title: HumanAorticEndothelialCells_Individual6_controlTreatment_rep2

description: control


title: HumanAorticEndothelialCells_Individual5_OxPAPCTreatment_rep2

status: Public on Jul 20 2011

type: RNA

city: La Jolla

first: Casey

last: Romanoski

state: CA

address: 9500 Gliman Dr.

country: USA

institute: UCSD

description: OxPAPC

hyb_protocol: According to Affymetrix standard protocol

data_processing: Data was processed with a custom CDF file (mask file HT_U133Amsk.cdf) using Just-RMA in Bioconductor/R and corrected for collection batch using ComBat in R

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: HumanAorticEndothelialCells

growth_protocol: Cells were grown in standard 6-well TC plates to confluence at 37C, 5%CO2

extract_protocol: Cytoplasmic RNA was extracted using the Rneasy protocol from Qiagen

treatment_protocol: Cells were treated for 4 hours with or without 40 ug/ul Ox-PAPC

tag: agent

value: OxPAPC

tag: individual id

tag: batch

tag: gender

value: Male

tag: replicate


title: HumanAorticEndothelialCells_Individual37_OxPAPCTreatment_rep1

description: OxPAPC

scan_protocol: According to Affymetrix standard protocol

value: Female


title: HumanAorticEndothelialCells_Individual9_OxPAPCTreatment_rep1

description: OxPAPC

label_protocol: According to Affymetrix standard protocol


title: HumanAorticEndothelialCells_Individual6_controlTreatment_rep1

description: control

value: control


title: HumanAorticEndothelialCells_Individual5_controlTreatment_rep2

description: control


title: HumanAorticEndothelialCells_Individual5_controlTreatment_rep1

description: control


title: HumanAorticEndothelialCells_Individual5_OxPAPCTreatment_rep1

description: OxPAPC


title: HumanAorticEndothelialCells_Individual2_OxPAPCTreatment_rep2

description: OxPAPC


title: HumanAorticEndothelialCells_Individual4_OxPAPCTreatment_rep2

description: OxPAPC


title: HumanAorticEndothelialCells_Individual4_OxPAPCTreatment_rep1

description: OxPAPC


title: HumanAorticEndothelialCells_Individual4_controlTreatment_rep2

description: control


title: HumanAorticEndothelialCells_Individual2_OxPAPCTreatment_rep1

description: OxPAPC


title: HumanAorticEndothelialCells_Individual2_controlTreatment_rep2

description: control


title: HumanAorticEndothelialCells_Individual4_controlTreatment_rep1

description: control


title: HumanAorticEndothelialCells_Individual564_OxPAPCTreatment_replicate2

description:
OxPAPC
5500024057485061409333_G11.cel

data_processing: Data was processed together with CEL files in GSE20060 using a custom CDF file using Just-RMA in Bioconductor/R and corrected for collection batch using ComBat in R


title: HumanAorticEndothelialCells_Individual564_controlTreatment_replicate2

description:
control
5500024057485061409333_H11.cel


title: HumanAorticEndothelialCells_Individual563_OxPAPCTreatment_replicate2

description:
OxPAPC
5500024057485061409333_D06.cel


title: HumanAorticEndothelialCells_Individual563_controlTreatment_replicate2

description:
control
5500024057485061409333_C06.cel


title: HumanAorticEndothelialCells_Individual2_controlTreatment_rep1

description: control


title: HumanAorticEndothelialCells_Individual562_controlTreatment_replicate2

description:
control
5500024057485061409333_E02.cel


title: HumanAorticEndothelialCells_Individual562_OxPAPCTreatment_replicate1

description:
OxPAPC
5500024057485061409333_H02.cel


title: HumanAorticEndothelialCells_Individual561_OxPAPCTreatment_replicate2

description:
OxPAPC
5500024063070081409291_C01.cel


title: HumanAorticEndothelialCells_Individual561_controlTreatment_replicate2

description:
control
5500024063070081409291_D01.cel


title: HumanAorticEndothelialCells_Individual564_controlTreatment_replicate1

description:
control
5500024057485061409333_F11.cel


title: HumanAorticEndothelialCells_Individual565_controlTreatment_replicate1

description:
control
5500024059565071603200_B09.cel


title: HumanAorticEndothelialCells_Individual563_OxPAPCTreatment_replicate1

description:
OxPAPC
5500024057485061409333_B06.cel


title: HumanAorticEndothelialCells_Individual560_OxPAPCTreatment_replicate2

description:
OxPAPC
5500024057485061409333_A03.cel


title: HumanAorticEndothelialCells_Individual565_OxPAPCTreatment_replicate2

description:
OxPAPC
5500024059565071603200_D09.cel


title: HumanAorticEndothelialCells_Individual563_controlTreatment_replicate1

description:
control
5500024057485061409333_A06.cel


title: HumanAorticEndothelialCells_Individual565_OxPAPCTreatment_replicate1

description:
OxPAPC
5500024059565071603200_A09.cel


title: HumanAorticEndothelialCells_Individual564_OxPAPCTreatment_replicate1

description:
OxPAPC
5500024057485061409333_E11.cel


title: HumanAorticEndothelialCells_Individual565_controlTreatment_replicate2

description:
control
5500024059565071603200_C09.cel


title: HumanAorticEndothelialCells_Individual562_OxPAPCTreatment_replicate2

description:
OxPAPC
5500024057485061409333_F02.cel


title: HumanAorticEndothelialCells_Individual562_controlTreatment_replicate1

description:
control
5500024057485061409333_G02.cel


title: HumanAorticEndothelialCells_Individual561_OxPAPCTreatment_replicate1

description:
OxPAPC
5500024063070081409291_A01.cel


title: HumanAorticEndothelialCells_Individual560_OxPAPCTreatment_replicate1

description:
OxPAPC
5500024057485061409333_C03.cel


title: HumanAorticEndothelialCells_Individual560_controlTreatment_replicate1

description:
control
5500024057485061409333_D03.cel


title: HumanAorticEndothelialCells_Individual559_controlTreatment_replicate2

description:
control
5500024063070081409291_C06.cel


title: HumanAorticEndothelialCells_Individual559_OxPAPCTreatment_replicate1

description:
OxPAPC
5500024063070081409291_B06.cel


title: HumanAorticEndothelialCells_Individual559_controlTreatment_replicate1

description:
control
5500024063070081409291_A06.cel


title: HumanAorticEndothelialCells_Individual557_OxPAPCTreatment_replicate2

description:
OxPAPC
5500024063070081409291_D07.cel


title: HumanAorticEndothelialCells_Individual558_controlTreatment_replicate2

description:
control
5500024057485061409333_H05.cel


title: HumanAorticEndothelialCells_Individual558_OxPAPCTreatment_replicate2

description:
OxPAPC
5500024057485061409333_F05.cel


title: HumanAorticEndothelialCells_Individual557_OxPAPCTreatment_replicate1

description:
OxPAPC
5500024063070081409291_A07.cel


title: HumanAorticEndothelialCells_Individual558_controlTreatment_replicate1

description:
control
5500024057485061409333_E05.cel


title: HumanAorticEndothelialCells_Individual559_OxPAPCTreatment_replicate2

description:
OxPAPC
5500024063070081409291_D06.cel


title: HumanAorticEndothelialCells_Individual555_controlTreatment_replicate2

description:
control
5500024063070081409291_F05.cel


title: HumanAorticEndothelialCells_Individual554_controlTreatment_replicate1

description:
control
5500024057485061409333_E09.cel


title: HumanAorticEndothelialCells_Individual553_controlTreatment_replicate2

description:
control
5500024063070081409291_F09.cel


title: HumanAorticEndothelialCells_Individual554_OxPAPCTreatment_replicate2

description:
OxPAPC
5500024057485061409333_G09.cel


title: HumanAorticEndothelialCells_Individual553_OxPAPCTreatment_replicate2

description:
OxPAPC
5500024063070081409291_E09.cel


title: HumanAorticEndothelialCells_Individual555_controlTreatment_replicate1

description:
control
5500024063070081409291_H05.cel


title: HumanAorticEndothelialCells_Individual556_OxPAPCTreatment_replicate1

description:
OxPAPC
5500024063070081409292_G11.cel


title: HumanAorticEndothelialCells_Individual557_controlTreatment_replicate1

description:
control
5500024063070081409291_C07.cel


title: HumanAorticEndothelialCells_Individual556_controlTreatment_replicate1

description:
control
5500024063070081409292_H11.cel


title: HumanAorticEndothelialCells_Individual555_OxPAPCTreatment_replicate1

description:
OxPAPC
5500024063070081409291_G05.cel


title: HumanAorticEndothelialCells_Individual554_controlTreatment_replicate2

description:
control
5500024057485061409333_H09.cel


title: HumanAorticEndothelialCells_Individual555_OxPAPCTreatment_replicate2

description:
OxPAPC
5500024063070081409291_E05.cel


title: HumanAorticEndothelialCells_Individual553_OxPAPCTreatment_replicate1

description:
OxPAPC
5500024063070081409291_H09.cel


title: HumanAorticEndothelialCells_Individual557_controlTreatment_replicate2

description:
control
5500024063070081409291_B07.cel


title: HumanAorticEndothelialCells_Individual552_controlTreatment_replicate1

description:
control
5500024059565071603200_A05.cel


title: HumanAorticEndothelialCells_Individual553_controlTreatment_replicate1

description:
control
5500024063070081409291_G09.cel


title: HumanAorticEndothelialCells_Individual552_OxPAPCTreatment_replicate1

description:
OxPAPC
5500024059565071603200_C05.cel


title: HumanAorticEndothelialCells_Individual556_controlTreatment_replicate2

description:
control
5500024063070081409291_H07.cel


title: HumanAorticEndothelialCells_Individual554_OxPAPCTreatment_replicate1

description:
OxPAPC
5500024057485061409333_F09.cel


title: HumanAorticEndothelialCells_Individual552_OxPAPCTreatment_replicate2

description:
OxPAPC
5500024059565071603200_B05.cel


title: HumanAorticEndothelialCells_Individual551_OxPAPCTreatment_replicate2

description:
OxPAPC
5500024059565071603200_H05.cel


title: HumanAorticEndothelialCells_Individual551_controlTreatment_replicate2

description:
control
5500024059565071603200_F05.cel


title: HumanAorticEndothelialCells_Individual551_controlTreatment_replicate1

description:
control
5500024059565071603200_G05.cel


title: HumanAorticEndothelialCells_Individual550_OxPAPCTreatment_replicate2

description:
OxPAPC
5500024057485061409333_E10.cel


title: HumanAorticEndothelialCells_Individual550_OxPAPCTreatment_replicate1

description:
OxPAPC
5500024057485061409333_G10.cel


title: HumanAorticEndothelialCells_Individual552_controlTreatment_replicate2

description:
control
5500024059565071603200_D05.cel


title: HumanAorticEndothelialCells_Individual549_controlTreatment_replicate2

description:
control
5500024059565071603200_B08.cel


title: HumanAorticEndothelialCells_Individual549_controlTreatment_replicate1

description:
control
5500024059565071603200_D08.cel


title: HumanAorticEndothelialCells_Individual548_controlTreatment_replicate2

description:
control
5500024059565071603200_E06.cel


title: HumanAorticEndothelialCells_Individual546_OxPAPCTreatment_replicate2

description:
OxPAPC
5500024057485061409333_G04.cel


title: HumanAorticEndothelialCells_Individual547_controlTreatment_replicate1

description:
control
5500024059565071603200_H10.cel


title: HumanAorticEndothelialCells_Individual546_controlTreatment_replicate2

description:
control
5500024057485061409333_H04.cel


title: HumanAorticEndothelialCells_Individual548_OxPAPCTreatment_replicate1

description:
OxPAPC
5500024059565071603200_F06.cel


title: HumanAorticEndothelialCells_Individual549_OxPAPCTreatment_replicate2

description:
OxPAPC
5500024059565071603200_A08.cel


title: HumanAorticEndothelialCells_Individual545_OxPAPCTreatment_replicate2

description:
OxPAPC
5500024063070081409291_F11.cel


title: HumanAorticEndothelialCells_Individual547_OxPAPCTreatment_replicate1

description:
OxPAPC
5500024059565071603200_E10.cel


title: HumanAorticEndothelialCells_Individual545_controlTreatment_replicate2

description:
control
5500024057485061409333_E06.cel


title: HumanAorticEndothelialCells_Individual546_OxPAPCTreatment_replicate1

description:
OxPAPC
5500024057485061409333_F04.cel


title: HumanAorticEndothelialCells_Individual549_OxPAPCTreatment_replicate1

description:
OxPAPC
5500024059565071603200_C08.cel


title: HumanAorticEndothelialCells_Individual550_controlTreatment_replicate1

description:
control
5500024057485061409333_F10.cel


title: HumanAorticEndothelialCells_Individual10_OxPAPCTreatment_rep1

description: OxPAPC


title: HumanAorticEndothelialCells_Individual547_OxPAPCTreatment_replicate2

description:
OxPAPC
5500024057485061409333_A12.cel


title: HumanAorticEndothelialCells_Individual545_controlTreatment_replicate1

description:
control
5500024057485061409333_H06.cel


title: HumanAorticEndothelialCells_Individual550_controlTreatment_replicate2

description:
control
5500024057485061409333_H10.cel


title: HumanAorticEndothelialCells_Individual548_OxPAPCTreatment_replicate2

description:
OxPAPC
5500024059565071603200_H06.cel


title: HumanAorticEndothelialCells_Individual545_OxPAPCTreatment_replicate1

description:
OxPAPC
5500024057485061409333_F06.cel


title: HumanAorticEndothelialCells_Individual544_controlTreatment_replicate2

description:
control
5500024063070081409291_D03.cel


title: HumanAorticEndothelialCells_Individual544_OxPAPCTreatment_replicate1

description:
OxPAPC
5500024063070081409291_A03.cel


title: HumanAorticEndothelialCells_Individual546_controlTreatment_replicate1

description:
control
5500024057485061409333_E04.cel


title: HumanAorticEndothelialCells_Individual544_OxPAPCTreatment_replicate2

description:
OxPAPC
5500024063070081409291_C03.cel


title: HumanAorticEndothelialCells_Individual548_controlTreatment_replicate1

description:
control
5500024059565071603200_G06.cel


title: HumanAorticEndothelialCells_Individual544_controlTreatment_replicate1

description:
control
5500024063070081409291_B03.cel


title: HumanAorticEndothelialCells_Individual543_OxPAPCTreatment_replicate2

description:
OxPAPC
5500024059565071603200_G11.cel


title: HumanAorticEndothelialCells_Individual541_OxPAPCTreatment_replicate1

description:
OxPAPC
5500024063070081409291_B11.cel


title: HumanAorticEndothelialCells_Individual541_controlTreatment_replicate2

description:
control
5500024063070081409291_A11.cel


title: HumanAorticEndothelialCells_Individual543_controlTreatment_replicate1

description:
control
5500024059565071603200_F11.cel


title: HumanAorticEndothelialCells_Individual541_OxPAPCTreatment_replicate2

description:
OxPAPC
5500024063070081409291_C11.cel


title: HumanAorticEndothelialCells_Individual543_OxPAPCTreatment_replicate1

description:
OxPAPC
5500024059565071603200_E11.cel


title: HumanAorticEndothelialCells_Individual543_controlTreatment_replicate2

description:
control
5500024059565071603200_H11.cel


title: HumanAorticEndothelialCells_Individual542_OxPAPCTreatment_replicate1

description:
OxPAPC
5500024063070081409291_G01.cel


title: HumanAorticEndothelialCells_Individual538_OxPAPCTreatment_replicate2

description:
OxPAPC
5500024057485061409333_H08.cel


title: HumanAorticEndothelialCells_Individual538_OxPAPCTreatment_replicate1

description:
OxPAPC
5500024057485061409333_F08.cel


title: HumanAorticEndothelialCells_Individual540_controlTreatment_replicate1

description:
control
5500024063070081409291_F03.cel


title: HumanAorticEndothelialCells_Individual551_OxPAPCTreatment_replicate1

description:
OxPAPC
5500024059565071603200_E05.cel


title: HumanAorticEndothelialCells_Individual541_controlTreatment_replicate1

description:
control
5500024063070081409291_D11.cel


title: HumanAorticEndothelialCells_Individual542_OxPAPCTreatment_replicate2

description:
OxPAPC
5500024063070081409291_E01.cel


title: HumanAorticEndothelialCells_Individual540_OxPAPCTreatment_replicate1

description:
OxPAPC
5500024063070081409291_E03.cel


title: HumanAorticEndothelialCells_Individual537_OxPAPCTreatment_replicate2

description:
OxPAPC
5500024057485061409333_C05.cel


title: HumanAorticEndothelialCells_Individual537_controlTreatment_replicate2

description:
control
5500024057485061409333_D05.cel


title: HumanAorticEndothelialCells_Individual538_controlTreatment_replicate2

description:
control
5500024057485061409333_G08.cel


title: HumanAorticEndothelialCells_Individual537_controlTreatment_replicate1

description:
control
5500024057485061409333_A05.cel


title: HumanAorticEndothelialCells_Individual536_OxPAPCTreatment_replicate2

description:
OxPAPC
5500024057485061409333_E01.cel


title: HumanAorticEndothelialCells_Individual537_OxPAPCTreatment_replicate1

description:
OxPAPC
5500024057485061409333_B05.cel


title: HumanAorticEndothelialCells_Individual542_controlTreatment_replicate1

description:
control
5500024063070081409291_F01.cel


title: HumanAorticEndothelialCells_Individual540_OxPAPCTreatment_replicate2

description:
OxPAPC
5500024063070081409291_H03.cel


title: HumanAorticEndothelialCells_Individual538_controlTreatment_replicate1

description:
control
5500024063070081409292_B11.cel


title: HumanAorticEndothelialCells_Individual540_controlTreatment_replicate2

description:
control
5500024063070081409291_G03.cel


title: HumanAorticEndothelialCells_Individual542_controlTreatment_replicate2

description:
control
5500024063070081409291_H01.cel


title: HumanAorticEndothelialCells_Individual534_OxPAPCTreatment_replicate1

description:
OxPAPC
5500024057485061409333_B11.cel


title: HumanAorticEndothelialCells_Individual535_OxPAPCTreatment_replicate2

description:
OxPAPC
5500024063070081409291_H06.cel


title: HumanAorticEndothelialCells_Individual536_OxPAPCTreatment_replicate1

description:
OxPAPC
5500024057485061409333_G01.cel


title: HumanAorticEndothelialCells_Individual534_OxPAPCTreatment_replicate2

description:
OxPAPC
5500024057485061409333_D11.cel


title: HumanAorticEndothelialCells_Individual533_controlTreatment_replicate2

description:
control
5500024057485061409333_D02.cel


title: HumanAorticEndothelialCells_Individual534_controlTreatment_replicate1

description:
control
5500024057485061409333_C11.cel


title: HumanAorticEndothelialCells_Individual533_OxPAPCTreatment_replicate2

description:
OxPAPC
5500024057485061409333_A02.cel


title: HumanAorticEndothelialCells_Individual533_OxPAPCTreatment_replicate1

description:
OxPAPC
5500024057485061409333_C02.cel


title: HumanAorticEndothelialCells_Individual558_OxPAPCTreatment_replicate1

description:
OxPAPC
5500024057485061409333_G05.cel


title: HumanAorticEndothelialCells_Individual533_controlTreatment_replicate1

description:
control
5500024057485061409333_B02.cel


title: HumanAorticEndothelialCells_Individual534_controlTreatment_replicate2

description:
control
5500024057485061409333_A11.cel


title: HumanAorticEndothelialCells_Individual536_controlTreatment_replicate2

description:
control
5500024063070081409291_G11.cel


title: HumanAorticEndothelialCells_Individual535_OxPAPCTreatment_replicate1

description:
OxPAPC
5500024063070081409291_E06.cel


title: HumanAorticEndothelialCells_Individual532_OxPAPCTreatment_replicate2

description:
OxPAPC
5500024063070081409291_A04.cel


title: HumanAorticEndothelialCells_Individual536_controlTreatment_replicate1

description:
control
5500024057485061409333_F01.cel


title: HumanAorticEndothelialCells_Individual535_controlTreatment_replicate2

description:
control
5500024063070081409291_G06.cel


title: HumanAorticEndothelialCells_Individual532_OxPAPCTreatment_replicate1

description:
OxPAPC
5500024063070081409291_C04.cel


title: HumanAorticEndothelialCells_Individual535_controlTreatment_replicate1

description:
control
5500024063070081409291_F06.cel


title: HumanAorticEndothelialCells_Individual531_controlTreatment_replicate2

description:
control
5500024059565071603200_C04.cel


title: HumanAorticEndothelialCells_Individual531_OxPAPCTreatment_replicate2

description:
OxPAPC
5500024059565071603200_D04.cel


title: HumanAorticEndothelialCells_Individual531_controlTreatment_replicate1

description:
control
5500024059565071603200_B04.cel


title: HumanAorticEndothelialCells_Individual532_controlTreatment_replicate1

description:
control
5500024063070081409291_B04.cel


title: HumanAorticEndothelialCells_Individual530_controlTreatment_replicate1

description:
control
5500024057485061409333_D08.cel


title: HumanAorticEndothelialCells_Individual530_controlTreatment_replicate2

description:
control
5500024057485061409333_B08.cel


title: HumanAorticEndothelialCells_Individual529_OxPAPCTreatment_replicate2

description:
OxPAPC
5500024059565071603200_G02.cel


title: HumanAorticEndothelialCells_Individual529_OxPAPCTreatment_replicate1

description:
OxPAPC
5500024059565071603200_F02.cel


title: HumanAorticEndothelialCells_Individual530_OxPAPCTreatment_replicate2

description:
OxPAPC
5500024057485061409333_A08.cel


title: HumanAorticEndothelialCells_Individual531_OxPAPCTreatment_replicate1

description:
OxPAPC
5500024059565071603200_A04.cel


title: HumanAorticEndothelialCells_Individual530_OxPAPCTreatment_replicate1

description:
OxPAPC
5500024057485061409333_C08.cel


title: HumanAorticEndothelialCells_Individual529_controlTreatment_replicate2

description:
control
5500024059565071603200_H02.cel


title: HumanAorticEndothelialCells_Individual528_controlTreatment_replicate1

description:
control
5500024063070081409291_G10.cel


title: HumanAorticEndothelialCells_Individual547_controlTreatment_replicate2

description:
control
5500024059565071603200_F10.cel


title: HumanAorticEndothelialCells_Individual529_controlTreatment_replicate1

description:
control
5500024059565071603200_E02.cel


title: HumanAorticEndothelialCells_Individual528_OxPAPCTreatment_replicate2

description:
OxPAPC
5500024063070081409291_E10.cel


title: HumanAorticEndothelialCells_Individual528_controlTreatment_replicate2

description:
control
5500024063070081409291_F10.cel


title: HumanAorticEndothelialCells_Individual527_OxPAPCTreatment_replicate1

description:
OxPAPC
5500024063070081409291_C10.cel


title: HumanAorticEndothelialCells_Individual527_controlTreatment_replicate2

description:
control
5500024063070081409291_A10.cel


title: HumanAorticEndothelialCells_Individual528_OxPAPCTreatment_replicate1

description:
OxPAPC
5500024063070081409291_H10.cel


title: HumanAorticEndothelialCells_Individual527_OxPAPCTreatment_replicate2

description:
OxPAPC
5500024063070081409291_B10.cel


title: HumanAorticEndothelialCells_Individual524_OxPAPCTreatment_replicate2

description:
OxPAPC
5500024057485061409333_D09.cel


title: 4742A-recut

type: genomic

city: South San Francisco

first: Zhaoshi

last: Jiang

address: 1 DNA Way

department: Bioinformatics

institute: Genentech, Inc

description: Tumor vs. Normal

hyb_protocol: Agilent's Oligonucleotide Array-Based CGH for Genomic DNA Analysis protocol

scan_protocol: Agilent's user manual (Agilent scanner)

data_processing: Tumor samples were assayed on Agilent Human Genome CGH 1X1M Microarrays. Human male genomic DNA (Promega P/N G1471) was used as reference.  Individual log2 ratios of background subtracted signal intensities were obtained from the Agilent Feature Extraction software version 10.7. The log2 ratios were centered to a median of zero and the resulting log2 ratio values for each probe were segmented using GLAD. All probes within the genomic bounds of a given GLAD-derived segment were given the mean copy number value of probes within that segment.

molecule: genomic DNA

source_name: GBM samples

label_protocol: Agilent's Genomic DNA Labeling Kit Plus

extract_protocol: Qiagen AllPrep extraction kit was used according to the manufacturer's instructions

treatment_protocol: Previosuly untreated, newly diagnosed GBM samples

tag: diagnosis

value: Glioblastoma (GBM)

tag: sampleID

tag: idh1 status

value: IDH1 WT

tag: prbid

tag: caseid

source_name: male genomic DNA (Promega P/N G1471)

value: male

tag: sample type

value: reference DNA (Promega P/N G1471)


title: HumanAorticEndothelialCells_Individual524_OxPAPCTreatment_replicate1

description:
OxPAPC
5500024057485061409333_B09.cel


title: passive smoker 293, cord blood

city: Prague 2

first: Hana

last: Bruchova

address: U nemocnice 1

department: Molecular Genetics

country: Czech Republic

institute: Institute of Hematology and Transfusion

description: 5-cm away from the site of cord insertion

hyb_protocol: 750 ng of biotinylated cRNA was hybridized to the array for 17 hours according to the manufacturer manual. Final staining was performed with streptavidin conjugated to Cy-3 fluorescent dye.

scan_protocol: Arrays were scaned using BeadArray Reader (Illumina) and bead level data were extracted by BeadStudio Software (Illumina).

data_processing: Bead summary data were imported into R statistical environment (www.r-project.org) and normalized by quantile method in Lumi package. Only probes, which reached detection P-value < 0.01 in all samples, were used for further analyses. Differentially expressed genes were analysed in the Limma package. A linear model was fitted for each gene given a series of arrays using lmFit function. Using Benjamini and Hochberg method P-values were corrected for multiple testing.

source_name: umbilical cord blood

label_protocol: Biotinylated cRNA was prepared from 200 ng of total RNA using Illumina TotalPrep RNA Amplification Kit (Ambion). In vitro transcription (IVT) was performed at 37°C for 14 hours.

extract_protocol: Umbilical cord bloods were sampled and processed using LeukoLOC Total RNA Isolation System (Ambion, Austin, TX, USA) according to the manufacturer manual. The system employs filter-based leukocyte-depletion technology to isolate leukocytes from whole blood and RNAlater™ (Ambion) to stabilize the cells on the filter. By removal of red blood cells, the RNA purified from captured leukocytes is inherently depleted of globin mRNA, which improves sample quality for expression profiling and other applications. The middle parts of placenta sections were frozen in RNA Later solution (Ambion) and stored at –20°C until RNA isolation. Placental total RNA was isolated using RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer instructions. Integrity of the total RNAs was assayed by Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA) and only samples with RNA integrity number (RIN) above 7.0 were used for gene expression profiling.

tag: smoking status

value: passive smoker

tag: age (years)

tag: maternal bmi

tag: parity

tag: gestational age (weeks)

tag: mode of delivery

value: vaginal

tag: placental weight (g)

value: unknown

tag: placental volume (cm3)

tag: newborn weight (g)

tag: newborn length (cm)

tag: apgar score (5s)

tag: baby's sex

value: F

tag: maternal blood cotinin (ng/ml)

tag: cord blood cotinin (ng/ml)


title: non-smoker 292, cord blood

value: non-smoker

value: M


title: non-smoker 294, cord blood


title: HumanAorticEndothelialCells_Individual524_controlTreatment_replicate2

description:
control
5500024057485061409333_A09.cel

tag: agent

tag: individual id

tag: batch

tag: gender

tag: replicate


title: passive smoker 295, cord blood

tag: smoking status

tag: age (years)

tag: maternal bmi


title: non-smoker 300, cord blood

tag: parity

tag: gestational age (weeks)

tag: mode of delivery


title: HumanAorticEndothelialCells_Individual527_controlTreatment_replicate1

description:
control
5500024063070081409291_D10.cel


title: passive smoker 289, cord blood

tag: placental weight (g)

tag: placental volume (cm3)

tag: newborn weight (g)


title: HumanAorticEndothelialCells_Individual523_OxPAPCTreatment_replicate2

description:
OxPAPC
5500024059565071603200_A03.cel


title: non-smoker 284, cord blood

tag: newborn length (cm)

tag: apgar score (5s)

tag: baby's sex


title: non-smoker 287, cord blood

tag: maternal blood cotinin (ng/ml)

tag: cord blood cotinin (ng/ml)


title: non-smoker 299, cord blood


title: non-smoker 291, cord blood


title: HumanAorticEndothelialCells_Individual523_OxPAPCTreatment_replicate1

description:
OxPAPC
5500024059565071603200_D03.cel

tag: agent

tag: individual id

tag: batch


title: 2009

description: Tumor vs. Normal

tag: diagnosis

tag: sampleID

tag: idh1 status

value: IDH1 mutant

tag: prbid

tag: caseid

tag: gender

tag: sample type


title: 5656A-recut

description: Tumor vs. Normal


title: HumanAorticEndothelialCells_Individual523_controlTreatment_replicate2

description:
control
5500024059565071603200_C03.cel

tag: replicate


title: 4765A

description: Tumor vs. Normal


title: 5234

description: Tumor vs. Normal


title: HumanAorticEndothelialCells_Individual523_controlTreatment_replicate1

description:
control
5500024059565071603200_B03.cel


title: passive smoker 270, cord blood

tag: smoking status

tag: age (years)

tag: maternal bmi

tag: parity

tag: gestational age (weeks)

tag: mode of delivery

value: caesarean

tag: placental weight (g)

tag: placental volume (cm3)

tag: newborn weight (g)


title: HumanAorticEndothelialCells_Individual522_OxPAPCTreatment_replicate1

description:
OxPAPC
5500024059565071603200_H09.cel

tag: agent

tag: individual id

tag: batch


title: non-smoker 268, cord blood

tag: newborn length (cm)

tag: apgar score (5s)

tag: baby's sex

tag: maternal blood cotinin (ng/ml)

tag: cord blood cotinin (ng/ml)


title: passive smoker 274, cord blood

tag: smoking status


title: 5196A

description: Tumor vs. Normal

tag: diagnosis

tag: sampleID

tag: idh1 status

tag: prbid

tag: caseid

tag: gender

tag: sample type


title: HumanAorticEndothelialCells_Individual524_controlTreatment_replicate1

description:
control
5500024057485061409333_C09.cel

tag: replicate


title: 2376

description: Tumor vs. Normal


title: HumanAorticEndothelialCells_Individual522_controlTreatment_replicate1

description:
control
5500024059565071603200_E09.cel

tag: agent


title: 5239

description: Tumor vs. Normal


title: HumanAorticEndothelialCells_Individual521_OxPAPCTreatment_replicate2

description:
OxPAPC
5500024059565071603200_C06.cel

tag: individual id


title: non-smoker 266, cord blood

tag: age (years)

tag: maternal bmi

tag: parity

tag: gestational age (weeks)

tag: mode of delivery

tag: placental weight (g)

tag: placental volume (cm3)

tag: newborn weight (g)


title: passive smoker 267, cord blood

tag: smoking status

tag: newborn length (cm)

tag: apgar score (5s)

tag: baby's sex

tag: maternal blood cotinin (ng/ml)

tag: cord blood cotinin (ng/ml)


title: non-smoker 265, cord blood


title: HumanAorticEndothelialCells_Individual522_controlTreatment_replicate2

description:
control
5500024059565071603200_G09.cel

tag: batch

tag: gender

tag: replicate


title: 6147A

description: Tumor vs. Normal

tag: diagnosis

tag: sampleID

tag: idh1 status

tag: prbid

tag: caseid

tag: sample type


title: 5337A

description: Tumor vs. Normal


title: 4686A

description: Tumor vs. Normal


title: 5865A

description: Tumor vs. Normal


title: 5303A

description: Tumor vs. Normal


title: passive smoker 262, cord blood

tag: age (years)

tag: maternal bmi

tag: parity

tag: gestational age (weeks)

tag: mode of delivery

tag: placental weight (g)

tag: placental volume (cm3)


title: HumanAorticEndothelialCells_Individual521_OxPAPCTreatment_replicate1

description:
OxPAPC
5500024059565071603200_B06.cel

tag: agent

tag: individual id


title: 5386A

description: Tumor vs. Normal

tag: gender


title: HumanAorticEndothelialCells_Individual521_controlTreatment_replicate2

description:
control
5500024059565071603200_D06.cel

tag: batch

tag: replicate


title: 5438A

description: Tumor vs. Normal

tag: diagnosis

tag: sampleID


title: 5548A

description: Tumor vs. Normal

tag: idh1 status

tag: prbid


title: 5476A

description: Tumor vs. Normal

tag: caseid

tag: sample type


title: HumanAorticEndothelialCells_Individual521_controlTreatment_replicate1

description:
control
5500024059565071603200_A06.cel


title: HumanAorticEndothelialCells_Individual520_controlTreatment_replicate2

description:
control
5500024057485061409333_B01.cel


title: HumanAorticEndothelialCells_Individual520_controlTreatment_replicate1

description:
control
5500024057485061409333_D01.cel


title: HumanAorticEndothelialCells_Individual522_OxPAPCTreatment_replicate2

description:
OxPAPC
5500024059565071603200_F09.cel


title: HumanAorticEndothelialCells_Individual520_OxPAPCTreatment_replicate2

description:
OxPAPC
5500024057485061409333_C01.cel


title: non-smoker 252, cord blood

tag: smoking status

tag: age (years)

tag: maternal bmi

tag: newborn weight (g)

tag: newborn length (cm)

tag: apgar score (5s)

tag: baby's sex

tag: maternal blood cotinin (ng/ml)

tag: cord blood cotinin (ng/ml)


title: passive smoker 253, cord blood

tag: parity

tag: gestational age (weeks)

tag: mode of delivery

tag: placental weight (g)

tag: placental volume (cm3)


title: 5428A-recut

description: Tumor vs. Normal

tag: diagnosis

tag: sampleID

tag: idh1 status

tag: prbid

tag: gender


title: passive smoker 256, cord blood

tag: smoking status

tag: age (years)

tag: maternal bmi


title: 5506A

description: Tumor vs. Normal

tag: caseid

tag: sample type


title: passive smoker 251, cord blood

tag: newborn weight (g)

tag: newborn length (cm)

tag: apgar score (5s)

tag: baby's sex

tag: maternal blood cotinin (ng/ml)


title: 5574A

description: Tumor vs. Normal


title: non-smoker 241, cord blood

tag: parity

tag: gestational age (weeks)

tag: mode of delivery

tag: placental weight (g)

tag: cord blood cotinin (ng/ml)


title: HumanAorticEndothelialCells_Individual519_OxPAPCTreatment_replicate1

description:
OxPAPC
5500024057485061409333_H07.cel

tag: agent

tag: individual id

tag: batch

tag: replicate


title: passive smoker 263, cord blood

tag: smoking status

tag: age (years)

tag: maternal bmi

tag: placental volume (cm3)


title: HumanAorticEndothelialCells_Individual519_OxPAPCTreatment_replicate2

description:
OxPAPC
5500024057485061409333_F07.cel

tag: gender


title: 5432A

description: Tumor vs. Normal

tag: diagnosis

tag: sampleID

tag: idh1 status

tag: prbid

tag: caseid

tag: sample type


title: HumanAorticEndothelialCells_Individual519_controlTreatment_replicate1

description:
control
5500024057485061409333_G07.cel


title: Bacterial nucleic acid sample  BMA_HPA_068

type: other

city: Salisbury

first: Karen

middle: Elizabeth

last: Kempsell

state: Wiltshire

address: Porton Down

department: Science Group

country: United Kingdom

institute: UK Health Security Agency

hyb_protocol: Slides were pre-hybridised in 5 x SSC, 0.1% SDS and 4 x Denhardts solution, washed in sterile, nuclease-free water followed by 100% propan-2-ol then air-dried. Cy3-labelled randomly-amplified target DNAs were denatured at 95 oC for 3 minutes then diluted to a final concentration of 80 μg/ml in 5 x SSC buffer (Sigma-Aldrich), 0.1% SDS, 4 x Denhardts solution at 50oC. 40 μl of hybridisation mix was applied to the microarray slide, which was then incubated in a humidified multi-slide chamber (Genetix Inc.) for 16 hours. The slides were then washed once in each of the following buffers for two minutes: (A) 1 x SSC, 0.2% SDS, 50oC, (B) 0.1 x SSC, 0.2% SDS, 50oC, (C) 0.1 x SSC, 0.2% SDS, 20oC, then centrifuged to dryness at 1000 rpm for 5 minutes

scan_protocol: scanned using an Affymetrix 428 microarray laser scanner at a gain of sixty

data_processing: After image capture files were saved in Tiff format then quantified using the scan analysis software Bluefuse™ (BlueGnome Inc. Cambridge UK), all data were normalised to the global median for each slide then replicate data points fused according to median fluorescent intensity and name. The data were sorted into pathogen relevant groups and each group analysed for statistical significance. Probe intensities were derived for each sample, the log(2) taken and p values calculated which were then sorted from lowest to highest values within each group. Data points for each group were then ranked first by decreasing fold intensity over human DNA control hybridisation values and then by significance (only oligonucleotides with p < 0.2 in each group were considered).

molecule: other

organism: Streptococcus agalactiae

source_name: In vitro grown bacterial cell culture

label_protocol:
The method used to generate randomly amplified DNA targets is a modification of the method published by Bohlander et al and has been described previously (see references 1 and 2 below)
Reference 1: Bohlander SK, Espinosa R 3rd, Le Beau MM, Rowley JD, Diaz MO. 1992  A method for the rapid sequence-independent amplification of microdissected chromosomal material. Genomics. 13:1322-4.
Reference 2: Burton, J. E., O. J. Oshota, E. North, M. J. Hudson, N. Polyanskaya, J. Brehm, G. Lloyd, and N. J. Silman. 2005. Development of a multi-pathogen oligonucleotide microarray for detection of Bacillus anthracis. Mol Cell Probes 19:349-57

growth_protocol: Bacterial cells  cultured overnight on 5%  horse blood/Brain Heart Infusion agar plates at 37 oC

extract_protocol: Bacterial colonies were isolated and re-suspended in 200 ul TEG buffer (10 mM Tris-Cl pH 8.0, 1 mM EDTA, 2% glucose). 500 ul Guanidine hydrochloride lysis buffer (8 M guanidine hydrochloride, 0.2% sodium sarkinosate) was added to the bacterial suspension which was then mixed by inversion, 200 ul of chloroform was added to the emulsion and centrifuged at 13000 g for 10 minutes. The DNA was recovered from the upper aqueous layer by precipitation with 100 % ethanol and collected by centrifugation. After washing twice with 70 % ethanol and drying, the DNA pellet was re-suspended in TE buffer (10 mM Tris-Cl pH 8.0, 1 mM EDTA) and stored at -20 oC prior to use.

tag: strain

tag: extracted molecule

value: total nucleic acids

tag: cell/tissue type

value: In vitro grown bacterial cell culture


title: HumanAorticEndothelialCells_Individual519_controlTreatment_replicate2

description:
control
5500024057485061409333_E07.cel

tag: agent

tag: individual id

value: Male


title: Bacterial nucleic acid sample  BMA_HPA_067

organism: Neisseria meningitidis

value: Z4673 (B2198) Serogroup B


title: Bacterial nucleic acid sample  BMA_HPA_066

value: Z5005 (B40) Serogroup A


title: passive smoker 246, cord blood

tag: parity

tag: gestational age (weeks)

tag: mode of delivery

tag: placental weight (g)

tag: newborn weight (g)

tag: newborn length (cm)

tag: apgar score (5s)

tag: baby's sex

tag: maternal blood cotinin (ng/ml)

tag: cord blood cotinin (ng/ml)


title: passive smoker 245, cord blood

tag: smoking status

tag: age (years)

tag: maternal bmi

tag: placental volume (cm3)


title: HumanAorticEndothelialCells_Individual517_OxPAPCTreatment_replicate1

description:
OxPAPC
5500024059565071603200_D02.cel

value: OxPAPC

tag: batch

tag: gender

tag: replicate


title: HumanAorticEndothelialCells_Individual518_OxPAPCTreatment_replicate2

description:
OxPAPC
5500024059565071603200_C10.cel

tag: agent

tag: individual id


title: HumanAorticEndothelialCells_Individual518_controlTreatment_replicate2

description:
control
5500024059565071603200_B10.cel

value: control


title: HumanAorticEndothelialCells_Individual518_controlTreatment_replicate1

description:
control
5500024059565071603200_D10.cel


title: Bacterial nucleic acid sample  BMA_HPA_065

organism: Neisseria lactamica

tag: strain

tag: extracted molecule

tag: cell/tissue type


title: HumanAorticEndothelialCells_Individual517_OxPAPCTreatment_replicate2

description:
OxPAPC
5500024059565071603200_A02.cel


title: HumanAorticEndothelialCells_Individual517_controlTreatment_replicate2

description:
control
5500024059565071603200_C02.cel


title: passive smoker 232, cord blood

tag: parity

tag: gestational age (weeks)

tag: mode of delivery

tag: placental weight (g)

tag: newborn weight (g)

tag: newborn length (cm)


title: BcaP overproduction vs. control - slide 185524

city: Groningen

first: Anne

middle: de

last: Jong

address: Nijenborgh 7

country: Netherlands

institute: university of Groningen

description:
Signal:ch1 is Cy3 in raw file
Signal:ch2 is Cy5 in raw file
Biological replicate 2 Vs Control 2; 1 hour after induction with nisin

hyb_protocol: The protocol was performed as described in Hendriksen et al., 2008 (PMID: 18024519)

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: Lactococcus cremoris subsp. cremoris NZ9000

source_name: BcaP overproduction

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 0.5 in GM17 media

extract_protocol: RNA was isolated and purified using the High Pure RNA isolation kit (Roche diagnostics) as described (Hendriksen et al., 2007; Hendriksen et al., 2008a). Contaminating genomic DNA was removed by treatment with RNase-free DNase I (Roche diagnostics). RNA was isolated from three replicate cultures.

tag: vector

tag: overproduction

value: BcaP

source_name: control


title: passive smoker 234, cord blood

tag: smoking status

tag: age (years)

tag: maternal bmi

tag: placental volume (cm3)

tag: apgar score (5s)

tag: baby's sex

tag: maternal blood cotinin (ng/ml)

tag: cord blood cotinin (ng/ml)


title: non-smoker 236, cord blood


title: HumanAorticEndothelialCells_Individual518_OxPAPCTreatment_replicate1

description:
OxPAPC
5500024059565071603200_A10.cel

tag: agent

tag: individual id

tag: batch

tag: gender

tag: replicate


title: Human nucleic acid sample 1 BMA_HPA_064

source_name: Human donor 1 whole blood

tag: extracted molecule

value: total DNA

tag: cell/tissue type

value: whole blood


title: non-smoker 238, cord blood

tag: parity

tag: gestational age (weeks)

tag: mode of delivery

value: vaginal

tag: placental weight (g)

tag: newborn weight (g)

tag: newborn length (cm)


title: non-smoker 240, cord blood

tag: smoking status

tag: age (years)

tag: maternal bmi

tag: placental volume (cm3)

tag: apgar score (5s)


title: non-smoker 231, cord blood

tag: baby's sex

tag: maternal blood cotinin (ng/ml)

tag: cord blood cotinin (ng/ml)


title: HumanAorticEndothelialCells_Individual517_controlTreatment_replicate1

description:
control
5500024059565071603200_B02.cel

tag: agent

tag: individual id

tag: batch

tag: gender

tag: replicate


title: non-smoker 248, cord blood

tag: parity

tag: gestational age (weeks)

tag: mode of delivery


title: non-smoker 226, cord blood

tag: placental weight (g)

tag: newborn weight (g)

tag: newborn length (cm)


title: HumanAorticEndothelialCells_Individual516_controlTreatment_replicate2

description:
control
5500024063070081409291_G02.cel

value: Female


title: No DNA Control sample  BMA_HPA_063

source_name: Buffer only control

tag: extracted molecule

tag: cell/tissue type

value: Buffer only control


title: D14P3

city: Bellaterra-Barcelona

first: Mariana

middle: Pereira Mónica

last: Teles

address: Campus Universitari

country: Spain

institute: Universitat Autònoma de Barcelona

description: Gene expression in liver of fish implanted with 200 µg/g body weight of cortisol during 14 days

hyb_protocol: Total RNA (500 ng) was amplified and Cy3-labeled with Agilent’s One-Color Microarray-Based Gene Expression Analysis (Quick Amp Labelling kit) along with Agilent’s One-Color RNA SpikeIn Kit. Each sample (1.65 μg of RNA) was hybridized to S. aurata array (ID 024502, Agilent) at 65 °C for 17 hours using Agilent’s GE Hybridisation Kit. Washes were conducted as recommended by the manufacturer using Agilent’s Gene Expression Wash Pack with stabilisation and drying solution.

scan_protocol: Microarrays slides were scanned with Agilent Technologies Scanner model G2505B. Spot intensities and other quality control features were extracted with Agilent’s Feature Extraction software version 10.4.0.0. One-channel TIFF images were imported into the GeneSpring software GX 11.0. After Percentile normalization, all data were filtered by comparison of the standard deviation expression among groups (filter by expression). The entities that had values lesser or greater than the standard deviation value were retained. This filter procedure allowed selected samples that have outlier entities, and filters out probes that have a high/low variation expression values across the samples.

data_processing: Statistical test were implemented in the GeneSpring software GX 11.0 used to select transcripts differentially expressed (P < 0.01) between control and treatments. One-way ANOVAs were used to explore differences in the transcriptomic profile between the treatments. The statistical tests were made using SPSS 17.0.

organism: Sparus aurata

source_name: Liver

label_protocol: A loop microarray design approach was used for the study, all experimental RNA samples were labelled with single colour dye (Cy3) and each stimulated sample was compared to the control sample (pool without stimulation) labelled with the same dye (Cy3). Denatured samples of RNA were reversed transcribed and indirectly labelled with Cy3. RNA labelling, hybridisations, and scanning were performed according to manufacturer’s instructions.

extract_protocol: Total RNA was individually extracted from tissues using 1ml/sample of TRI reagent (Molecular Research Center Inc.) following the manufacturer's protocol. Quantification was carried out with a Nanodrop1000 (Thermo Scientific) and the quality of the RNA was checked with a Bioanalyser (Agilent Technologies). All RIN values obtained were >8, indicative of excellent RNA integrity and quality.

treatment_protocol:
Sparus aurata (gilthead sea bream) specimens (108 g mean weight) were obtained from a local fish farm (Piscifactoria Andrès, Spain). Fish were acclimatized to laboratory conditions for at least 15 days, maintained in a closed freshwater flow circuit, at 15°C, in a 12 h light/12 h dark cycle. Fish were fed with a commercial diet once a day and fasted 24 h before the experimental procedures and during the experiment. Water quality indicators, such as dissolved oxygen, pH, nitrite and ammonia were analyzed periodically, and the measured values were acceptable considering gilthead sea bream physiological requirements. All experimental procedures agree with the “International Guiding Principles for Biomedical Research Involving Animals” and they were supervised by the ethical committee of the University.
Three experimental groups of six fish were slightly anaesthetized with tricaine methane sulphonate (MS222) and injected intraperitoneally (ip) with coconut oil implants. Cortisol implants were prepared by warming the coconut oil at 30°C and mixing the desired amount of cortisol (hydrocortisone hemisuccinate). Fish were ip injected with the implants (5 μl/g body weight - bw) of coconut oil alone (controls) or with the implants containing two different concentrations of cortisol (50 or 200 µg/g bw) to simulate a cortisol secretion after chronic stress. After that, fish were returned to their respective tanks. One extra group of fish without the implant (untreated fish) was maintained under the same conditions and sampled at day zero (time 0 control). After seven and forteen days of cortisol implantation fish were randomly sampled from the duplicated tanks used for each experimental group and sacrificed by over-anesthetization with MS222. Blood was collected with heparinized syringes from the caudal vein and used for plasma isolation. Different organs, including liver, were carefully dissected out and immediately frozen in liquid nitrogen.

tag: tissue

value: Liver

tag: age

value: adults

tag: treatment


title: HumanAorticEndothelialCells_Individual516_OxPAPCTreatment_replicate2

description:
OxPAPC
5500024063070081409291_H02.cel


title: Patient nucleic acid sample  BMA_HPA_062

source_name: Patient 7 Cerebrospinal fluid Sample

treatment_protocol: CSF samples were centrifuged for 5 minutes at 1000 g to remove cellular debris, 200 ul aliquots of the supernatant fraction were then removed and centrifuged at 13000 g for 10 minutes. The pellet and supernatant fractions were recovered and processed separately. The pellet fraction was re-suspended in 200 ul of TBE buffer prior to further processing.

value: cerebrospinal fluid


title: HumanAorticEndothelialCells_Individual516_OxPAPCTreatment_replicate1

description:
OxPAPC
5500024063070081409291_F02.cel


title: Patient nucleic acid sample  BMA_HPA_061


title: D14P2

value: liver of fish implanted with 200 µg/g body weight of cortisol during 14 days


title: Patient nucleic acid sample  BMA_HPA_060

source_name: Patient 6 Cerebrospinal fluid Sample

value: total nucleic acids


title: non-smoker 228, cord blood

tag: smoking status

value: non-smoker

tag: age (years)

tag: maternal bmi

tag: placental volume (cm3)

tag: apgar score (5s)

tag: baby's sex

value: F

tag: maternal blood cotinin (ng/ml)

tag: cord blood cotinin (ng/ml)


title: Patient nucleic acid sample  BMA_HPA_059


title: BcaP overproduction vs. control - slide 185523

description:
Signal:ch1 is Cy5 in raw file
Signal:ch2 is Cy3 in raw file
Biological replicate1 Vs Control 1; 1 hour after induction with nisin

tag: vector

tag: overproduction


title: passive smoker 225, cord blood

value: passive smoker

tag: parity

tag: gestational age (weeks)

tag: mode of delivery

tag: placental weight (g)

tag: newborn weight (g)

value: M


title: HumanAorticEndothelialCells_Individual516_controlTreatment_replicate1

description:
control
5500024063070081409291_E02.cel

tag: agent

tag: individual id

tag: batch

tag: gender

tag: replicate


title: HumanAorticEndothelialCells_Individual515_OxPAPCTreatment_replicate2

description:
OxPAPC
5500024057485061409333_B10.cel

value: OxPAPC

value: Male


title: non-smoker 218, cord blood

tag: smoking status

tag: age (years)

tag: maternal bmi

tag: placental volume (cm3)

tag: newborn length (cm)


title: D14P1

tag: tissue

tag: age

tag: treatment


title: Patient nucleic acid sample  BMA_HPA_058

source_name: Patient 5 Cerebrospinal fluid Sample

tag: extracted molecule

tag: cell/tissue type


title: non-smoker 222, cord blood

tag: parity

tag: gestational age (weeks)

tag: mode of delivery

value: caesarean

tag: placental weight (g)

tag: apgar score (5s)

tag: baby's sex

tag: maternal blood cotinin (ng/ml)

tag: cord blood cotinin (ng/ml)


title: D7P2

description: Gene expression in liver of fish implanted with 200 µg/g body weight of cortisol during 7 days


title: D7P3

value: liver of fish implanted with 200 µg/g body weight of cortisol during 7 days


title: HumanAorticEndothelialCells_Individual515_OxPAPCTreatment_replicate1

description:
OxPAPC
5500024057485061409333_D10.cel

tag: agent

tag: individual id

tag: batch

tag: gender

tag: replicate


title: D7P1

tag: tissue

tag: age


title: Patient nucleic acid sample  BMA_HPA_057

tag: extracted molecule


title: HumanAorticEndothelialCells_Individual515_controlTreatment_replicate1

description:
control
5500024057485061409333_C10.cel

value: control


title: HumanAorticEndothelialCells_Individual515_controlTreatment_replicate2

description:
control
5500024057485061409333_A10.cel


title: passive smoker 258, cord blood

tag: smoking status

tag: age (years)

tag: maternal bmi

value: vaginal

value: unknown

tag: placental volume (cm3)

tag: newborn weight (g)

tag: newborn length (cm)


title: passive smoker 219, cord blood

tag: parity

tag: gestational age (weeks)

tag: mode of delivery

tag: placental weight (g)

tag: apgar score (5s)

tag: baby's sex


title: Patient nucleic acid sample  BMA_HPA_056

source_name: Patient 4 Cerebrospinal fluid Sample

tag: cell/tissue type


title: ControlP3

description: Gene expression of control group

tag: treatment


title: ControlP2

description: Gene expression of control group

tag: tissue


title: passive smoker 215, cord blood

tag: maternal blood cotinin (ng/ml)

tag: cord blood cotinin (ng/ml)

value: no sample


title: passive smoker 212, cord blood

tag: smoking status


title: HumanAorticEndothelialCells_Individual514_OxPAPCTreatment_replicate2

description:
OxPAPC
5500024057485061409333_D04.cel

tag: agent

tag: individual id

tag: batch

tag: gender

tag: replicate


title: ControlP1

description: Gene expression of control group

value: Liver

tag: age


title: non-smoker 211, cord blood

tag: age (years)

tag: maternal bmi

tag: parity

tag: gestational age (weeks)

tag: placental volume (cm3)

tag: newborn weight (g)

tag: newborn length (cm)


title: HumanAorticEndothelialCells_Individual514_OxPAPCTreatment_replicate1

description:
OxPAPC
5500024057485061409333_B04.cel


title: Patient nucleic acid sample  BMA_HPA_052

source_name: Patient 2 Cerebrospinal fluid Sample

tag: extracted molecule

tag: cell/tissue type


title: Patient nucleic acid sample  BMA_HPA_055


title: non-smoker 210, cord blood

tag: mode of delivery

tag: placental weight (g)

tag: apgar score (5s)

tag: baby's sex

tag: maternal blood cotinin (ng/ml)

tag: cord blood cotinin (ng/ml)


title: HumanAorticEndothelialCells_Individual520_OxPAPCTreatment_replicate1

description:
OxPAPC
5500024057485061409333_A01.cel

tag: agent

tag: individual id

tag: batch

tag: gender

tag: replicate


title: Patient nucleic acid sample  BMA_HPA_050

source_name: Patient 1 Cerebrospinal fluid Sample


title: Patient nucleic acid sample  BMA_HPA_054

source_name: Patient 3 Cerebrospinal fluid Sample


title: HumanAorticEndothelialCells_Individual514_controlTreatment_replicate2

description:
control
5500024057485061409333_A04.cel

source_name: HumanAorticEndothelialCells


title: Patient nucleic acid sample  BMA_HPA_053


title: HumanAorticEndothelialCells_Individual514_controlTreatment_replicate1

description:
control
5500024057485061409333_C04.cel


title: Patient nucleic acid sample  BMA_HPA_051


title: HumanAorticEndothelialCells_Individual513_OxPAPCTreatment_replicate1

description:
OxPAPC
5500024057485061409333_H03.cel


title: passive smoker 209, cord blood

tag: smoking status

tag: age (years)

tag: maternal bmi

tag: parity

tag: gestational age (weeks)


title: passive smoker 201, cord blood

tag: placental volume (cm3)

tag: newborn weight (g)

tag: newborn length (cm)


title: HumanAorticEndothelialCells_Individual513_OxPAPCTreatment_replicate2

description:
OxPAPC
5500024057485061409333_E03.cel


title: p75High/p75Low-replicate2

city: Rouen

first: nicolas

last: guerout

state: Normandy

address: 22 Bd Gambetta

country: France

institute: Faculty of medecine of Rouen

description: Biological replicate 2 of 4.

hyb_protocol: The corresponding Cy3 and Cy5 labeled cDNAs were combined and hybridized overnight (17 hours, 65°C) to an Agilent Whole Rat Genome Oligo Microarrays 4x44K using Agilent's recommended hybridization chamber and oven.

scan_protocol: Agilent Technologies Scanner G2505C

data_processing: Images were quantified using Agilent Feature Extraction Software (version 10.5). Background was substracted and data were normalized by linear Lowess.

organism: Rattus norvegicus

source_name: p75High OEC

label_protocol: SuperAmp RNA amplification was performed according to Miltenyi Biotec's undisclosed procedure. The amplification is based on a global PCR protocol using mRNA-derived cDNA. 250 ng of each of the cDNAs were used as template for Cy3 and Cy5 labeling which was performed according to Miltenyi Biotec's undisclosed protocol. p75 High-OECs are labeled with Cy5 and p75 Low-OECs are labeled with Cy3.

growth_protocol: OECs were cultivated with the same protocol (A. Ramon-Cueto and M. Nieto-Sampedro, 1992).

extract_protocol: Cells samples were lysed using SuperAmp Lysis Buffer and strored appropriately according to the instructions of the SuperAmp Preparation Kit (Miltenyi Biotec). mRNA was isolated via magnetic bead technology.

treatment_protocol: P75Low and p75High OECs were sorted using a FACSAria flow cytometer (BD Biosciences). Briefly, OECs were sorted based on their differential expression of p75,  purification of each sorting experiments were assessed (98% purity).

tag: strain

value: Fischer

source_name: p75Low OEC


title: HumanAorticEndothelialCells_Individual513_controlTreatment_replicate2

description:
control
5500024057485061409333_G03.cel


title: p75High/p75Low-replicate1

description: Biological replicate 1 of 4.


title: p75High/p75Low-replicate4

description: Biological replicate 4 of 4.


title: non-smoker 204, cord blood

source_name: umbilical cord blood

tag: mode of delivery

tag: placental weight (g)

tag: apgar score (5s)

tag: baby's sex


title: Human nucleic acid sample 2 BMA_HPA_048

source_name: Human donor 2 whole blood

tag: extracted molecule

value: total DNA

tag: cell/tissue type

value: whole blood


title: non-smoker 300, placenta

description: middle part of the placenta villi parenchyma sections

source_name: term placenta

tag: maternal blood cotinin (ng/ml)

tag: cord blood cotinin (ng/ml)


title: HumanAorticEndothelialCells_Individual513_controlTreatment_replicate1

description:
control
5500024057485061409333_F03.cel

tag: agent

tag: individual id

tag: batch

tag: gender

tag: replicate


title: 2i Nam-treated completely Max-null clone 35

city: Hidaka

first: Akihiko

last: Okuda

state: Saitama

address: 1397-1 Yamane

department: Research Center for Genomic Medicine

country: Japan

institute: Saitama Medical University

hyb_protocol: Labelled samples were hybridized to the microarrays according to the manufacturer’s protocol with Affymetrix Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix GeneArray Scanner 3000. Scanning was preformed as described elsewhere. (Irizarry et al, Nucleic Acids Res 31, e15, 2003)

data_processing:
The data was background-subtracted and normalized with the robust multi-array analysis (RMA; Irizarry et al.  Nucleic Acids Res  31(4): e15, 2003) via R/Bioconductor 2.7 affy package using default analysis settings.
Matrix values are logarithmic (log2) of expression measure from CEL files.

organism: Mus musculus

source_name: 2i NAM-treated completely Max-null ES clone 35

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

growth_protocol: Dox-untread or -treated Max-null ESCs cultured under conventional ES culture condition with LIF and serum or 2i/Nam condition. Nanog-rescued Max-null ESCs and wild-type ESCs were cultured under conventional and 2i/Nam conditions, respectively.

extract_protocol: Total RNAs were prepared by using TRIzol reagent from invitrogen (15596-026).

value: male

tag: tissue

value: ES cells


title: non-smoker 299, placenta

tag: smoking status

value: non-smoker

tag: age (years)

tag: maternal bmi

tag: parity

tag: gestational age (weeks)

tag: placental volume (cm3)

tag: newborn weight (g)


title: non-smoker 298, placenta

tag: mode of delivery

tag: placental weight (g)

tag: newborn length (cm)

tag: apgar score (5s)

tag: baby's sex

value: F


title: p75High/p75Low-replicate3

description: Biological replicate 3 of 4.

tag: strain


title: 2i Nam-treated completely Max-null clone 32

source_name: 2i NAM-treated completely Max-null ES clone 32


title: Human nucleic acid sample 1 BMA_HPA_047

source_name: Human donor 1 whole blood

tag: extracted molecule

tag: cell/tissue type


title: HumanAorticEndothelialCells_Individual512_OxPAPCTreatment_replicate1

description:
OxPAPC
5500024063070081409291_D05.cel

tag: agent

tag: individual id

tag: batch

tag: gender

tag: replicate


title: 2i Nam-treated completely Max-null clone 31

source_name: 2i NAM-treated completely Max-null ES clone 31

tag: tissue


title: Patient nucleic acid sample  BMA_HPA_049

value: total nucleic acids

value: cerebrospinal fluid


title: No DNA Control sample  BMA_HPA_046

source_name: Buffer only control

value: Buffer only control


title: HumanAorticEndothelialCells_Individual512_controlTreatment_replicate2

description:
control
5500024063070081409291_A05.cel

value: Male


title: HumanAorticEndothelialCells_Individual512_OxPAPCTreatment_replicate2

description:
OxPAPC
5500024063070081409291_B05.cel

value: OxPAPC


title: HumanAorticEndothelialCells_Individual512_controlTreatment_replicate1

description:
control
5500024063070081409291_C05.cel

value: control


title: 2i Nam-treated WT ES

description: Wild-type ES; reference sample to compare with three clones of Max-null ESCs from which Dox-regulatable Max cDNA had been removed

source_name: 2i NAM-treated WT ES (EBRTcH3)


title: Patient nucleic acid sample  BMA_HPA_044

source_name: Patient 7 Cerebrospinal fluid Sample


title: Patient nucleic acid sample  BMA_HPA_043

source_name: Patient 6 Cerebrospinal fluid Sample


title: Patient nucleic acid sample  BMA_HPA_045


title: non-smoker 296, placenta

tag: smoking status

tag: age (years)

tag: maternal bmi

tag: parity

tag: gestational age (weeks)

value: vaginal

tag: maternal blood cotinin (ng/ml)

tag: cord blood cotinin (ng/ml)


title: Patient nucleic acid sample  BMA_HPA_042


title: non-smoker 297, placenta

tag: mode of delivery

tag: placental weight (g)

value: unknown

tag: placental volume (cm3)

tag: newborn weight (g)

tag: newborn length (cm)

tag: apgar score (5s)

tag: baby's sex

value: M


title: passive smoker 203, cord blood

value: passive smoker

value: caesarean


title: Patient nucleic acid sample  BMA_HPA_041

source_name: Patient 5 Cerebrospinal fluid Sample

tag: extracted molecule

tag: cell/tissue type


title: Nanog (WT)-rescued Max-null ES

source_name: Dox-treated Max-null ES rescued with Nanog (WT)

tag: gender

tag: strain

tag: tissue


title: Max-null ES Dox-treated (6 day) ver2

description: Reference sample for unrescued Max-null ES to compared with the rescued using WT or R67G mutant of Nanog

source_name: Max-null ES Dox treated for 6 days


title: Nanog (D67G)-rescued Max-null ES

source_name: Dox-treated Max-null ES rescued with Nanog (D67G)


title: HumanAorticEndothelialCells_Individual511_OxPAPCTreatment_replicate1

description:
OxPAPC
5500024059565071603200_E08.cel

source_name: HumanAorticEndothelialCells

tag: agent

tag: individual id

tag: batch

value: Female

tag: replicate


title: non-smoker 292, placenta

tag: smoking status

tag: age (years)

tag: maternal bmi

tag: parity

tag: gestational age (weeks)

tag: maternal blood cotinin (ng/ml)

tag: cord blood cotinin (ng/ml)


title: non-smoker 294, placenta

tag: mode of delivery

tag: placental weight (g)

tag: placental volume (cm3)

tag: newborn weight (g)

tag: newborn length (cm)

tag: apgar score (5s)

tag: baby's sex


title: passive smoker 295, placenta


title: HumanAorticEndothelialCells_Individual511_OxPAPCTreatment_replicate2

description:
OxPAPC
5500024059565071603200_H08.cel

tag: agent

tag: individual id

tag: gender


title: non-smoker 291, placenta

tag: smoking status


title: passive smoker 289, placenta

tag: age (years)


title: HumanAorticEndothelialCells_Individual511_controlTreatment_replicate1

description:
control
5500024059565071603200_F08.cel

tag: batch

tag: replicate


title: HumanAorticEndothelialCells_Individual511_controlTreatment_replicate2

description:
control
5500024059565071603200_G08.cel


title: Patient nucleic acid sample  BMA_HPA_040

tag: extracted molecule

tag: cell/tissue type


title: Max-null ES Dox-treated (8 day)

source_name: Max-null ES Dox treated for 8 days

tag: strain

tag: tissue


title: Max-null ES Dox untreated ver3

description: Reference sample for Max-null ES cells rescued with WT or R67G mutant of Nanog

source_name: Max-null ES Dox untreated ver3


title: HumanAorticEndothelialCells_Individual510_OxPAPCTreatment_replicate2

description:
OxPAPC
5500024059565071603200_H03.cel


title: HumanAorticEndothelialCells_Individual510_OxPAPCTreatment_replicate1

description:
OxPAPC
5500024059565071603200_E03.cel


title: non-smoker 287, placenta

tag: maternal bmi

tag: parity

tag: gestational age (weeks)

tag: mode of delivery

tag: placental weight (g)

tag: maternal blood cotinin (ng/ml)

tag: cord blood cotinin (ng/ml)


title: Patient nucleic acid sample  BMA_HPA_038

source_name: Patient 4 Cerebrospinal fluid Sample


title: HumanAorticEndothelialCells_Individual510_controlTreatment_replicate2

description:
control
5500024059565071603200_G03.cel

tag: agent

tag: individual id


title: Patient nucleic acid sample  BMA_HPA_039


title: Max-null ES Dox-treated (4 day)

source_name: Max-null ES Dox treated for 4 days

tag: gender


title: Max-null ES Dox untreated ver2

description: Reference sample for Max-null ES cells Dox-treated for 6 and 8 days

source_name: Max-null ES Dox untreated


title: Patient nucleic acid sample  BMA_HPA_037

source_name: Patient 3 Cerebrospinal fluid Sample


title: Patient  nucleic acid sample  BMA_HPA_035

source_name: Patient 2 Cerebrospinal fluid Sample


title: Patient nucleic acid sample  BMA_HPA_036


title: Max-null ES Dox-treated (6 day)


title: Max-null ES Dox-treated (2 day)

source_name: Max-null ES Dox treated for 2 days


title: non-smoker 282, placenta

source_name: term placenta

tag: smoking status

tag: age (years)

tag: placental volume (cm3)

tag: newborn weight (g)

tag: newborn length (cm)

tag: apgar score (5s)

tag: baby's sex


title: Max-null ES Dox-treated (3 day)

source_name: Max-null ES Dox treated for 3 days

tag: strain

tag: tissue


title: passive smoker 274, placenta

tag: maternal bmi

tag: parity

tag: gestational age (weeks)


title: non-smoker 284, placenta

tag: mode of delivery

tag: placental weight (g)

tag: maternal blood cotinin (ng/ml)


title: non-smoker 275, placenta

tag: cord blood cotinin (ng/ml)


title: HumanAorticEndothelialCells_Individual509_OxPAPCTreatment_replicate2

description:
OxPAPC
5500024059565071603200_H07.cel

tag: agent

tag: individual id

tag: batch

tag: gender

tag: replicate


title: Patient nucleic acid sample  BMA_HPA_034

tag: extracted molecule

tag: cell/tissue type


title: Patient nucleic acid sample  BMA_HPA_033

source_name: Patient 1 Cerebrospinal fluid Sample


title: Max-null ES Dox-treated (1 day)

source_name: Max-null ES Dox treated for 1 day


title: HumanAorticEndothelialCells_Individual509_OxPAPCTreatment_replicate1

description:
OxPAPC
5500024059565071603200_F07.cel


title: HumanAorticEndothelialCells_Individual510_controlTreatment_replicate1

description:
control
5500024059565071603200_F03.cel


title: passive smoker 270, placenta

tag: smoking status

tag: age (years)

tag: placental volume (cm3)

tag: newborn weight (g)

tag: newborn length (cm)

tag: apgar score (5s)

tag: baby's sex


title: passive smoker 267, placenta

tag: maternal bmi

tag: parity

tag: gestational age (weeks)

tag: mode of delivery

tag: placental weight (g)


title: HumanAorticEndothelialCells_Individual509_controlTreatment_replicate1

description:
control
5500024059565071603200_E07.cel

tag: agent

tag: individual id

tag: batch


title: HumanAorticEndothelialCells_Individual509_controlTreatment_replicate2

description:
control
5500024059565071603200_G07.cel

tag: gender

tag: replicate


title: Max-null ES Dox untreated

description: Reference sample for Max-null ES cells Dox-treated for 1-4 days

tag: strain

tag: tissue


title: Rbp2-/- ES 6 days without LIF biological replicate 2

city: New Haven

first: Qin

last: Yan

state: CT

address: Department of Pathology, PO Box 208023

institute: Yale School of Medicine

hyb_protocol: 15ug of the fragmented cRNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C. The chips are transferred to a fluidics instrument that performs washes to remove cRNA that has not hybridized to its complementary oligonucleotide probe. The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE.

scan_protocol: Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured. These measures provide the basis of subsequent biostatistical analysis.

data_processing: Analysis of the raw gene expression profiling data was performed using dChip software (Li and Hung Wong, 2001)

source_name: Rbp2-/- ES cells 6 days without LIF

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

extract_protocol: RNA isolation using RNeasy mini kit with on-column DNase digestion (Qiagen)

tag: cell type

value: embryonic stem cells

tag: genotype/variation

tag: culture medium

value: absence of LIF for 6 days


title: non-smoker 268, placenta

tag: smoking status

tag: age (years)

tag: placental volume (cm3)

tag: newborn weight (g)

tag: newborn length (cm)

tag: apgar score (5s)

tag: maternal blood cotinin (ng/ml)

tag: cord blood cotinin (ng/ml)


title: Patient nucleic acid sample  BMA_HPA_032

tag: extracted molecule

tag: cell/tissue type


title: Bacterial nucleic acid sample  BMA_HPA_030

source_name: In vitro grown bacterial cell culture

value: In vitro grown bacterial cell culture


title: Patient nucleic acid sample  BMA_HPA_031

organism: Neisseria flavescens


title: Bacterial nucleic acid sample  BMA_HPA_029


title: Bacterial nucleic acid sample  BMA_HPA_028


title: Bacterial nucleic acid sample  BMA_HPA_027

value: NCTC13275 Unknown Serogroup


title: HumanAorticEndothelialCells_Individual508_OxPAPCTreatment_replicate1

description:
OxPAPC
5500024059565071603200_C07.cel

tag: agent

tag: individual id

tag: batch

tag: gender


title: Rbp2-/- ES 6 days without LIF biological replicate 1

tag: cell type


title: non-smoker 261, placenta

value: non-smoker

tag: maternal bmi

tag: parity

tag: gestational age (weeks)

tag: mode of delivery

tag: placental weight (g)

tag: baby's sex

value: F


title: Bacterial nucleic acid sample  BMA_HPA_026

tag: strain

value: NCTC13273 Unknown Serogroup

value: total nucleic acids


title: HumanAorticEndothelialCells_Individual508_controlTreatment_replicate1

description:
control
5500024059565071603200_D07.cel

value: Male

tag: replicate


title: Bacterial nucleic acid sample  BMA_HPA_025

value: NCTC13225 Unknown Serogroup


title: HumanAorticEndothelialCells_Individual508_OxPAPCTreatment_replicate2

description:
OxPAPC
5500024059565071603200_A07.cel

value: OxPAPC


title: Rbp2-/- ES biological replicate 1

source_name: Rbp2-/- ES cells

tag: genotype/variation

tag: culture medium

value: presence of LIF


title: Rbp2f/f ES 6 days without LIF biological replicate 2

source_name: Rbp2f/f ES cells 6 days without LIF


title: Rbp2f/f ES 6 days without LIF biological replicate 1


title: HumanAorticEndothelialCells_Individual508_controlTreatment_replicate2

description:
control
5500024059565071603200_B07.cel

source_name: HumanAorticEndothelialCells

value: control


title: Rbp2-/- ES biological replicate 2


title: non-smoker 266, placenta

tag: smoking status

tag: age (years)

value: vaginal

tag: placental volume (cm3)

tag: newborn weight (g)

tag: newborn length (cm)

tag: apgar score (5s)

tag: maternal blood cotinin (ng/ml)

tag: cord blood cotinin (ng/ml)


title: HumanAorticEndothelialCells_Individual507_controlTreatment_replicate2

description:
control
5500024063070081409291_D09.cel

tag: agent

tag: individual id

tag: batch

tag: gender


title: HumanAorticEndothelialCells_Individual507_OxPAPCTreatment_replicate2

description:
OxPAPC
5500024063070081409291_C09.cel


title: passive smoker 263, placenta

value: passive smoker

tag: maternal bmi

tag: parity

tag: gestational age (weeks)

tag: mode of delivery

tag: placental weight (g)

value: unknown

tag: baby's sex


title: HumanAorticEndothelialCells_Individual507_OxPAPCTreatment_replicate1

description:
OxPAPC
5500024063070081409291_A09.cel

tag: replicate


title: Rbp2f/f ES biological replicate 1

source_name: Rbp2f/f ES cells

tag: cell type

tag: genotype/variation

tag: culture medium


title: passive smoker 262, placenta

tag: smoking status

tag: age (years)

value: caesarean

tag: placental volume (cm3)

tag: newborn weight (g)

tag: newborn length (cm)

tag: apgar score (5s)

value: M


title: non-smoker 260, placenta

tag: maternal blood cotinin (ng/ml)

tag: cord blood cotinin (ng/ml)


title: non-smoker 265, placenta

tag: maternal bmi

tag: parity


title: Bacterial nucleic acid sample  BMA_HPA_024

tag: strain

tag: extracted molecule

tag: cell/tissue type


title: Rbp2f/f ES biological replicate 2

value: embryonic stem cells


title: HumanAorticEndothelialCells_Individual507_controlTreatment_replicate1

description:
control
5500024063070081409291_B09.cel

tag: agent

tag: individual id

tag: batch

tag: gender

tag: replicate


title: non-smoker 259, placenta

tag: smoking status

tag: age (years)

tag: gestational age (weeks)

tag: mode of delivery

tag: placental weight (g)

tag: baby's sex


title: passive smoker 258, placenta

tag: placental volume (cm3)

tag: newborn weight (g)

tag: newborn length (cm)

tag: apgar score (5s)

tag: maternal blood cotinin (ng/ml)

tag: cord blood cotinin (ng/ml)


title: Bacterial nucleic acid sample  BMA_HPA_022

tag: strain

value: NCTC13218 Unknown Serogroup

tag: extracted molecule

tag: cell/tissue type

value: In vitro grown bacterial cell culture


title: Bacterial nucleic acid sample  BMA_HPA_023

value: NCTC13223 Unknown Serogroup


title: Bacterial nucleic acid sample  BMA_HPA_021

value: NCTC13214 Unknown Serogroup


title: Bacterial nucleic acid sample  BMA_HPA_020

value: NCTC13198 Unknown Serogroup


title: Bacterial nucleic acid sample  BMA_HPA_019

value: NCTC13152 Unknown Serogroup

value: total nucleic acids


title: HumanAorticEndothelialCells_Individual506_OxPAPCTreatment_replicate1

description:
OxPAPC
5500024059565071603200_F04.cel

tag: agent

tag: individual id

tag: batch

tag: gender

value: Male


title: HumanAorticEndothelialCells_Individual506_OxPAPCTreatment_replicate2

description:
OxPAPC
5500024059565071603200_G04.cel

value: OxPAPC

tag: replicate


title: Bacterial nucleic acid sample  BMA_HPA_018

value: NCTC10793 Serogroup Z-prime


title: HumanAorticEndothelialCells_Individual505_OxPAPCTreatment_replicate2

description:
OxPAPC
5500024063070081409291_A08.cel

value: Female


title: HumanAorticEndothelialCells_Individual506_controlTreatment_replicate2

description:
control
5500024059565071603200_H04.cel

value: control


title: non-smoker 248, placenta

tag: smoking status

value: non-smoker

tag: age (years)

tag: maternal bmi

tag: parity

tag: gestational age (weeks)

tag: mode of delivery

value: vaginal

value: F


title: Bacterial nucleic acid sample  BMA_HPA_017

value: NCTC10792 Serogroup Z


title: passive smoker 251, placenta

value: passive smoker

value: caesarean

tag: placental weight (g)

tag: placental volume (cm3)

tag: newborn weight (g)

tag: newborn length (cm)

tag: apgar score (5s)

tag: baby's sex

value: M


title: HumanAorticEndothelialCells_Individual506_controlTreatment_replicate1

description:
control
5500024059565071603200_E04.cel

tag: agent


title: non-smoker 241, placenta

tag: maternal blood cotinin (ng/ml)

tag: cord blood cotinin (ng/ml)


title: passive smoker 256, placenta


title: Wild type BY4741

city: Lincoln

first: Dmitri

middle: E

last: Fomenko

state: NE

department: Biochemistry

institute: University of Nebraska

hyb_protocol: Agilent standard hybridization protocol

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.

organism: Saccharomyces cerevisiae

source_name: BY4741 wild-type - untreated

label_protocol: Agilent standard labeling protocol

growth_protocol: BY4741 wild type, yap1Δ, gcn2Δ, gcn4Δ mutant cells were grown to an optical density of 0.2-0.3 at 600 nm in 200 ml YPD medium

extract_protocol: Ambion Yeast RNA purification kit

treatment_protocol: 20 mM boric acid treatment for 1 hour

tag: strain

tag: genotype/variation

value: wild-type

source_name: BY4741 wild-type + 20mM boric acid


title: HumanAorticEndothelialCells_Individual505_controlTreatment_replicate2

description:
control
5500024063070081409291_B08.cel

tag: individual id

tag: batch

tag: gender

tag: replicate


title: non-smoker 238, placenta

tag: smoking status

tag: age (years)

tag: maternal bmi

tag: parity

tag: gestational age (weeks)


title: non-smoker 240, placenta

tag: mode of delivery

tag: placental weight (g)

tag: placental volume (cm3)

tag: newborn weight (g)

tag: newborn length (cm)


title: Yap1Δ mutant cells

source_name: BY4741 Yap1Δ - untreated

source_name: BY4741 Yap1Δ + 20mM boric acid


title: Gcn4Δ mutant cells

source_name: BY4741 Gcn4Δ - untreated

source_name: BY4741 Gcn4Δ + 20mM boric acid


title: passive smoker 245, placenta

tag: apgar score (5s)

tag: baby's sex

tag: maternal blood cotinin (ng/ml)

tag: cord blood cotinin (ng/ml)


title: HumanAorticEndothelialCells_Individual505_controlTreatment_replicate1

description:
control
5500024063070081409291_D08.cel

tag: agent

tag: individual id

tag: batch


title: Bacterial nucleic acid sample  BMA_HPA_016

tag: strain

value: NCTC10791 Serogroup Y

tag: extracted molecule

tag: cell/tissue type

value: In vitro grown bacterial cell culture


title: non-smoker 236, placenta

tag: smoking status

tag: age (years)

tag: maternal bmi

tag: parity


title: Bacterial nucleic acid sample  BMA_HPA_015

value: NCTC10790 Serogroup X


title: HumanAorticEndothelialCells_Individual505_OxPAPCTreatment_replicate1

description:
OxPAPC
5500024063070081409291_C08.cel

tag: gender

tag: replicate


title: Leaf_rep3

city: Gainesville

first: Andre

last: Chanderbali

state: FL

address: Museum Road

institute: Univrsity of Florida

hyb_protocol: Arrays were hybridized in accordance with the Agilent Microarrray processing protocol

scan_protocol: Arrays were scanned with and Agilent DNA microarray scanner using Agilent’s Feature Extraction Software 9.1.3 (Agilent Technologies)

data_processing: Arrays were background-corrected and loess normalized within arrays and A-quantile normalized between arrays , using the Bioconductor package Limma. Significantly differentially expressed genes among the eight tissue samples were identifed using a one-way empirical Bayes ANOVA using single channel analysis while considering correlation between channels at each spot.

organism: Nuphar advena

source_name: Leaves

label_protocol: RNA transcripts were labeled using the Low-input RNA Labeling Kit (Agilent Technologies)

growth_protocol: wild populations of water lily in Pennsylvania, USA

extract_protocol: Total RNA was extracted from all tissue samples using the RNeasy Plant Mini Kit (Qiagen).

treatment_protocol: harvested tissues were flash frozen in liquid nitrogen

tag: tissue

value: Vegetative


title: passive smoker 234, placenta

source_name: term placenta

tag: gestational age (weeks)

tag: mode of delivery

tag: placental weight (g)

tag: placental volume (cm3)

tag: newborn weight (g)

tag: newborn length (cm)

tag: apgar score (5s)


title: Fruit_rep3

source_name: Young Fruits

value: Reproductive


title: HumanAorticEndothelialCells_Individual504_OxPAPCTreatment_replicate1

description:
OxPAPC
5500024063070081409291_B02.cel

tag: agent

value: OxPAPC

tag: individual id

tag: batch

value: Male


title: YBud_rep4

source_name: Pre-microsporangial floral bud


title: Bacterial nucleic acid sample  BMA_HPA_012

tag: strain

value: NCTC9714 Serogroup D

tag: extracted molecule

value: total nucleic acids

tag: cell/tissue type


title: Bacterial nucleic acid sample  BMA_HPA_010

value: Z8948 (FAM18) Serogroup C


title: Bacterial nucleic acid sample  BMA_HPA_011

value: Z6904 (ROY) Serogroup W135


title: Bacterial nucleic acid sample  BMA_HPA_013

value: NCTC11423 Strain 73-M6


title: passive smoker 232, placenta

tag: smoking status

tag: age (years)

tag: maternal bmi

tag: parity

value: vaginal

tag: baby's sex

value: F

tag: maternal blood cotinin (ng/ml)

tag: cord blood cotinin (ng/ml)


title: HumanAorticEndothelialCells_Individual504_controlTreatment_replicate1

description:
control
5500024063070081409291_C02.cel

value: control

tag: gender

tag: replicate


title: MBud_rep4

source_name: Pre-meiotic floral  buds

tag: tissue


title: HumanAorticEndothelialCells_Individual504_controlTreatment_replicate2

description:
control
5500024063070081409291_A02.cel


title: HumanAorticEndothelialCells_Individual504_OxPAPCTreatment_replicate2

description:
OxPAPC
5500024063070081409291_D02.cel


title: non-smoker 231, placenta

value: non-smoker

tag: gestational age (weeks)

tag: mode of delivery

tag: placental weight (g)

tag: placental volume (cm3)

tag: newborn weight (g)

tag: newborn length (cm)

tag: apgar score (5s)


title: Fruit_rep4


title: passive smoker 225, placenta

tag: smoking status

value: passive smoker

value: M


title: non-smoker 228, placenta

tag: age (years)


title: non-smoker 226, placenta

tag: maternal bmi


title: HumanAorticEndothelialCells_Individual503_controlTreatment_replicate2

description:
control
5500024063070081409291_H08.cel

tag: agent

tag: individual id

tag: batch


title: InnerTepal_rep4

source_name: Inner Tepals dissected  from mature floral bud


title: HumanAorticEndothelialCells_Individual503_OxPAPCTreatment_replicate1

description:
OxPAPC
5500024063070081409291_F08.cel


title: HumanAorticEndothelialCells_Individual503_OxPAPCTreatment_replicate2

description:
OxPAPC
5500024063070081409291_G08.cel


title: HumanAorticEndothelialCells_Individual503_controlTreatment_replicate1

description:
control
5500024063070081409291_E08.cel


title: Carpel_rep4

source_name: Carpels dissected  from mature floral bud


title: non-smoker 222, placenta

tag: parity

value: caesarean

tag: baby's sex

tag: maternal blood cotinin (ng/ml)

tag: cord blood cotinin (ng/ml)


title: Bacterial nucleic acid sample  BMA_HPA_008

source_name: In vitro grown bacterial cell culture

tag: strain

value: Z5005 (B40) Serogroup A

tag: extracted molecule

tag: cell/tissue type

value: In vitro grown bacterial cell culture


title: Bacterial nucleic acid sample  BMA_HPA_007

organism: Staphylococcus aureus

value: ATCC 29213 (MSSA)


title: HumanAorticEndothelialCells_Individual502_OxPAPCTreatment_replicate2

description:
OxPAPC
5500024057485061409333_D07.cel

value: OxPAPC

tag: gender

tag: replicate


title: Bacterial nucleic acid sample  BMA_HPA_006

value: EMRSA-16 (MRSA)


title: Leaf_rep4

tag: tissue

value: Vegetative


title: YBud_rep3

value: Reproductive


title: Bacterial nucleic acid sample  BMA_HPA_005

value: total nucleic acids


title: passive smoker 219, placenta

tag: gestational age (weeks)

tag: mode of delivery

tag: placental weight (g)

tag: placental volume (cm3)

tag: newborn weight (g)

tag: newborn length (cm)

tag: apgar score (5s)


title: non-smoker 220, placenta

tag: smoking status

tag: age (years)

tag: maternal bmi

tag: parity


title: Bacterial nucleic acid sample  BMA_HPA_004

organism: Streptococcus pneumoniae

tag: strain


title: HumanAorticEndothelialCells_Individual502_OxPAPCTreatment_replicate1

description:
OxPAPC
5500024057485061409333_B07.cel

tag: agent

tag: individual id

tag: batch

value: Male


title: Bacterial nucleic acid sample  BMA_HPA_003

organism: Listeria monocytogenes

tag: extracted molecule

tag: cell/tissue type


title: Stamen_rep3

source_name: Stamens dissected from mature floral bud

tag: tissue


title: OuterTepal_rep3

source_name: Outer Tepals dissected from mature floral bud


title: passive smoker 215, placenta

tag: gestational age (weeks)

tag: mode of delivery

tag: baby's sex

tag: maternal blood cotinin (ng/ml)

tag: cord blood cotinin (ng/ml)

value: no sample


title: Carpel_rep3


title: HumanAorticEndothelialCells_Individual502_controlTreatment_replicate1

description:
control
5500024057485061409333_C07.cel

source_name: HumanAorticEndothelialCells

tag: gender

tag: replicate


title: HumanAorticEndothelialCells_Individual502_controlTreatment_replicate2

description:
control
5500024057485061409333_A07.cel


title: Stamen_rep4


title: non-smoker 218, placenta

tag: smoking status

tag: age (years)

value: vaginal

tag: placental weight (g)

tag: placental volume (cm3)

tag: newborn weight (g)

tag: newborn length (cm)

tag: apgar score (5s)


title: Bacterial nucleic acid sample  BMA_HPA_002

organism: Haemophilus influenzae

tag: strain

tag: extracted molecule


title: InnerTepal_rep3

tag: tissue


title: Bacterial nucleic acid sample  BMA_HPA_009

value: Z4673 (B2198) Serogroup B

tag: cell/tissue type


title: HumanAorticEndothelialCells_Individual501_OxPAPCTreatment_replicate1

description:
OxPAPC
5500024059565071603200_A11.cel

tag: agent

tag: individual id

tag: batch


title: passive smoker 212, placenta

tag: maternal bmi

tag: parity

tag: gestational age (weeks)

tag: mode of delivery

tag: baby's sex

value: F

tag: maternal blood cotinin (ng/ml)

tag: cord blood cotinin (ng/ml)


title: non-smoker 211, placenta

tag: smoking status

value: non-smoker

tag: age (years)

tag: placental weight (g)

tag: placental volume (cm3)

tag: newborn weight (g)


title: HumanAorticEndothelialCells_Individual501_controlTreatment_replicate2

description:
control
5500024057485061409333_H12.cel

value: control

tag: gender

tag: replicate


title: HumanAorticEndothelialCells_Individual501_OxPAPCTreatment_replicate2

description:
OxPAPC
5500024059565071603200_C11.cel

tag: agent


title: Bacterial nucleic acid sample  BMA_HPA_001

tag: strain

value: HPA

tag: extracted molecule

tag: cell/tissue type


title: MBud_rep3

tag: tissue


title: Leaf_rep2


title: non-smoker 210, placenta

tag: maternal bmi

tag: parity

tag: gestational age (weeks)

tag: newborn length (cm)

tag: apgar score (5s)

value: M


title: MBud_rep2


title: passive smoker 209, placenta

tag: smoking status

value: passive smoker

tag: mode of delivery

tag: baby's sex

tag: maternal blood cotinin (ng/ml)

tag: cord blood cotinin (ng/ml)


title: HumanAorticEndothelialCells_Individual501_controlTreatment_replicate1

description:
control
5500024059565071603200_B11.cel

tag: individual id

tag: batch

tag: gender


title: YBud_rep2


title: passive smoker 207, placenta

tag: age (years)

tag: placental weight (g)

tag: placental volume (cm3)

tag: newborn weight (g)


title: non-smoker 204, placenta

tag: maternal bmi


title: non-smoker 205, placenta

tag: parity

value: caesarean


title: non-smoker 208, placenta

tag: gestational age (weeks)


title: passive smoker 206, placenta

value: unknown

tag: newborn length (cm)


title: Stamen_rep2

tag: tissue


title: Fruit_rep2


title: time-24h, dosage-5ng, rep-4

city: New York

first: Ajish

middle: D

last: George

state: NY

address: 1425 Madison Ave

department: Dept of Genetics & Genomics

institute: Mt Sinai School of Medicine

description: Gene expression data from cells treated with 5ng for 24h

hyb_protocol: Samples were hybridized to WT Human Gene 1.0 ST arrays using Affymetrix hybridization kit materials, according to the manufacturrer's instructions.

scan_protocol: Arrays were scanned on a GeneChip Scanner 3000 7G (Affymetrix).

data_processing: Raw CEL file data from Affymetrix GeneChip Operating Software (GCOS) were background corrected, normalized, and summarized using both gcrma and plier functions in parallel using the Affymetrix power tools package (http://www.affymetrix.com/partners_programs/programs/developer/tools/powertools.affx). The power tools package was also used to estimate a p value for expression of gene in each array according to the Detection Above Background (DABG) method. The data was imported into an R Bioconductor session. Genes that were not expressed at DABG p < 10^ 8 in all replicates of a set were discarded. Linear models of differential expression were fit to each of the transformed data sets using the R Bioconductor limma package, and contrasts were estimated between each group of p53 regulated samples and its corresponding set of controls. The genes were tested for significant differential expression between each pair of groups at a level of p <=0.05 after multiple testing correction according to Benjamini Hochberg procedure (Benjamini & Hochberg, 1995).

source_name: time-24h, dosage-5ng, rep-4

label_protocol: WT expression kit (Ambion), WT Terminal Labeling Kit (Affymetrix), according to the manufatcturer's instructions

growth_protocol: The immortalized B5/589 human mammary epithelial cells (Stampfer and Bartley, 1985) were maintained in RPMI 1640 medium (Invitrogen) supplemented with 10% fetal bovine serum (Invitrogen), 1% penicillin/streptomycin (GIBCO) and 5 ng/ml hEGF (Peprotech). Cells were cultured at 37 °C in a humidified atmosphere containing 5% CO2.

extract_protocol: Total RNA was isolated with an RNAeasy kit (QIAGEN).

treatment_protocol: For all experiments, cells were plated at 800,000 cells/10cm plate 12 24h before treatment, induced with doxycycline at the same time and collected after indicated time periods. Media with or without doxycycline were replaced every 24h.  Doxycycline was purchased from Clontech (631311). Doxorubicin was purchased from Sigma (D1515). TrypLE Express Stable Trypsin Replacement Enzyme (Invitrogen, 12604) was used for the dissociation of attached cells.

tag: cell line

tag: time

tag: treatment

value: 5ng Dox

tag: transgene

value: inducible p53


title: passive smoker 246, placenta

tag: smoking status

tag: mode of delivery

tag: apgar score (5s)

tag: baby's sex

tag: maternal blood cotinin (ng/ml)

tag: cord blood cotinin (ng/ml)


title: passive smoker 203, placenta

tag: age (years)

tag: placental weight (g)

tag: placental volume (cm3)


title: Carpel_rep2


title: Salmonella enterica serovar Typhimurium GidA mutant 3

city: Madison

first: Daniel

last: Shippy

address: 1675 Observatory Dr

institute: University of Wisconsin-Madison

description: This sample is of a Salmonella enterica serovar Typhimurium 14028 delta GidA mutant. It is the first of three wild-type biological replicates used in this experiment, each from separate cultures.

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.). The data received from Nimblegen was analyzed using ArrayStar.

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Salmonella enterica serovar Typhimurium 14028 wild-type and delta GidA mutant cultures were grown in LB medium to mid-log phase (O.D.600nm 0.6) at 37°C.

extract_protocol: Total bacterial RNA was extracted and treated with DNase I using the RiboPure-Bacteria RNA Isolation kit (Ambion, Austin, TX) following manufacturer’s instructions.

treatment_protocol: All cultures were washed twice with PBS prior to extraction.

tag: genotype

value: single deletion mutant delta GidA


title: Salmonella enterica serovar Typhimurium GidA mutant 2

source_name: Salmonella enterica serovar Typhimurium 14028 delta GidA mutant


title: time-24h, dosage-5ng, rep-3

source_name: time-24h, dosage-5ng, rep-3

value: immortalized B5/589 human mammary epithelial cells


title: MBud_rep1

value: Reproductive


title: OuterTepal_rep2


title: Salmonella enterica serovar Typhimurium wt 3

description: This sample is of wild-type Salmonella enterica serovar Typhimurium 14028. It is the first of three wild-type biological replicates used in this experiment, each from separate cultures.

source_name: Salmonella enterica serovar Typhimurium 14028 wild-type

value: wild-type


title: Salmonella enterica serovar Typhimurium GidA mutant 1


title: Salmonella enterica serovar Typhimurium wt 2


title: time-24h, dosage-5ng, rep-1

source_name: time-24h, dosage-5ng, rep-1


title: 22 IM

city: Cambridge

first: Muna

last: Affara

address: Tennis Court Road

department: Pathology

institute: University of Cambridge

description: HUVEC, Inflammatory mediator treated, Biological replicate 8

hyb_protocol: 10 µg biotin incorporated cRNA was fragmented and then denatured. The denatured cRNA was slowly loaded into the bioarray flex chamber without the introduction of air bubbles. All samples were loaded within 30 minutes of cRNA denaturation. The sealed bioarrays were left to hybridise in a 37°C shaker-incubator for 18 hours. The slides were washed and placed in a solution of Cy5-streptavidin for 30 minutes, before stringent washes were used to remove any unbound dye.

scan_protocol: All microarray slides were scanned using an Axon 4100B scanner at the following settings; 635mn wavelength, 600V PMT voltage, 100% laser power, 10µm pixel size

data_processing: The scanned Tagged Image File Format (TIFF) files were pre-processed using CodeLink Expression Analysis v4.0 software. Subsequent normalisation was carried out using Loess normalisation in R.

label: Biotin

source_name: HUVEC, Inflammatory mediator treated

label_protocol: Total RNA was converted to cDNA. This was then used in an invitro transcription (IVT) reaction with biotin to generate biotin incorporated cRNA.

growth_protocol: HUVEC isolates from different individuals were cultured in fully supplemented media until passage 4 (P4).

extract_protocol: Cell cultures were washed with 1 x PBS and lysed using TRIzol® reagent. Total RNA was extracted using phenol chloroform, with the precipitated RNA washed in 70% ethanol and resuspended in Rnase free water. RNA concentration and quality was assess by spectrophotometer and Agilent BioAnalyser.

treatment_protocol: Passage 4 cultured HUVEC isolates were treated with an inflammatory cocktail of 10ng/ml TNF-α, Il-1β, Il-8 for 24 hours prior to RNA extraction.

value: Primary endothelial cells

tag: culture

value: Passage 4 cultured HUVECs


title: Salmonella enterica serovar Typhimurium wt 1


title: 23 IM

description: HUVEC, Inflammatory mediator treated, Biological replicate 9


title: YBud_rep1


title: high glucose HG6

city: Melbourne

first: Assam

last: El-Osta

address: 75 Commercial Road

country: Australia

institute: Baker Heart and Diabetes Institute

description:
HAEC cells grown in medium containing high glucose level (30mM)
4662010041_D

hyb_protocol: according to Illumina standard protocol for iSCAN

data_processing: Illumina Genome Studio, remove backgroung and Cubic Spline normalisation

source_name: Endothelial cell response to glucose levels/ test sample

growth_protocol: Primary HAECs (human aortic endothelial cells), purchased from Lonza (Walkersville, MD, USA), were cultured in EBM-2 medium (Lonza) containing EGM-2 growth factors and supplements (Lonza) and 10% fetal bovine serum (Gibco).

extract_protocol: TriReagent + Qiagen Rneasy mini as described in Tothill et al, Cancer Research 2008

treatment_protocol: Glucose response was analyzed in cells treated 48 hours with medium containing 30 mM high glucose (HG) or 5.5 mM low glucose (LG).

tag: cell type

value: primary human aortic endothelial cells

value: high glucose


title: time-24h, dosage-3ng, rep-2

description: Gene expression data from cells treated with 3ng for 24h

source_name: time-24h, dosage-3ng, rep-2

value: 3ng Dox


title: time-24h, dosage-5ng, rep-2

source_name: time-24h, dosage-5ng, rep-2


title: time-24h, dosage-3ng, rep-3

source_name: time-24h, dosage-3ng, rep-3


title: A14 IM

description: HUVEC, Inflammatory mediator treated, Biological replicate 6

tag: tissue


title: Carpel_rep1


title: A11 IM

description: HUVEC, Inflammatory mediator treated, Biological replicate 5


title: normal glucose LG6

description:
HAEC cells grown in medium containing normal glucose level (4mM)
4662010041_C

scan_protocol: according to Illumina standard protocol for iSCAN

source_name: Endothelial cell response to glucose levels/ control

value: normal glucose


title: time-24h, dosage-3ng, rep-1

source_name: time-24h, dosage-3ng, rep-1

tag: cell line


title: normal glucose LG5

description:
HAEC cells grown in medium containing normal glucose level (4mM)
4662010040_E

label_protocol: according to Illumina standard protocol for iSCAN


title: Bacterial nucleic acid sample  BMA_HPA_014

tag: strain

tag: extracted molecule

value: total nucleic acids

tag: cell/tissue type

value: In vitro grown bacterial cell culture


title: OuterTepal_rep4


title: Fruit_rep1

source_name: Young Fruits


title: Stamen_rep1


title: 12 IM

description: HUVEC, Inflammatory mediator treated, Biological replicate 7


title: InnerTepal_rep1

source_name: Inner Tepals dissected  from mature floral bud


title: time-24h, dosage-3ng, rep-4

source_name: time-24h, dosage-3ng, rep-4

tag: time

tag: treatment

tag: transgene


title: OuterTepal_rep1

source_name: Outer Tepals dissected from mature floral bud


title: time-24h, dosage-0ng, rep-4

description: Gene expression data from cells treated with 0ng for 24h

source_name: time-24h, dosage-0ng, rep-4

value: 0ng Dox


title: A7 IM

description: HUVEC, Inflammatory mediator treated, Biological replicate 3


title: normal glucose LG4

description:
HAEC cells grown in medium containing normal glucose level (4mM)
4662010040_A


title: high glucose HG3

description:
HAEC cells grown in medium containing high glucose level (30mM)
4676008067_F


title: high glucose HG4

description:
HAEC cells grown in medium containing high glucose level (30mM)
4662010040_B


title: A5 IM

description: HUVEC, Inflammatory mediator treated, Biological replicate 2


title: InnerTepal_rep2


title: A9 IM

description: HUVEC, Inflammatory mediator treated, Biological replicate 4


title: time-24h, dosage-0ng, rep-2

source_name: time-24h, dosage-0ng, rep-2