title: erStress_twins_Cauc_1710twin2_500nM_thapsigargin_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1710:2 treated with 500nM thapsigargin.

source_name: Lymphoblastoid cell lines derived from family 1710, member 2


title: erStress_twins_Cauc_1710twin1_DMSO_4h

status: Public on Mar 30 2010

type: RNA

city: Philadelphia

first: Renuka

last: Nayak

state: PA

address: 3516 Civic Center Blvd

country: USA

institute: HHMI, University of Pennsylvania

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1710:1 treated with DMSO.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16-18 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix print default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Lymphoblastoid cell lines derived from family 1710, member 1

label_protocol: Biotinylated cRNA were prepared according to the Ambion MessageAmp Premier RNA Amplification Kit protocol from 500 ng total RNA (MessageAmp Premier RNA Amplification Kit Instruction Manual, 2008, Ambion).

growth_protocol: The cells were grown at a density of 1 million cells/ ml in RPMI 1640 with 15% FBS, 1% penicillin-streptomycin, 2mM L-glutamine at 37°C in a humidified 5% CO2 chamber.

extract_protocol: RNA was extracted using the Rneasy Mini-Kit (Qiagen) as per the manufacturer's instructions

treatment_protocol: DMSO 4 hours

tag: cell line

value: lymphoblastoid cell line

tag: family id

tag: coriell cell line repository identifier

tag: individual

value: Twin number 1

tag: agent

value: DMSO

tag: time

value: 4 hours


title: erStress_twins_Cauc_1706twin2_DMSO_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1706:2 treated with DMSO.

source_name: Lymphoblastoid cell lines derived from family 1706, member 2

value: Twin number 2


title: erStress_twins_Cauc_1710twin2_DMSO_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1710:2 treated with DMSO.


title: erStress_twins_Cauc_1704twin1_500nM_thapsigargin_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1704:1 treated with 500nM thapsigargin.

source_name: Lymphoblastoid cell lines derived from family 1704, member 1

treatment_protocol: 500nM thapsigargin 4 hours

value: thapsigargin

tag: dose


title: erStress_twins_Cauc_1715twin1_500nM_thapsigargin_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1715:1 treated with 500nM thapsigargin.

source_name: Lymphoblastoid cell lines derived from family 1715, member 1


title: erStress_twins_Cauc_1704twin1_DMSO_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1704:1 treated with DMSO.


title: erStress_twins_Cauc_1704twin2_DMSO_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1704:2 treated with DMSO.

source_name: Lymphoblastoid cell lines derived from family 1704, member 2


title: erStress_twins_Cauc_1700twin1_500nM_thapsigargin_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1700:1 treated with 500nM thapsigargin.

source_name: Lymphoblastoid cell lines derived from family 1700, member 1


title: erStress_twins_AA_1757twin2_500nM_thapsigargin_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1757:2 treated with 500nM thapsigargin.

source_name: Lymphoblastoid cell lines derived from family 1757, member 2


title: erStress_twins_Cauc_1700twin2_DMSO_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1700:2 treated with DMSO.

source_name: Lymphoblastoid cell lines derived from family 1700, member 2


title: erStress_twins_Cauc_1700twin2_500nM_thapsigargin_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1700:2 treated with 500nM thapsigargin.


title: erStress_twins_Cauc_1715twin1_DMSO_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1715:1 treated with DMSO.


title: erStress_twins_AA_1757twin2_DMSO_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1757:2 treated with DMSO.


title: erStress_twins_AA_1744twin2_500nM_thapsigargin_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1744:2 treated with 500nM thapsigargin.

source_name: Lymphoblastoid cell lines derived from family 1744, member 2


title: erStress_twins_Cauc_1700twin1_DMSO_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1700:1 treated with DMSO.


title: erStress_twins_Cauc_1706twin1_DMSO_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1706:1 treated with DMSO.

source_name: Lymphoblastoid cell lines derived from family 1706, member 1


title: erStress_twins_AA_1757twin1_500nM_thapsigargin_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1757:1 treated with 500nM thapsigargin.

source_name: Lymphoblastoid cell lines derived from family 1757, member 1


title: erStress_twins_AA_1757twin1_DMSO_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1757:1 treated with DMSO.


title: erStress_twins_AA_1744twin1_500nM_thapsigargin_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1744:1 treated with 500nM thapsigargin.

source_name: Lymphoblastoid cell lines derived from family 1744, member 1


title: erStress_twins_AA_1743twin2_DMSO_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1743:2 treated with DMSO.

source_name: Lymphoblastoid cell lines derived from family 1743, member 2


title: erStress_twins_AA_1744twin2_DMSO_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1744:2 treated with DMSO.


title: erStress_twins_AA_1734twin1_500nM_thapsigargin_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1734:1 treated with 500nM thapsigargin.

source_name: Lymphoblastoid cell lines derived from family 1734, member 1


title: erStress_twins_AA_1736twin2_DMSO_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1736:2 treated with DMSO.

source_name: Lymphoblastoid cell lines derived from family 1736, member 2


title: erStress_twins_AA_1744twin1_DMSO_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1744:1 treated with DMSO.


title: erStress_twins_AA_1734twin2_500nM_thapsigargin_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1734:2 treated with 500nM thapsigargin.

source_name: Lymphoblastoid cell lines derived from family 1734, member 2


title: erStress_twins_AA_1743twin1_DMSO_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1743:1 treated with DMSO.

source_name: Lymphoblastoid cell lines derived from family 1743, member 1


title: erStress_twins_AA_1736twin2_500nM_thapsigargin_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1736:2 treated with 500nM thapsigargin.


title: erStress_twins_AA_1733twin2_DMSO_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1733:2 treated with DMSO.

source_name: Lymphoblastoid cell lines derived from family 1733, member 2


title: erStress_twins_AA_1727twin1_DMSO_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1727:1 treated with DMSO.

source_name: Lymphoblastoid cell lines derived from family 1727, member 1


title: erStress_twins_AA_1733twin2_500nM_thapsigargin_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1733:2 treated with 500nM thapsigargin.


title: erStress_twins_AA_1733twin1_500nM_thapsigargin_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1733:1 treated with 500nM thapsigargin.

source_name: Lymphoblastoid cell lines derived from family 1733, member 1


title: erStress_twins_AA_1734twin1_DMSO_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1734:1 treated with DMSO.


title: erStress_twins_AA_1743twin2_500nM_thapsigargin_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1743:2 treated with 500nM thapsigargin.


title: erStress_twins_AA_1743twin1_500nM_thapsigargin_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1743:1 treated with 500nM thapsigargin.


title: erStress_twins_AA_1725twin2_500nM_thapsigargin_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1725:2 treated with 500nM thapsigargin.

source_name: Lymphoblastoid cell lines derived from family 1725, member 2


title: erStress_twins_AA_1736twin1_DMSO_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1736:1 treated with DMSO.

source_name: Lymphoblastoid cell lines derived from family 1736, member 1


title: erStress_twins_AA_1727twin2_DMSO_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1727:2 treated with DMSO.

source_name: Lymphoblastoid cell lines derived from family 1727, member 2


title: erStress_twins_AA_1733twin1_DMSO_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1733:1 treated with DMSO.


title: erStress_twins_AA_1736twin1_500nM_thapsigargin_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1736:1 treated with 500nM thapsigargin.


title: erStress_twins_AA_1725twin1_DMSO_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1725:1 treated with DMSO.

source_name: Lymphoblastoid cell lines derived from family 1725, member 1


title: erStress_twins_AA_1734twin2_DMSO_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1734:2 treated with DMSO.


title: erStress_twins_AA_1725twin1_500nM_thapsigargin_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1725:1 treated with 500nM thapsigargin.


title: erStress_twins_AA_1725twin2_DMSO_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1725:2 treated with DMSO.


title: erStress_twins_AA_1727twin2_500nM_thapsigargin_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1727:2 treated with 500nM thapsigargin.


title: erStress_twins_AA_1727twin1_500nM_thapsigargin_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1727:1 treated with 500nM thapsigargin.


title: erStress_twins_AA_1720twin2_DMSO_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1720:2 treated with DMSO.

source_name: Lymphoblastoid cell lines derived from family 1720, member 2


title: erStress_twins_AA_1720twin2_500nM_thapsigargin_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1720:2 treated with 500nM thapsigargin.


title: erStress_twins_AA_1717twin2_500nM_thapsigargin_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1717:2 treated with 500nM thapsigargin.

source_name: Lymphoblastoid cell lines derived from family 1717, member 2


title: erStress_twins_AA_1720twin1_500nM_thapsigargin_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1720:1 treated with 500nM thapsigargin.

source_name: Lymphoblastoid cell lines derived from family 1720, member 1


title: erStress_twins_AA_1720twin1_DMSO_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1720:1 treated with DMSO.


title: erStress_twins_AA_1712twin2_DMSO_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1712:2 treated with DMSO.

source_name: Lymphoblastoid cell lines derived from family 1712, member 2


title: erStress_twins_AA_1724twin2_DMSO_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1724:2 treated with DMSO.

source_name: Lymphoblastoid cell lines derived from family 1724, member 2


title: erStress_60grandparents_GM12875_DMSO_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM12875 treated with DMSO 8 hours.

source_name: Lymphoblastoid cell lines derived from GM12875

treatment_protocol: DMSO 8 hours

value: 8 hours


title: erStress_60grandparents_GM12891_DMSO_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM12891 treated with DMSO 8 hours.

source_name: Lymphoblastoid cell lines derived from GM12891


title: erStress_twins_AA_1712twin1_DMSO_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1712:1 treated with DMSO.

source_name: Lymphoblastoid cell lines derived from family 1712, member 1


title: erStress_60grandparents_GM12873_4_ug_ml_tunicamycin_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM12873 treated with 4 ug/ml tunicamycin 8 hours.

source_name: Lymphoblastoid cell lines derived from GM12873

treatment_protocol: 4 ug/ml tunicamycin 8 hours

value: tunicamycin

value: 4 ug/ml


title: erStress_60grandparents_GM12873_DMSO_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM12873 treated with DMSO 8 hours.


title: erStress_60grandparents_GM12891_4_ug_ml_tunicamycin_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM12891 treated with 4 ug/ml tunicamycin 8 hours.


title: erStress_twins_AA_1712twin2_500nM_thapsigargin_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1712:2 treated with 500nM thapsigargin.


title: erStress_60grandparents_GM12875_4_ug_ml_tunicamycin_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM12875 treated with 4 ug/ml tunicamycin 8 hours.


title: erStress_twins_AA_1717twin1_500nM_thapsigargin_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1717:1 treated with 500nM thapsigargin.

source_name: Lymphoblastoid cell lines derived from family 1717, member 1


title: erStress_twins_AA_1717twin1_DMSO_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1717:1 treated with DMSO.


title: erStress_60grandparents_GM12892_DMSO_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM12892 treated with DMSO 8 hours.

source_name: Lymphoblastoid cell lines derived from GM12892


title: erStress_60grandparents_GM12874_DMSO_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM12874 treated with DMSO 8 hours.

source_name: Lymphoblastoid cell lines derived from GM12874


title: erStress_60grandparents_GM12892_4_ug_ml_tunicamycin_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM12892 treated with 4 ug/ml tunicamycin 8 hours.


title: erStress_60grandparents_GM12872_DMSO_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM12872 treated with DMSO 8 hours.

source_name: Lymphoblastoid cell lines derived from GM12872


title: erStress_twins_AA_1712twin1_500nM_thapsigargin_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1712:1 treated with 500nM thapsigargin.


title: erStress_60grandparents_GM12874_4_ug_ml_tunicamycin_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM12874 treated with 4 ug/ml tunicamycin 8 hours.


title: erStress_twins_AA_1724twin1_DMSO_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1724:1 treated with DMSO.

source_name: Lymphoblastoid cell lines derived from family 1724, member 1


title: erStress_twins_AA_1724twin2_500nM_thapsigargin_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1724:2 treated with 500nM thapsigargin.


title: erStress_60grandparents_GM12872_4_ug_ml_tunicamycin_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM12872 treated with 4 ug/ml tunicamycin 8 hours.


title: erStress_twins_AA_1724twin1_500nM_thapsigargin_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1724:1 treated with 500nM thapsigargin.


title: erStress_60grandparents_GM12814_DMSO_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM12814 treated with DMSO 8 hours.

source_name: Lymphoblastoid cell lines derived from GM12814


title: erStress_60grandparents_GM12815_DMSO_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM12815 treated with DMSO 8 hours.

source_name: Lymphoblastoid cell lines derived from GM12815


title: erStress_60grandparents_GM12815_4_ug_ml_tunicamycin_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM12815 treated with 4 ug/ml tunicamycin 8 hours.


title: erStress_60grandparents_GM12763_4_ug_ml_tunicamycin_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM12763 treated with 4 ug/ml tunicamycin 8 hours.

source_name: Lymphoblastoid cell lines derived from GM12763


title: erStress_60grandparents_GM12762_4_ug_ml_tunicamycin_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM12762 treated with 4 ug/ml tunicamycin 8 hours.

source_name: Lymphoblastoid cell lines derived from GM12762


title: erStress_twins_Cauc_1716twin1_DMSO_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1716:1 treated with DMSO.

source_name: Lymphoblastoid cell lines derived from family 1716, member 1


title: erStress_60grandparents_GM12762_DMSO_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM12762 treated with DMSO 8 hours.


title: erStress_60grandparents_GM12760_DMSO_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM12760 treated with DMSO 8 hours.

source_name: Lymphoblastoid cell lines derived from GM12760


title: erStress_60grandparents_GM12763_DMSO_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM12763 treated with DMSO 8 hours.


title: erStress_60grandparents_GM12760_4_ug_ml_tunicamycin_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM12760 treated with 4 ug/ml tunicamycin 8 hours.


title: erStress_60grandparents_GM12761_DMSO_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM12761 treated with DMSO 8 hours.

source_name: Lymphoblastoid cell lines derived from GM12761


title: erStress_60grandparents_GM12812_4_ug_ml_tunicamycin_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM12812 treated with 4 ug/ml tunicamycin 8 hours.

source_name: Lymphoblastoid cell lines derived from GM12812


title: erStress_60grandparents_GM12812_DMSO_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM12812 treated with DMSO 8 hours.


title: erStress_60grandparents_GM12813_4_ug_ml_tunicamycin_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM12813 treated with 4 ug/ml tunicamycin 8 hours.

source_name: Lymphoblastoid cell lines derived from GM12813


title: erStress_60grandparents_GM12813_DMSO_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM12813 treated with DMSO 8 hours.


title: erStress_60grandparents_GM12751_4_ug_ml_tunicamycin_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM12751 treated with 4 ug/ml tunicamycin 8 hours.

source_name: Lymphoblastoid cell lines derived from GM12751


title: erStress_60grandparents_GM12814_4_ug_ml_tunicamycin_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM12814 treated with 4 ug/ml tunicamycin 8 hours.


title: erStress_60grandparents_GM12717_4_ug_ml_tunicamycin_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM12717 treated with 4 ug/ml tunicamycin 8 hours.

source_name: Lymphoblastoid cell lines derived from GM12717


title: erStress_60grandparents_GM12761_4_ug_ml_tunicamycin_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM12761 treated with 4 ug/ml tunicamycin 8 hours.


title: erStress_60grandparents_GM12750_DMSO_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM12750 treated with DMSO 8 hours.

source_name: Lymphoblastoid cell lines derived from GM12750


title: erStress_60grandparents_GM12264_DMSO_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM12264 treated with DMSO 8 hours.

source_name: Lymphoblastoid cell lines derived from GM12264


title: erStress_60grandparents_GM12716_DMSO_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM12716 treated with DMSO 8 hours.

source_name: Lymphoblastoid cell lines derived from GM12716


title: erStress_60grandparents_GM12751_DMSO_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM12751 treated with DMSO 8 hours.


title: erStress_60grandparents_GM12248_DMSO_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM12248 treated with DMSO 8 hours.

source_name: Lymphoblastoid cell lines derived from GM12248


title: erStress_60grandparents_GM12156_DMSO_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM12156 treated with DMSO 8 hours.

source_name: Lymphoblastoid cell lines derived from GM12156


title: erStress_60grandparents_GM12155_DMSO_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM12155 treated with DMSO 8 hours.

source_name: Lymphoblastoid cell lines derived from GM12155


title: erStress_60grandparents_GM12249_DMSO_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM12249 treated with DMSO 8 hours.

source_name: Lymphoblastoid cell lines derived from GM12249


title: erStress_60grandparents_GM12239_4_ug_ml_tunicamycin_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM12239 treated with 4 ug/ml tunicamycin 8 hours.

source_name: Lymphoblastoid cell lines derived from GM12239


title: erStress_60grandparents_GM12236_4_ug_ml_tunicamycin_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM12236 treated with 4 ug/ml tunicamycin 8 hours.

source_name: Lymphoblastoid cell lines derived from GM12236


title: erStress_60grandparents_GM12716_4_ug_ml_tunicamycin_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM12716 treated with 4 ug/ml tunicamycin 8 hours.


title: erStress_60grandparents_GM12249_4_ug_ml_tunicamycin_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM12249 treated with 4 ug/ml tunicamycin 8 hours.


title: erStress_60grandparents_GM12236_DMSO_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM12236 treated with DMSO 8 hours.


title: erStress_60grandparents_GM12239_DMSO_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM12239 treated with DMSO 8 hours.


title: erStress_60grandparents_GM12155_4_ug_ml_tunicamycin_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM12155 treated with 4 ug/ml tunicamycin 8 hours.


title: erStress_60grandparents_GM12234_DMSO_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM12234 treated with DMSO 8 hours.

source_name: Lymphoblastoid cell lines derived from GM12234


title: erStress_60grandparents_GM12154_DMSO_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM12154 treated with DMSO 8 hours.

source_name: Lymphoblastoid cell lines derived from GM12154


title: erStress_60grandparents_GM12248_4_ug_ml_tunicamycin_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM12248 treated with 4 ug/ml tunicamycin 8 hours.


title: erStress_60grandparents_GM12264_4_ug_ml_tunicamycin_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM12264 treated with 4 ug/ml tunicamycin 8 hours.


title: erStress_60grandparents_GM12717_DMSO_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM12717 treated with DMSO 8 hours.


title: erStress_60grandparents_GM12156_4_ug_ml_tunicamycin_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM12156 treated with 4 ug/ml tunicamycin 8 hours.


title: erStress_60grandparents_GM12146_DMSO_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM12146 treated with DMSO 8 hours.

source_name: Lymphoblastoid cell lines derived from GM12146


title: erStress_60grandparents_GM12234_4_ug_ml_tunicamycin_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM12234 treated with 4 ug/ml tunicamycin 8 hours.


title: erStress_60grandparents_GM12144_4_ug_ml_tunicamycin_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM12144 treated with 4 ug/ml tunicamycin 8 hours.

source_name: Lymphoblastoid cell lines derived from GM12144


title: erStress_60grandparents_GM12057_4_ug_ml_tunicamycin_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM12057 treated with 4 ug/ml tunicamycin 8 hours.

source_name: Lymphoblastoid cell lines derived from GM12057


title: erStress_60grandparents_GM12144_DMSO_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM12144 treated with DMSO 8 hours.


title: erStress_60grandparents_GM12145_DMSO_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM12145 treated with DMSO 8 hours.

source_name: Lymphoblastoid cell lines derived from GM12145


title: erStress_60grandparents_GM12057_DMSO_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM12057 treated with DMSO 8 hours.


title: erStress_60grandparents_GM12056_DMSO_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM12056 treated with DMSO 8 hours.

source_name: Lymphoblastoid cell lines derived from GM12056


title: erStress_60grandparents_GM12044_4_ug_ml_tunicamycin_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM12044 treated with 4 ug/ml tunicamycin 8 hours.

source_name: Lymphoblastoid cell lines derived from GM12044


title: erStress_60grandparents_GM12043_DMSO_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM12043 treated with DMSO 8 hours.

source_name: Lymphoblastoid cell lines derived from GM12043


title: erStress_60grandparents_GM12154_4_ug_ml_tunicamycin_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM12154 treated with 4 ug/ml tunicamycin 8 hours.


title: erStress_60grandparents_GM12146_4_ug_ml_tunicamycin_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM12146 treated with 4 ug/ml tunicamycin 8 hours.


title: erStress_60grandparents_GM12056_4_ug_ml_tunicamycin_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM12056 treated with 4 ug/ml tunicamycin 8 hours.


title: erStress_60grandparents_GM12145_4_ug_ml_tunicamycin_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM12145 treated with 4 ug/ml tunicamycin 8 hours.


title: erStress_60grandparents_GM12044_DMSO_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM12044 treated with DMSO 8 hours.


title: erStress_60grandparents_GM12043_4_ug_ml_tunicamycin_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM12043 treated with 4 ug/ml tunicamycin 8 hours.


title: erStress_60grandparents_GM12003_DMSO_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM12003 treated with DMSO 8 hours.

source_name: Lymphoblastoid cell lines derived from GM12003


title: erStress_60grandparents_GM11994_4_ug_ml_tunicamycin_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM11994 treated with 4 ug/ml tunicamycin 8 hours.

source_name: Lymphoblastoid cell lines derived from GM11994


title: erStress_60grandparents_GM11995_DMSO_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM11995 treated with DMSO 8 hours.

source_name: Lymphoblastoid cell lines derived from GM11995


title: erStress_60grandparents_GM12005_4_ug_ml_tunicamycin_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM12005 treated with 4 ug/ml tunicamycin 8 hours.

source_name: Lymphoblastoid cell lines derived from GM12005


title: erStress_60grandparents_GM12003_4_ug_ml_tunicamycin_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM12003 treated with 4 ug/ml tunicamycin 8 hours.


title: erStress_60grandparents_GM12006_4_ug_ml_tunicamycin_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM12006 treated with 4 ug/ml tunicamycin 8 hours.

source_name: Lymphoblastoid cell lines derived from GM12006


title: erStress_60grandparents_GM12006_DMSO_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM12006 treated with DMSO 8 hours.


title: erStress_60grandparents_GM11993_4_ug_ml_tunicamycin_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM11993 treated with 4 ug/ml tunicamycin 8 hours.

source_name: Lymphoblastoid cell lines derived from GM11993


title: erStress_60grandparents_GM11992_4_ug_ml_tunicamycin_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM11992 treated with 4 ug/ml tunicamycin 8 hours.

source_name: Lymphoblastoid cell lines derived from GM11992


title: erStress_60grandparents_GM12004_4_ug_ml_tunicamycin_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM12004 treated with 4 ug/ml tunicamycin 8 hours.

source_name: Lymphoblastoid cell lines derived from GM12004


title: erStress_60grandparents_GM12004_DMSO_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM12004 treated with DMSO 8 hours.


title: erStress_60grandparents_GM11881_DMSO_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM11881 treated with DMSO 8 hours.

source_name: Lymphoblastoid cell lines derived from GM11881


title: erStress_60grandparents_GM11995_4_ug_ml_tunicamycin_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM11995 treated with 4 ug/ml tunicamycin 8 hours.


title: erStress_60grandparents_GM11840_4_ug_ml_tunicamycin_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM11840 treated with 4 ug/ml tunicamycin 8 hours.

source_name: Lymphoblastoid cell lines derived from GM11840


title: erStress_60grandparents_GM11881_4_ug_ml_tunicamycin_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM11881 treated with 4 ug/ml tunicamycin 8 hours.


title: erStress_60grandparents_GM11994_DMSO_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM11994 treated with DMSO 8 hours.


title: erStress_60grandparents_GM11840_DMSO_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM11840 treated with DMSO 8 hours.


title: erStress_60grandparents_GM12005_DMSO_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM12005 treated with DMSO 8 hours.


title: erStress_60grandparents_GM11993_DMSO_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM11993 treated with DMSO 8 hours.


title: erStress_60grandparents_GM11992_DMSO_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM11992 treated with DMSO 8 hours.


title: erStress_60grandparents_GM11882_4_ug_ml_tunicamycin_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM11882 treated with 4 ug/ml tunicamycin 8 hours.

source_name: Lymphoblastoid cell lines derived from GM11882


title: erStress_60grandparents_GM11839_4_ug_ml_tunicamycin_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM11839 treated with 4 ug/ml tunicamycin 8 hours.

source_name: Lymphoblastoid cell lines derived from GM11839


title: erStress_60grandparents_GM11882_DMSO_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM11882 treated with DMSO 8 hours.


title: erStress_60grandparents_GM11831_DMSO_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM11831 treated with DMSO 8 hours.

source_name: Lymphoblastoid cell lines derived from GM11831


title: erStress_60grandparents_GM11839_DMSO_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM11839 treated with DMSO 8 hours.


title: erStress_60grandparents_GM11830_DMSO_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM11830 treated with DMSO 8 hours.

source_name: Lymphoblastoid cell lines derived from GM11830


title: erStress_60grandparents_GM11832_4_ug_ml_tunicamycin_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM11832 treated with 4 ug/ml tunicamycin 8 hours.

source_name: Lymphoblastoid cell lines derived from GM11832


title: erStress_60grandparents_GM11832_DMSO_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM11832 treated with DMSO 8 hours.


title: erStress_60grandparents_GM11830_4_ug_ml_tunicamycin_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM11830 treated with 4 ug/ml tunicamycin 8 hours.


title: erStress_60grandparents_GM07357_DMSO_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM07357 treated with DMSO 8 hours.

source_name: Lymphoblastoid cell lines derived from GM07357


title: erStress_60grandparents_GM07345_DMSO_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM07345 treated with DMSO 8 hours.

source_name: Lymphoblastoid cell lines derived from GM07345


title: erStress_60grandparents_GM11829_DMSO_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM11829 treated with DMSO 8 hours.

source_name: Lymphoblastoid cell lines derived from GM11829


title: erStress_60grandparents_GM07056_4_ug_ml_tunicamycin_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM07056 treated with 4 ug/ml tunicamycin 8 hours.

source_name: Lymphoblastoid cell lines derived from GM07056


title: erStress_60grandparents_GM11829_4_ug_ml_tunicamycin_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM11829 treated with 4 ug/ml tunicamycin 8 hours.


title: erStress_60grandparents_GM07034_4_ug_ml_tunicamycin_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM07034 treated with 4 ug/ml tunicamycin 8 hours.

source_name: Lymphoblastoid cell lines derived from GM07034


title: erStress_60grandparents_GM07055_DMSO_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM07055 treated with DMSO 8 hours.

source_name: Lymphoblastoid cell lines derived from GM07055


title: erStress_60grandparents_GM07055_4_ug_ml_tunicamycin_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM07055 treated with 4 ug/ml tunicamycin 8 hours.


title: erStress_60grandparents_GM07000_4_ug_ml_tunicamycin_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM07000 treated with 4 ug/ml tunicamycin 8 hours.

source_name: Lymphoblastoid cell lines derived from GM07000


title: erStress_twins_AA_1717twin2_DMSO_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1717:2 treated with DMSO.

source_name: Lymphoblastoid cell lines derived from family 1717, member 2


title: erStress_60grandparents_GM07034_DMSO_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM07034 treated with DMSO 8 hours.


title: erStress_60grandparents_GM07056_DMSO_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM07056 treated with DMSO 8 hours.


title: erStress_60grandparents_GM06994_4_ug_ml_tunicamycin_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM06994 treated with 4 ug/ml tunicamycin 8 hours.

source_name: Lymphoblastoid cell lines derived from GM06994


title: erStress_60grandparents_GM07022_DMSO_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM07022 treated with DMSO 8 hours.

source_name: Lymphoblastoid cell lines derived from GM07022


title: erStress_60grandparents_GM06993_DMSO_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM06993 treated with DMSO 8 hours.

source_name: Lymphoblastoid cell lines derived from GM06993


title: erStress_60grandparents_GM06994_DMSO_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM06994 treated with DMSO 8 hours.


title: 6.5% ethanol replicate 3

city: East Geelong

first: Dragana

last: Stanley

state: Victoria

address: 5 Portarlington Rd

department: AAHL

country: Australia

institute: CSIRO

description: normal dye direction (sample red, pool green)

hyb_protocol: Quigene purified labeled samples were resuspended in Hybing solution containing 10 mg ml-1 of yeast tRNA and 10 mg ml-1 of Samon sperm DNA in Dig Easy Hyb solution (Roche)

scan_protocol: GenePix-Pro 4000B

data_processing: GenowizTM 4.0.2.1 software (Ocimum Biosolutions). Dye swapped samples were reversed by Genowiz software. Minimum normalized ratio was set to 0.01 (-100 fold) and maximum normalized ratio was set to 100.

label: AlexaFluor 647

organism: Saccharomyces cerevisiae

source_name: Total RNA from third culture grown at 6.5% ethanol

label_protocol: Invitrogen “SuperScript TM Plus Indirect cDNA Labeling Module” (#L1014-04) was used for both cDNA synthesis and labelling with the AlexaFluor (AF647/AF555) dyes that were also supplied in the kit.

growth_protocol: The strain used in this study was S. cerevisiae W303-1A (MATa leu2-3, 122 trp1-1 can1-100 ura 3-1 ade2-1 his3-11, 15), a haploid laboratory strain.  Cultures were cultivated in YEPD (20 g/l glucose, 20 g/l bactopeptone and 10 g/l yeast extract) at 30C and 110 rpm in the presence and absence of added ethanol.

extract_protocol: RNA was extracted from equal numbers of yeast cells using the glass bead extraction method, essentially as described by Collart and Oliviero (1997), followed by DNase treatment using the Ambion DNA-FreeTM

treatment_protocol: Inoculum from unstressed late exponentioal parent culture was added to 3 separate cultures containing 0% ethanol and to other 3 cultures containing 6.5% ethanol.

tag: test

value: ethanol stressed culture 3

label: AlexaFluor 555

source_name: Total RNA made by pooling Total RNA extracted from 3 cultures grown at 0% ethanol

tag: reference

value: 0% ethanol reference pool


title: erStress_60grandparents_GM07000_DMSO_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM07000 treated with DMSO 8 hours.


title: erStress_60grandparents_GM07345_4_ug_ml_tunicamycin_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM07345 treated with 4 ug/ml tunicamycin 8 hours.


title: erStress_60grandparents_GM07357_4_ug_ml_tunicamycin_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM07357 treated with 4 ug/ml tunicamycin 8 hours.


title: erStress_60grandparents_GM07022_4_ug_ml_tunicamycin_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM07022 treated with 4 ug/ml tunicamycin 8 hours.


title: 6.5% ethanol replicate 2

source_name: Total RNA from second culture grown at 6.5% ethanol

value: ethanol stressed culture 2


title: erStress_60grandparents_GM06985_DMSO_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM06985 treated with DMSO 8 hours.

source_name: Lymphoblastoid cell lines derived from GM06985


title: erStress_60grandparents_GM06985_4_ug_ml_tunicamycin_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM06985 treated with 4 ug/ml tunicamycin 8 hours.


title: erStress_60grandparents_GM06993_4_ug_ml_tunicamycin_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM06993 treated with 4 ug/ml tunicamycin 8 hours.


title: 0% ethanol replicate 2

source_name: Total RNA from second culture grown at 0% ethanol

value: non stressed culture 2


title: 6.5% ethanol replicate 1

description: dye swapped experiment with pool labeled red

source_name: Total RNA from first culture grown at 6.5% ethanol

value: ethanol stressed culture 1


title: 0% ethanol replicate 3

source_name: Total RNA from third culture grown at 0% ethanol

value: non stressed culture 3


title: TN4b-control

city: Ann Arbor

first: Preethi

last: Sankaranarayanan

state: MI

address: 1552 MSRB2,1150 W. Medical Center Drive

department: Department of Internal Medicine - Division of Nephrology

institute: University of Michigan

description: Gene expression data from glomeruli of patient after Tumor Nephrectomy - this serves as control.

hyb_protocol: Affymetrix Expression Analysis Technical Manual protocol was followed

data_processing: RMA-Express was used for normalization and Genepattern and Genomatix software suites were used for statistical analysis

source_name: kidney biopsy from patient after Tumor Nephrectomy

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

extract_protocol: Silica Gel column extraction of total RNA was performed according to the manufacturer's instructions.(Agilent Technologies, Waldbronn, Germany)Total RNA was isolated from microdissected  glomeruli, reverse-transcribed, and linearly amplified.

tag: tissue

value: glomeruli of human kidney

tag: disease state

value: control


title: NSC15

description: Gene expression data from glomeruli of patient with Nephrosclerosis.

scan_protocol: Affymetrix Expression Analysis Technical Manual protocol was followed

source_name: kidney biopsy from patient with NSC

value: nephrosclerosis


title: TN2b-control


title: NSC16


title: TN3b-control


title: NSC13


title: NSC18


title: NSC8


title: NSC11


title: NSC6


title: NSC5


title: NSC7


title: TN1b-control


title: NSC14


title: Bone Marrow Stromal Cells vs. Repair Tissue Comparison 3

city: Lexington

first: Michael

middle: J.

last: Mienaltowski

email: M.Mski@uky.edu, mmienalt@health.usf.edu

state: KY

address: 108 Gluck Equine Research Center

department: Veterinary Science

institute: University of Kentucky

description:
This "sample" represents an average of two dye swap slides. The actual channel assignments were as follows:
Source_name_ch1 = Horse R8 repair tissue 532
Source_name_ch2 = Horse 3 BMSCs 635
Source_name_ch1 = Horse 3 BMSCs 532
Source_name_ch2 = Horse R8 repair tissue 635

hyb_protocol: Samples were labeled with an indirect labeling protocol using amino-allyl dUTP and hybridized 48 hours at 42C.

scan_protocol: DyeSaver2 was applied each slide with one dip. Slides were scanned with a Molecular Devices GenePix Personal 4100A Scanner using GenePix Pro 5.0.

data_processing: Data analyzed by planned linear contrast, followed by SAS-based one sample t-test.

label: AlexaFluor555, AlexaFluor647

organism: Equus caballus

source_name: Bone Marrow Stromal Cells (Horse 3)

label_protocol: Invitrogen Indirect PLUS Labeling

extract_protocol: Amplified RNA from total RNA

tag: Bone marrow stromal cells isolated from Thoroughbred Horse #3 and expanded to monolayer confluence.

label: AlexaFluor647, AlexaFluor555

source_name: Repair Tissue (R8)

tag: Articular repair tissue from stifles of an adult Quarterhorse ("R8")


title: Bone Marrow Stromal Cells vs. Repair Tissue Comparison 4

description:
This "sample" represents an average of two dye swap slides. The actual channel assignments were as follows:
Source_name_ch1 = Horse R9 repair tissue 532
Source_name_ch2 = Horse 4 BMSCs 635
Source_name_ch1 = Horse 4 BMSCs 532
Source_name_ch2 = Horse R9 repair tissue 635

source_name: Bone Marrow Stromal Cells (Horse 4)

tag: Bone marrow stromal cells isolated from Thoroughbred Horse #4 and expanded to monolayer confluence.

source_name: Repair Tissue (R9)

tag: Articular repair tissue from stifles of an adult Quarterhorse ("R9")


title: NSC12


title: Neonatal Articular Cartilage vs. Repair Tissue Comparison 4

description:
This "sample" represents an average of two dye swap slides. The actual channel assignments were as follows:
Source_name_ch1 = Horse R9 repair tissue 532
Source_name_ch2 = Foal 8 articular cartilage 635
Source_name_ch1 = Foal 8 articular cartilage 532
Source_name_ch2 = Horse R9 repair tissue 635

source_name: Neonatal Articular Cartilage (Foal 8)

tag: Articular cartilage from neonatal Thoroughbred ("Foal 8")


title: NSC4


title: Bone Marrow Stromal Cells vs. Repair Tissue Comparison 1

description:
This "sample" represents an average of two dye swap slides. The actual channel assignments were as follows:
Source_name_ch1 = Horse R5 repair tissue 532
Source_name_ch2 = Horse 1 BMSCs 635
Source_name_ch1 = Horse 1 BMSCs 532
Source_name_ch2 = Horse R5 repair tissue 635

source_name: Bone Marrow Stromal Cells (Horse 1)

tag: Bone marrow stromal cells isolated from Thoroughbred Horse #1 and expanded to monolayer confluence.

source_name: Repair Tissue (R5)

tag: Articular repair tissue from stifles of an adult Quarterhorse ("R5")


title: Bone Marrow Stromal Cells vs. Repair Tissue Comparison 2

description:
This "sample" represents an average of two dye swap slides. The actual channel assignments were as follows:
Source_name_ch1 = Horse R7 repair tissue 532
Source_name_ch2 = Horse 2 BMSCs 635
Source_name_ch1 = Horse 2 BMSCs 532
Source_name_ch2 = Horse R7 repair tissue 635

source_name: Bone Marrow Stromal Cells (Horse 2)

tag: Bone marrow stromal cells isolated from Thoroughbred Horse #2 and expanded to monolayer confluence.

source_name: Repair Tissue (R7)

tag: Articular repair tissue from stifles of an adult Quarterhorse ("R7")


title: Neonatal Articular Cartilage vs. Repair Tissue Comparison 2

description:
This "sample" represents an average of two dye swap slides. The actual channel assignments were as follows:
Source_name_ch1 = Horse R7 repair tissue 532
Source_name_ch2 = Foal 2 articular cartilage 635
Source_name_ch1 = Foal 2 articular cartilage 532
Source_name_ch2 = Horse R7 repair tissue 635

source_name: Neonatal Articular Cartilage (Foal 2)

tag: Articular cartilage from neonatal Thoroughbred ("Foal 2")


title: NSC1


title: 0% ethanol replicate 1

source_name: Total RNA made by pooling Total RNA extracted from 3 cultures grown at 0% ethanol

source_name: Total RNA from first culture grown at 0% ethanol

value: non stressed culture 1


title: Neonatal Articular Cartilage vs. Repair Tissue Comparison 3

description:
This "sample" represents an average of two dye swap slides. The actual channel assignments were as follows:
Source_name_ch1 = Horse R8 repair tissue 532
Source_name_ch2 = Foal 4 articular cartilage 635
Source_name_ch1 = Foal 4 articular cartilage 532
Source_name_ch2 = Horse R8 repair tissue 635

source_name: Neonatal Articular Cartilage (Foal 4)

tag: Articular cartilage from neonatal Thoroughbred ("Foal 4")


title: Neonatal Articular Cartilage vs. Repair Tissue Comparison 1

description:
This "sample" represents an average of two dye swap slides. The actual channel assignments were as follows:
Source_name_ch1 = Horse R5 repair tissue 532
Source_name_ch2 = Foal 1 articular cartilage 635
Source_name_ch1 = Foal 1 articular cartilage 532
Source_name_ch2 = Horse R5 repair tissue 635

source_name: Neonatal Articular Cartilage (Foal 1)

tag: Articular cartilage from neonatal Thoroughbred ("Foal 1")


title: NSC2


title: De-differentiated Chondrocytes vs. Repair Tissue Comparison 4

description:
This "sample" represents an average of two dye swap slides. The actual channel assignments were as follows:
Source_name_ch1 = Horse R9 repair tissue 532
Source_name_ch2 = Star DDC 635
Source_name_ch1 = Star DDC 532
Source_name_ch2 = Horse R9 repair tissue 635

source_name: De-differentiated Chondrocytes ("Star")

tag: Chondrocytes isolated from adult Thoroughbred and maintained in monolayer culture with 3 passages over 28 days.


title: De-differentiated Chondrocytes vs. Repair Tissue Comparison 1

description:
This "sample" represents an average of two dye swap slides. The actual channel assignments were as follows:
Source_name_ch1 = Horse R5 repair tissue 532
Source_name_ch2 = Blaze DDC 635
Source_name_ch1 = Blaze DDC 532
Source_name_ch2 = Horse R5 repair tissue 635


title: Rp22 Vs Erus replicate 3

status: Public on Mar 29 2010

city: Marseille

first: LEROY

last: Quentin

address: 27 Boulevard Jean Moulin

country: France

institute: URMITE

description: Comparison of biological replicate 3

hyb_protocol: Hybridizations were performed for 17 h at 60°C in dedicated microchambers with 50 pmol of both control or eschar samples. Stringent washings were then performed according to manufacturer’s instructions.

scan_protocol: Slides were scanned with XDR range at a 5-µm resolution. Feature Extractor 7.1 (Agilent Technologies) was used for image analysis.

data_processing: Data filtering and normalisation were then performed using the Midas module of TM4. The background-subtracted signals were normalised by local substraction method, and intensity signals were normalised by global lowess method. Normalised signals were used for analysis with the TMev module of TM4.

organism: Rickettsia prowazekii str. Rp22

source_name: Rp22 replicate 3

label_protocol: Twenty nanograms of cDNA were amplified using the GenomiPhi DNA amplication kit (Amersham Biosciences, Uppsala, Sweden) and labeled with Cy3-dCTP or Cy5-dCTP dyes (Amersham Biosciences) using the BioPrime DNA labeling System (Invitrogen, Cergy-Pontoise, France). Following purification with Qiaquick columns (Qiagen), the levels of Cy3-dCTP and Cy5-dCTP incorporation were quantified by absorbance measurement at 550 nm and 650 nm, respectively.

growth_protocol: Growth in L929 at 32°C with EMEM medium with 4% SVF and 1% L-glutamine

extract_protocol: Total RNA extraction and purification from purified bacteria was carried out using the RNeasy kit (Qiagen) with some modifications. Briefly, pellet of bacteria were resuspended with 100µl of TE + Lyzoyme (10mg/ml) and incubated for 10 min at RT.Then The amount and quality of obtained RNA were determined with the microfluidic-based platform (Agilent 2100 Bioanalyzer) and using the RNA 6000 Nano Labchip kit (Agilent). cDNA was synthesized as described by La et al. (2008) using the M-MLV Reverse Transcriptase (Invitrogen, Cergy-Pontoise, France).

tag: Purifed bacteria by lysing the infected cells with 1% trypsin and cell debris were eliminated by successive centrifugations at 1000 rpm. Bacteria were stored at -80°C before RNA extraction

organism: Rickettsia prowazekii

source_name: Erus replicate 3


title: De-differentiated Chondrocytes vs. Repair Tissue Comparison 2

description:
This "sample" represents an average of two dye swap slides. The actual channel assignments were as follows:
Source_name_ch1 = Horse R7 repair tissue 532
Source_name_ch2 = Felicity DDC 635
Source_name_ch1 = Felicity DDC 532
Source_name_ch2 = Horse R7 repair tissue 635


title: array Erus 2

first: Yassina

last: Bechah

address: 27 bd J. Moulin

institute: CNRS

description: HMEC endothelial cells  infected with R. prowazekii Erus strain

hyb_protocol: as recommanded by the manufacturer

scan_protocol: Slides were scanned at a 5-µm resolution with a G2505B DNA microarray scanner (Agilent)

data_processing:
Agilent Feature Extractor Software A.9.1.3 was used for image analysis. The microarray grid was automatically placed, outlier spots were flagged and feature intensities and backgrounds were accurately determined.
Further data processing was performed using Resolver software 7.1 (Rosetta Inpharmatics), and its error model-based transformation pipeline was used to map replicate reporters to genes and to normalise inter-array data sets. The fold change (FC) was calculated using pairs Erus vs. Control, Evir vs. Control and Rp22 vs. Control. Only genes that had an absolute FC over 2.0 (p<0.01) for at least one of them were considered to be regulated and kept for further statistical analysis.

source_name: Erus 2

label_protocol: Labelled cRNA was synthesised from cDNA using T7 RNA polymerase and cyanine 3-labeled CTP (Cy-3) fluorescent dyes with the One-Color Low RNA Input Linear Amplification KitPLUS (Agilent).

growth_protocol: Human endothelial cells (HMEC-1 cell line) were cultured in MCDB 131 medium (Gibco) supplemented with 10% of SVF and 1% of L-glutamine

extract_protocol: Total RNA was extracted using RNeasy Mini kit (Qiagen).

treatment_protocol: Human endothelial cells (HMEC-1 cell line) were infected with R. prowazekii Erus strain (50:1 bacterium-to-cell ratio) for 6 hours at 37°C.

tag: cell type

value: HMEC endothelial cells

tag: infection

value: R. prowazekii Erus strain


title: array Rp22 4

description: HMEC endothelial cells infected with R. prowazekii Rp22 strain

treatment_protocol: Human endothelial cells (HMEC-1 cell line) were infected with R. prowazekii Rp22 strain (50:1 bacterium-to-cell ratio) for 6 hours at 37°C.

value: R. prowazekii Rp22 strain


title: Rp22 Vs Erus replicate 2

description: Comparison of biological replicate 2

source_name: Rp22 replicate 2

source_name: Erus replicate 2

treatment_protocol: Total RNA extraction and purification from purified bacteria was carried out using the RNeasy kit (Qiagen) with some modifications. Briefly, pellet of bacteria were resuspended with 100µl of TE + Lyzoyme (10mg/ml) and incubated for 10 min at RT.Then The amount and quality of obtained RNA were determined with the microfluidic-based platform (Agilent 2100 Bioanalyzer) and using the RNA 6000 Nano Labchip kit (Agilent). cDNA was synthesized as described by La et al. (2008) using the M-MLV Reverse Transcriptase (Invitrogen, Cergy-Pontoise, France).


title: array Evir 1

description: HMEC endothelial cells  infected with R. prowazekii Evir strain

source_name: Evir 1

treatment_protocol: Human endothelial cells (HMEC-1 cell line) were infected with R. prowazekii Evir strain (50:1 bacterium-to-cell ratio) for 6 hours at 37°C.

value: R. prowazekii Evir strain


title: array Erus 4

source_name: Erus 4


title: array Evir 4

source_name: Evir 4


title: array Evir 2

source_name: Evir 2


title: array Erus 3

source_name: Erus 3


title: array controle 4

description: HMEC endothelial cells non infected with R. prowazekii strain

source_name: Controle 4

treatment_protocol: Human endothelial cells (HMEC-1 cell line) were infected or not with R. prowazekii (50:1 bacterium-to-cell ratio) for 6 hours at 37°C.


title: De-differentiated Chondrocytes vs. Repair Tissue Comparison 3

description:
This "sample" represents an average of two dye swap slides. The actual channel assignments were as follows:
Source_name_ch1 = Horse R8 repair tissue 532
Source_name_ch2 = Riches DDC 635
Source_name_ch1 = Riches DDC 532
Source_name_ch2 = Horse R8 repair tissue 635

source_name: Repair Tissue (R8)


title: array Rp22 2


title: Induced sputum, deficits in FEV1/FVC, Asthmatic child 18

city: Subiaco

first: Anthony

last: Bosco

state: WA

address: 100 Roberts Road

institute: Telethon Kids Institute

hyb_protocol: The samples were hybridized to HuGene ST1.0 microarrays according to standardized protocols and reagents from Affymetrix.

scan_protocol: The samples were scanned on a GeneChip® Scanner 3000 7G (Affymetrix).

data_processing: The microarray data were preprocessed in Expression Consol software (Affymetrix) employing the probe logarithmic intensity error algorithm (PLIER, parameters - PM-GCBG background subtraction, quantile normalization, iterPLIER summarization).

source_name: Induced sputum cells obtained during an exacerbation.

label_protocol: The samples were labelled according to standardized protocols and reagents from Affymetrix.

growth_protocol: Asthmatic children were instructed to visit the study center within 24 h of experiencing an exacerbation.

extract_protocol: Total RNA was extracted from total sputum cells using TRIzol followed by RNeasy.

treatment_protocol: Induced sputum cells were processed in 0.1 % Dithiothreitol on a shaking water bath at 37 °C for 15 minutes with intermittent aspiration via pipetting every 5 minutes.

tag: phenotype

value: Asthmatic child with deficits in FEV1/FVC


title: array Rp22 3


title: erStress_60grandparents_GM11831_4_ug_ml_tunicamycin_8_hours_rep1

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM11831 treated with 4 ug/ml tunicamycin 8 hours.

source_name: Lymphoblastoid cell lines derived from GM11831

tag: cell line

value: lymphoblastoid cell line

tag: coriell cell line repository identifier

tag: agent

value: tunicamycin

tag: dose

tag: time

value: 8 hours


title: array Rp22 1

treatment_protocol: Human endothelial cells (HMEC-1 cell line) were infected with R. prowazekii  Rp22 strain (50:1 bacterium-to-cell ratio) for 6 hours at 37°C.


title: array controle 2

source_name: Controle 2


title: array controle 3

source_name: Controle 3


title: Induced sputum, deficits in FEV1/FVC, Asthmatic child 19


title: array Erus 1

source_name: Erus 1


title: heart_RCS_rep5

city: Newark

first: Jiyeon

last: Park

state: NJ

address: 185 South Orange Ave.

department: Department of Cell Biology and Molecular Medicine

institute: Rutgers New Jersey Medical School

description: Gene expression data from RCS (repeating 6 episodes of 90 min coronary artery stenosis 12 hrs apart)

hyb_protocol: The Affymetrix arrays (Porcine Genome Array) were hybridized and washed using the manufacturer's protocol.

scan_protocol: Affymetrix arrays were scanned with the Affymetrix GeneArray scanner.

data_processing: The microarray data were normalized using the Robust Multichip Average (RMA) method. We discarded probe sets that did not have signals above background in more than 75% of the arrays for all samples using the Affymetrix MAS5 present/absent calls.

organism: Sus scrofa

source_name: pig heart in RCS

label_protocol: cDNA synthesis (SuperScript, Invitrogen) was performed from 10 μg total RNA with a T7-oligo(24)dT primer. The DNA was transcribed into biotin-labeled RNA (Bioarray RNA Labeling Kit, ENZO)

growth_protocol: No growth protocol. Samples were taken from animals in vivo.

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

treatment_protocol: No treatment prior to experiment was applied.

tag: tissue

value: heart

tag: gender

value: female

tag: protocol

value: RCS


title: Induced sputum, deficits in FEV1/FVC, Asthmatic child 20


title: Induced sputum, deficits in FEV1/FVC, Asthmatic child 16


title: Induced sputum, deficits in FEV1/FVC, Asthmatic child 14


title: Induced sputum, deficits in FEV1/FVC, Asthmatic child 15


title: heart_RCS_rep3


title: Induced sputum, deficits in FEV1/FVC, Asthmatic child 12


title: heart_RCS_rep1


title: heart_RCS_rep2


title: heart_SWOP_rep3

description: Gene expression data from SWOP (two 10 min episodes of coronary artery occlusion followed by 24 hr reperfusion)

source_name: pig heart in SWOP

value: SWOP


title: Induced sputum, deficits in FEV1/FVC, Asthmatic child 13


title: heart_SWOP_rep2


title: heart_SWOP_rep1


title: heart_SWOP_rep4


title: Induced sputum, normal FEV1/FVC, Asthmatic child 08

value: Asthmatic child with normal FEV1/FVC


title: heart_RCS_rep4


title: Rp22 Vs Erus replicate 1

description: Comparison of biological replicate 1

source_name: Rp22 replicate 1

source_name: Erus replicate 1


title: Induced sputum, normal FEV1/FVC, Asthmatic child 10


title: Induced sputum, normal FEV1/FVC, Asthmatic child 06


title: Induced sputum, normal FEV1/FVC, Asthmatic child 09


title: Induced sputum, deficits in FEV1/FVC, Asthmatic child 11


title: array controle 1

source_name: Controle 1


title: array Evir 3

source_name: Evir 3


title: Induced sputum, normal FEV1/FVC, Asthmatic child 07


title: heart_RCO_rep4

description: Gene expression data from RCO (repeating 6 episodes of 10 min coronary artery occlusion 12 hrs apart)

source_name: pig heart in RCO

value: RCO


title: heart_RCO_rep2


title: heart_RCO_rep5


title: heart_RCO_rep3


title: heart_control_rep5

description: Gene expression data from Control (sham-operated)

source_name: pig heart in sham operation

value: control


title: heart_RCO_rep1


title: Induced sputum, normal FEV1/FVC, Asthmatic child 03


title: Induced sputum, normal FEV1/FVC, Asthmatic child 02


title: Induced sputum, normal FEV1/FVC, Asthmatic child 01


title: Induced sputum, normal FEV1/FVC, Asthmatic child 04


title: heart_SWOP_rep5


title: heart_control_rep2


title: heart_control_rep4


title: Calvaria_WT5

status: Public on Mar 27 2010

city: Jacksonville

first: Yan

middle: W.

last: Asmann

state: FL

address: 4500 San Pablo Road South

institute: Mayo Clinic

hyb_protocol: The single-stranded PCR product was hybridized to the Ilumina Mouseref-8 Beadchip, where the labelled strand binds to the bead on the array containing the complementary address sequence

scan_protocol: Illumina BeadArray Reader

data_processing: Gene level expression values were exported from BeadStudio without normalization nor background subtraction.

organism: Mus musculus

label_protocol: Varying amounts of total RNA were polyadenylated and then converted to cDNA using a biotinylated oligo-dT primer with a universal PCR sequence at its 5’ end.  This was followed by annealing of a miRNA-specific oligonucleotide pool (MSO) which consists of three parts: a universal PCR priming site at the 5’ end, an address sequence complementary to a capture sequence on the BeadArray and a microRNA-specific sequence at the 3’ end.  Extension of MSO was facilitated by addition of a polymerase, but only if their 3’ bases were complementary to the cognate sequence in the cDNA template.  Common primers were used to amplify the cDNA templates; the primer complimentary to the BeadArray was fluorescently labelled.

growth_protocol: Calvarial samples were extracted from decapitated mice, digested for 20 minutes with collegenase under standard conditions, rinsed, frozen at -80.

extract_protocol: Total RNA was extracted using Trizol® LS (Invitrogen, Corp., Carlsbad, CA).

value: calvaria

tag: age

value: 5 days postnatal

tag: genotype/variation

value: Wildtype

tag: litter pair


title: Calvaria_KO2

value: Conditional Osterix-Cre Null


title: Calvaria_KO1


title: Calvaria_KO6


title: Calvaria_KO5


title: Calvaria_KO7


title: heart_control_rep3


title: Induced sputum, deficits in FEV1/FVC, Asthmatic child 17


title: Calvaria_KO3


title: Calvaria_KO4


title: Calvaria_KO8


title: heart_control_rep1


title: Calvaria_WT6


title: Calvaria_WT7


title: Calvaria_WT3


title: Calvaria_WT8


title: Calvaria_WT2


title: Calvaria_WT4


title: RAW 264.7 cells

city: Northbrook

last: Falduto

state: IL

address: 1808 Janke, Unit M

institute: GenUs BioSystems, Inc.

hyb_protocol: 1 µg of purified cRNA was fragmented to uniform size and applied to Agilent Whole Mouse Genome microarrays (Agilent Technologies, Santa Clara, CA) in hybridization buffer. Arrays were hybridized at 65° C for 17 hrs. in a rotating incubator, washed at 37° C for 1 min, and stained with Streptavidin-Alexa555.

scan_protocol: Rinsed and dried arrays were scanned with an Agilent G2565 Microarray Scanner (Agilent Technologies, Santa Clara, CA) at 5 µm resolution.

data_processing: Agilent Feature Extraction software was used to process the scanned images from arrays (gridding and feature intensity extraction) and the data generated for each probe on the array was analyzed with GeneSpring GX v7.3.1 software (Agilent Technologies, Santa Clara, CA). Intensity values are normalized to the 75th percentile intensity of each array.

source_name: RAW 264.7 cells

label_protocol: First and second strand cDNA was prepared from the total RNA samples. cRNA target was prepared from the DNA template and verified on the Bioanalyzer.  cRNA was fragmented to uniform size and verified on the Bioanalyzer.

growth_protocol: RAW 264.7 cells were cultured with DMEM containing 10% FBS.

extract_protocol: Total RNA was isolated using RNAzol reagent (Biotecx Labs, Houston, TX) from ground based control (Xg) and microgravity (μXg) stimulated with RANKL.

treatment_protocol: RAW 264.7 cells (1.5 x 106 /ml) were loaded in RCCS with DMEM containing 10% FBS for 24 h. The cells were stimulated with RANKL (80 ng/ml) for 24 h in parallel with ground based control cells.

tag: treatment group


title: Primary bladder cancer BT148

status: Public on Mar 26 2010

city: Daejeon

first: Seon-Kyu

last: Kim

address: 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Korea

department: Personalized Genomic Medicine Research Center

country: South Korea

institute: Korea Research Institutue of Bioscience & Biotechnology

description: To export to gene expression data based on unique gene, we use Sample Gene Profile option of Illumina BeadStudio software.  Therefore, a total of 5553 probe data which have duplicated gene aggregated unique genes from the whole 48701 probes on the Human-6 beadChip ver. 2.

hyb_protocol: Labeled, amplified material (1,500 ng per array) was hybridized to a ver. 2 of the Illumina Human-6 BeadChip (48K) according to the Manufacturer's instructions (Illumina, Inc., San Diego, CA). Array signals were developed by Amersham fluorolink streptavidin-Cy3 (GE Healthcare Bio-Sciences, Little Chalfont, UK) following the BeadChip manual.

scan_protocol: Arrays were scanned with an Illumina Bead array Reader confocal scanner (BeadStation 500GXDW; Illumina, Inc., San Diego, CA) according to the Manufacturer's instructions.

data_processing: Array data processing were performed on Illumina BeadStudio software. We normalized gene expression data using Quantile normalization and log2 transformatoin. To export to a data matrix, Sample Gene Profile option of this software was used.

source_name: Primary bladder cancer

label_protocol: Biotin-labeled cRNA samples for hybridization were prepared according to Illumina’s recommended sample labeling procedure: 500 ng of total RNA was used for cDNA synthesis, followed by an amplification/labeling step (in vitro transcription) to synthesize biotin-labeled cRNA using the Illumina® TotalPrep RNA Amplification kit (Ambion Inc., Austin, TX). cRNA concentrations using RiboGreen were measured (Quant-iTTM RiboGreen® RNA assay kit; Invitrogen-Molecular Probes, ON, Canada) by the Victor3 spectrophotometer (PerkinElmer, CT) and cRNA quality was checked on a 1% agarose gel.

extract_protocol: Total RNA was isolated from tissues with TRIzol (Life Technologies, NY) reagent according to the manufacturer’s protocol. RNA quality and integrity were confirmed by electrophoresis on agarose gel stained with ethidium bromide and examined under ultraviolet light.

tag: biological source

value: primary bladder cancer

tag: SEX

value: M

tag: AGE

tag: invasiveness

value: non-muscle invasive

tag: intravesical therapy

value: Yes

tag: systemic chemo

value: No

tag: grade

value: low

tag: recurrence

tag: progression

tag: overall survival

value: survival

tag: cancer specific survival

tag: survival month


title: RAW 264.7 cells_RCCS_24hrs

tag: cell line

value: RCCS


title: Primary bladder cancer BT151


title: Primary bladder cancer BT146


title: Primary bladder cancer BT137

value: death


title: Primary bladder cancer BT141

value: high


title: Primary bladder cancer BT152


title: Primary bladder cancer BT134


title: Primary bladder cancer BT138


title: Calvaria_WT1

tag: tissue

tag: age


title: Primary bladder cancer BT140


title: Primary bladder cancer BT139

value: F


title: Primary bladder cancer BT132


title: Primary bladder cancer BT109


title: Primary bladder cancer BT114


title: Primary bladder cancer BT133


title: Primary bladder cancer BT104


title: Primary bladder cancer BT087


title: Primary bladder cancer BT116


title: Primary bladder cancer BT113


title: Primary bladder cancer BT107


title: Primary bladder cancer BT082


title: Primary bladder cancer BT083


title: Primary bladder cancer BT119


title: Primary bladder cancer BT079


title: Primary bladder cancer BT094


title: Primary bladder cancer BT084


title: Primary bladder cancer BT085


title: Primary bladder cancer BT078


title: Primary bladder cancer BT075


title: Primary bladder cancer BT067


title: Primary bladder cancer BT059


title: Primary bladder cancer BT063


title: Primary bladder cancer BT046


title: Primary bladder cancer BT053


title: Primary bladder cancer BT055


title: Primary bladder cancer BT051


title: Primary bladder cancer BT047


title: Primary bladder cancer BT062


title: Primary bladder cancer BT023


title: Primary bladder cancer BT034


title: Primary bladder cancer BT038


title: Primary bladder cancer BT042


title: Primary bladder cancer BT039


title: Primary bladder cancer BT004


title: Primary bladder cancer BT017


title: Primary bladder cancer BT028


title: Induced sputum, normal FEV1/FVC, Asthmatic child 05

tag: phenotype

value: Asthmatic child with normal FEV1/FVC


title: Patient_52 (miRNA)

city: Little Rock

first: Yiming

last: Zhou

state: AR

address: 4301 West Markham St., Slot 776

institute: Myeloma Institute for Research and Therapy

description: miRNA expression of CD138 selected plasma cells

data_processing:
Purified miRNA was hybridized to the Human miRNA Microarray platform (Agilent, Santa Clara, CA) following the Agilent version 2.0 protocol (June 2008) explicitly for target labeling, hybridization, washing, scanning, and image analysis.
Total gene signal from GeneView data files, which were extracted using default miRNA settings in Agilent Feature Extraction (v9.5.x), was used as signal for miRNAs. We took advantage of spiked-in controls spotted in Agilent's platform, which were external references and served as microarray controls in the hybridization protocol. We averaged intensities of positive controls on each array and then normalized miRNA signals by equalizing these averages among all  arrays.

source_name: CD138 selected plasma cells

extract_protocol: TRIzol reagent (Invitrogen, Carlsbad, CA) (500 µl) was added to dry cell pellets, which were vigorously pipetted. After incubation at room temperature (5 minutes), chloroform (100 µl) was added, and the sample was briefly vortexed and again incubated at room temperature (5 minutes). After centrifugation (15 minutes, 12,000g, 4°C), the upper aqueous phase of samples was transferred to a new RNase-free microcentrifuge tube containing 250 µl of isopropanol. Following pulse-vortexing and incubation at room temperature (5 minutes), total RNA was precipitated (20 minutes, 14,000g, 4°C). Following removal of the supernatant, the RNA pellet was washed in 500 µl of 70% ethanol (30 minutes, 14,000g, 4°C), RNA pellets were allowed to air-dry (10 minutes) and were resuspended in 20 µl of RNase-free water. Total RNA samples were evaluated spectrophotometrically using a Nanodrop spectrophotometer. A260 values were used to quantify the samples, and A260/A280 ratios were used to determine relative purity; generally, RNA samples with A260/A280 ≥1.6 were routed to analysis.

tag: patient

tag: disease state

value: multiple myeloma

tag: cell type

value: CD138+ selected plasma cells


title: Normal_02 (miRNA)

hyb_protocol: Purified miRNA was hybridized to the Human miRNA Microarray platform (Agilent, Santa Clara, CA) following the Agilent version 2.0 protocol (June 2008) explicitly for target labeling, hybridization, washing, scanning, and image analysis.

value: normal


title: Normal_01 (miRNA)

scan_protocol: Purified miRNA was hybridized to the Human miRNA Microarray platform (Agilent, Santa Clara, CA) following the Agilent version 2.0 protocol (June 2008) explicitly for target labeling, hybridization, washing, scanning, and image analysis.


title: Primary bladder cancer BT001

tag: biological source

tag: SEX

tag: AGE


title: Primary bladder cancer BT015

tag: invasiveness

tag: intravesical therapy

tag: systemic chemo


title: 14C_12S

city: Castanet Tolosan

first: Caroline

last: Molette

address: Avenue de l'Agrobiopole

institute: ENSAT

description: dye switch design

hyb_protocol: Hybridization experiments were carried out with an automatic hybridization chamber (Discovery from Ventana Medical System). Briefly, microarray was prehybridized with a solution of 1% BSA, 2X SSC, 0.1% SDS over 30 min at 42°C. After automatic washing, microarray was hybridized overnight at 42°C in 200 µl of ChipHybe buffer containing 10 µl of each labeled cDNA purified (approximately 2000 pmol of each incorporated dye). Slides were then manually washed twice for 2 min in a 2X SSC, 0.1% SDS solution and for 2 min in 0.1X SSC.

scan_protocol: The microarray slides were scanned using a laser scanner (GenePix 4000B from Axon Instruments) at 532 nm for Cy3 fluorescence (green signal) and 635 nm for Cy5 fluorescence (red signal) keeping a PMT difference between both channels lower than 100. The two images generated for each slide were then analysed with GenePix Pro 6.1 software (Axon Instruments).

data_processing: The two images from each slide were analyzed with GenepixPro 4.0 software (Axon instruments, Inc., Union City, CA). Data filtering and normalisation were performed using the Bioconductor package Limma (Linear Models for Microarray Analysis) in the R project statistical (version 2.2.1) (http://www.r-project.org) (http://www.bioconductor.org). A filter procedure eliminated non informative spots according to two criterions: 1) the genepix flag automatically performed by Genepix Pro 6.1 software which indicated spots found or not, 2) the SNR (Signal to Noise Ratio) also provided  by Genepix Pro which was set to 0. Background was not substracted in the normalisation process. The ratio Cy5/Cy3 used was expressed as the Log(base 2) of the ratio of median pixel intensity of the two red and green spots. Log2 median ratio values were then normalized by “Robustspline” normalization. Only spots conform to the filtering step were used for the normalization. Log2 ratios in VALUE column of sample tables represents restrained sample/control sample.

organism: Gallus gallus

source_name: Muscle collected 5min post mortem

label_protocol: Five microg of each RNA sample were reverse-transcribed and Cy3 or Cy5 fluorescent-labelled using the ChipShotTM direct labelling kit (Promega, Charbonnieres, France). Microarray analysis were realised on six animals of each experimental group selected on the base of their corticosterone levels (i.e. animals the most representives of the mean of each experimental group). Each fluorescent dye was used to label cDNA from three "control" animals and three "treated" animals (dye switch method). Cy5 or Cy3-labelled cDNA from control animals was hybridized to the microarray with Cy3 or Cy5-labelled cDNA from treated animals, respectively, according to the Biochips plateform of "Genopole Toulouse Midi-Pyrenees" procedure.

extract_protocol: Muscle samples from each animal were ground into a fine powder in a mortar cooled by liquid nitrogen and 100 mg was added to 1 ml of prechilled TRIzol Reagent (Invitrogen Cergy Pontoise, France). Total RNA extractions were carried out according to manufacturer's directions and were further purified by passage through RNeasy mini-columns (RNeasy MinElute kit, Qiagen, Courtaboeuf, France) according to manufacturer's protocols for RNA cleanup. DNA was digested using an RNase-free DNase set (Qiagen, Courtaboeuf, France) during RNA purification. Total RNA was quantified by spectrophotometer (NanoDrop®) and its integrity was assessed on an Agilent 2100 Bioanalyser (RNA 6000 Nano LabChip, Agilent Technologies, Massy, France).

tag: muscle name

value: tensor fascia latae and biceps femoris

tag: treatment

value: control

value: restrained and transport for two hours


title: Primary bladder cancer BT007

value: primary bladder cancer

value: M

tag: grade

tag: recurrence

tag: progression

tag: overall survival

tag: cancer specific survival


title: Patient_51 (miRNA)

label_protocol: Purified miRNA was hybridized to the Human miRNA Microarray platform (Agilent, Santa Clara, CA) following the Agilent version 2.0 protocol (June 2008) explicitly for target labeling, hybridization, washing, scanning, and image analysis.


title: 6C_23S

description: dye switch design


title: Patient_50 (miRNA)


title: Patient_49 (miRNA)


title: Patient_48 (miRNA)


title: 10C_28S

description: dye switch design


title: Patient_46 (miRNA)


title: Patient_47 (miRNA)


title: 18C_8S

description: dye switch design

data_processing: The two images from each slide were analyzed with GenepixPro 4.0 software (Axon instruments, Inc., Union City, CA). Data filtering and normalisation were performed using the Bioconductor package Limma (Linear Models for Microarray Analysis) in the R project statistical (version 2.2.1) (http://www.r-project.org) (http://www.bioconductor.org). A filter procedure eliminated non informative spots according to two criterions: 1) the genepix flag automatically performed by Genepix Pro 6.1 software which indicated spots found or not, 2) the SNR (Signal to Noise Ratio) also provided  by Genepix Pro which was set to 0. Background was not substracted in the normalisation process. The ratio Cy5/Cy3 used was expressed as the Log(base 2) of the ratio of median pixel intensity of the two red and green spots. Log2 median ratio values were then normalized by “Robustspline” normalization. Only spots conform to the filtering step were used for the normalisation. Log2 ratios in VALUE column of sample tables represents restrained sample/control sample.


title: Patient_52

description: Gene expression data from CD138+ selected plasma cells

hyb_protocol: mRNA purification, cDNA synthesis, cRNA preparation, and hybridization to the Human Genome U133Plus 2.0 GeneChip microarrays (Affymetrix, Santa Clara, CA) were performed as previously described PMID: 17105814

scan_protocol: mRNA purification, cDNA synthesis, cRNA preparation, and hybridization to the Human Genome U133Plus 2.0 GeneChip microarrays (Affymetrix, Santa Clara, CA) were performed as previously described PMID: 17105815

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

label_protocol: mRNA purification, cDNA synthesis, cRNA preparation, and hybridization to the Human Genome U133Plus 2.0 GeneChip microarrays (Affymetrix, Santa Clara, CA) were performed as previously described PMID: 17105813

extract_protocol: mRNA purification, cDNA synthesis, cRNA preparation, and hybridization to the Human Genome U133Plus 2.0 GeneChip microarrays (Affymetrix, Santa Clara, CA) were performed as previously described in PMID: 17105813

tag: risk score

tag: proliferation index


title: 26C_15S

description: dye switch design


title: Patient_50

tag: patient

tag: disease state


title: Patient_45 (miRNA)

tag: cell type


title: Patient_44 (miRNA)


title: Patient_42 (miRNA)


title: Patient_51


title: Patient_41 (miRNA)


title: Patient_40 (miRNA)


title: STT4711-SFT-FFPE-aRNA

city: Stanford

first: Andrew

last: Beck

state: CA

address: Stanford

institute: Stanford University

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-05/83673.gif

hyb_protocol: not provided

scan_protocol: Scanner Model = GenePix 4000A

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

source_name: aUHR

label_protocol: not provided

extract_protocol: not provided

tag: reference

value: aUHR

source_name: STT4711-SFT-formalin fixed paraffin embedded tissue-aRNA

tag: preservation

value: formalin fixed paraffin embedded tissue

value: solitary fibrous tumor


title: Patient_45


title: Patient_48


title: Patient_44


title: Patient_39 (miRNA)


title: Patient_49


title: Patient_47


title: Patient_43


title: Patient_43 (miRNA)


title: STT2162-SFT-FFPE-aRNA

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-05/83671.gif

source_name: STT2162-SFT-formalin fixed paraffin embedded tissue-aRNA


title: Patient_38 (miRNA)


title: STT5388-SFT-FFPE-aRNA

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-05/83674.gif

source_name: STT5388-SFT-formalin fixed paraffin embedded tissue-aRNA


title: Patient_42


title: Patient_37 (miRNA)


title: Patient_36 (miRNA)


title: STT200-SFT-FFPE-aRNA

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-05/83669.gif

source_name: STT200-SFT-formalin fixed paraffin embedded tissue-aRNA


title: STT3524-SFT-FFPE-aRNA

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-05/83672.gif

source_name: STT3524-SFT-formalin fixed paraffin embedded tissue-aRNA


title: STT5386-DTF-FFPE-aRNA

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-05/83667.gif

source_name: STT5386-DTF-formalin fixed paraffin embedded tissue-aRNA

value: desmoid type fibromatosis


title: STT4327-DTF-FFPE-aRNA

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-05/83665.gif

source_name: STT4327-DTF-formalin fixed paraffin embedded tissue-aRNA


title: STT1079-SFT-FFPE-aRNA

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-05/83670.gif

source_name: STT1079-SFT-formalin fixed paraffin embedded tissue-aRNA


title: Patient_32 (miRNA)


title: Patient_35 (miRNA)


title: Patient_33 (miRNA)


title: Patient_31 (miRNA)


title: STT5387-DTF-FFPE-aRNA

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-05/83668.gif

source_name: STT5387-DTF-formalin fixed paraffin embedded tissue-aRNA


title: Patient_40


title: Patient_38


title: Patient_41


title: Patient_36


title: Patient_46


title: STT5385-DTF-FFPE-aRNA

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-05/83666.gif

source_name: STT5385-DTF-formalin fixed paraffin embedded tissue-aRNA


title: Patient_35


title: Patient_34 (miRNA)


title: Patient_29 (miRNA)


title: Patient_28 (miRNA)


title: Patient_37


title: Patient_24 (miRNA)


title: Patient_23 (miRNA)


title: Patient_30


title: Patient_29


title: Patient_28


title: Patient_26 (miRNA)


title: Patient_27 (miRNA)


title: Patient_25 (miRNA)


title: Patient_33


title: Patient_26


title: Patient_27


title: Patient_20 (miRNA)


title: Patient_30 (miRNA)


title: Patient_32


title: Patient_19 (miRNA)


title: Patient_22 (miRNA)


title: Patient_21 (miRNA)


title: Patient_17 (miRNA)


title: Patient_16 (miRNA)


title: Patient_18 (miRNA)


title: Patient_15 (miRNA)


title: Patient_14 (miRNA)


title: Patient_23


title: Patient_13 (miRNA)


title: Patient_24


title: Patient_22


title: Patient_25


title: Patient_21


title: Patient_12 (miRNA)


title: Patient_18


title: Patient_20


title: Patient_19


title: Patient_39


title: Patient_17


title: Patient_16


title: Patient_15


title: Patient_11 (miRNA)


title: Patient_08 (miRNA)


title: Patient_10 (miRNA)


title: Patient_09 (miRNA)


title: Patient_13


title: Patient_07 (miRNA)


title: Patient_12


title: Patient_14


title: Patient_10


title: Patient_11


title: Patient_34


title: Patient_09


title: Patient_06 (miRNA)


title: Patient_05 (miRNA)


title: STT1986a-Fibromatosis

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68317.gif

source_name: UHR

value: UHR

value: frozen


title: STT1969a-Fibromatosis

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68316.gif


title: Patient_08


title: Patient_03 (miRNA)


title: Patient_04 (miRNA)


title: Patient_06


title: Inoculated cotyledons at T1+T2, biological rep2

city: SOPHIA ANTIPOLIS

first: Attard

last: Agnes

address: 400 route des chappes

institute: INRA

hyb_protocol: RNA samples from the “early” and “late” compatible interaction, and from the water-treated control (5 µg each) were submitted to hybridizations on Affymetrix ATH1 GeneChips

scan_protocol: Signals were revealed with the Gene Array Scanner Model G2500A (Agilent Technologies, Massy, France).

data_processing: Signal intensities, and the 'presence-absence' expression for each of the duplicated samples were computed using Microarray Suite (MAS 5.0; Affymetrix) with default parameters.

organism: Arabidopsis thaliana

source_name: Mixed samples of  Arabidopsis thaliana inoculated with H. arabidopsidis at T1=8 hours after inoculation and T2=24 hours after inoculation.

label_protocol: Hybridized probes were labeled with streptavidin-phycoerythrin conjugate and anti streptavidine antibody,

growth_protocol: Seeds from A. thaliana ecotype Wassilewskija (WS) were sown on a soil/sand mixture, stratified for 3 days at 4 °C, and then grown under a 12 h photoperiod in a growth chamber at 20 °C.

extract_protocol: In two independent experiments, cotyledons from the ecotype Wassilewskija (WS) were inoculated with water, or with H. arabidopsidis to establish a compatible interaction. Total RNA was extracted using the NucleoSpin Plant RNA preparation kit according to the manufacturer’s instructions (Macherey-Nagel, Hoerd, France). Equal amounts of RNA extracted at 8 h and 24 h after inoculation were mixed to produce the “early” interaction samples. Equal amounts of RNA from cotyledons at 4 d and 6 d after inoculation were mixed to produce the “late” interaction samples.

treatment_protocol: For infection, 10-day-old plants were spray-inoculated to saturation with a spore suspension of 40,000 spores/ml (strain  Emwa1)

tag: tissue

value: Cotyledons

tag: genotype

value: Wassilewskija

tag: infection

value: Hyaloperonospora arabidopsidis strain Emwa1


title: Inoculated cotyledons at T3+T4, biological rep1

source_name: Mixed samples of  Arabidopsis thaliana inoculated with H. arabidopsidis at T3=4 days after inoculation and T4=6 days after inoculation.


title: Patient_07

value: multiple myeloma


title: STT4934-SFT-FS

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-10/70699.gif


title: STT4711-SFT

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68315.gif


title: Patient_05

value: CD138+ selected plasma cells


title: Patient_31


title: mock inoculated, biological rep2

source_name: Mixed samples of  Arabidopsis thaliana inoculated with water.

value: no


title: Inoculated cotyledons at T3+T4, biological rep2


title: STT3237-SFT-FS

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-10/70700.gif


title: mock inoculated, biological rep1


title: STT2435-Fibromatosis-FS

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-10/70697.gif


title: STT3125a-Fibromatosis

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-06/68802.gif


title: STT3524-SFT

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68611.gif


title: STT3119a-Fibromatosis

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-06/68776.gif


title: STT1079c-SFT

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68613.gif


title: STT2913-Fibromatosis

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-06/68777.gif


title: STT2774a-SFT

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-06/68778.gif


title: STT3120a-Fibromatosis

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-06/68783.gif


title: STT1637c-SFT

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68614.gif


title: STT3122b-Fibromatosis

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68605.gif


title: STT1968b-Fibromatosis

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68604.gif


title: Inoculated cotyledons at T1+T2, biological rep1


title: u87mg

status: Public on Mar 25 2010

city: Huntsville

first: Preti

last: Jain

state: AL

address: 601 Genome Way

institute: Hudsonalpha Institute for Biotechnology

hyb_protocol: llumina Homo sapiens 6 BeadChips were hybridized, washed, stained and scanned according to Illuminas protocol

scan_protocol: Processed arrays were read using Illumina BeadReader according to the manufacturer's instructions.

data_processing: The data was extracted and normalized the data with the rank-invariant method (Illumina BeadStudio software).

source_name: Human glioblastoma-astrocytoma, epithelial-like cell line

label_protocol: Cy3 using standard protocols

extract_protocol: RNA samples were prepared using Qiagen RNeasy Micro Kit (Qiagen) and then assayed using the NanoDrop (ThermoScientific) to ensure that high-quality RNA was used for the array experiments.

tag: cell line


title: hela

source_name: cervical carcinoma

value: cervical carcinoma

value: hela


title: Patient_02

description: Gene expression data from CD138+ selected plasma cells

source_name: CD138 selected plasma cells


title: Patient_04


title: hct116

source_name: colorectal carcinoma

value: colorectal carcinoma


title: Unexpanded CD34+ cells

city: Randwick

first: Kap-Hyoun

last: Ko

state: NSW

address: High Street

department: Cord and Marrow Transplant Facility

institute: Sydney Children's Hospital

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using average normalisation with Illumina Beadstudio

label: Biotin

source_name: Umbilical cord blood

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

growth_protocol: CD34+ cells were seeded at a density of 1-2 x 105 cells/ml in Iscove’s Modified Dulbecco’s medium (IMDM) with 10% heat-inactivated foetal calf serum (FCS), 2mM L-glutamine, 100U/ml penicillin/streptomycin and a cytokine cocktail of Flt3 ligand (FLT3L), stem cell factor (SCF) and thrombopoietin (TPO), all at a concentration of 100ng/ml

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: Umbilical cord blood


title: ags

source_name: gastric adenocarcinoma

value: gastric adenocarcinoma

value: ags


title: hepg2

source_name: liver carcinoma

value: liver carcinoma


title: Expanded CD34+ cells


title: t98g

source_name: fibroblast

value: fibroblast


title: Patient_03


title: STT3237-SFT-FFPE-aRNA

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-09/76722.gif

source_name: aRNA-UHR

value: aRNA-UHR

source_name: STT3237-SFT-formalin fixed paraffin embedded tissue-aRNA

value: formalin fixed paraffin embedded tissue

value: solitary fibrous tumor


title: Patient_02 (miRNA)

description: miRNA expression of CD138 selected plasma cells


title: Blastocysts from synchronized heifers rep3

city: Fort Collins

first: Ahmed

last: Gad

state: Colorado

address: 3107 Rampart Rd

department: Biomedical Sciences

institute: Colorado State University

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr on GeneChip Bovine Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450/250.

scan_protocol: GeneChips were scanned using the GeneChip scanner 3000 integrated with Affymetrix® Microarray Suitesoftware.

data_processing: R software (www.r-project.org) and bioconductor packages (www.bioconductor.org) were used to generate GC-RMA data.

organism: Bos taurus

source_name: Bovine blastocysts cultured under non superovulation environment from day2 until day7

label_protocol: Biotinylated cRNA was labeled using a biotinylated nucleotide analog/ribonucleotide mix in the second IVT reaction using GeneChip IVT Labeling Kit (Affymetrix, Inc., Santa Clara, CA, USA).

extract_protocol: Total RNA isolation was performed using the PicoPureTM RNA Isolation Kit (ARCTURS, Munich, Germany) according to the manufacturer's instruction.

value: Blastocysts

tag: age

value: 7 days


title: Blastocysts from superovulated heifers rep2

source_name: Bovine blastocysts cultured under superovulation environment until day7


title: STT2435-Fibromatosis-FFPE-aRNA

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-09/76719.gif

source_name: STT2435-Fibromatosis-formalin fixed paraffin embedded tissue-aRNA

value: desmoid type fibromatosis


title: Blastocysts from synchronized heifers rep2


title: ht1080

source_name: human fibrosarcoma

value: human fibrosarcoma


title: g402

source_name: human renal leiomyoblastoma cell line

value: human renal leiomyoblastoma cell line


title: Blastocysts from superovulated heifers rep3


title: Blastocysts from superovulated heifers rep1


title: Blastocysts from synchronized heifers rep1


title: NPd14_2 biological rep2

city: Bonn

first: Dessie

last: Salilew-Wondim

state: NRW

address: Endenicher Allee 15

department: Animal breeding and husbandry group

country: Germany

institute: University of Bonn

hyb_protocol: The biotin-labeled cRNA was fragmented. Following this, a hybridization cocktail consisting of fragmented and labeled cRNA, control oligonucleotide B2 (3nM), 20X eukaryotic hybridization controls (bioB, bioC, bioD, cre), 2X hybridization mix, DMSO and RNAse free water were mixed to a final volume of 200 µl and heated to 99°C for 5 followed by warming at 45°C for 5 min. The samples were then hybridized to GeneChip® Bovine Genome Array for 16 h at 45°C in hybridization oven. For each sample of CDd7, CDd14, NPd7 or NPd14, three biotin labeled cRNA hybridizations were performed.

scan_protocol: The arrays were washed and stained using Fluidics Station 450/250 and scanned using the GeneChip® scanner 3000 integrated with Affymetrix® Microarray Suite software as recommended in GeneChip® expression wash, stain and scan user manual (P/N 702731).

data_processing: The microarray data normalization and background correction was performed using guanine cytosine robust multi-array analysis (gcrma) . The quality of the arrays after hybridization was evaluated by assessing the absent and present calls of the control probesets. Differentially expressed genes were generated using linear models for microarray data analysis (LIMMA).  For this, we used R software, (www.r-project.org) and bioconductor packages (www.bioconductor.org).

source_name: Endometrial biopsy collected at day 14 of the oestrous ccycle from hiefers resulted in no pregnancy after embryo transfer

label_protocol: The cRNA  was biotin labeled using the GeneChip® IVT Labeling Kit (Affymetrix, Inc., Santa Clara, CA, USA) according to GeneChip® expression analysis technical manual (P/N 702232)

extract_protocol:
Total RNA was extracted from three pools of each endometrial sample (CDd7, CDd14, NPd7 or NPd14 ) using RNeasy mini kit (Qiagen).
RNA amplification was perfomed using MEGAscript® T7 Kit (Ambion, Inc., Austin, TX, USA) according to GeneChip® expression analysis technical manual (P/N 702232)

tag: day of the oestrous cycle

tag: pregnancy

value: no