051: Brain_TCGA-06-0167


title: laird-00051: Brain_TCGA-06-0122

value: OVERLAPPING LESION OF BRAIN


title: laird-00224: TCGA-13-0807-01B-02D-0402-05


title: laird-00051: Brain_TCGA-08-0373


title: laird-00051: Brain_TCGA-02-0070


title: laird-00224: TCGA-13-0913-02A-01D-0807-05

source_name: Recurrent Solid Tumor


title: laird-00224: TCGA-13-1491-01A-01D-0475-05


title: laird-00051: Brain_TCGA-02-0014


title: laird-00051: Brain_TCGA-02-0011


title: laird-00051: Brain_TCGA-02-0069


title: laird-00224: TCGA-13-0761-01A-01D-0359-05

value: IV


title: laird-00224: TCGA-61-2102-01A-01D-0667-05


title: laird-00051: Brain_TCGA-02-0015


title: laird-00224: TCGA-13-0913-01A-01D-0402-05


title: laird-00224: TCGA-25-2042-01A-01D-0708-05


title: laird-00224: TCGA-25-1633-01A-01D-0536-05


title: laird-00051: Brain_TCGA-02-0115


title: laird-00051: Brain_TCGA-02-0075


title: laird-00051: Brain_TCGA-06-0241


title: laird-00224: TCGA-09-1675-01B-01D-0563-05

value: IC


title: laird-00224: TCGA-20-0991-01A-03D-0432-05

value: Serous Cystadenocarcinoma

value: IIB


title: laird-00051: Brain_TCGA-06-0185


title: laird-00224: TCGA-10-0931-01A-01D-0402-05

value: Ovary

value: IIIC


title: laird-00051: Brain_TCGA-02-0106

value: GLIOBLASTOMA MULTIFORME


title: laird-00224: TCGA-24-2290-01A-01D-0708-05

value: OMENTUM

value: FEMALE


title: laird-00224: TCGA-09-1670-01A-01D-0563-05

value: IIIA

value: NOT SPECIFIED


title: laird-00051: Brain_TCGA-12-0616

value: Brain

value: MALIGNANT


title: laird-00224: TCGA-31-1959-01A-01D-0652-05


title: laird-00051: Brain_TCGA-06-0182

value: TEMPORAL LOBE


title: laird-00224: TCGA-61-1917-01A-01D-0652-05

value: IIIB


title: laird-00051: Brain_TCGA-06-0195

value: FRONTAL LOBE


title: laird-00224: TCGA-25-1626-01A-01D-0536-05


title: laird-00224: TCGA-36-1577-01A-01D-0536-05

value: IIC


title: laird-00224: TCGA-30-1856-01A-01D-0581-05


title: laird-00051: Brain_TCGA-12-0615

value: OVERLAPPING LESION OF BRAIN


title: laird-00051: Brain_TCGA-06-0409


title: laird-00051: Brain_TCGA-02-0290


title: laird-00051: Brain_TCGA-02-0060


title: laird-00224: TCGA-24-1603-01A-01D-0501-05


title: laird-00224: TCGA-01-0631-11A-01D-0383-05

source_name: Solid normal_tissue

value: Serous cystadenocarcinoma

value: many


title: laird-00224: TCGA-61-1903-01A-01D-0581-05

value: Serous Cystadenocarcinoma

value: IB


title: laird-00051: Brain_TCGA-06-0413


title: laird-00224: TCGA-13-0894-01B-01D-0460-05

value: Ovary

value: IIIC


title: laird-00224: TCGA-20-1685-01A-01D-0563-05


title: laird-00051: Brain_TCGA-06-0126

value: GLIOBLASTOMA MULTIFORME


title: laird-00051: Brain_TCGA-08-0345

value: PARIETAL LOBE


title: laird-00051: Brain_TCGA-02-0113


title: laird-00224: TCGA-36-1575-01A-01D-0536-05

value: FEMALE


title: laird-00224: TCGA-30-1857-01A-02D-0581-05

value: IV

value: NOT SPECIFIED


title: laird-00051: Brain_TCGA-02-0001

value: Brain

value: MALIGNANT

value: BRAIN, NOS


title: laird-00224: TCGA-25-1321-01A-01D-0460-05


title: laird-00051: Brain_TCGA-06-0150


title: laird-00224: TCGA-13-1510-01A-02D-0475-05


title: laird-00051: Brain_TCGA-06-0127


title: laird-00051: Brain_TCGA-02-0339


title: laird-00224: TCGA-24-1104-01A-01D-0432-05


title: laird-00051: Brain_TCGA-02-0007

value: TEMPORAL LOBE


title: laird-00224: TCGA-29-1704-01B-01D-0807-05


title: laird-00224: TCGA-23-1026-01B-01D-0432-05


title: laird-00051: Brain_TCGA-06-0238


title: laird-00224: TCGA-29-1704-02A-01D-0807-05


title: laird-00051: Brain_TCGA-02-0023


title: laird-00051: Brain_TCGA-02-0317


title: laird-00051: Brain_TCGA-08-0360


title: laird-00224: TCGA-25-2409-01A-01D-0708-05


title: laird-00051: Brain_TCGA-06-0158


title: laird-00051: Brain_TCGA-08-0518

value: FRONTAL LOBE


title: laird-00224: TCGA-04-1519-01A-01D-0536-05


title: laird-00051: Brain_TCGA-02-0440


title: laird-00224: TCGA-24-1548-01A-01D-0536-05


title: laird-00224: TCGA-29-1690-01A-01D-0563-05


title: laird-00224: TCGA-61-1728-01A-01D-0652-05


title: laird-00224: TCGA-25-1326-01A-01D-0460-05


title: laird-00051: Brain_TCGA-02-0028


title: laird-00224: TCGA-30-1887-01A-01D-0652-05


title: laird-00051: Brain_TCGA-02-0422


title: laird-00224: TCGA-25-1329-01A-01D-0460-05


title: laird-00224: TCGA-09-1674-01A-01D-0563-05


title: laird-00224: TCGA-29-1769-01A-01D-0581-05


title: laird-00051: Brain_TCGA-06-0169

value: OVERLAPPING LESION OF BRAIN


title: laird-00051: Brain_TCGA-08-0529


title: laird-00224: TCGA-13-0901-01B-01D-0460-05


title: laird-00224: TCGA-04-1351-01A-01D-0460-05


title: laird-00224: TCGA-13-1488-01A-01D-0475-05


title: laird-00051: Brain_TCGA-06-0221


title: laird-00051: Brain_TCGA-06-0147


title: laird-00224: TCGA-13-0804-01A-01D-0359-05


title: laird-00224: TCGA-59-2351-01A-01D-0708-05


title: laird-00224: TCGA-25-1313-01A-01D-0460-05


title: laird-00051: Brain_TCGA-06-0168


title: laird-00224: TCGA-07-0227-20A-01D-0536-05

source_name: Control Cell Line


title: laird-00224: TCGA-23-1107-01A-01D-0432-05


title: laird-00051: Brain_TCGA-02-0026


title: laird-00224: TCGA-07-0227-20A-01D-0581-05


title: laird-00224: TCGA-07-0227-20A-01D-0460-05


title: laird-00051: Brain_TCGA-02-0084


title: laird-00051: Brain_TCGA-02-0004


title: laird-00051: Brain_TCGA-08-0344


title: laird-00224: TCGA-07-0227-20A-01D-0402-05


title: laird-00051: Brain_TCGA-02-0333


title: laird-00224: TCGA-07-0227-20A-01D-0563-05


title: laird-00224: TCGA-07-0227-20A-01D-0807-05


title: laird-00051: Brain_TCGA-06-0646


title: laird-00051: Brain_TCGA-06-0175


title: laird-00051: Brain_TCGA-06-0143


title: laird-00224: TCGA-07-0227-20A-01D-0432-05


title: laird-00051: Brain_TCGA-02-0051


title: laird-00051: Brain_TCGA-06-0137


title: laird-00224: TCGA-07-0227-20A-01D-0359-05


title: laird-00051: Brain_TCGA-08-0244


title: laird-00224: TCGA-07-0227-20A-01D-0667-05


title: laird-00051: Brain_TCGA-02-0006


title: laird-00224: TCGA-07-0227-20A-01D-0652-05


title: laird-00051: Brain_TCGA-02-0010


title: laird-00051: Brain_TCGA-06-0132


title: laird-00224: TCGA-07-0227-20A-01D-0708-05


title: laird-00051: Brain_TCGA-02-0080


title: laird-00051: Brain_TCGA-06-0142


title: laird-00224: TCGA-25-2393-01A-01D-0708-05


title: laird-00051: Brain_TCGA-06-0133


title: laird-00051: Brain_TCGA-06-0197


title: laird-00224: TCGA-29-1696-01A-01D-0563-05


title: laird-00051: Brain_TCGA-08-0357


title: laird-00051: Brain_TCGA-02-0043


title: laird-00051: Brain_TCGA-06-0159


title: laird-00224: TCGA-13-1496-01A-01D-0475-05


title: laird-00051: Brain_TCGA-02-0052


title: laird-00224: TCGA-25-2408-01A-01D-0708-05


title: laird-00051: Brain_TCGA-02-0027


title: laird-00224: TCGA-13-0805-01A-01D-0359-05


title: laird-00051: Brain_TCGA-06-0394


title: laird-00224: TCGA-13-1506-01A-01D-0475-05


title: laird-00224: TCGA-29-1701-01A-01D-0563-05


title: laird-00051: Brain_TCGA-02-0451


title: laird-00051: Brain_TCGA-06-0152


title: laird-00224: TCGA-25-1630-01A-01D-0536-05


title: laird-00051: Brain_TCGA-08-0520


title: laird-00051: Brain_TCGA-02-0048


title: laird-00224: TCGA-24-1555-01A-01D-0501-05


title: laird-00051: Brain_TCGA-06-0184


title: laird-00224: TCGA-09-2048-01A-01D-0708-05


title: laird-00224: TCGA-36-1576-01A-01D-0536-05


title: laird-00224: TCGA-24-1556-01A-01D-0536-05

value: IIB


title: laird-00051: Brain_TCGA-06-0130


title: laird-00224: TCGA-01-0638-11A-02D-0383-05

value: many


title: laird-00224: TCGA-29-1705-01A-01D-0563-05

value: Serous Cystadenocarcinoma


title: laird-00051: Brain_TCGA-06-0125


title: laird-00051: Brain_TCGA-06-0188


title: laird-00224: TCGA-29-1705-02A-01D-0807-05


title: laird-00224: TCGA-61-1915-01A-01D-0581-05

value: IIC


title: laird-00224: TCGA-61-1918-01A-01D-0652-05

value: Ovary


title: laird-00224: TCGA-59-2355-01A-01D-0708-05


title: laird-00051: Brain_TCGA-06-0145


title: laird-00224: TCGA-04-1337-01A-01D-0432-05

value: IIIC


title: laird-00051: Brain_TCGA-08-0352

value: GLIOBLASTOMA MULTIFORME


title: laird-00051: Brain_TCGA-06-0141

value: OCCIPITAL LOBE


title: laird-00051: Brain_TCGA-02-0003


title: laird-00224: TCGA-24-2020-01A-01D-0652-05

value: FEMALE


title: laird-00224: TCGA-24-2038-01A-01D-0667-05

value: IIIA

value: GB


title: laird-00224: TCGA-09-1672-01A-01D-0563-05

value: NOT SPECIFIED


title: laird-00224: TCGA-57-1584-01A-01D-0536-05


title: laird-00051: Brain_TCGA-02-0116

value: Brain

value: MALIGNANT


title: laird-00051: Brain_TCGA-02-0071


title: laird-00051: Brain_TCGA-08-0510


title: laird-00224: TCGA-24-1546-01A-01D-0536-05


title: laird-00224: TCGA-04-1349-01A-01D-0460-05

value: IV


title: laird-00051: Brain_TCGA-02-0439


title: laird-00224: TCGA-13-0908-01B-01D-0460-05


title: laird-00224: TCGA-61-2101-01A-01D-0667-05


title: laird-00051: Brain_TCGA-02-0002


title: laird-00224: TCGA-25-2401-01A-01D-0708-05


title: laird-00051: Brain_TCGA-06-0121


title: laird-00051: Brain_TCGA-02-0025


title: laird-00051: Brain_TCGA-08-0375


title: laird-00224: TCGA-61-1899-01A-01D-0581-05


title: laird-00051: Brain_TCGA-08-0356


title: laird-00224: TCGA-23-1109-01A-01D-0432-05


title: laird-00051: Brain_TCGA-02-0114

value: FRONTAL LOBE


title: laird-00224: TCGA-13-1492-01A-01D-0475-05


title: laird-00051: Brain_TCGA-08-0386


title: laird-00051: Brain_TCGA-02-0057


title: laird-00224: TCGA-25-1632-01A-01D-0536-05


title: laird-00051: Brain_TCGA-06-0208


title: laird-00224: TCGA-24-1424-01A-01D-0475-05


title: laird-00224: TCGA-13-0903-01A-01D-0402-05


title: laird-00224: TCGA-13-0726-01A-01D-0359-05

value: GX


title: laird-00051: Brain_TCGA-08-0525

value: ANAPLASTIC ASTROCYTOMA

value: PARIETAL LOBE


title: laird-00051: Brain_TCGA-02-0024


title: laird-00051: Brain_TCGA-02-0260


title: laird-00224: TCGA-31-1951-01A-01D-0652-05

value: Serous Cystadenocarcinoma


title: laird-00051: Brain_TCGA-06-0237

value: OVERLAPPING LESION OF BRAIN


title: laird-00051: Brain_TCGA-06-0194

value: TEMPORAL LOBE


title: laird-00224: TCGA-24-1423-01A-01D-0475-05

value: Ovary

value: IIIC


title: laird-00224: TCGA-10-0937-01A-02D-0402-05


title: laird-00051: Brain_TCGA-06-0151

value: GLIOBLASTOMA MULTIFORME


title: laird-00224: TCGA-09-1661-01B-01D-0536-05

value: FEMALE


title: laird-00051: Brain_TCGA-06-0414


title: laird-00224: TCGA-24-2262-01A-01D-0708-05


title: laird-00051: Brain_TCGA-02-0099

value: OCCIPITAL LOBE


title: laird-00224: TCGA-13-0906-01A-01D-0402-05


title: laird-00051: Brain_TCGA-08-0517

value: GLIOMA MIXED


title: laird-00224: TCGA-23-1124-01A-01D-0432-05

value: NOT SPECIFIED


title: laird-00051: Brain_TCGA-02-0258

value: Brain


title: laird-00051: Brain_TCGA-06-0148

value: MALIGNANT


title: laird-00224: TCGA-24-0970-01B-01D-0432-05


title: laird-00224: TCGA-01-0636-11A-01D-0383-05

value: many


title: laird-00051: Brain_TCGA-02-0446


title: laird-00224: TCGA-24-1614-01A-01D-0501-05


title: laird-00224: TCGA-09-2045-01A-01D-0708-05

value: IV


title: laird-00224: TCGA-31-1944-01A-01D-0652-05


title: laird-00051: Brain_TCGA-02-0016


title: laird-00051: Brain_TCGA-08-0380

value: FRONTAL LOBE


title: laird-00224: TCGA-29-1703-01A-01D-0563-05


title: laird-00224: TCGA-61-1741-01A-02D-0581-05

value: IIIB


title: laird-00224: TCGA-20-0990-01A-01D-0432-05


title: laird-00224: TCGA-13-0717-01A-01D-0359-05


title: laird-00051: Brain_TCGA-02-0456


title: laird-00224: TCGA-13-0921-01A-01D-0402-05


title: laird-00051: Brain_TCGA-02-0039


title: laird-00051: Brain_TCGA-06-0206


title: laird-00224: TCGA-61-2009-01A-01D-0667-05


title: laird-00224: TCGA-24-1847-01A-01D-0563-05


title: laird-00051: Brain_TCGA-08-0346


title: laird-00051: Brain_TCGA-02-0009


title: laird-00224: TCGA-24-1564-01A-01D-0501-05


title: laird-00224: TCGA-10-0925-01B-01D-0652-05


title: laird-00051: Brain_TCGA-02-0085


title: laird-00051: Brain_TCGA-02-0083


title: laird-00051: Brain_TCGA-06-0402


title: laird-00051: Brain_TCGA-02-0111


title: laird-00224: TCGA-13-0888-01A-01D-0402-05


title: laird-00224: TCGA-13-0766-01A-02D-0359-05


title: laird-00224: TCGA-04-1343-01A-01D-0432-05


title: laird-00224: TCGA-24-2267-01A-01D-0708-05

value: IIB


title: laird-00051: Brain_TCGA-08-0509

value: PARIETAL LOBE


title: laird-00051: Brain_TCGA-08-0350


title: laird-00051: Brain_TCGA-06-0189


title: laird-00224: TCGA-04-1356-01A-01D-0460-05

value: Serous Cystadenocarcinoma

value: IIC


title: laird-00051: Brain_TCGA-02-0086


title: laird-00224: TCGA-59-2354-01A-01D-0708-05

value: Ovary


title: laird-00224: TCGA-24-1551-01A-01D-0501-05

value: IIIC


title: laird-00051: Brain_TCGA-02-0087

value: GLIOBLASTOMA MULTIFORME


title: laird-00051: Brain_TCGA-06-0119


title: laird-00051: Brain_TCGA-06-0166


title: laird-00051: Brain_TCGA-06-0129

value: OVERLAPPING LESION OF BRAIN


title: laird-00224: TCGA-23-1022-01A-02D-0432-05

value: FEMALE


title: laird-00051: Brain_TCGA-06-0410


title: laird-00224: TCGA-04-1338-01A-01D-0432-05


title: laird-00051: Brain_TCGA-02-0269


title: laird-00051: Brain_TCGA-12-0618


title: laird-00051: Brain_TCGA-02-0325


title: laird-00051: Brain_TCGA-06-0210


title: laird-00224: TCGA-13-0889-01A-01D-0402-05

value: GX


title: laird-00051: Brain_TCGA-08-0392


title: laird-00224: TCGA-24-1426-01A-01D-0475-05

value: NOT SPECIFIED


title: laird-00051: Brain_TCGA-02-0047

value: Brain

value: TEMPORAL LOBE


title: laird-00051: Brain_TCGA-06-0211

value: MALIGNANT


title: laird-00051: Brain_TCGA-02-0089


title: laird-00051: Brain_TCGA-06-0124


title: laird-00224: TCGA-13-0768-01A-01D-0359-05


title: laird-00051: Brain_TCGA-06-0160


title: laird-00051: Brain_TCGA-06-0171


title: laird-00224: TCGA-57-1583-01A-01D-0536-05


title: laird-00051: Brain_TCGA-08-0349


title: laird-00224: TCGA-25-2397-01A-01D-0708-05

value: IV


title: laird-00051: Brain_TCGA-12-0620


title: laird-00051: Brain_TCGA-02-0033

value: OCCIPITAL LOBE


title: laird-00224: TCGA-13-1500-01A-01D-0475-05


title: laird-00051: Brain_TCGA-02-0430


title: laird-00051: Brain_TCGA-02-0330


title: laird-00051: Brain_TCGA-02-0055


title: laird-00051: Brain_TCGA-06-0178

value: FRONTAL LOBE


title: laird-00224: TCGA-24-1431-01A-01D-0475-05


title: laird-00224: TCGA-25-2400-01A-01D-0708-05


title: laird-00224: TCGA-13-0755-01A-01D-0359-05


title: laird-00224: TCGA-09-0364-01A-02D-0359-05


title: laird-00051: Brain_TCGA-02-0046


title: laird-00051: Brain_TCGA-02-0059


title: laird-00051: Brain_TCGA-02-0321


title: laird-00224: TCGA-24-2297-01A-01D-0708-05


title: laird-00051: Brain_TCGA-02-0037


title: laird-00224: TCGA-13-0924-01A-01D-0402-05


title: laird-00224: TCGA-13-0890-01A-01D-0402-05


title: laird-00051: Brain_TCGA-02-0337


title: laird-00224: TCGA-24-2271-01A-01D-0708-05


title: laird-00051: Brain_TCGA-06-0214


title: laird-00224: TCGA-20-1687-01A-01D-0563-05


title: laird-00224: TCGA-04-1332-01A-01D-0432-05


title: laird-00224: TCGA-04-1525-01A-01D-0536-05


title: laird-00224: TCGA-61-1736-01B-01D-0667-05


title: laird-00051: Brain_TCGA-06-0156

value: GLIOBLASTOMA


title: laird-00224: TCGA-13-0730-01A-01D-0359-05


title: laird-00224: TCGA-24-1557-01A-01D-0536-05


title: laird-00224: TCGA-13-0912-01A-01D-0402-05


title: laird-00224: TCGA-04-1336-01A-01D-0432-05

value: IIIB


title: laird-00224: TCGA-25-1323-01A-01D-0460-05

value: Serous Cystadenocarcinoma


title: laird-00224: TCGA-01-0630-11A-01D-0383-05

value: many


title: laird-00224: TCGA-61-2098-01A-01D-0667-05

value: Ovary


title: laird-00224: TCGA-61-1910-01A-01D-0581-05

value: IIC


title: Mouse brain tissue mock injected, biological rep3

type: RNA

city: Singapore

first: Timothy

middle: Weixin

last: Kwang

address: 46 Kim Yan Road, The Herencia #01-14/15

country: Singapore

institute: Tessa Therapeutics Pte. Ltd.

description:
Mock-3 purification methods.
Gene expression data from brain tissue around site injected with mock supernatant.

hyb_protocol: Hybridization mixes with 15 μg of fragmented cRNA were prepared according to the standard protocol from Affymetrix GeneChip Hybridization, Wash and Stain kit. 200µl of clarified hybridization cocktail (15 µg of labeled cRNA) was hybridized onto arrays for 16 h at 45 °C. Arrays were washed and stained with streptavidin-phycoerythrin in Affymetrix GeneChip Fluidics Station 450 using recommended reagents from Affymetrix Hybridization, Wash and Stain kit.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: The data were acquired with GCOS v 1.4.0.036, scaling and normalization factors were set to user-defined values of 1. The statistical expression algorithm was used for analysis.

molecule: total RNA

organism: Mus musculus

source_name: Mouse brain tissue mock injected

label_protocol: 5μg of purified RNA was used to prepare labeled cRNA using Affymetrix One Cycle Target Labeling and Control reagents and Kreactech RNA ampULSE amplification labeling kit.

extract_protocol: Total RNA was isolated from brain tissue using Trizol according to the manufacturer's instructions and cleaned up using Qiagen RNeasy Mini column.

treatment_protocol: 3 adult male immunocompetent BALB/c mice were used for each group of Mock, MC+HS- and HS-purified baculovirus injections. 1E8 BV-HSVtk viral particles in 10 μl (purified by HS or MC+HS) were injected stereotaxically into each side of the mouse brain striatum (anteroposterior: 0.0 mm, mediolateral: +2.0 mm, and dorsoventral: -3.0 mm from bregma and dura) using a 10 μl Hamilton syringe connected with a 30 G needle. Brain samples around the injection sites were collected 2 days after virus inoculation and placed in Trizol. Mock virus preparation refers to Sf9 culture medium containing no baculovirus subjected to purification by MC+HS.

tag: strain/background

value: BALB/c

tag: tissue

value: brain

value: adult

value: male

tag: treatment

value: mock

tag: bv-hsvtk purification method


title: Mouse brain tissue mock injected, biological rep1

description:
Mock-1 purification methods.
Gene expression data from brain tissue around site injected with mock supernatant.


title: Mouse brain tissue injected with MC+HS-purified BV, biological rep2

description:
Membrane purification-2 purification methods.
Gene expression data from brain tissue around site injected with MC+HS-purified BV-HSVtk.

source_name: Mouse brain tissue injected with MC+HS-purified BV-HSVtk

value: BV-HSVtk

value: membrane chromatography with high-speed centrifugation (MC+HS)


title: laird-00224: TCGA-29-1761-01A-01D-0563-05

value: IIIC

value: FEMALE

value: NOT SPECIFIED


title: Mouse brain tissue mock injected, biological rep2

description:
Mock-2 purification methods.
Gene expression data from brain tissue around site injected with mock supernatant.


title: Mouse brain tissue injected with HS-purified BV, biological rep3

description:
HS centrifugation-3 purification.
Gene expression data from brain tissue around site injected with HS-purified BV-HSVtk.

source_name: Mouse brain tissue injected with HS-purified BV-HSVtk

value: high-speed centrifugation (HS)


title: Mouse brain tissue injected with HS-purified BV, biological rep2

description:
HS centrifugation-2 purification.
Gene expression data from brain tissue around site injected with HS-purified BV-HSVtk.


title: Mouse brain tissue injected with HS-purified BV, biological rep1

description:
HS centrifugation-1 purification.
Gene expression data from brain tissue around site injected with HS-purified BV-HSVtk.


title: laird-00224: TCGA-30-1718-01A-01D-0563-05


title: laird-00224: TCGA-04-1331-01A-01D-0432-05


title: laird-00224: TCGA-13-1404-01A-01D-0460-05


title: laird-00224: TCGA-23-1121-01A-01D-0432-05


title: laird-00224: TCGA-29-1694-01A-01D-0563-05

value: GX


title: laird-00224: TCGA-13-0762-01A-01D-0359-05


title: Mouse brain tissue injected with MC+HS-purified BV, biological rep1

description:
Membrane purification-1 purification methods.
Gene expression data from brain tissue around site injected with MC+HS-purified BV-HSVtk.


title: laird-00224: TCGA-25-1315-01A-01D-0460-05


title: laird-00224: TCGA-24-1852-02A-01D-0807-05


title: ExVivoBlood_CONTROL_rep3

city: Greensboro

first: Mulumebet

last: Worku

state: North Carolina

address: 1601 E market Street

department: Animal Sciences

institute: North Carolina Agricultural and Technical State University

description: Gene expression after 30 min incubation of cow whole blood with no treatment

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Bovine v2 4×44k Oligo Microarrays (G2519F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan default setting for 1x44k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent) using default parameters (GE1-v5_95_Feb07) to obtain background subtracted and spatially detrended Processed Signal intensities. Data normalization and statistical analysis were performed using GeneSpring software 13.0 (Agilent). Fold changes in gene expression, t-test, gene ontology and pathway analysis were generated using the GeneSpring software.

organism: Bos taurus

source_name: BovinePeripheral Blood, CONTROL, replicate 3

label_protocol: All microarray procedures used were per manufacturer’s recommendation (Agilent Technologies, Santa Clara, CA). Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: All experimental procedures were approved by the North Carolina A&T State University committee of animal care and use. Experimental animals were clinically healthy with no mastitis during the period of blood collection. Blood was collected from animals at the end of 60-day study of receiving FastTrack Microbial (Probiotics) pack (Conklin Company, Kansas City, MO).

extract_protocol: Total RNA was extracted using the ZR whole blood RNA miniPrep kit (ZYMO RESEARCH, Irvine, CA) following the manufacturer's recommendations.  The isolation protocol includes differential lysis of red and white blood cells, and an on-column DNase digestion.  Total RNA was quantified using a NanoDrop-1000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA)  and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). All samples displayed a 260/280 ratio greater than 1.8 and RNA integrity number (RIN) greater than 7.

treatment_protocol: Freshly drawn peripheral blood from Holstein Friesian cows (n = 5) was treated with 10 ug/ml of cowpea leaf phenolic extract. Untreated samples served as negative control. The samples were incubated for 30 min at 37 ºC in a humidified incubator with 5% CO2.

tag: breed

value: Holstein Friesian

value: whole blood

tag: gender

value: Female


title: laird-00224: TCGA-24-1852-01A-01D-0807-05

tag: diseasestate

value: Serous Cystadenocarcinoma

tag: organismpart

value: Ovary


title: ExVivoBloodTreatment_CPE_rep4

description: Gene expression after 30 min treatment of cow whole blood with 10ug of cowpea phenolic extract

source_name: BovinePeripheral Blood, CPE, replicate 4


title: ExVivoBlood_CONTROL_rep2

source_name: BovinePeripheral Blood, CONTROL, replicate 2


title: ExVivoBlood_CONTROL_rep4

source_name: BovinePeripheral Blood, CONTROL, replicate 4


title: ExVivoBloodTreatment_CPE_rep1

source_name: BovinePeripheral Blood, CPE, replicate 1


title: laird-00224: TCGA-61-1895-01A-01D-0581-05

tag: diseasestaging

value: IIIB

tag: individual


title: laird-00224: TCGA-23-1110-01A-01D-0432-05

tag: Sex

tag: age


title: Mouse brain tissue injected with MC+HS-purified BV, biological rep3

description:
Membrane purification-3 purification methods.
Gene expression data from brain tissue around site injected with MC+HS-purified BV-HSVtk.

value: BALB/c

value: brain


title: laird-00224: TCGA-36-1569-01A-01D-0536-05

tag: external id

tag: tumorgrading


title: ExVivoBloodTreatment_CPE_rep2

source_name: BovinePeripheral Blood, CPE, replicate 2


title: laird-00224: TCGA-04-1357-01A-01D-0460-05

tag: pathologic status


title: LOVO ISD2

city: Miami

first: Tianli

last: Xia

state: FL

address: 1550 NW 10th Ave

department: Sylvester Comprehensive Cancer Center

institute: University of Miami

description: replicate 2

hyb_protocol: standard as recommended by illumina

scan_protocol: standard as recommended by illumina

data_processing: The data was preprocessed by Bioconductor lumi package (version 2.20.2). It was log2 transformed and quantile normalized.

label: Biotin

source_name: LOVO

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

growth_protocol: DMEM supplemented with 10% FBS, 37 Â°C, 5% CO2

extract_protocol: total RNA extraction using QIAGEN RNeasy mini kit following kit instruction

treatment_protocol: DNA transfection using lipofectamin 2000 following invitrogen standard transfection protocols

tag: cell line

value: LOVO

value: Colon


title: SW480 L2

description: replicate 2


title: HT116 L2

description: replicate 2


title: ExVivoBlood_CONTROL_rep1

source_name: BovinePeripheral Blood, CONTROL, replicate 1


title: HT116 ISD2

description: replicate 2


title: HT29 L2

description: replicate 2


title: COLO205 ISD2

description: replicate 2


title: ExVivoBloodTreatment_CPE_rep3

source_name: BovinePeripheral Blood, CPE, replicate 3


title: laird-00224: TCGA-01-0633-11A-01D-0383-05

value: many


title: FHC L2

description: replicate 2

source_name: FHC

value: FHC


title: FHC ISD2

description: replicate 2


title: SW480 ISD2

description: replicate 2


title: COLO205 L2

description: replicate 2


title: LOVO L2

description: replicate 2


title: laird-00224: TCGA-13-0923-01A-01D-0402-05

source_name: Primary solid_tumor

value: IIIC

tag: clinical diagnosis


title: HT29 ISD1

description: replicate 1


title: HT116 L1

description: replicate 1


title: laird-00224: TCGA-30-1862-01A-02D-0652-05

value: IV

value: FEMALE


title: SW480 ISD1

description: replicate 1


title: LOVO ISD1

description: replicate 1


title: HT116 ISD1

description: replicate 1


title: HT29 ISD2

description: replicate 2


title: HT29 L1

description: replicate 1


title: laird-00224: TCGA-13-0910-01A-01D-0402-05

value: NOT SPECIFIED


title: laird-00224: TCGA-24-1103-01A-01D-0432-05


title: laird-00224: TCGA-61-2002-01A-01D-0667-05


title: laird-00224: TCGA-61-1727-01A-01D-0581-05

value: IC


title: laird-00224: TCGA-25-2392-01A-01D-0708-05


title: laird-00224: TCGA-24-2260-01A-01D-0667-05


title: Embryonic WT Kupffer cells, biological replicate 2

city: Zwijnaarde

first: Liesbet

last: Martens

address: Technologiepark 927

department: VIB Inflammation Research Center

country: Belgium

institute: VIB-University of Ghent

description: Adult Kupffer cells from WT mice

hyb_protocol: Standard Affymetrix protocol. cDNA was hybrised on Affymetrix GeneChip Mouse Gene 1.0 ST Arrays (GPL6246).

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using Bioconductor. Normalisation was done by RMA.
probe_group_file:  = MoGene-1_0-st-v1.r4.pgf
meta-probeset_file:  = MoGene-1_0-st-v1.r4.mps

label_protocol: Affymetrix WT Terminal Labeling Kit

growth_protocol: Livers were isolated from the mice between 6-12 weeks of age

extract_protocol: Livers were perfused with PBS and subsequently digested with 1mg/ml Collagenase A and 10U/ul DNase (20mins at 37oC). Kupffer cells were isolated from single cell suspensions by FACS.

treatment_protocol: Indicated KC-DTR mice received 50ng DT at the designated time prior to FACS-purification of liver Kupffer cells

value: Liver

tag: genotype

value: DTR WT


title: LOVO L1

description: replicate 1

tag: tissue


title: COLO205 ISD1

description: replicate 1


title: FHC ISD1

description: replicate 1


title: laird-00224: TCGA-13-0794-01A-01D-0359-05


title: COLO205 L1

description: replicate 1


title: Monocyte Kupffer cells (Mo-KCs) from KC-DTR mouse, 30 days after DT treatment, biological replicate 4

description: Kupffer cells from transgenic DT-receptor mice, treated with DT on day 30

source_name: KC_DTR_Tg, DT30

value: DTR Tg


title: FHC L1

description: replicate 1


title: Embryonic WT Kupffer cells, biological replicate 3

description: Adult Kupffer cells from WT mice


title: laird-00224: TCGA-13-0797-01A-01D-0359-05

value: Serous Cystadenocarcinoma


title: patient 099_non-cancerous_copy number

city: Bunkyo-ku

first: Kaoru

last: Mogushi

state: Tokyo

address: 2-1-1 Hongo

department: Intractable Disease Research Center

country: Japan

institute: Juntendo University

description:
Hybridized to 250K_Sty
reference sample

hyb_protocol: Using Genome-Wide Human SNP Sty assay kit (Affymetrix), DNA was prepared and was hybridized to each array according to the manufacturer's instructions.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner 3000.

data_processing: Copy number analysis was performed using Genotyping Console software (Affymetrix). The intensity data of the reference samples were used internally to estimate the copy number state in the cancer tissue. Therefore there are no processed data for the reference samples.

source_name: surgically resected material

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from surgical materials using the QIAamp DNA Micro Kit (Qiagen) for tumor tissue or the QIAamp DNA Mini Kit (Qiagen) for non-cancerous tissue. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and agarose gel electrophoresis.

treatment_protocol: Tumor tissue was extracted using laser-capture microdissection. Whole tissue was used for analysis of non-tumor specimens.

value: non-cancerous colorectal tissue, homogenized


title: SW480 L1

description: replicate 1


title: patient 097_non-cancerous_copy number

description:
Hybridized to 250K_Sty
reference sample


title: patient 098_non-cancerous_copy number

description:
Hybridized to 250K_Sty
reference sample


title: laird-00224: TCGA-24-1430-01A-01D-0475-05

value: Ovary


title: patient 096_non-cancerous_copy number

description:
Hybridized to 250K_Sty
reference sample


title: laird-00224: TCGA-24-0966-01A-01D-0402-05


title: Monocyte Kupffer cells (Mo-KCs) from KC-DTR mouse, 30 days after DT treatment, biological replicate 3


title: Monocyte Kupffer cells (Mo-KCs) from KC-DTR mouse, 30 days after DT treatment, biological replicate 5


title: Embryonic WT Kupffer cells, biological replicate 1

description: Adult Kupffer cells from WT mice


title: laird-00224: TCGA-29-1778-01A-01D-0581-05


title: patient 094_non-cancerous_copy number

description:
Hybridized to 250K_Sty
reference sample


title: laird-00224: TCGA-13-0904-01A-02D-0402-05


title: patient 089_non-cancerous_copy number

description:
Hybridized to 250K_Sty
reference sample


title: patient 088_non-cancerous_copy number

description:
Hybridized to 250K_Sty
reference sample


title: laird-00224: TCGA-01-0628-11A-01D-0383-05

source_name: Solid normal_tissue

value: Serous cystadenocarcinoma


title: patient 095_non-cancerous_copy number

description:
Hybridized to 250K_Sty
reference sample


title: laird-00224: TCGA-04-1362-01A-01D-0460-05

value: IIC


title: laird-00224: TCGA-25-2398-01A-01D-0708-05


title: patient 065_non-cancerous_copy number

description:
Hybridized to 250K_Sty
reference sample


title: patient 078_non-cancerous_copy number

description:
Hybridized to 250K_Sty
reference sample


title: patient 073_non-cancerous_copy number

description:
Hybridized to 250K_Sty
reference sample


title: nonCSCs2

city: London

first: Ilaria

last: Malanchi

address: 1 Midland Rd,

country: United Kingdom

institute: The Francis Crick Institute

description:
14 CD24+ CD90-
replicate2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Raw data was transformed using variance-stabilizing transformation before quantile normalisation using the lumi package in R.

source_name: FACS isolation CD24+CD90-cancer cells from primary MMTVpyMT tumours

label_protocol: Standard Illumina biotin labelling protocol

extract_protocol: Tissue was digested with collagenase and reduced to signle cell suspention. Cells where stained with CD45, CD31 and 7AAD for the lineage depletion and CD24 and CD90 for the positive selection. Samples were FACS sorted and the indicated labelled cancer cells were isolated.

tag: strain

value: MMTVpyMT FVB

tag: cell type


title: patient 063_non-cancerous_copy number

description:
Hybridized to 250K_Sty
reference sample


title: laird-00224: TCGA-10-0934-01A-02D-0402-05


title: patient 070_non-cancerous_copy number

description:
Hybridized to 250K_Sty
reference sample


title: patient 068_non-cancerous_copy number

description:
Hybridized to 250K_Sty
reference sample


title: patient 083_non-cancerous_copy number

description:
Hybridized to 250K_Sty
reference sample


title: laird-00224: TCGA-61-2104-01A-01D-0667-05


title: patient 041_non-cancerous_copy number

description:
Hybridized to 250K_Sty
reference sample


title: patient 082_non-cancerous_copy number

description:
Hybridized to 250K_Sty
reference sample


title: patient 072_non-cancerous_copy number

description:
Hybridized to 250K_Sty
reference sample


title: laird-00224: TCGA-20-1686-01A-01D-0563-05


title: patient 036_non-cancerous_copy number

description:
Hybridized to 250K_Sty
reference sample


title: laird-00224: TCGA-25-2396-01A-01D-0708-05


title: patient 034_non-cancerous_copy number

description:
Hybridized to 250K_Sty
reference sample


title: patient 033_non-cancerous_copy number

description:
Hybridized to 250K_Sty
reference sample


title: CSCs

description: CD24+CD90+prim 11

source_name: FACS isolation CD24+CD90+cancer cells from primary MMTVpyMT tumours


title: patient 086_non-cancerous_copy number

description:
Hybridized to 250K_Sty
reference sample


title: laird-00224: TCGA-13-0911-01A-01D-0402-05


title: laird-00224: TCGA-29-1710-02A-01D-0807-05

source_name: Recurrent Solid Tumor


title: patient 061_non-cancerous_copy number

description:
Hybridized to 250K_Sty
reference sample


title: patient 031_non-cancerous_copy number

description:
Hybridized to 250K_Sty
reference sample


title: nonCSCs1

description:
2 CD24+ CD90-
replicate1

value: CD24+CD90-cancer cells from primary MMTVpyMT tumours


title: patient 028_non-cancerous_copy number

description:
Hybridized to 250K_Sty
reference sample


title: laird-00224: TCGA-23-2079-01A-01D-0667-05


title: patient 030_non-cancerous_copy number

description:
Hybridized to 250K_Sty
reference sample


title: patient 026_non-cancerous_copy number

description:
Hybridized to 250K_Sty
reference sample


title: laird-00224: TCGA-29-1710-01A-02D-0563-05


title: patient 025_non-cancerous_copy number

description:
Hybridized to 250K_Sty
reference sample


title: laird-00224: TCGA-61-1730-01A-01D-0581-05


title: patient 023_non-cancerous_copy number

description:
Hybridized to 250K_Sty
reference sample


title: laird-00224: TCGA-04-1365-01A-01D-0460-05

value: IIIB


title: laird-00224: TCGA-09-1665-01B-01D-0536-05


title: Faki rep5

city: Saint Louis

first: David

last: DeNardo

state: MO

address: 425 S. Euclid Avenue

institute: Washington University in St. louis

hyb_protocol: 1.5 ug of Cy5-labelled cRNA (specific activity >10.0 pmol Cy5/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2X Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Mouse 8x60K Expression Microarrays for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one-color scan setting for 8x60K array slides (Scan resolution 10um, Red Dye channel, PMT 100%).

data_processing: Raw data values were log2-transformed and quantile normalized across all samples. Detectable genes were defined as those with a detected call in at least 10% of samples studied. R software package “limma” was used to detect differentially expressed genes. Significant genes were determined at p<0.05 and absolute fold-change >=1.5.

source_name: KP mice_FAKi

label_protocol: Cyanine-5 (Cy5) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA from tumor tissues of KP tumor-bearing mice treated with vehicle and FAKi was isolated using NucleoSpin Kit according to the manufacturer's instruction.

treatment_protocol: We treated KP orthotopic tumor-bearing mice with vehicle and FAKi (50mg/kg) by gavage

tag: strain background

tag: genotype/variation

value: KP orthotopic tumor-bearing mice

value: female

value: 8 weeks

tag: treated with

value: FAK inhibitor (FAKi) for 14 days


title: patient 155_non-cancerous_copy number

description:
Hybridized to 250K_Sty
reference sample


title: laird-00224: TCGA-29-1695-01A-01D-0563-05

tag: diseasestate

tag: organismpart

value: IIIC

value: FEMALE

value: NOT SPECIFIED


title: patient 017_non-cancerous_copy number

description:
Hybridized to 250K_Sty
reference sample


title: Faki rep6

tag: gender


title: Faki rep4


title: patient 129_non-cancerous_copy number

description:
Hybridized to 250K_Sty
reference sample


title: patient 133_non-cancerous_copy number

description:
Hybridized to 250K_Sty
reference sample


title: laird-00224: TCGA-57-1993-01A-01D-0652-05

tag: diseasestaging

tag: individual

tag: Sex


title: patient 130_non-cancerous_copy number

description:
Hybridized to 250K_Sty
reference sample


title: patient 125_non-cancerous_copy number

description:
Hybridized to 250K_Sty
reference sample


title: laird-00224: TCGA-24-1849-01A-01D-0581-05

tag: age

tag: external id

tag: tumorgrading


title: Faki rep1


title: Veh rep6

source_name: KP mice_vehicle

value: vehicle for 14 days


title: Faki rep2


title: patient 027_non-cancerous_copy number

description:
Hybridized to 250K_Sty
reference sample


title: patient 123_non-cancerous_copy number

description:
Hybridized to 250K_Sty
reference sample


title: Faki rep3


title: Veh rep5


title: patient 124_non-cancerous_copy number

description:
Hybridized to 250K_Sty
reference sample


title: laird-00224: TCGA-10-0933-01A-01D-0402-05

tag: clinical diagnosis

tag: pathologic status


title: patient 110_non-cancerous_copy number

description:
Hybridized to 250K_Sty
reference sample

tag: tissue


title: laird-00224: TCGA-61-1900-01A-01D-0581-05


title: patient 109_non-cancerous_copy number

description:
Hybridized to 250K_Sty
reference sample


title: patient 108_non-cancerous_copy number

description:
Hybridized to 250K_Sty
reference sample


title: patient 106_non-cancerous_copy number

description:
Hybridized to 250K_Sty
reference sample


title: laird-00224: TCGA-09-0367-01A-01D-0359-05


title: patient 102_non-cancerous_copy number

description:
Hybridized to 250K_Sty
reference sample


title: patient 101_non-cancerous_copy number

description:
Hybridized to 250K_Sty
reference sample


title: laird-00224: TCGA-24-1604-01A-01D-0501-05


title: patient 103_non-cancerous_copy number

description:
Hybridized to 250K_Sty
reference sample


title: laird-00224: TCGA-20-1682-01A-01D-0563-05

value: GX


title: Veh rep4


title: patient 127_non-cancerous_copy number

description:
Hybridized to 250K_Sty
reference sample


title: Veh rep3


title: laird-00224: TCGA-24-2026-01A-01D-0652-05

value: Serous Cystadenocarcinoma


title: Veh rep2


title: patient 117_non-cancerous_copy number

description:
Hybridized to 250K_Sty
reference sample

value: non-cancerous colorectal tissue, homogenized


title: laird-00224: TCGA-01-0629-11A-01D-0383-05

value: Ovary

value: many


title: laird-00224: TCGA-23-1122-01A-01D-0432-05


title: laird-00224: TCGA-29-1762-01A-01D-0563-05

value: IV


title: laird-00224: TCGA-09-2049-01D-01D-0708-05


title: laird-00224: TCGA-13-0916-01A-01D-0402-05


title: laird-00224: TCGA-36-1581-01A-01D-0536-05

value: IIC


title: Veh rep1


title: laird-00224: TCGA-04-1364-01A-01D-0460-05


title: laird-00224: TCGA-23-1113-01A-01D-0432-05


title: patient 097_cancer_copy number

description: Hybridized to 250K_Sty

data_processing: Copy number analysis was performed using Genotyping Console software (Affymetrix). The intensity data of the reference samples were used internally to estimate the copy number state in the cancer tissue.

tag: metastasis

value: colorectal cancer, LCM


title: laird-00224: TCGA-29-1699-01A-01D-0563-05


title: patient 095_cancer_copy number

description: Hybridized to 250K_Sty


title: patient 083_cancer_copy number

description: Hybridized to 250K_Sty

value: distant metastasis


title: patient 088_cancer_copy number

description: Hybridized to 250K_Sty


title: patient 086_cancer_copy number

description: Hybridized to 250K_Sty


title: laird-00224: TCGA-24-2295-01A-01D-0708-05


title: patient 082_cancer_copy number

description: Hybridized to 250K_Sty


title: patient 073_cancer_copy number

description: Hybridized to 250K_Sty


title: patient 096_cancer_copy number

description: Hybridized to 250K_Sty


title: patient 072_cancer_copy number

description: Hybridized to 250K_Sty


title: laird-00224: TCGA-10-0935-01A-03D-0402-05


title: patient 089_cancer_copy number

description: Hybridized to 250K_Sty


title: laird-00224: TCGA-61-1901-01A-01D-0581-05


title: patient 055_cancer_copy number

description: Hybridized to 250K_Sty


title: patient 099_cancer_copy number

description: Hybridized to 250K_Sty


title: patient 098_cancer_copy number

description: Hybridized to 250K_Sty


title: patient 094_cancer_copy number

description: Hybridized to 250K_Sty


title: patient 061_cancer_copy number

description: Hybridized to 250K_Sty


title: patient 068_cancer_copy number

description: Hybridized to 250K_Sty


title: laird-00224: TCGA-24-1558-01A-01D-0536-05


title: patient 046_cancer_copy number

description: Hybridized to 250K_Sty


title: patient 048_cancer_copy number

description: Hybridized to 250K_Sty


title: patient 065_cancer_copy number

description: Hybridized to 250K_Sty


title: patient 063_cancer_copy number

description: Hybridized to 250K_Sty


title: patient 078_cancer_copy number

description: Hybridized to 250K_Sty


title: laird-00224: TCGA-13-0725-01A-01D-0359-05


title: laird-00224: TCGA-61-1906-01A-01D-0581-05


title: patient 070_cancer_copy number

description: Hybridized to 250K_Sty


title: patient 052_cancer_copy number

description: Hybridized to 250K_Sty


title: patient 044_cancer_copy number

description: Hybridized to 250K_Sty


title: laird-00224: TCGA-29-1697-01A-01D-0563-05


title: patient 045_cancer_copy number

description: Hybridized to 250K_Sty


title: patient 041_cancer_copy number

description: Hybridized to 250K_Sty


title: patient 036_cancer_copy number

description: Hybridized to 250K_Sty


title: laird-00224: TCGA-24-1553-01A-01D-0501-05

value: IIIB


title: patient 053_cancer_copy number

description: Hybridized to 250K_Sty


title: patient 034_cancer_copy number

description: Hybridized to 250K_Sty


title: laird-00224: TCGA-23-1028-01A-01D-0432-05


title: patient 028_cancer_copy number

description: Hybridized to 250K_Sty


title: patient 030_cancer_copy number

description: Hybridized to 250K_Sty


title: patient 033_cancer_copy number

description: Hybridized to 250K_Sty


title: patient 057_cancer_copy number

description: Hybridized to 250K_Sty


title: laird-00224: TCGA-25-1316-01A-01D-0460-05


title: laird-00224: TCGA-24-1417-01A-01D-0475-05


title: laird-00224: TCGA-01-0637-11A-01D-0383-05

value: Serous cystadenocarcinoma


title: laird-00224: TCGA-13-1495-01A-01D-0475-05


title: patient 026_cancer_copy number

description: Hybridized to 250K_Sty


title: patient 031_cancer_copy number

description: Hybridized to 250K_Sty


title: laird-00224: TCGA-10-0927-01A-02D-0402-05


title: laird-00224: TCGA-01-0639-11A-01D-0383-05


title: laird-00224: TCGA-61-2000-01A-01D-0667-05


title: patient 025_cancer_copy number

description: Hybridized to 250K_Sty


title: laird-00224: TCGA-61-1916-02A-01D-0807-05


title: patient 027_cancer_copy number

description: Hybridized to 250K_Sty


title: patient 241_cancer_copy number

description: Hybridized to 250K_Sty


title: patient 231_cancer_copy number

description: Hybridized to 250K_Sty


title: laird-00224: TCGA-09-1668-01B-01D-0536-05


title: patient 240_cancer_copy number

description: Hybridized to 250K_Sty


title: laird-00224: TCGA-61-1916-01A-01D-0807-05


title: patient 234_cancer_copy number

description: Hybridized to 250K_Sty


title: patient 226_cancer_copy number

description: Hybridized to 250K_Sty


title: laird-00224: TCGA-20-1683-01A-01D-0563-05


title: patient 244_cancer_copy number

description: Hybridized to 250K_Sty


title: patient 222_cancer_copy number

description: Hybridized to 250K_Sty


title: patient 023_cancer_copy number

description: Hybridized to 250K_Sty


title: patient 229_cancer_copy number

description: Hybridized to 250K_Sty


title: laird-00224: TCGA-29-2425-01A-01D-0708-05


title: patient 230_cancer_copy number

description: Hybridized to 250K_Sty


title: patient 215_cancer_copy number

description: Hybridized to 250K_Sty


title: patient 243_cancer_copy number

description: Hybridized to 250K_Sty


title: patient 242_cancer_copy number

description: Hybridized to 250K_Sty


title: patient 227_cancer_copy number

description: Hybridized to 250K_Sty


title: patient 219_cancer_copy number

description: Hybridized to 250K_Sty


title: patient 214_cancer_copy number

description: Hybridized to 250K_Sty


title: patient 223_cancer_copy number

description: Hybridized to 250K_Sty


title: patient 220_cancer_copy number

description: Hybridized to 250K_Sty


title: patient 235_cancer_copy number

description: Hybridized to 250K_Sty


title: patient 217_cancer_copy number

description: Hybridized to 250K_Sty


title: patient 221_cancer_copy number

description: Hybridized to 250K_Sty


title: laird-00224: TCGA-13-0802-01A-01D-0359-05


title: patient 211_cancer_copy number

description: Hybridized to 250K_Sty


title: patient 210_cancer_copy number

description: Hybridized to 250K_Sty


title: patient 207_cancer_copy number

description: Hybridized to 250K_Sty


title: patient 209_cancer_copy number

description: Hybridized to 250K_Sty


title: patient 202_cancer_copy number

description: Hybridized to 250K_Sty


title: patient 201_cancer_copy number

description: Hybridized to 250K_Sty


title: patient 203_cancer_copy number

description: Hybridized to 250K_Sty


title: laird-00224: TCGA-09-2054-01A-01D-0667-05


title: patient 213_cancer_copy number

description: Hybridized to 250K_Sty


title: laird-00224: TCGA-04-1360-01A-01D-0460-05

value: IA


title: patient 196_cancer_copy number

description: Hybridized to 250K_Sty


title: patient 195_cancer_copy number

description: Hybridized to 250K_Sty


title: patient 191_cancer_copy number

description: Hybridized to 250K_Sty


title: patient 197_cancer_copy number

description: Hybridized to 250K_Sty


title: laird-00224: TCGA-04-1346-01A-01D-0432-05


title: patient 181_cancer_copy number

description: Hybridized to 250K_Sty


title: laird-00224: TCGA-30-1891-01A-01D-0652-05


title: laird-00224: TCGA-24-1422-01A-01D-0475-05


title: patient 017_cancer_copy number

description: Hybridized to 250K_Sty


title: laird-00224: TCGA-13-1494-01A-01D-0475-05


title: patient 190_cancer_copy number

description: Hybridized to 250K_Sty


title: patient 180_cancer_copy number

description: Hybridized to 250K_Sty


title: patient 188_cancer_copy number

description: Hybridized to 250K_Sty


title: patient 175_cancer_copy number

description: Hybridized to 250K_Sty


title: laird-00224: TCGA-30-1866-01A-02D-0652-05


title: patient 184_cancer_copy number

description: Hybridized to 250K_Sty


title: laird-00224: TCGA-13-0919-01A-01D-0402-05


title: patient 178_cancer_copy number

description: Hybridized to 250K_Sty


title: patient 204_cancer_copy number

description: Hybridized to 250K_Sty


title: patient 179_cancer_copy number

description: Hybridized to 250K_Sty


title: laird-00224: TCGA-57-1586-01A-02D-0563-05


title: patient 194_cancer_copy number

description: Hybridized to 250K_Sty


title: laird-00224: TCGA-13-1512-01A-01D-0475-05


title: patient 173_cancer_copy number

description: Hybridized to 250K_Sty


title: patient 169_cancer_copy number

description: Hybridized to 250K_Sty


title: laird-00224: TCGA-04-1347-01A-01D-0432-05


title: laird-00224: TCGA-13-1481-01A-01D-0475-05


title: laird-00224: TCGA-01-0642-11A-02D-0383-05


title: patient 171_cancer_copy number

description: Hybridized to 250K_Sty


title: laird-00224: TCGA-13-1477-01A-01D-0475-05


title: laird-00224: TCGA-36-1568-01A-01D-0536-05


title: patient 168_cancer_copy number

description: Hybridized to 250K_Sty


title: laird-00224: TCGA-36-1571-01A-01D-0536-05


title: laird-00224: TCGA-23-2078-01A-01D-0667-05


title: patient 156_cancer_copy number

description: Hybridized to 250K_Sty


title: patient 150_cancer_copy number

description: Hybridized to 250K_Sty


title: laird-00224: TCGA-04-1649-01A-01D-0581-05


title: patient 147_cancer_copy number

description: Hybridized to 250K_Sty


title: laird-00224: TCGA-24-2024-01A-02D-0667-05


title: laird-00224: TCGA-24-1469-01A-01D-0501-05


title: patient 155_cancer_copy number

description: Hybridized to 250K_Sty


title: patient 158_cancer_copy number

description: Hybridized to 250K_Sty


title: patient 162_cancer_copy number

description: Hybridized to 250K_Sty


title: patient 146_cancer_copy number

description: Hybridized to 250K_Sty


title: patient 164_cancer_copy number

description: Hybridized to 250K_Sty


title: patient 015_cancer_copy number

description: Hybridized to 250K_Sty


title: laird-00224: TCGA-61-1995-01A-01D-0667-05


title: patient 157_cancer_copy number

description: Hybridized to 250K_Sty


title: patient 200_cancer_copy number

description: Hybridized to 250K_Sty


title: patient 143_cancer_copy number

description: Hybridized to 250K_Sty


title: laird-00224: TCGA-04-1542-01A-01D-0501-05


title: patient 142_cancer_copy number

description: Hybridized to 250K_Sty


title: laird-00224: TCGA-61-1919-01A-01D-0652-05


title: patient 136_cancer_copy number

description: Hybridized to 250K_Sty


title: patient 148_cancer_copy number

description: Hybridized to 250K_Sty


title: patient 144_cancer_copy number

description: Hybridized to 250K_Sty


title: laird-00224: TCGA-25-1325-01A-01D-0460-05


title: patient 187_cancer_copy number

description: Hybridized to 250K_Sty


title: patient 141_cancer_copy number

description: Hybridized to 250K_Sty


title: patient 140_cancer_copy number

description: Hybridized to 250K_Sty


title: patient 135_cancer_copy number

description: Hybridized to 250K_Sty


title: patient 129_cancer_copy number

description: Hybridized to 250K_Sty


title: patient 125_cancer_copy number

description: Hybridized to 250K_Sty


title: patient 127_cancer_copy number

description: Hybridized to 250K_Sty


title: patient 133_cancer_copy number

description: Hybridized to 250K_Sty


title: patient 130_cancer_copy number

description: Hybridized to 250K_Sty


title: patient 123_cancer_copy number

description: Hybridized to 250K_Sty


title: patient 117_cancer_copy number

description: Hybridized to 250K_Sty


title: Pancreatic cancer tissue 4

status: Public on Nov 20 2015

city: Xi'an

first: Shibin

last: Qu

state: Shaanxi

address: 127 West Changle Road

department: Department of Hepatobiliary Surgery

country: China

institute: Xijing Hospital

description:
C4
circRNA
Circular RNA expression in pancreatic cancer tissue 4.

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Human circRNA Array (8x15K, Arraystar).

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

data_processing:
Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the R software package. Differentially expressed circRNAs with statistical significance between two groups were identified through Volcano Plot filtering. Differentially expressed circRNAs between two samples were identified through Fold Change filtering. Hierarchical Clustering was performed to show the distinguishable circRNAs expression pattern among samples.
The Sample data table includes the detectable signals.

source_name: pancreatic cancer 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.

growth_protocol: Tissue samples were obtained from pancreatic ductal adenocarcinoma patients. This study was approved by the institutional Ethics Review Board of the Xijing Hospital of the Fourth Military Medical University.

extract_protocol: Total RNA was isolated from six PDAC and paired adjacent normal tissues using Trizol reagent (Invitrogen, Carlsbad, CA, USA), according to the manufacturer's protocol.

treatment_protocol: Each sample was snap-frozen in liquid nitrogen immediately after resection, then stored at -130°C until use.

tag: disease state

value: pancreatic ductal adenocarcinoma (PDAC)

value: pancreatic cancer tissue

value: female

tag: patient id


title: Pancreatic cancer tissue 6

description:
C6
circRNA
Circular RNA expression in pancreatic cancer tissue 6.


title: Pancreatic cancer tissue 5

description:
C5
circRNA
Circular RNA expression in pancreatic cancer tissue 5.

value: male


title: Pancreatic cancer tissue 3

description:
C3
circRNA
Circular RNA expression in pancreatic cancer tissue 3.


title: laird-00224: TCGA-25-1878-01A-01D-0652-05

value: IIIC

value: FEMALE


title: Normal pancreatic tissue 5

description:
N5
circRNA
Circular RNA expression in normal pancreatic tissue 5.

source_name: adjacent normal pancreatic tissue

value: adjacent normal pancreatic tissue


title: Normal pancreatic tissue 6

description:
N6
circRNA
Circular RNA expression in normal pancreatic tissue 6.


title: Pancreatic cancer tissue 1

description:
C1
circRNA
Circular RNA expression in pancreatic cancer tissue 1.


title: patient 174_cancer_copy number

description: Hybridized to 250K_Sty


title: Pancreatic cancer tissue 2

description:
C2
circRNA
Circular RNA expression in pancreatic cancer tissue 2.


title: Normal pancreatic tissue 4

description:
N4
circRNA
Circular RNA expression in normal pancreatic tissue 4.


title: patient 139_cancer_copy number

description: Hybridized to 250K_Sty


title: patient 108_cancer_copy number

description: Hybridized to 250K_Sty


title: patient 106_cancer_copy number

description: Hybridized to 250K_Sty


title: patient 109_cancer_copy number

description: Hybridized to 250K_Sty


title: patient 116_cancer_copy number

description: Hybridized to 250K_Sty


title: patient 101_cancer_copy number

description: Hybridized to 250K_Sty


title: patient 006_cancer_copy number

description: Hybridized to 250K_Sty


title: patient 103_cancer_copy number

description: Hybridized to 250K_Sty


title: patient 008_cancer_copy number

description: Hybridized to 250K_Sty


title: patient 110_cancer_copy number

description: Hybridized to 250K_Sty


title: patient 124_cancer_copy number

description: Hybridized to 250K_Sty


title: Normal pancreatic tissue 3

description:
N3
circRNA
Circular RNA expression in normal pancreatic tissue 3.


title: Normal pancreatic tissue 2

description:
N2
circRNA
Circular RNA expression in normal pancreatic tissue 2.


title: patient 102_cancer_copy number

description: Hybridized to 250K_Sty


title: C33-A transfected with HPV16 variant E-C188/G350 (1)

city: Mexico

first: Sandra

middle: Lorena

last: Romero-Cordoba

state: Mexico

address: Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan. México, D.F.

department: Cancer Genomics

country: Mexico

institute: National Instute of Genomic Medicine

hyb_protocol: Samples were hybridized with  Gene Chip Human Transcriptome Array (HTA) 2.0 (Affymetrix) and scanned at the INMEGEN Microarray Core Facility

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix) in the GeneChip Fluidics Station 450(Affymetrix)

data_processing: The probe arrays were scanned using The GeneChip Scanner 3000 7G (Affmetrix, Santa Clara CA, USA). Array signal intensities were analyzed with Affymetrix Expression Console software, probeset analysis . Briefly, raw data probes were normalized using robust multiarray analysis (RMA) for the background correction and quantile algorithm

source_name: C33-A transfected with E-C188/G350 variant

label_protocol: cDNA synthesis, amplification, and gene expression profiling were done with the WT PLUS Reagent Kit for fresh samples (Affymetrix) and and labeled with the Genechip hybridization wash and stain kit (Affymetrix).

growth_protocol: The cervical carcinoma cell line C33-A used in a previous report (Del Moral- Hernández, et al., 2010), was grown at 37 °C in 5% CO2, using MEM supplemented with 10% fetal bovine serum (Gibco, Life Technologies, USA), 100 U/ml penicillin and 100 μg/ml streptomycin.

extract_protocol: Total RNA was extracted from non-transfected C33-A cell cultures, stably transfected cell cultures and cells transfected with an empty vector, using Trizol (Invitrogen) and following the manufacturer’s protocol. Equimolar concentrations of total RNA from 3 independent experiments were pooled, a total of 2 biological pools (n=3) per condition were made

treatment_protocol: Cells were stably transfected using the standard calcium phosphate coprecipitation method (Jordan et al., 2004). Briefly, cells were grown for 24 h, transfected with 10 μg of each DNA construct and selected in MEM medium supplemented with 500μg/ml G418 (Invitrogen, Corp.). After 4 weeks of selection, GFP-positive cells were sorted by FACS (FACS Calibur, BD, Mountain View, CA, USA) to obtain a purity of greater tan 90%. The transfected cells were not cloned, but each experiment was repeated in at least three different independent assays.

tag: cell line

value: cervical carcinoma cell line C33-A

tag: transfection


title: C33-A transfected with mock (2)

source_name: C33-A transfected with mock

value: Mock


title: C33-A WT (2)

source_name: C33-A wt

value: WT- No tranfection


title: C33-A transfected with HPV16 E-protype (2)

source_name: C33-A transfected with E-protype

value: E-prototype (E-A176)


title: C33-A transfected with HPV16 variant AAc (2)

source_name: C33-A transfected with AAc variant

value: AAc


title: C33-A transfected with mock (1)


title: C33-A transfected with HPV16 variant E-C188/G350 (2)


title: C33-A transfected with HPV16 E-protype (1)


title: C33-A transfected with HPV16 variant G350 (1)

source_name: C33-A transfected with G350 variant


title: C33-A transfected with HPV16 variant AAa (2)

source_name: C33-A transfected with AAa variant

value: AAa


title: C33-A transfected with HPV16 variant E-A176/G350 (2)

source_name: C33-A transfected with E-A176/G350 variant


title: C33-A transfected with HPV16 variant AAa (1)


title: C33-A transfected with HPV16 variant G350 (2)


title: C33-A transfected with HPV16 variant E-A176/G350 (1)


title: C33-A WT (1)


title: nontransfected KSL cells (p21-/- vs p21+/+)

city: Izumo

first: Seiji

last: Fukuda

state: Shimane

address: 89-1 Enya

department: Pediatrics

institute: Shimane University

description:
biological replicate 1 of 1, freshly isolated KSL cells from p21-/-  and p21+/+ mice
Sample 1

hyb_protocol: The hybridization procedure was performed according to the Agilent 60-mer oligo microarray processing protocol using the Agilent Gene Expression Hybridization Kit (Agilent Technologies). Briefly, 300 ng of the corresponding Cy3- and Cy5-labeled fragmented cRNA were combined and hybridized overnight (17 hours, 65 °C) to Agilent Whole Mouse Genome Oligo Microarrays 8x60K using Agilent’s recommended hybridization chamber and oven. Finally, the microarray was washed once with the Agilent Gene Expression Wash Buffer 1 for 1 min at room temperature followed by a second wash with preheated Agilent Gene Expression Wash Buffer 2 (37 °C) for 1 min. The last washing step was performed with acetonitrile.

scan_protocol: Fluorescence signals of the hybridized Agilent Oligo Microarrays were detected using Agilent’s DNA microarray scanner (Agilent Technologies).

data_processing: The Agilent Feature Extraction Software (FES) was used to read out and process the microarray image files. The software determines feature intensities and ratios (including background subtraction and normalization), rejects outliers and calculates statistical confidences (p-values). For determination of differential gene expression FES derived output data files were further analyzed using the Rosetta Resolver gene expression data analysis system (Rosetta Biosoftware).

source_name: marrow KSL cells from p21-/- mouse

label_protocol: For the linear T7-based amplification step, 50 ng of each total RNA sample was used. To produce Cy3- and Cy5-labeled cRNA, the RNA samples were amplified and labeled using the Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer’s protocol. Yields of cRNA and the dye-incorporation rate were measured with the ND-1000 Spectrophotometer (NanoDrop Technologies).

growth_protocol: Marrow cells were harvested from p21-/- or p21+/+ mice. KSL cells were FACS sorted and frozen for storage. The remaining samples were cultured in the presence of murine stem cell factor, human Flt3-ligand and human thrombopoietin for 48 hours. Cells were then incubated with retroviral supernatant containing Flt3/ITD cDNA obtained from human AML patients (N51-Flt3/ITD, Kelly et al. Blood 2001) and cultured for 2 weeks in the absence of growth factors. KSL cells were FACS sorted and frozen.

extract_protocol: Total RNA was isolated from the frozen cells using standard RNA extraction protocols (NucleoSpin Ⓡ RNA II, Machery-Nagel).

value: bone marrow

tag: cell type

value: KSL

tag: genotype

tag: transfection construct

value: none, freshly isolated

source_name: marrow KSL cells from p21+/+ mouse


title: Flt3/ITD transfected KSL cells (p21-/- vs p21+/+)_rep3

description:
biological replicate 3 of 3,  KSL cells overexpressing Flt3/ITD from p21-/-  and p21+/+ mice, the same donors used in sample 1
Sample 4

value: Flt3/ITD transfected


title: TTPKO_29Mo_VE_Cerebellum_rep3

description: Ttpa-/-, 29Mo, Cerebellum, VE

hyb_protocol: Hybridization was performed according to the manufacturer's instruction.

scan_protocol: Microarrays were scanned by G2505C (Agilent) according to the manufacturer's instruction.

data_processing: Obtained data were processed using Feature Extraction Software version 10.1.1.1.

source_name: Ttpa-/-, 29Mo, Cerebellum, Vitamin E supplemented diet

label_protocol: Labeling was performed according to the manufacturer's instruction.

extract_protocol: RNA was isolated using mirVana mRNA isolation kit (Ambion) according to the manufacturer’s protocol. RNA concen-tration was quantified with NanoDrop Spectrometer (NanoDrop technologies) at a wavelength of 260nm and an Agilent 2100 Bioanalizer was used to evaluate its integrity.

treatment_protocol: Wild-type and Ttpa-/- mice were fed on a normal (36 mg of alpha-tocopherol/kg), alpha-tocopherol-supplemented (600 mg of alpha-tocopherol/kg), or alpha-tocopherol-deficient diet until the time of use. The background mouse strain is C57Bl/6 for all mice. The Animal Experiment Committee of Tokyo Medical and Dental University approved animal experiments.

value: Ttpa-/-

value: Cerebellum

tag: diet

value: Vitamin E supplemented


title: TTPKO_29Mo_VE_Cerebellum_rep4

description: Ttpa-/-, 29Mo, Cerebellum, VE


title: TTPKO_29Mo_VE_Cerebellum_rep2

description: Ttpa-/-, 29Mo, Cerebellum, VE


title: TTPKO_29Mo_noVE_Cerebellum_rep4

description: Ttpa-/-, 29Mo, Cerebellum, no VE

source_name: Ttpa-/-, 29Mo Cerebellum, Vitamin E deficient diet

value: Vitamin E deficient


title: TTPKO_29Mo_noVE_Cerebellum_rep3

description: Ttpa-/-, 29Mo, Cerebellum, no VE


title: TTPKO_29Mo_noVE_Cerebellum_rep2

description: Ttpa-/-, 29Mo, Cerebellum, no VE


title: WT_2Mo_Cerebellum_rep4

description: Wild type, 2Mo Cerebellum

source_name: Wild type, 2Mo Cerebellum, normal diet

value: Wild type

value: Normal


title: TTPKO_29Mo_VE_Cerebellum_rep1

description: Ttpa-/-, 29Mo, Cerebellum, VE


title: TTPKO_29Mo_noVE_Cerebellum_rep1

description: Ttpa-/-, 29Mo, Cerebellum, no VE


title: Normal pancreatic tissue 1

description:
N1
circRNA
Circular RNA expression in normal pancreatic tissue 1.

value: pancreatic ductal adenocarcinoma (PDAC)

value: adjacent normal pancreatic tissue

tag: gender

value: female


title: WT_29Mo_noVE_Cerebellum_rep4

description: Wild type, 29Mo, Cerebellum, no VE

source_name: Wild type, 29Mo Cerebellum, Vitamin E deficient diet


title: WT_29Mo_Cerebellum_rep3

description: Wild type, 29Mo Cerebellum

source_name: Wild type, 29Mo Cerebellum, normal diet


title: WT_29Mo_Cerebellum_rep2

description: Wild type, 29Mo Cerebellum


title: TTPKO_29Mo_noVE_Cortex_rep1

description: Ttpa-/-, 29Mo, Cortex, no VE

source_name: Ttpa-/-, 29Mo Cortex, Vitamin E deficient diet

value: Cortex


title: WT_2Mo_Cerebellum_rep2

description: Wild type, 2Mo Cerebellum


title: TTPKO_29Mo_VE_Cortex_rep2

description: Ttpa-/-, 29Mo, Cortex, VE

source_name: Ttpa-/-, 29Mo, Cortex, Vitamin E supplemented diet


title: WT_29Mo_Cerebellum_rep1

description: Wild type, 29Mo Cerebellum


title: WT_2Mo_Cerebellum_rep3

description: Wild type, 2Mo Cerebellum


title: TTPKO_29Mo_noVE_Cortex_rep3

description: Ttpa-/-, 29Mo, Cortex, no VE


title: TTPKO_29Mo_VE_Cortex_rep4

description: Ttpa-/-, 29Mo, Cortex, VE


title: TTPKO_29Mo_noVE_Cortex_rep4

description: Ttpa-/-, 29Mo, Cortex, no VE


title: TTPKO_29Mo_noVE_Cortex_rep2

description: Ttpa-/-, 29Mo, Cortex, no VE


title: WT_29Mo_noVE_Cerebellum_rep3

description: Wild type, 29Mo, Cerebellum, no VE


title: WT_29Mo_noVE_Cerebellum_rep1

description: Wild type, 29Mo, Cerebellum, no VE


title: WT_29Mo_noVE_Cerebellum_rep2

description: Wild type, 29Mo, Cerebellum, no VE


title: TTPKO_29Mo_VE_Cortex_rep1

description: Ttpa-/-, 29Mo, Cortex, VE


title: Flt3/ITD transfected KSL cells (p21-/- vs p21+/+)_rep2

description:
biological replicate 2 of 3,  KSL cells overexpressing Flt3/ITD from p21-/-  and p21+/+ mice
Sample 3


title: WT_29Mo_noVE_Cortex_rep2

description: Wild type, 29Mo, Cortex, no VE

source_name: Wild type, 29Mo Cortex, Vitamin E deficient diet


title: WT_29Mo_Cerebellum_rep4

description: Wild type, 29Mo Cerebellum


title: WT_29Mo_noVE_Cortex_rep4

description: Wild type, 29Mo, Cortex, no VE


title: TTPKO_29Mo_VE_Cortex_rep3

description: Ttpa-/-, 29Mo, Cortex, VE


title: WT_2Mo_Cerebellum_rep1

description: Wild type, 2Mo Cerebellum


title: C33-A transfected with HPV16 variant AAc (1)

value: cervical carcinoma cell line C33-A


title: WT_29Mo_noVE_Cortex_rep3

description: Wild type, 29Mo, Cortex, no VE


title: WT_29Mo_noVE_Cortex_rep1

description: Wild type, 29Mo, Cortex, no VE


title: WT_29Mo_Cortex_rep3

description: Wild type, 29Mo Cortex

source_name: Wild type, 29Mo Cortex, normal diet


title: WT_2Mo_Cortex_rep2

description: Wild type, 2Mo Cortex

source_name: Wild type, 2Mo Cortex, normal diet


title: WT_29Mo_Cortex_rep4

description: Wild type, 29Mo Cortex


title: WT_29Mo_Cortex_rep2

description: Wild type, 29Mo Cortex


title: WT_2Mo_Cortex_rep1

description: Wild type, 2Mo Cortex


title: WT_29Mo_Cortex_rep1

description: Wild type, 29Mo Cortex


title: WT_2Mo_Cortex_rep3

description: Wild type, 2Mo Cortex


title: WT_2Mo_Cortex_rep4

description: Wild type, 2Mo Cortex


title: OsMADS26 downregulated line 2, osmotic stresscondition, rep2

city: Montpellier

first: Pascal

last: Gantet

address: Avenue Agropolis

department: IRD

country: France

institute: Université Montpellier 2

description:
Gene expression data from roots and shoots of 7 days old transgenic seedlings down-regulated for OsMADS26 expression and cultivated in osmotic stress (100 mM manitol) condition
DR3_M_2

hyb_protocol: All steps of Microarray hybridization and data processing were performed according manufacturer’s instructions (Affymetrix). Equipments were provided by Affymetrix Company. Twelve μg of biotin-labelled antisens RNAs were fragmented and hybridized to GeneChip Rice Genome Arrays (Affymetrix) for 16h at 45°C and 60rpm in a Hybridization Oven 645.

scan_protocol: Arrays were washed, labeled with phycoerythrin on the Fluidic Station 450 and read with the Scanner 3000 7G.

data_processing:
Data acquisition was done with the GeneChip Command Console. Array pictures were analyzed with MAS5 algorithm of the Expression Console software (Affymetrix).
Default parameters were applied, global scaling method was used to normalize data (TGT value set at 100).

organism: Oryza sativa

source_name: down-regulated line transformed with a pANDA plasmid containing the GST targeting the 3'UTR of OsMADS26 mRNA cultivated in in osmotic stress condition (100 mM manitol)

label_protocol: Antisense RNA strand were biotynilated according the Affymetrix (Affymetrix, CA, USA) IVT Express protocol.

growth_protocol: dehulled and surface sterilized seeds of Oryza sativa, cv. Nipponbare were incubated in sterile distilled water in a growth chamber (16 h of light per day, 500 µE m-2 s-1, 28°C/25°C day/night) for 2 days at 25°C. Imbibed seeds were transferred in square Petri dishes (245 mm x 245 mm, Corning, 7 seeds per dish) containing 250 ml of half strength Murashige and Skoog (Duchefa) standard medium (MS/2) solidified with 8 g L-1 of agarose type II (Sigma). These dishes were transferred and placed vertically in a growth chamber at 28°C under 16h light.

extract_protocol: Roots and shoots of 7 day-old seedlings of 7 plantlets were collected, pooled and used for transcriptome analyses.total RNA was extracted from 100 mg of frozen leaves and roots using a RNeasy Plant Mini Kit (Quiagen) according to manufacturer’s instructions. Residual genomic DNA was removed with the RNAse-Free DNase Set (Quiagen) during RNA purification. Two independent biological experiments were used for each studied plant line.

treatment_protocol:
The isolation of OsMADS26 (Os08g02070) cDNA from O. sativa cv Nipponbare was achieved by RT-PCR. For over-expression of OsMADS26, a BP tailed OsMADS26 PCR-amplified cDNA was cloned with the BP recombinase in a modified pCAMBIA 1300 binary vector for over-expression named PC5300.OE where the Ccdb gene surrounded by the BP recombination sites were cloned between the constitutive promoter of ubiquitin gene from maize and the terminator of the nopaline syntase gene from Agrobacterium. tumefaciens (J.C. Breitler, CIRAD, unpublished). The plasmid named PC5300.OE-PC8 was transferred into A. tumefaciens strain EHA105. For down-regulation of OsMADS26 by RNA interference, the BP tailed amplified GST1 (targeting the 5’UTR of OsMADS26 mRNA) or GST2 (targeting the 3’UTR of OsMADS26 mRNA) were cloned by BP recombination in the pDON207 entry plasmid (Invitrogen) and transferred with the LR recombinase (Invitrogen) in the siRNA binary plasmid pANDA (Miki and Shimamoto, 2004, Plant Cell Physiol 45, 490_495). The resulting plasmids, were mobilized into A. tumefaciens strain EHA105 for plant transformation. Transgenic plants were obtained by co-culture of seed embryo-derived callus with A. tumefaciens strain EHA105 carrying the adequate binary plasmids following the procedure detailed in (Sallaud et al., 2003, Theor Appl Genet 106, 1396_1408). Single locus and homozygous T2 lines were selected on the basis of the segregation of the antibiotic resistance gene carried by the T-DNA and Southern blot analysis. The over-expression or down-regulation of OsMADS26 in selected transgenic lines was assessed by RT-qPCR using specific primers. On this base two independent lines ove-rexpressing OsMADS26 (called OX1 and OX2) or one line down-regulated for OsMADS26 obtained by the expression of each of the two GST designed to target OsMAS26 5’UTR or 3’UTR (called DR5 or DR3 respectively) were selected for transcriptome analysis. One transgenic lines obtained by transformation with each PC5300.OE or pANDA empty plasmids (called OX0 or DR0 respectively) were used as control.
Osmotic stress was obtained by adding Manitol (100 mM) to the culture medium.

value: root and shoot

value: 7 day old seedlings

tag: cultivar

value: Nipponbare


title: control line, empty pANDA, osmotic stresscondition, rep1

description:
Gene expression data from roots and shoots of 7 days old transgenic seedlings transformed with the empty pANDA plasmid and cultivated in osmotic stress (100 mM manitol) condition
DR0_M_1

source_name: control line transformed with an empty pANDA plasmid cultivated in in osmotic stress condition (100 mM manitol)

tag: age


title: control line, empty PC5300.OE,osmotic stresscondition, rep2

description:
Gene expression data from roots and shoots of 7 days old transgenic seedlings transformed with the empty PC5300.OE plasmid and cultivated in osmotic stress (100 mM manitol) condition
OX0_M_2

source_name: control line transformed with an empty PC5300.0E plasmid cultivatedin osmotic stress condition (100 mM manitol)


title: OsMADS26 over-expressing line 1, osmotic stresscondition, rep1

description:
Gene expression data from roots and shoots of 7 days old transgenic seedlings over-expressing OsMADS26 and cultivated in osmotic stress (100 mM manitol) condition
OX1_M_1

source_name: over-expressing line transformed with a PC5300.OE plasmid containing the OsMADS26 cDNA cultivated in in osmotic stress condition (100 mM manitol)


title: OsMADS26 over-expressing line 1, osmotic stresscondition, rep2

description:
Gene expression data from roots and shoots of 7 days old transgenic seedlings over-expressing OsMADS26 and cultivated in osmotic stress (100 mM manitol) condition
OX1_M_2


title: OsMADS26 downregulated line 2, standardculturecondition, rep2

description:
Gene expression data from roots and shoots of 7 days old transgenic seedlings down-regulated for OsMADS26 expression and cultivated in standard condition
DR3_2

source_name: down-regulated line transformed with a pANDA plasmid containing the GST targeting the 3'UTR of OsMADS26 mRNA cultivated in standard condition


title: OsMADS26 downregulated line 1, osmotic stresscondition, rep1

description:
Gene expression data from roots and shoots of 7 days old transgenic seedlings down-regulated for OsMADS26 expression and cultivated in osmotic stress (100 mM manitol) condition
DR5_M_1

source_name: down-regulated line transformed with a pANDA plasmid containing the GST targeting the 5'UTR of OsMADS26 mRNA cultivated in in osmotic stress condition (100 mM manitol)


title: OsMADS26 over-expressing line 2, standardculturecondition, rep1

description:
Gene expression data from roots and shoots of 7 days old transgenic seedlings over-expressing OsMADS26 and cultivated in standard condition
OX2_1

source_name: over-expressing line transformed with a PC5300.OE plasmid containing the OsMADS26 cDNA cultivated in standard condition


title: OsMADS26 over-expressing line 2, osmotic stresscondition, rep1

description:
Gene expression data from roots and shoots of 7 days old transgenic seedlings over-expressing OsMADS26 and cultivated in osmotic stress (100 mM manitol) condition
OX2_M_1


title: OsMADS26 downregulated line 2, standardculturecondition, rep1

description:
Gene expression data from roots and shoots of 7 days old transgenic seedlings down-regulated for OsMADS26 expression and cultivated in standard condition
DR3_1


title: control line, empty PC5300.OE, standardculturecondition, rep2

description:
Gene expression data from roots and shoots of 7 days old transgenic seedlings transformed with the empty PC5300.OE plasmid and cultivated in standard condition
OX0_2

source_name: control line transformed with an empty PC5300.0E plasmid cultivated in standard condition


title: OsMADS26 downregulated line 1, osmotic stresscondition, rep2

description:
Gene expression data from roots and shoots of 7 days old transgenic seedlings down-regulated for OsMADS26 expression and cultivated in osmotic stress (100 mM manitol) condition
DR5_M_2


title: OsMADS26 downregulated line 2, osmotic stresscondition, rep1

description:
Gene expression data from roots and shoots of 7 days old transgenic seedlings down-regulated for OsMADS26 expression and cultivated in osmotic stress (100 mM manitol) condition
DR3_M_1


title: OsMADS26 downregulated line 1, standardculturecondition, rep1

description:
Gene expression data from roots and shoots of 7 days old transgenic seedlings down-regulated for OsMADS26 expression and cultivated in standard condition
DR5_1

source_name: down-regulated line transformed with a pANDA plasmid containing the GST targeting the 5'UTR of OsMADS26 mRNA cultivated in standard condition


title: OsMADS26 over-expressing line 2, osmotic stresscondition, rep2

description:
Gene expression data from roots and shoots of 7 days old transgenic seedlings over-expressing OsMADS26 and cultivated in osmotic stress (100 mM manitol) condition
OX2_M_2


title: control line, empty pANDA, standardculturecondition, rep1

description:
Gene expression data from roots and shoots of 7 days old transgenic seedlings transformed with the empty pANDA plasmid and cultivated in standard condition
DR0_1

source_name: control line transformed with an empty pANDA plasmid cultivated in standard condition


title: control line, empty pANDA, standardculturecondition, rep2

description:
Gene expression data from roots and shoots of 7 days old transgenic seedlings transformed with the empty pANDA plasmid and cultivated in standard condition
DR0_2


title: control line, empty PC5300.OE, osmotic stresscondition, rep1

description:
Gene expression data from roots and shoots of 7 days old transgenic seedlings transformed with the empty PC5300.OE plasmid and cultivated in osmotic stress (100 mM manitol) condition
OX0_M_1

source_name: control line transformed with an empty PC5300.0E plasmid cultivated in osmotic stress condition (100 mM manitol)


title: T-ALL_1054_14

city: Paris

first: Andre

last: Bortolini Silveira

address: 26 rue d'Ulm

institute: Institut Curie

hyb_protocol: Samples were hybridized on the GeneChip Human Gene 1.0 ST Arrays (Affymetrix, Inc.), according to the manufacturer's instructions. Arrays were washed and stained with the GeneChip Fluidics Station 450.

scan_protocol: Arrays were scanned with the GeneChip Scanner 3000, according to the manufacturer's instructions.

data_processing: Arrays were normalized and expression values were obtained with the default transcript level iterPLIER algorithm of the Affymetrix Expression Console software.

source_name: Bone marrow mononuclear cells obtained from patient with newly diagnosed T-ALL

label_protocol: Samples were processed with the WT Expression Kit (Ambion, Inc., Austin, TX, USA) and GeneChip WT Terminal Labeling and Controls Kit (Affymetrix, Inc., Santa Clara, CA, USA), according to the manufacturer's instructions.

extract_protocol: Primary T-ALL samples were obtained at diagnosis from bone marrow and/or peripheral blood with high leukemia involvement (>85%), and enriched by density centrifugation over Ficoll-Paque. Thymic samples, obtained from children undergoing cardiac surgery, were gently minced in culture medium and subsequently subjected to density centrifugation. Total RNA was extracted from lysates preserved in guanidine isothiocyanate solution using the Illustra RNAspin Mini RNA Isolation Kit (GE Healthcare).

tag: age (years)

value: Female

value: T-ALL sample


title: Thymocytes_T8

source_name: Thymocytes sample obtained from child undergoing cardiac surgery

value: Human thymocytes


title: OsMADS26 downregulated line 1, standardculturecondition, rep2

description:
Gene expression data from roots and shoots of 7 days old transgenic seedlings down-regulated for OsMADS26 expression and cultivated in standard condition
DR5_2


title: control line, empty pANDA, osmotic stresscondition, rep2

description:
Gene expression data from roots and shoots of 7 days old transgenic seedlings transformed with the empty pANDA plasmid and cultivated in osmotic stress (100 mM manitol) condition
DR0_M_2


title: T-ALL_1720_25

value: Male


title: Thymocytes_T11


title: T-ALL_1001_11


title: T-ALL_979_10


title: T-ALL_1732_27


title: control line, empty PC5300.OE, standardculturecondition, rep1

description:
Gene expression data from roots and shoots of 7 days old transgenic seedlings transformed with the empty PC5300.OE plasmid and cultivated in standard condition
OX0_1


title: OsMADS26 over-expressing line 2, standardculturecondition, rep2

description:
Gene expression data from roots and shoots of 7 days old transgenic seedlings over-expressing OsMADS26 and cultivated in standard condition
OX2_2


title: OsMADS26 over-expressing line 1, standardculturecondition, rep2

description:
Gene expression data from roots and shoots of 7 days old transgenic seedlings over-expressing OsMADS26 and cultivated in standard condition
OX1_2


title: OsMADS26 over-expressing line 1, standardculturecondition, rep1

description:
Gene expression data from roots and shoots of 7 days old transgenic seedlings over-expressing OsMADS26 and cultivated in standard condition
OX1_1


title: S784

city: Houston

first: Valerie

last: LeBleu

state: TX

address: 1881 East Road

institute: MDACC

description: Mouse 9

data_processing: Genome Studio 5.0

source_name: pancreas tumor

extract_protocol: RNA was extracted with Trizol reagent,Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Mice spontaneously developed pancreas tumors

value: KPC;SnailcKO

value: pancreas tumor


title: Treg.SP.SPF#3

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

hyb_protocol: Ambion WT Expression Kit

scan_protocol: Affymetrix GeneChip Scanner

data_processing: The datasets was pre-filtered to keep only those probesets for which a gene symbol could be found in the Affymetrix annotation. CEL files were normalized using Affymetrix Power Tools on the predefined probeset ID list mentioned above, and using the standard RMA workflow (background adjustment, quantile normalization, median polish probeset summarization). Output on 2^ scale.

source_name: Spleen

label_protocol: Affymetrix GeneChip WT Terminal Labeling and Controls Kit

extract_protocol: TriZol

value: 6 Weeks Old

tag: genetic background

tag: Sex

tag: cell family

value: CD4 TReg Cell

tag: phenotype markers

tag: source prep description

value: Spleen dissociation and digestion

tag: separation method

value: Dissection / Trimming

tag: amplification technique

value: Ambion WT Expression Kit


title: T-ALL_609_6


title: T-ALL_783


title: U755

description: Mouse 3

value: KPC

tag: tissue


title: BB.SP.2h.IFN#1

value: B Cell

value: CD19+ IGM+


title: U513

description: Mouse 7


title: 4188

description: Mouse 4

value: KPC;TwistcKO


title: T-ALL_134


title: BB.SP.2h.IFN#2


title: DC.SP.SPF#3

value: Dendritic Cell

value: CD11c+ FLT3+


title: T4.SP.SPF#3

value: CD4 TConv Cell


title: U509

description: Mouse 8


title: 4081

description: Mouse 1


title: S874

description: Mouse 6


title: B1ab.PC.2h.IFN#2


title: 4055

description: Mouse 2


title: NK.SP.SPF#3

value: NK Cell


title: T8.SP.SPF#3

value: CD8 T Cell


title: BB.SP.SPF#3

value: Male

value: CD19+ Igm+


title: B1ab.PC.SPF#3


title: Tgd.SPF.SPF#3

value: gdT Cell

value: TCRgd+


title: GN.SP.2h.IFN#1

value: 6 Weeks Old

value: Neutrophil


title: Flt3/ITD transfected KSL cells (p21-/- vs p21+/+)_rep1

description:
biological replicate 1 of 3,  KSL cells overexpressing Flt3/ITD from p21-/-  and p21+/+ mice
Sample 2

source_name: marrow KSL cells from p21-/- mouse

value: bone marrow

value: KSL

value: Flt3/ITD transfected

source_name: marrow KSL cells from p21+/+ mouse


title: DC.SP.2h.IFN#2

value: CD11c+ Flt3+

value: Spleen dissociation and digestion

value: Dissection / Trimming

value: Ambion WT Expression Kit


title: 3854

description: Mouse 5

value: KPC;TwistcKO

value: pancreas tumor


title: NKT.SP.SPF#3

value: NKT Cell

value: NK1.1+ TCRB+


title: Tgd.SP.2h.IFN#2

value: Male


title: GN.SP.2h.IFN#2


title: DC.SP.2h.IFN#1

value: Dendritic Cell


title: Tgd.SP.2h.IFN#1

value: gdT Cell


title: T8.SP.2h.IFN#2

value: CD8 T Cell


title: Treg.SP.2h.IFN#1

value: 6 Weeks Old

value: CD4 TReg Cell


title: T4.SP.2h.IFN#2

value: CD4 TConv Cell

value: 11 cell set with after 2h interferon injection


title: DC.SP.SPF#1

value: CD11c+ FTL3+

value: spleen dissocation and stain


title: T8.SP.2h.IFN#1

value: Spleen dissociation and digestion


title: Treg.SP.2h.IFN#2

value: Dissection / Trimming


title: NKT.SP.2h.IFN#2

value: NK1.1+ TCRb+

value: Ambion WT Expression Kit


title: Treg.SP.SPF#1

value: spleen dissociation and stain


title: NK.SP.SPF#2

value: NK Cell

value: NK1.1+ TCRb-


title: NK.SP.SPF#1

value: Male


title: NKT.SP.SPF#1

value: NKT Cell

value: Spleen dissociation and stain


title: NK.SP.2h.IFN#2


title: B1ab.PC.SPF#1

value: B Cell

value: Spleen aspiration and seperation


title: B1ab.PC.SPF#2

value: 6 Weeks Old


title: DC.SP.SPF#2

value: Dendritic Cell


title: Treg.SP.SPF#2

value: CD4 TReg Cell


title: NKT.SP.SPF#2


title: NK.SP.2h.IFN#1

value: 11 cell set with after 2h interferon injection


title: Tgd.SP.SPF#2

value: gdT Cell

value: gdT+ TCRB-


title: GN.SP.SPF#2

value: Neutrophil

value: Dissection / Trimming


title: T4.SP.2h.IFN#1

value: CD4 TConv Cell

value: Ambion WT Expression Kit


title: T4.SP.SPF#2

value: Spleen dissiociation and stain


title: T4.SP.SPF#1


title: T8.SP.SPF#2

source_name: Blood

value: CD8 T Cell

value: spleen dissociation and stain


title: NKT.SP.2h.IFN#1

value: Male

value: NKT Cell

value: NK1.1+ TCRb+


title: T8.SP.SPF#1


title: BB.SP.SPF#1

value: B Cell

value: Spleen aspiration and seperation


title: Tgd.SP.SPF#1

value: 6 Weeks Old


title: Slide 345314

city: STOCKHOLM

first: Sulman

last: Shafeeq

address: nobel vag 16

department: MTC

country: Sweden

institute: Karolinska Institutet

description: Sample 2

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

scan_protocol: Scanning was done using the Genepix 4200AL laser scanner

data_processing: Dual-channel array images were analyzed with ArrayPro 4.5 software (Media Cybernetics Inc.). Spots were screened visually to identify those of low quality. Slide data were processed with MicroPreP as previously described (15, 18, 49). Prior to analysis, automatically and manually flagged spots and spots with very low background subtracted signal intensity (5% of the weakest spots [sum of Cy3 and Cy5 net signals]) were filtered out of all data sets.Net signal intensities were calculated by grid-based background subtraction. A grid-based Lowess transformation was performed for slide normalization, negative and empty values were removed, and outliers were removed by the deviation test. Expression ratios of mutant strain over the wild-type strain were calculated. Further analysis was performed with a Cyber-T Student t test for paired data.

organism: Streptococcus pneumoniae D39

source_name: D39 wild-type

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

growth_protocol: Cells were grown to OD600 of 0.2 in CDM medium with and without 0.3 mM Ni

extract_protocol: RNA was isolated and purified using the High Pure RNA isolation kit (Roche diagnostics) as described (Kloosterman et al., 2006; Shafeeq et al., 2011). Contaminating genomic DNA was removed by treatment with RNase-free DNase I (Roche diagnostics). RNA was isolated from three replicate cultures.

tag: genotype/variation

value: Wild type

source_name: D39 ΔpsaR

value: psaR Mutant


title: Slide 345315

description: Sample 3


title: BB.SP.SPF#2


title: Slide 347295

description: Avarage ratio of inter slide replicates

source_name: F550 mean

growth_protocol: Cells were grown to OD600 of 0.2 in CDM medium with and without 0.5 mM Ni2+

tag: strain

value: wildtype

tag: ni concentration

value: 0.5 mM Ni2

source_name: B650 mean

value: 0 mM Ni2


title: Slide 347294

description: Avarage ratio of inter slide replicates

tag: genotype


title: GN.SP.SPF#1

value: Neutrophil

value: Spleen dissociation and stain

value: Dissection / Trimming


title: Slide 347191

description: Sample 2

source_name: F532 Mean

growth_protocol: Cells were grown to OD600 of 0.2 in CDM medium with 0.3 mM Ni2+

value: adcR mutant

source_name: F635 Mean


title: Slide 347189

description: Sample 1


title: Slide 345313

description: Sample 1


title: 19.BB.SP.5.5H.IFN#1

tag: dose

tag: time course

value: CD19+ Igm+

value: Time course serious with itnerferon injections. Spleen dissociation and B cell sort.

value: Ambion WT Expression Kit


title: 26.BB.SP.0.15H.IFN#1

value: Male


title: 18.BB.SP.5H.IFN#1


title: 27.BB.SP.9H.IFN#1


title: 24.BB.SP.1.25H.IFN#1


title: 30.BB.SP.13H.IFN#1


title: 25.BB.SP.0.75H.IFN#1


title: 20.BB.SP.6H.IFN#1


title: 21.BB.SP.6.5H.IFN#1


title: 5.BB.SP.11H.IFN#1

value: Time Course Serious treated with Interferon and sorted B cells from spleen


title: 17.BB.SP.4.5H.IFN#1

value: B Cell


title: 4.BB.SP.1H.IFN#1


title: 23.BB.SP.8H.IFN#1


title: 28.BB.SP.10H.IFN#1


title: 3.BB.SP.14H.IFN#1


title: 2.BB.SP.0.5H.IFN#1


title: 29.BB.SP.12H.IFN#1


title: 22.BB.SP.7H.IFN#1


title: 1.BB.SP.15H.IFN#1


title: 6.BB.SP.1.5H.IFN#1


title: 10.BB.SP.2.5H.IFN#1


title: 8.BB.SP.2H.IFN#1


title: 11.BB.SP.2.75H.IFN#1


title: 12.BB.SP3H.IFN#1


title: 16.BB.SP.4H.IFN#1


title: B.IFN.1000U/ml#3

tag: ifna dose

value: EasySep Neg Sel. & IFN in vitro


title: B.IFN.1000U/ml#2

tag: age

value: 6 Weeks Old


title: 14.BB.SP.3.5H.IFN#1


title: 15.BB.SP.3.75H.IFN#1


title: B.IFN.100U/ml#2


title: B.IFN.100U/ml#1


title: B.IFN.10U/ml#1


title: B.IFN.1U/ml#2


title: B.IFN.1U/ml#1


title: FG-3149 treated PKCe left ventricle, biological rep12

city: San Francisco

first: Mark

middle: D.

last: Sternlicht

state: CA

address: 409 Illinois Street

department: Molecular Biology

institute: FibroGen, Inc.

hyb_protocol: Following fragmentation, labeled cRNA were hybridized on Affymetrix mouse genome 430A 2.0 microarrays using the Affymetrix GeneChip Hybridization, Wash, and Stain kit (P/N 901241) and standard protocol.  Hybridization was performed for 16hrs at 45°C, 60rpm in an Affymetrix GeneChip Hybridization Oven 640 and staining and washing were performed using an Affymetrix GeneChip Fluidics Station 450 using the manufacturer's recommended fluidics script for 430Av2 genechips (FS450_0002).

scan_protocol: GeneChips were scanned using an Affymetrix GeneChip Scanner 7G.  Scanning was performed using AGCC software and resulting CEL files were exported to GCOS v1.4.0.036 to generate CEL files compatible with Agilent GeneSpring GX 7.3.1 analysis software.

data_processing: CEL data were preprocessed using the GC content-based Robust Multi-Array (GCRMA) algorithm and imported into GeneSpring GX 7.3.1.  Between-group gene expression comparisons were performed on median per-gene normalized data using parametric t-tests without assuming equal variances or correcting for multiple comparisons.

source_name: FG-3149 treated PKCe left ventricle

label_protocol: Biotinylated cRNA were prepared from 250ng total RNA using the Affymetrix GeneChip 3'IVT Express kit (P/N 901229) according the manufacturer's standard protocol.

extract_protocol: Total RNA was isolated from frozen LV tissue using TRIzol Reagent (Invitrogen) and purified using the Qiagen RNeasy Mini RNA purification kit with DNase treatment per the manufacturer's recommended methods.  RNA quantity and integrity were determined using a NanoDrop ND-1000 spectrophotometer and an Agilent 2100 Bioanalyzer and Agilent RNA 6000 Nano assay kit.

treatment_protocol: All animal procedures were carried out in accordance with institutional and national guidelines.  Mice with cardiomyocyte-specific expression of a constitutively active (A159E) rabbit PKCε transgene driven by the mouse Myh6 gene promoter on an FVB/N background (PKCε mice) were kindly provided by Dr. Peipei Ping, University of California, Los Angeles.  Nontransgenic FVB/N mice (Charles River Laboratories) served as controls.  Three-month-old mice underwent baseline echocardiography and were randomly assigned to one of four groups: FVB/N mice that received nonimmune mouse immunoglobulin (IgG) (n=10), FVB/N mice that received the anti-CTGF antibody FG-3149 (n=12), PKCε mice that received IgG (n=10), or PKCε mice that received FG-3149 (n=12).  IgG and FG-3149 antibodies (FibroGen, San Francisco, CA) were administered by intraperitoneal injection twice weekly at 30 mg/kg for three months.  After three months of treatment, mice underwent echocardiography and LV catheterization, after which hearts were excised, rapidly frozen in liquid N2, and stored at -80C.

tag: mouse id

tag: strain background

value: FVB/N

value: PKCε transgenic

tag: gender

value: male

tag: treatment

value: anti-CTGF antibody FG-3149

value: left ventricle


title: B.IFN.100U/ml#3

tag: genetic background

tag: Sex

tag: cell family

tag: phenotype markers


title: 9.BB.SP.2.25H.IFN#1

tag: source prep description

tag: separation method

tag: amplification technique


title: B.IFN.10U/ml#3


title: B.IFN.0.1U/ml#1


title: FG-3149 treated PKCe left ventricle, biological rep11

tag: genotype/variation

tag: tissue


title: B.IFN.1000U/ml#1


title: B.IFN.0U/ml#2


title: FG-3149 treated PKCe left ventricle, biological rep10


title: FG-3149 treated PKCe left ventricle, biological rep8

value: female


title: B.IFN.0.1U/ml#3


title: B.IFN.0U/ml#1


title: FG-3149 treated PKCe left ventricle, biological rep9


title: B.IFN.0.1U/ml#2


title: FG-3149 treated PKCe left ventricle, biological rep7


title: FG-3149 treated PKCe left ventricle, biological rep6


title: B.IFN.1U/ml#3


title: B.IFN.10U/ml#2


title: FG-3149 treated PKCe left ventricle, biological rep5