title: BM_MSC 31M A

status: Public on Sep 30 2013

type: RNA

city: Taipei

first: Jui-Yu

last: Hsieh

address: No. 155, Sec 2, Li-Nong Street

country: Taiwan

institute: National Yang-Ming University

description: normal mesenchymal stem cells

hyb_protocol: cRNA were hybridized, washed and stained on U133 plus 2.0 chips according to standard Affymetrix protocol.

scan_protocol: Chips are stained on Affymetrix GCS3000 scanner (scanner type M10)

data_processing: The CEL file was loaded to R/Bioconductor software and normalized by GC-RMA with default settings.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: MSC, human bone marrow

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: All MSCs were cultured in MesenCult (Stem Cells Technology) medium at 37°C in a 5% CO2 humidified incubator.

extract_protocol: Total RNA was extracted by Tri-Reagent (Sigma) according to the manufacturer's instructions.

tag: tissue

value: bone marrow

tag: cell type

value: normal mesenchymal stem cells

tag: passages

value: < 10 passages


title: BM_H_MSC1_2

description: normal mesenchymal stem cells


title: BM_H_MSC1

description: normal mesenchymal stem cells


title: S0119-040-UcMSC-2

description: normal mesenchymal stem cells

source_name: MSC, human Wharton's jelly of umbilical cord

value: Wharton's jelly of umbilical cord


title: S0119-042-UcMSC-4

description: normal mesenchymal stem cells


title: S0119-043-UcMSC-3

description: normal mesenchymal stem cells


title: BM_H_MSC1_1

description: normal mesenchymal stem cells


title: Clone 19- 10uM MDV3100 24h rep2

city: Cambridge

first: Joshua

middle: M

last: Korn

state: MA

address: 250 Mass Ave

country: USA

institute: Novartis

description: Gene expression data from resistant cells treated with 10uM MDV3100

hyb_protocol: Affymetrix GeneChip eukaryotic hybridization protocol (Affymetrix Inc.)

scan_protocol: GeneChip Scanner 3000 (Affymetrix Inc.)

data_processing: Micorarray Analysis Suite version 5.0 (MAS 5.0) background correction, scaled to 150

source_name: MDV Resistant LNCaP

label_protocol: Nugen Ovation RNA Amplification System+ WB + FL cDNA Biotin Module V2 (NuGen Lts)

growth_protocol: All lines were cultured in RPMI-1640 supplemented with 10% FCS

extract_protocol: RNeasy Plus kit (qiagen) following the manufacturers instructions

treatment_protocol: 300K cells were seeded in 6 wells for 3d prior to treatment for 24 h

tag: cell line

value: LNCaP

tag: clone

tag: mdv sensitivity

value: insensitive

tag: agent


title: Clone 24- 10uM MDV3100 24h rep2


title: Clone 15- 0.1% DMSO 24h rep2

description: Gene expression data from resistant cells treated with DMSO

value: 0.1% DMSO


title: Clone 14- 0.1% DMSO 24h rep2


title: Clone 24- 0.1% DMSO 24h rep2


title: Clone 1- 10uM MDV3100 24h rep2


title: Clone 15- 10uM MDV3100 24h rep2


title: Clone 19- 0.1% DMSO 24h rep2


title: Clone 10- 10uM MDV3100 24h rep2


title: Clone 14- 10uM MDV3100 24h rep2


title: Clone 9- 10uM MDV3100 24h rep2


title: Clone 9- 0.1% DMSO 24h rep2


title: Clone 1- 0.1% DMSO 24h rep2


title: M+R- 10uM MDV3100 24h rep2

description: Gene expression data from control LNCaP cells treated with 10uM MDV3100

source_name: Control 3 LNCaP

value: control

value: sensitive


title: D+E- 10uM MDV3100 24h rep2

source_name: Control 1 LNCaP


title: D+E- 0.1% DMSO 24h rep2

description: Gene expression data from control LNCaP cells treated with DMSO


title: M+R- 0.1% DMSO 24h rep2


title: Clone 10- 0.1% DMSO 24h rep2


title: D+R- 0.1% DMSO 24h rep2

source_name: Control 2 LNCaP


title: Clone 19- 10uM MDV3100 24h rep1


title: Clone 1- 10uM MDV3100 24h rep1


title: Clone 24- 0.1% DMSO 24h rep1


title: Clone 15- 10uM MDV3100 24h rep1


title: Clone 10- 0.1% DMSO 24h rep1


title: Clone 19- 0.1% DMSO 24h rep1


title: Clone 14- 10uM MDV3100 24h rep1


title: D+R- 10uM MDV3100 24h rep2


title: Clone 9- 0.1% DMSO 24h rep1


title: M+R- 10uM MDV3100 24h rep1


title: Clone 14- 0.1% DMSO 24h rep1


title: Clone 1- 0.1% DMSO 24h rep1


title: Clone 10- 10uM MDV3100 24h rep1


title: Clone 24- 10uM MDV3100 24h rep1


title: D+R- 0.1% DMSO 24h rep1


title: Clone 9- 10uM MDV3100 24h rep1


title: 14- NTC- F876L Dox+ MDV+ #2

description: Gene expression data from F876L/T877A AR overexpressing cells treated with 10uM MDV

source_name: F876L/T877A Mut MDV+ rep 2

growth_protocol: All lines were cultured in RPMI-1640 supplemented with 10% FCS and 100ng/ml Doxycycline for 3d prior to treatment with 0.1% DMSO or 10uM MDV3100 for 24h.

treatment_protocol: 300K cells were seeded in 6 wells for 3d with 100ng/ml doxyxycline prior to treatment for 24 h

tag: genotype/variation

value: F876L/T877A Mut overexpression

value: partially insensitive


title: 15- NTC- W741C Dox+ MDV+ #1

description: Gene expression data from W741C/T877A overexpressing cells treated with 10uM MDV

source_name: W741C/T877A Mut MDV+ rep 1

value: W741C/T877A Mut overexpression


title: Clone 15- 0.1% DMSO 24h rep1


title: 11- NTC- T877A WT Dox+ MDV+ #1

description: Gene expression data from T877A AR overexpressing LNCaPs treated with 10uM MDV

source_name: T877A WT MDV+ rep 1

value: T877A WT overexpression


title: M+R- 0.1% DMSO 24h rep1


title: 12- NTC- T877A WT Dox+ MDV+ #2

source_name: T877A WT MDV+ rep 2


title: D+R- 10uM MDV3100 24h rep1


title: 5- NTC- F876L Dox+ MDV- #1

description: Gene expression data from F876L/T877A AR overexpressing cells treated with 0.1% DMSO

source_name: F876L/T877A Mut MDV- rep 1


title: 7- NTC- W741C Dox+ MDV- #1

description: Gene expression data from W741C/T877A overexpressing cells treated with 0.1% DMSO

source_name: W741C/T877A Mut MDV- rep 1


title: 6- NTC- F876L Dox+ MDV- #2

source_name: F876L/T877A Mut MDV- rep 2


title: D+E- 0.1% DMSO 24h rep1


title: D+E- 10uM MDV3100 24h rep1


title: 16- NTC- W741C Dox+ MDV+ #2

source_name: W741C/T877A Mut MDV+ rep 2


title: 10- NTC- p121 Vec Dox+ MDV+ #2

description: Gene expression data from vec control cells treated with 10uM MDV

source_name: Vec control MDV+ rep 2

value: Vec control


title: 2- NTC- p121 Vec Dox+ MDV- #2

description: Gene expression data from vec control cells treated with 0.1% DMSO

source_name: Vec control MDV- rep 2


title: 1- NTC- p121 Vec Dox+ MDV- #1

source_name: Vec control MDV- rep 1


title: 13- NTC- F876L Dox+ MDV+ #1

source_name: F876L/T877A Mut MDV+ rep 1


title: 8- NTC- W741C Dox+ MDV- #2

source_name: W741C/T877A Mut MDV- rep 2


title: 4- NTC- T877A WT Dox+ MDV- #2

description: Gene expression data from T877A AR overexpressing LNCaPs treated with 0.1% DMSO

source_name: T877A WT MDV- rep 2


title: JH_101019_TweakCaki_19_TW212

city: Watertown

first: Mary

last: Simcox

address: 500 Arsenal St

institute: Forma Therapeutics

description:
Human cells were implanted as xenografts.  Treated xenografts were removed and processed for hybridization to human chips to investigate tumor changes.
Kidney, carcinoma_kidney_CC, Caucasian, Male

hyb_protocol: Hybridization followed manufacturer's recommendations

scan_protocol: GC_scanner3000 Affymetrix scanner was utilized with AGCC

data_processing: Statistical analysis was done by simple linear modeling using Partek Genomics Suite software.  A model containing fixed effects for treatment and time and their interaction was calculated, and contrasts were constructed for the overall TWEAK vs. vehicle treatment comparison and for each individual time point.  Relevant gene lists of interesting genes and patterns of genes were created.  Lists were generated for probesets where treatment induced changes had significance p values of <0.05 and which change at least 1.8-fold at 2 time points.

source_name: CAKI-1 cells, treated with TW212 for 24hours

label_protocol: 5'IVT Express kit was followed according to manufacturer's recommendations

growth_protocol: Human cancer cell lines used in tumor xenograft studies were obtained from the ATCC.  These cells were cultured according to instructions provided by the ATCC.  Cell numbers for implantation were determined in previous tumor growth kinetic studies.  Matrigel (BD Biosciences, Bedford, MA) was added 1:1 to cold sterile PBS for cells requiring this supplement for growth in a final cell inoculum volume of 0.2 ml per mouse.  Cells were implanted subcutaneously (sc) in the right hind flank of each mouse using a 1 cc syringe and 26 gauge needle.  All tumor cell lines tested negative for mycoplasma within 1 week of tumor implantation.  After implantation mice were randomized according to tumor volume so that all groups had similar starting mean tumor volumes of 100 – 200 mm3.

extract_protocol: total RNA was extracted using Qiagen Rneasy Minikit.

treatment_protocol: Anti-TWEAK antibodies were stored at -80° C, thawed and diluted immediately prior to use with Histidine buffer (10 mM Histidine, 140 mM NaCl, pH 6.0) and administered intraperitoneally (ip) to tumor-bearing mice.  The anti-VEGF antibody, B20.4.1, was obtained from Roche Diagnostics GmbH (Penzberg, Germany).  All stock antibodies were kept frozen at -80° C, thawed prior to use and diluted to the desired concentration for in vivo administration.

tag: tissue type

value: xenograft

value: kidney carcinoma

tag: implant host

value: Athymic, Nu/Nu nude mice


title: JH_101019_TweakCaki_16_Vehicle

source_name: CAKI-1 cells, treated with Vehicle_Control for 24hours


title: JH_101019_TweakCaki_12_TW212


title: 3- NTC- T877A WT Dox+ MDV- #1

source_name: T877A WT MDV- rep 1


title: U133Plus2_030810sp_XenograftTweak_35

description: ACHN xenografts, Kidney, adenocarcinoma, Caucasian, Male

source_name: ACHN xenografts, treated with Vehicle_Control for 72hours

value: ACHN

value: kidney adenocarcinoma


title: U133Plus2_040710sp_XenograftTweak_51


title: JH_101019_TweakCaki_18_TW212


title: U133Plus2_042210sp_XenograftTweak_19

source_name: ACHN xenografts, treated with Vehicle_Control for 24hours


title: JH_101019_TweakCaki_15_Vehicle


title: U133Plus2_030810sp_XenograftTweak_12


title: U133Plus2_040710sp_XenograftTweak_57


title: JH_101019_TweakCaki_11_Vehicle


title: JH_101019_TweakCaki_14_TW212


title: JH_101019_TweakCaki_17_Vehicle


title: U133Plus2_040710sp_XenograftTweak_40

source_name: ACHN xenografts, treated with Vehicle_Control for 8hours


title: U133Plus2_030810sp_XenograftTweak_19


title: U133Plus2_030810sp_XenograftTweak_30


title: U133Plus2_040710sp_XenograftTweak_50


title: U133Plus2_030810sp_XenograftTweak_09


title: U133Plus2_030810sp_XenograftTweak_29


title: U133Plus2_040710sp_XenograftTweak_53


title: U133Plus2_040710sp_XenograftTweak_47

source_name: ACHN xenografts, treated with Vehicle_Control for 4hours


title: U133Plus2_040710sp_XenograftTweak_37


title: U133Plus2_030810sp_XenograftTweak_32


title: U133Plus2_030810sp_XenograftTweak_41


title: U133Plus2_030810sp_XenograftTweak_06


title: U133Plus2_030810sp_XenograftTweak_02


title: 9- NTC- p121 Vec Dox+ MDV+ #1

source_name: Vec control MDV+ rep 1


title: U133Plus2_030810sp_XenograftTweak_23


title: U133Plus2_040710sp_XenograftTweak_38

source_name: ACHN xenografts, treated with TW212 for 72hours


title: U133Plus2_030810sp_XenograftTweak_14


title: U133Plus2_040710sp_XenograftTweak_60


title: U133Plus2_030810sp_XenograftTweak_05


title: U133Plus2_030810sp_XenograftTweak_27

source_name: ACHN xenografts, treated with TW212 for 8hours


title: U133Plus2_030810sp_XenograftTweak_26

source_name: ACHN xenografts, treated with TW212 for 24hours


title: U133Plus2_040710sp_XenograftTweak_45


title: U133Plus2_030810sp_XenograftTweak_20


title: U133Plus2_040710sp_XenograftTweak_43


title: U133Plus2_040710sp_XenograftTweak_55


title: U133Plus2_030810sp_XenograftTweak_03


title: U133Plus2_040710sp_XenograftTweak_39


title: U133Plus2_040710sp_XenograftTweak_48

source_name: ACHN xenografts, treated with TW212 for 4hours


title: U133Plus2_040710sp_XenograftTweak_22


title: U133Plus2_030810sp_XenograftTweak_36


title: U133Plus2_040710sp_XenograftTweak_44


title: U133Plus2_030810sp_XenograftTweak_07


title: U133Plus2_030810sp_XenograftTweak_21


title: U133Plus2_040710sp_XenograftTweak_49

source_name: ACHN xenografts, treated with B20_4_1_antibody for 72hours


title: U133Plus2_030810sp_XenograftTweak_31


title: U133Plus2_030810sp_XenograftTweak_01


title: U133Plus2_040710sp_XenograftTweak_52


title: U133Plus2_030810sp_XenograftTweak_17


title: U133Plus2_030810sp_XenograftTweak_10


title: U133Plus2_030810sp_XenograftTweak_25


title: U133Plus2_040710sp_XenograftTweak_28

source_name: ACHN xenografts, treated with B20_4_1_antibody for 24hours


title: U133Plus2_042210sp_XenograftTweak_08


title: U133Plus2_040710sp_XenograftTweak_42


title: U133Plus2_030810sp_XenograftTweak_11


title: U133Plus2_030810sp_XenograftTweak_13

source_name: ACHN xenografts, treated with B20_4_1_antibody for 8hours


title: U133Plus2_030810sp_XenograftTweak_24


title: U133Plus2_040710sp_XenograftTweak_56

source_name: ACHN xenografts, treated with B20_4_1_antibody for 4hours


title: U133Plus2_040710sp_XenograftTweak_58


title: U133Plus2_030810sp_XenograftTweak_34


title: U133Plus2_040710sp_XenograftTweak_33


title: U133Plus2_030810sp_XenograftTweak_04


title: U133Plus2_030810sp_XenograftTweak_46


title: U133Plus2_030810sp_XenograftTweak_16


title: JH_120319_Tweak_Cell_Lines_105

source_name: ACHN cells, treated with 100ng_per_ml TWEAK for 8hours

growth_protocol: Cells were seeded in appropriate media with 2% heat-inactivated FBS in humidified 95% air, 5% CO2 overnight in 6-well plates at 37oC.

treatment_protocol: 100 ng/ml TWEAK or media control was added on day 2 to subconfluent cells. For each time point and treatment, five replicates were generated.  One replicate from each treatment group was used for QC as assessed with immunoblotting for Fn14 expression. Samples were collected in all cell lines after 4 h, 8 h or 24 h of stimulation or control treatment with five replicates. For the U2OS and MDA-MB-436 arrays, 15 min and 1 h time points were also collected.

tag: cell line origin

value: kidney

value: adenocarcinoma

tag: gender

value: male

tag: race

value: caucasian


title: JH_120319_Tweak_Cell_Lines_106

source_name: ACHN cells, treated with 100ng_per_ml TWEAK for 24hours


title: JH_120319_Tweak_Cell_Lines_079


title: JH_120319_Tweak_Cell_Lines_082


title: U133Plus2_040710sp_XenograftTweak_59


title: U133Plus2_030810sp_XenograftTweak_15


title: U133Plus2_030810sp_XenograftTweak_18


title: JH_120319_Tweak_Cell_Lines_103


title: JH_120319_Tweak_Cell_Lines_085

source_name: ACHN cells, treated with 0ng_per_ml TWEAK for 8hours


title: JH_120319_Tweak_Cell_Lines_098

source_name: ACHN cells, treated with 0ng_per_ml TWEAK for 4hours


title: JH_120319_Tweak_Cell_Lines_089


title: JH_120319_Tweak_Cell_Lines_100


title: JH_120319_Tweak_Cell_Lines_080

source_name: ACHN cells, treated with 0ng_per_ml TWEAK for 24hours


title: JH_120319_Tweak_Cell_Lines_094


title: JH_120319_Tweak_Cell_Lines_101

source_name: ACHN cells, treated with 100ng_per_ml TWEAK for 4hours


title: U133Plus2_030810sp_XenograftTweak_54


title: JH_120319_Tweak_Cell_Lines_108


title: JH_120319_Tweak_Cell_Lines_099


title: JH_120319_Tweak_Cell_Lines_107


title: JH_120319_Tweak_Cell_Lines_102


title: JH_120319_Tweak_Cell_Lines_090


title: JH_120319_Tweak_Cell_Lines_096


title: JH_120319_Tweak_Cell_Lines_088


title: U133Plus2_030810sp_XenograftTweak_08


title: JH_120319_Tweak_Cell_Lines_097


title: JH_120319_Tweak_Cell_Lines_073


title: JH_100927_Tweak_MDA-MB-436_242_TWEAK_24hrs

source_name: MDA-MB-436 cells, treated with 100ng_per_ml TWEAK for 24hours

value: mammary

value: ductal carcinoma

value: female


title: JH_100927_Tweak_MDA-MB-436_207_TWEAK_24hrs


title: JH_120319_Tweak_Cell_Lines_078


title: JH_100927_Tweak_MDA-MB-436_246_TWEAK_8hrs

source_name: MDA-MB-436 cells, treated with 100ng_per_ml TWEAK for 8hours


title: JH_100927_Tweak_MDA-MB-436_211_TWEAK_8hrs


title: JH_100927_Tweak_MDA-MB-436_230_TWEAK_4hrs

source_name: MDA-MB-436 cells, treated with 100ng_per_ml TWEAK for 4hours


title: JH_100927_Tweak_MDA-MB-436_224_TWEAK_24hrs


title: JH_100927_Tweak_MDA-MB-436_206_TWEAK_8hrs


title: JH_100927_Tweak_MDA-MB-436_233_TWEAK_4hrs


title: JH_100927_Tweak_MDA-MB-436_248_TWEAK_24hrs


title: JH_100927_Tweak_MDA-MB-436_225_TWEAK_24hrs


title: JH_100927_Tweak_MDA-MB-436_243_TWEAK_8hrs


title: JH_100927_Tweak_MDA-MB-436_205_TWEAK_8hrs


title: JH_100927_Tweak_MDA-MB-436_239_TWEAK_4hrs


title: JH_100927_Tweak_MDA-MB-436_231_TWEAK_4hrs


title: JH_100927_Tweak_MDA-MB-436_214_TWEAK_4hrs


title: JH_100927_Tweak_MDA-MB-436_247_TWEAK_1hrs

source_name: MDA-MB-436 cells, treated with 100ng_per_ml TWEAK for 1hours


title: JH_100927_Tweak_MDA-MB-436_223_TWEAK_1hrs


title: JH_100927_Tweak_MDA-MB-436_212_TWEAK_1hrs


title: JH_100927_Tweak_MDA-MB-436_221_TWEAK_1hrs


title: JH_100927_Tweak_MDA-MB-436_249_TWEAK_0_25hrs

source_name: MDA-MB-436 cells, treated with 100ng_per_ml TWEAK for 0.25hours


title: JH_100927_Tweak_MDA-MB-436_237_TWEAK_0_25hrs


title: JH_120319_Tweak_Cell_Lines_095


title: JH_100927_Tweak_MDA-MB-436_216_TWEAK_1hrs


title: JH_100927_Tweak_MDA-MB-436_236_Control_24hrs

source_name: MDA-MB-436 cells, treated with 0ng_per_ml TWEAK for 24hours


title: JH_100927_Tweak_MDA-MB-436_219_TWEAK_0_25hrs


title: JH_100927_Tweak_MDA-MB-436_220_Control_24hrs


title: JH_100927_Tweak_MDA-MB-436_203_Control_24hrs


title: JH_120319_Tweak_Cell_Lines_104


title: JH_100927_Tweak_MDA-MB-436_245_TWEAK_0_25hrs


title: JH_100927_Tweak_MDA-MB-436_228_Control_24hrs


title: JH_100927_Tweak_MDA-MB-436_250_Control_8hrs

source_name: MDA-MB-436 cells, treated with 0ng_per_ml TWEAK for 8hours


title: JH_100927_Tweak_MDA-MB-436_201_TWEAK_0_25hrs


title: JH_100927_Tweak_MDA-MB-436_235_Control_1hrs

source_name: MDA-MB-436 cells, treated with 0ng_per_ml TWEAK for 1hours


title: JH_100927_Tweak_MDA-MB-436_226_Control_8hrs


title: JH_100927_Tweak_MDA-MB-436_234_Control_8hrs


title: JH_100927_Tweak_MDA-MB-436_217_Control_4hrs

source_name: MDA-MB-436 cells, treated with 0ng_per_ml TWEAK for 4hours


title: JH_100927_Tweak_MDA-MB-436_213_Control_8hrs


title: JH_100927_Tweak_MDA-MB-436_208_Control_4hrs


title: JH_100927_Tweak_MDA-MB-436_244_Control_4hrs


title: JH_100927_Tweak_MDA-MB-436_218_Control_1hrs


title: JH_100927_Tweak_MDA-MB-436_232_Control_0_25hrs

source_name: MDA-MB-436 cells, treated with 0ng_per_ml TWEAK for 0.25hours


title: JH_100927_Tweak_MDA-MB-436_222_Control_8hrs


title: JH_100927_Tweak_MDA-MB-436_209_Control_0_25hrs


title: JH_100927_Tweak_MDA-MB-436_204_Control_4hrs


title: JH_100927_Tweak_MDA-MB-436_240_Control_1hrs


title: JH_100927_Tweak_MDA-MB-436_229_Control_1hrs


title: JH_100927_Tweak_MDA-MB-436_215_Control_1hrs


title: JH_100927_Tweak_MDA-MB-436_241_Control_0_25hrs


title: JH_100927_Tweak_MDA-MB-436_210_Control_0_25hrs


title: U2OS, Untreated 8 hours rep2

source_name: U2OS, Untreated 8 hours

tag: disease

value: osteosarcoma

value: Female

tag: ethnicity

value: Caucasian

tag: tweak treated

value: no

tag: time point

value: 8 hrs


title: U2OS, Untreated 4 hours rep1

source_name: U2OS, Untreated 4 hours

value: 4 hrs


title: U2OS, Untreated 24 hours rep4

source_name: U2OS, Untreated 24 hours

value: 24 hrs


title: U2OS, Untreated 4 hours rep2


title: U2OS, Untreated 4 hours rep5


title: U2OS, Untreated 24 hours rep2


title: U2OS, Untreated 24 hours rep1


title: U2OS, Untreated 15 minute rep4

source_name: U2OS, Untreated 15 minute

value: 15 min


title: U2OS, Untreated 4 hours rep3


title: U2OS, Untreated 24 hours rep3


title: U2OS, Untreated 8 hours rep4


title: JH_100927_Tweak_MDA-MB-436_227_Control_4hrs


title: U2OS, Untreated 24 hours rep5


title: U2OS, Untreated 4 hours rep4


title: U2OS, Untreated 15 minute rep5


title: U2OS, Untreated 15 minute rep3


title: U2OS, Untreated 15 minute rep2


title: U2OS, Untreated 8 hours rep1


title: U2OS, Untreated 1 hour rep1

source_name: U2OS, Untreated 1 hour

value: 1 hr


title: U2OS, Untreated 1 hour rep4


title: U2OS, Untreated 1 hour rep3


title: U2OS, Untreated 15 minute rep1


title: U2OS, TWEAK treated 8 hours rep5

source_name: U2OS, TWEAK treated 8 hours

value: yes


title: U2OS, Untreated 1 hour rep5


title: U2OS, Untreated 1 hour rep2


title: U2OS, TWEAK treated 8 hours rep3


title: U2OS, TWEAK treated 4 hours rep5

source_name: U2OS, TWEAK treated 4 hours


title: U2OS, TWEAK treated 8 hours rep1


title: U2OS, TWEAK treated 4 hours rep4


title: U2OS, TWEAK treated 8 hours rep4


title: U2OS, TWEAK treated 8 hours rep2


title: U2OS, TWEAK treated 24 hours rep3

source_name: U2OS, TWEAK treated 24 hours


title: U2OS, TWEAK treated 24 hours rep5


title: U2OS, TWEAK treated 4 hours rep3


title: U2OS, TWEAK treated 24 hours rep4


title: U2OS, TWEAK treated 15 minute rep2

source_name: U2OS, TWEAK treated 15 minute


title: U2OS, TWEAK treated 4 hours rep2


title: U2OS, TWEAK treated 24 hours rep2


title: U2OS, TWEAK treated 1 hour rep4

source_name: U2OS, TWEAK treated 1 hour


title: U2OS, TWEAK treated 15 minute rep1


title: JH_100927_Tweak_MDA-MB-436_238_Control_24hrs


title: U2OS, TWEAK treated 15 minute rep4


title: U2OS, TWEAK treated 1 hour rep5


title: U2OS, TWEAK treated 4 hours rep1


title: U2OS, TWEAK treated 1 hour rep1


title: U2OS, TWEAK treated 24 hours rep1


title: CM_530 12h normoxia

city: rotterdam

first: Mario

last: Pescatori

address: Westplein 11

country: Netherlands

institute: Health e-genomics

description: SAMPLE 11

hyb_protocol: Standard affymetrix protocol using the wash & stain kit.

scan_protocol: Standa affymetrix settings for the gene chip scanner

data_processing: Transcript abundance values were summarised from probesets, log2 transformed and normalised using rma as implemented in BRB ArrayTools. Data exploration and statistical analysis was also performed in BRB aArrayTools using the class comparison and class discovery tools implemented in the software package.

label_protocol: Standard affymetrix protocol with no amplification. Biotin labelled cRNA stained with Phycoeritrin.

growth_protocol: HUVEC cells were grown in Human Endothelial-SFM (Invitrogen) supplemented with 20% heat inactivated new born calf serum, 10% heat inactivated human serum, 100 ng/ml bFGF and 100 ng/ml EGF, on 0,1% gelatin coated flasks

extract_protocol: Total RNA was extracted from treated or untreated HUVEC cells using the Qiagen RNAeasy purification kit.

treatment_protocol: HUVECs were treated with melanoma conditioned medium or DMEM 10% FCS for 12 hours under normoxia or hypoxia.

value: HUVEC cells (#33)

tag: media

value: melanoma conditioned medium (MCM)

tag: condition

value: Normoxia


title: U2OS, TWEAK treated 1 hour rep3


title: U2OS, TWEAK treated 15 minute rep3


title: CM_M14 12h normoxia

description: SAMPLE 9

tag: cell type


title: U2OS, TWEAK treated 1 hour rep2

tag: cell line


title: CM_Mel57 12h normoxia

description: SAMPLE 10


title: CM_Mel57 12h hypoxia

description: SAMPLE 5

value: Hypoxia


title: DMEM 12h normoxia rep1

description: SAMPLE 6

value: DMEM


title: CM_M14 12h hypoxia

description: SAMPLE 4


title: CM_1F6 12h normoxia

description: SAMPLE 8


title: DMEM 12h hypoxia rep1

description: SAMPLE 1


title: CM_1F6 12h hypoxia

description: SAMPLE 3


title: DMEM 12h normoxia rep2

description: SAMPLE 7


title: hESC transfected with shTS2, bio repeat 1

first: Chun

middle: Ying

last: Yu

address: 128 Academia Road, Section 2

department: Genomic Research center

institute: Academia sinica

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Array. GeneChips were washed and stained

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: Raw data were normalized by RMA (Robust Multichip Average) Genespring XI and the weakly expressed signals (<20% of total samples) were excluded.

source_name: disrupting the tsNCRMS expression in hESC

label_protocol: biotin-labeled cRNA probes were generated according to the manufacturer’s protocol

growth_protocol: Human ESCs were grown on MEF feeders (2 × 104 cells/cm2) in DMEM/F12 medium plus 20% Knockout Serum Replacement and 4 ng/ml bFGF

extract_protocol: Total RNA was isolated using TRI Reagent  according to the manufacturer’s protocol

treatment_protocol: Human ESCs were transfected with shLuc or shTS2 for 7 days

tag: transfection

value: embryonic stem cell


title: hESC transfected with shLuc, bio repeat 1

source_name: hESC using shLuc as transfection control

value: shLuc


title: hESC transfected with shTS2, bio repeat 2


title: DMEM 12h hypoxia rep2

description: SAMPLE 2


title: Izmir-5 tumor sample

city: Ankara

first: Mehmet

last: Ozturk

address: Faculty of Science Building

department: BilGen Genetics and Biotechnology Research Center

country: Turkey

institute: Bilkent University

description: Gene expression data from male patient HCC tissue

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Gene Array Scanner. GeneChip Opreating Software (GCOS, Affymetrix) was used to collect and store the data.

data_processing: The data were analyzed with Robust Multichip Average (RMA) using Affymetrix default analysis settings and global scaling as normalization method. The signal intensity was converted to log2 values using Bioconductor package in R 2.4.0.

source_name: Izmir HCC tissue

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Surgically resected samples were immediately snap frozen in liquid nitrogen, and stored in -80C until RNA extraction.

extract_protocol: Tissues were homogenized using 0.8 mm needle before processing. The total RNA were extracted using Nucleospin RNA II kit (MN) according to the manufecturer's protocol.

treatment_protocol: Frozen tissue samples were cut into thirty 20 um thick slices, and scraped into microtubes for RNA extraction. Two 6 um thick slides were cut for pathological examination.

tag: tissue

value: Liver

tag: age

value: Male


title: hESC transfected with shLuc, bio repeat 2


title: Ankara-8 cirrhosis sample

description: Gene expression data from 30 years old age female cirrhosis tissue

source_name: Ankara cirrhosis tissue

tag: genotype

value: HBV positive

value: Female 30


title: Ankara-5 cirrhosis sample

description: Gene expression data from male patient cirrhosis tissue


title: Izmir-3 cirrhosis sample

description: Gene expression data from 65 years old age male cirrhosis tissue

source_name: Izmir cirrhosis tissue

value: Male 65


title: Ankara-12 cirrhosis sample

description: Gene expression data from 41 years old age male cirrhosis tissue

value: HBV+HDV positive

value: Male 41


title: Izmir-2 tumor sample

description: Gene expression data from 44 years old age female HCC tissue

value: Female 44


title: NCTC8325 185::ermB

city: He Fei

first: Haipeng

last: Sun

state: An Hui

address: Huangshan Road

department: School of Life Sciences

country: China

institute: University of Science and Technology of China

description: Gene expression in SAOUHSC_00184-85 mutated strain

hyb_protocol: total of 600 ng cy5-labeled cDNA was used for hybridization sample using Gene Expression Hybridization Kit (Agilent p/n5188-4242) following the manufacturer’s instruction. 40 ul of the hybridization samples were added onto the microarray slide and hybridized in an Agilent hybridization oven to rotate at 10 rpm at 65 °C for 17 hours. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x15k array slides (Scan resolution 5 um, Dye channel is set to Red and Red PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent). Quantity normalization were analyzed with GENESPRING 11.5 (Agilent).

organism: Staphylococcus aureus subsp. aureus NCTC 8325

source_name: S. aureus growth culture, OD600=2.0

label_protocol: 5 ug RNA was used to synthesize cDNA, and labeled with cy5. This process was accomplished using FairPlay III Microarray Labeling Kit (Aglilent p/n252012). Labeled cDNA was purified and quantified with NanoDrop Spectrophotometer (Thermo G2939A).

growth_protocol: Overnight culture were diluted 1:100 in TSB and grow until OD600=2.0.

extract_protocol: Total RNA was prepared using mirVana RNA Isolation Kit (Applied Biosystem p/n AM1556) following the manufacturer’s instruction.

treatment_protocol: In order to lysis the cell wall, cells were collected and incubated in 37°C with 10 mg/ml lysozyme and 40 ug/ml lysostaphin for 5 minutes. Then, cells were centrifuged and resuspended in TRIzol immediately.

tag: strain

value: SAOUHSC_00184-85 mutated strain


title: CD86 positive DCs LLC/SeV/GM rep1

city: Fukuoka

first: kenzaburo

last: tani

address: 3-1-1 Maidashi

department: Medical Institute of Bioregulation

country: Japan

institute: Kyushu University

description: Gene expression after 2days in LLC/SeV/GM cell injected-mouse tumor draining lymph nodes

hyb_protocol: 1.5 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Microarray 4x44K v2 (Probe Name version) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Mus musculus

source_name: Axillary lymph nodes, LLC/SeV/GM, replicate1

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

extract_protocol: Total RNA was extracted using TRIzol .

value: female

value: Tumor draining lymph nodes

value: CD86 positive DCs

tag: treatment

value: LLC/SeV/GM


title: NCTC8325 wild type

description: Gene expression in wild type NCTC8325

value: wild type NCTC8325


title: NCTC8325 1980::ermB

description: Gene expression in SAOUHSC_01980-1981 mutated strain

value: SAOUHSC_01980-1981 mutated strain


title: Ankara-3 cirrhosis sample

description: Gene expression data from 62 years old age male cirrhosis tissue

value: HCV positive

value: Male 62


title: U2OS, Untreated 8 hours rep3

source_name: U2OS, Untreated 8 hours

value: osteosarcoma

value: Female

value: Caucasian

value: no

value: 8 hrs


title: ang_010

city: Newtown

first: Jennifer

middle: R

last: Gamble

state: NSW

address: Locked Bag No. 6

country: Australia

institute: CENTENARY INSTITUTE

hyb_protocol: Samples were hybridised to Ambion mirVana miRNA Probe Set 1564v1 arrays for 4 hours at 62oC in dark conditions and subsequently washed.

scan_protocol: Arrays were scanned on an Axon® GenePix 4000B scanner and GenePix Pro software v4.0 was used to obtain raw probe intensities.

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Statistics in Microarray Analysis” package (http://www.stat.berkeley.edu/∼terry/zarray/software/smacode.html) was used.

label_protocol: the Message Amp aRNA Kit (Ambion; Austin, TX) was used to convert 0.5 μg of the total RNA from each time point to cDNA and then linearly amplify the mRNA ∼400-fold. The amplified RNA (aRNA) was generated incorporating 5-(3-aminoallyl)-UTP and subsequently coupled to Cy3 and Cy5 dyes according to manufacture's protocol of Ambion mirVana miRNA labelling kit

growth_protocol: Human umbilical vein endothelial cells (HUVECs) were isolated ) and cultured in gelatin-coated flasks in medium 199 (M199) with Earles' balanced salts and 0.68 mM glutamine, 20 mM HEPES, 20% FCS, 15 μg/ml endothelial cell growth supplement (ECGS; BD Biosciences; Bedford, MA), 50 U/ml penicillin, 50 U/ml streptomycin, and 15 μg/ml heparin (Sigma; St. Louis, MO). The protocol for the harvesting of HUVECs was performed with approval from the Royal Adelaide Hospital Research Ethics Committee.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: 6.4 × 104 cells/160 μl HUVEC medium were plated onto 100 μl gelled bovine type I collagen (Celtrix Laboratories; Palo Alto, CA) in 96-well flat-bottomed microtiter plates. Capillary tube formation was stimulated by the addition of 20 ng/ml phorbol myristate acetate (PMA) and an antibody against α2β1-integrin (RMAC11), which promotes the formation of complex multicellular tubes.

value: HUVEC


title: ang_011


title: NCTC8325 1314::ermB

description: Gene expression in SAOUHSC_01313-1314 mutated strain

value: SAOUHSC_01313-1314 mutated strain


title: 42WT

city: Coral Gables

first: Nanette

middle: Hahr

last: Bishopric

state: FL

address: 10 Edgewater Drive, Apt. 9A

department: Medicine

institute: Nanette Bishopric

description:
raw data: block 10-12
low molecular weight RNA

hyb_protocol: Labeled LMW RNA samples were hybridized to the MicroRNA microarrays according to conditions recommended in the Flash Tag RNA labeling Kit manual.

scan_protocol: The microarrays were scanned on an Axon Genepix 4000B scanner, and data was extracted from images using GenePix V4.1 software.

data_processing: Date for 4 arrays were extracted from a single microarray image in to a single text file using GenePix version 4.1 software. The raw text files were split in to four subfiles based on block assignment. Blocks 1-3 contained data for array A, block 4-6 contained data for array B, block 7-9 contained data for array C, and block 10-12 contained data for array D. Spot intensities were obtained for the 2340 features on each microarray by subtracting the median local background from the median local foreground for each spot. Detection Thresholds for each array were determined by calculating the 10% trim mean intensity of the negative controls spots and adding 5X the standard deviation of the background (non-spot area). The spot intensities and the Threshold (T) were transformed by taking the log (base 2) of each value. The normalization factor (N) for each microarray was determined by obtaining the 20% trim mean of the mouse probes intensities above threshold in all samples. The log2-transformed spot intensities for all 2340 features were normalized, by subtracting N from each spot intensity, and scaled by adding the grand mean of N across all microarrays. The mean probe intensities for each of the 1141 oligonucleotide probes were then determined by averaging the duplicate spot intensities. Spots flagged as poor quality during data extraction were omitted prior to averaging.

label: Oyster-550 Dendrimer

source_name: Left ventricular myocardium, wildtype

label_protocol: The samples were DNAse digested and low-molecular weight (LMW) RNA was isolated by ultrafiltration through YM-100 columns (Millipore) and subsequent purification using the RNeasy MinElute Clean-Up Kit (Qiagen). The LMW RNA samples were 3’-end labeled with Oyster-550 fluorescent dye using the Flash Tag RNA labeling Kit (Genisphere).

growth_protocol: Mice littermates were maintained in standard housing in a virus and antigen-free facility until weaning.

extract_protocol: RNA was extracted from left ventricular homogenates in Trizol following the manufacturer's instructions.

treatment_protocol: 34TG, 33TG and 39TG mice are heterozygous for a transgene expressing HA-tagged human EP300 driven by the murine alpha-myosin heavy chain promoter; 42WT littermate is null (Wei JQ et al, Circulation 2008).  Mice were sacrificed at 13 weeks of age.

value: Heart

tag: line

tag: date of birth


title: U2OS, Untreated 8 hours rep5

tag: gender


title: ang_009


title: CD86 positive DCs LLC/SeV/GFP rep1

description: Gene expression after 2days in LLC/SeV/GFP cell injected-mouse tumor draining lymph nodes

source_name: Axillary lymph nodes, LLC/SeV/GFP, replicate1

value: LLC/SeV/GFP


title: 39TG

description:
raw data: block 7-9
low molecular weight RNA

source_name: Left ventricular myocardium, Ep300 transgenic


title: ang_008


title: 34TG

description:
raw data: block 1-3
low molecular weight RNA


title: 33TG

description:
raw data: block 4-6
low molecular weight RNA


title: CD86 positive DCs LLC rep1

description: Gene expression after 2days in LLC cell injected-mouse tumor draining lymph nodes

source_name: Axillary lymph nodes, LLC, replicate1

value: female

value: LLC


title: JH_100927_Tweak_MDA-MB-436_202_Control_0_25hrs

source_name: MDA-MB-436 cells, treated with 0ng_per_ml TWEAK for 0.25hours

tag: cell line origin

value: mammary

value: ductal carcinoma

tag: race

value: caucasian


title: ang_004


title: ang_007


title: LncapAto (miRNA)

city: Northbrook

first: Michael

last: Falduto

state: IL

address: 1808 Janke, Unit M

institute: GenUs BioSystems, Inc.

hyb_protocol: Labeled target was applied to Agilent miRNA 8x15K arrays (Design ID#029297) and hybridized overnight.

scan_protocol: Slides were washed and 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).

source_name: Lncap cells, treated with 10uM of Atorvastatin

label_protocol: Total RNA samples were dephosphorylated, denatured, and end-labeled according to Agilent's protocols.

growth_protocol: Human prostate cancer cells (PC3 cells and LNCaP cells) were purchased from the American Type Culture Collection (Manassas, VA).  All prostate cancer cell lines were cultured in RPMI medium containing 10% FBS. PC3 and LNCaP cells were seeded in culture dishes so that cells reached ~30% confluence on Day 2.

extract_protocol: Total RNA to be used in both mRNA and miRNA assays was isolated and purified using the Ribopure RNA isolation kit (Invitrogen, Grand Island, NY).

treatment_protocol: On day 2, culture medium was replaced and cells were exposed to Atorvastatin (ATO) (10 µM) for 24 h.

value: LNCaP


title: LncapCtrl (miRNA)

source_name: Lncap cells, no treatment control


title: PC3Ctrl (miRNA)

source_name: PC3 cells, no treatment control


title: PC3Ato (miRNA)

source_name: PC3 cells, treated with 10uM of Atorvastatin


title: ang_005


title: 2012 mock treated grapes, EL38,biological replicate 3

city: Lisboa

first: Ana

middle: Margarida

last: Fortes

address: Campus da FCUL

department: Plant Biology

country: Portugal

description: Gene expression data from skin and pulp of mock treated grapes at harvest stage

hyb_protocol: Each sample was added to a hybridization solution containing 100mM 2-(N-morpholino) ethanesulfonic acid, 1 M NaCl, and 20mM of EDTA in the presence of 0.01% of Tween-20 to a final cRNA concentration of 0.05 µg/ml. Hybridization was performed for 16 h at 45ºC .

scan_protocol: Each microarray was washed and stained with streptavidin-phycoerythrin in a Fluidics station 450 (Affymetrix) and scanned at 1.56 µm resolution in a GeneChip® Scanner 3000 7G System (Affymetrix).

data_processing: Robust Muti-array Analysis (RMA, Bioconductor) algorithm was used for background correction, normalization and expression levels summarization. Next, differential expression analysis was performed with the Bayes t-statistics from the linear models for Microarray data (limma), included in the affylmGUI package. P-values were corrected for multiple-testing using the Benjamini-Hochberg’s method

organism: Vitis vinifera

source_name: harvest stage grapes

label_protocol: cDNA was synthesized from 4 µg of total RNA using One-cycle target labeling and control reagents (Affymetrix, Santa Clara, CA) to produce biotin labeled cRNA which was then fragmented at 94ºC for 35 min into 35-200 bases in length

growth_protocol: Grapevine plants were growing at Plansel´s vines located in Montemor-o-Novo (Southern Portugal).

extract_protocol: Total RNA was isolated essentially as described by Rerie et al. (1991, Mol Gen Genet) using phenol/ chloroform with modifications

treatment_protocol: Berries of Trincadeira grapevine cultivar (Vitis vinifera L.), were collected at 10 pm during 2010 season at Plansel´s vineyard in Montemor (Alentejo, Southern Portugal). The application of polyamine oxidase inhibitor, guazatine, on berries was done at 7 pm and their sampling were performed based on E-L system, developed by (Coombe, 1995). It was considered five developmental stages for the applications (EL32; EL34; EL35; EL36 and EL37) and three stages (EL35; EL36 and EL38) for collection. Four biological replicates at each stage were done by gathering 40-50 berries from 4 to 5 plants; they were immediately frozen in liquid nitrogen, and stored at -80 ºC until further use.

value: pulp and skin

value: mock

tag: variety

value: Trincadeira


title: 2011 mock treated grapes, EL38,biological replicate 2


title: ang_006


title: 2010 mock treated grapes, EL38,biological replicate 1


title: 2010 guazatine treated grapes, EL38,biological replicate 1

description: Gene expression data from skin and pulp of guazatine treated grapes at harvest stage

value: guazatine


title: marrow CD3 T cells_pre_R2 (responder)

city: Boston

first: Pavan

last: Bachireddy

address: 77 Avenue Louis Pasteur

institute: Dana-Farber Cancer Institute

description: Gene expression data from marrow derived CD3+ T cells in responder (R2) before DLI

hyb_protocol: Total RNA was amplified followed by cDNA synthesis (Ovation Pico WTA System V2, NuGEN, San Carlos, CA) and samples were hybridized to Affymetrix U133A+ 2.0 arrays (Santa Cruz, CA) at the DFCI Microarray Core Facility

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

data_processing: The data were analyzed using Robust Multichip Average (RMA) as in implemented in the R package affy. Probe level data were averaged to the gene level, and the resulting values were converted to a log2 scale for downstream analysis.

source_name: marrow derived CD3+ T cells, before DLI

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

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

treatment_protocol: BMMCs from DLI responders and nonresponders were thawed, and CD3+ T cells were enriched using magnetic bead sorting (Miltenyi Biotec).

tag: patient

value: responder

value: bone marrow-derived CD3+ T cells


title: marrow CD3 T cells_post_R4 (responder)

description: Gene expression data from marrow derived CD3+ T cells in responder (R4) after DLI

source_name: marrow derived CD3+ T cells, after DLI


title: marrow CD3 T cells_pre_NR1 (nonresponder)

description: Gene expression data from marrow derived CD3+ T cells in non-responder (NR1) before DLI

value: nonresponder


title: ang_003

value: HUVEC


title: ang_002


title: 2010 guazatine treated grapes, EL38,biological replicate 2


title: marrow CD3 T cells_pre_R3 (responder)

description: Gene expression data from marrow derived CD3+ T cells in responder (R3) before DLI


title: marrow CD3 T cells_post_R2 (responder)

description: Gene expression data from marrow derived CD3+ T cells in responder (R2) after DLI


title: marrow CD3 T cells_post_NR1 (nonresponder)

description: Gene expression data from marrow derived CD3+ T cells in non-responder (NR1) after DLI


title: marrow CD3 T cells_pre_R4 (responder)

description: Gene expression data from marrow derived CD3+ T cells in responder (R4) before DLI


title: marrow CD3 T cells_post_R3 (responder)

description: Gene expression data from marrow derived CD3+ T cells in responder (R3) after DLI


title: marrow CD3 T cells_post_R1 (responder)

description: Gene expression data from marrow derived CD3+ T cells in responder (R1) after DLI


title: marrow CD3 T cells_post_NR2 (nonresponder)

description: Gene expression data from marrow derived CD3+ T cells in non-responder (NR2) after DLI


title: 2010 guazatine treated grapes, EL38,biological replicate 3


title: marrow CD3 T cells_pre_NR2 (nonresponder)

description: Gene expression data from marrow derived CD3+ T cells in non-responder (NR2) before DLI


title: MCF7_PALB2_RA 24h_rep3

city: Miami

first: Alessandro

last: Gardini

address: 1501 NW 10 Avenue

department: Sylvester Comprehensive Cancer Center

institute: University of Miami

description: PALB2 24_rep3

hyb_protocol: Biotin labeled aRNA at 750ng was hybridized  to  Illumina HumanHT-12V4 expression Beadchip with Illumina  HumanHT-12 v4 Expression BeadChip Kit(cat# BD-103-0204 )         Subsequent steps include washing, blocking, and streptavadin-Cy3 staining of the beadchip.

scan_protocol: Fluorescence emission by Cy3 is quantitatively detected with Illumina BeadArray Reader (scan software : Illumina BeadSacn) and GenomeStudio  software provides results in standard file format.

data_processing: Intensity raw data were log2 transformed and normalized by quantile normalization using BeadArray package (version 2.8.1) on R.

source_name: MCF7_PALB2_RA 24h

label_protocol: samples were biotin-labeled using the TargetAmp™-Nano Labeling Kit for Illumina Expression BeadChip (Epicentre)

growth_protocol: MCF7 cells were infected with sh vectors and selected in puromycin for 3 days, medium was DMEM + 10% FBS

extract_protocol: cells were harvested and lysed in RLT buffer (Qiagen), total RNA was extracted with Rneasy mini kit

treatment_protocol: cells were treated with 10 microM of all-trans Retinoic acid

value: breast adenocarcinoma cells

tag: infected with

value: PALB2 shRNAs

tag: cell subtype

value: PALB2 depleted cells

tag: stimulated with

value: 10microM Retinoic Acid (RA) for 24 h


title: MCF7_BRCA1_unstimuated_rep3

description: BRCA1 0_rep3

tag: cell line

tag: cell type

value: BRCA1 shRNAs

value: BRCA1 depleted cells

value: none (unstimulated)


title: marrow CD3 T cells_pre_R1 (responder)

description: Gene expression data from marrow derived CD3+ T cells in responder (R1) before DLI


title: MCF7_SCR_RA 24h_rep3

description: SCR 24_rep3

source_name: MCF7_SCR_RA 24h

value: non-targeting (SCR) shRNAs

value: control cells


title: MCF7_SCR_unstimuated_rep3

description: SCR 0_rep3


title: MCF7_BRCA1_RA 24h_rep2

description: BRCA1 24_rep2

source_name: MCF7_BRCA1_RA 24h


title: MCF7_PALB2_unstimuated_rep2

description: PALB2 0_rep2


title: MCF7_SCR_RA 24h_rep2

description: SCR 24_rep2


title: MCF7_BRCA1_RA 24h_rep3

description: BRCA1 24_rep3


title: MCF7_BRCA1_unstimuated_rep2

description: BRCA1 0_rep2


title: MCF7_SCR_unstimuated_rep2

description: SCR 0_rep2


title: MCF7_SCR_RA 24h_rep1

description: SCR 24_rep1


title: U2OS, TWEAK treated 15 minute rep5

source_name: U2OS, TWEAK treated 15 minute

tag: disease

value: osteosarcoma

value: Female

tag: ethnicity

value: Caucasian

tag: tweak treated

value: yes

tag: time point

value: 15 min


title: MCF7_PALB2_RA 24h_rep2

description: PALB2 24_rep2


title: MCF7_SCR_unstimuated_rep1

description: SCR 0_rep1


title: MCF7_PALB2_unstimuated_rep1

description: PALB2 0_rep1


title: MCF7_PALB2_unstimulated rep3

description: PALB2 0h_rep3

hyb_protocol: Biotin labeled aRNA at 750ng was hybridized  to  Illumina HumanHT-12V4 expression Beadchip with Illumina  HumanHT-12 v4 Expression BeadChip Kit (cat# BD-103-0204 )         Subsequent steps include washing, blocking, and streptavadin-Cy3 staining of the beadchip.

scan_protocol: Fluorescence emission by Cy3 is quantitatively detected with Illumina BeadArray Reader (scan software : Illumina BeadSacn) and GenomeStudio  software provides results in standard file format

data_processing: Intensity raw data were log2 transformed and normalized by quantile normalization using BeadArray package  (version 2.8.1) on R.

treatment_protocol: cells were treated with 10 ng/ml of TNF-alpha for 1h


title: MCF7_p65_TNF 1h rep3

description: p65 1h_rep3

value: p65/RelA shRNAs

value: p65/RelA depleted cells

value: 10ng/ml of TNF-alpha for 1h


title: MCF7_SCR_TNF 1h rep3

description: SCR 1h_rep3

value: breast adenocarcinoma cells


title: MCF7_p65_TNF 1h rep2

description: p65 1h_rep2


title: MCF7_BRCA1_unstimuated_rep1

description: BRCA1 0_rep1


title: MCF7_BRCA1_RA 24h_rep1

description: BRCA1 24_rep1


title: MCF7_PALB2_RA 24h_rep1

description: PALB2 24_rep1

value: PALB2 shRNAs


title: MCF7_PALB2_TNF 1h rep3

description: PALB2 1h_rep3

value: PALB2 depleted cells


title: MCF7_BRCA1_TNF 1h rep3

description: BRCA1 1h_rep3


title: MCF7_p65_unstimulated rep2

description: p65 0h_rep2


title: MCF7_p65_unstimulated rep3

description: p65 0h_rep3


title: MCF7_SCR_unstimulated rep3

description: SCR 0h_rep3


title: MCF7_SCR_TNF 1h rep2

description: SCR 1h_rep2


title: MCF7_PALB2_TNF 1h rep2

description: PALB2 1h_rep2


title: MCF7_BRCA1_unstimulated rep3

description: BRCA1 0h_rep3


title: MCF7_BRCA1_unstimulated rep2

description: BRCA1 0h_rep2


title: MCF7_p65_TNF 1h rep1

description: p65 1h_rep1


title: MCF7_BRCA1_TNF 1h rep2

description: BRCA1 1h_rep2


title: MCF7_p65_unstimulated rep1

description: p65 0h_rep1


title: MCF7_PALB2_unstimulated rep1

description: PALB2 0h_rep1


title: MCF7_SCR_unstimulated rep2

description: SCR 0h_rep2


title: MCF7_PALB2_unstimulated rep2

description: PALB2 0h_rep2


title: MCF7_PALB2_TNF 1h rep1

description: PALB2 1h_rep1


title: MCF7_BRCA1_TNF 1h rep1

description: BRCA1 1h_rep1


title: MCF7_SCR_TNF 1h rep1

description: SCR 1h_rep1


title: MCF7_SCR_unstimulated rep1

description: SCR 0h_rep1


title: MCF10A MOCK

city: Lyon

first: stéphane

last: ansieau

address: 28 rue Laennec

department: Centre Léon Bérard

country: France

institute: Inserm U590

description: MCF10A cells

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol with iScan from Illumina

data_processing: The data were normalised using quantile normalisation with Genome Studio Software 2010 from Illumina

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

growth_protocol: HMEC cells were grown in DMEM/HAMF12 medium supplemented with penicillin/strptomycin, L-glutamin, 10% fetal bovine serum, 10ng/ml hEGF, 0.5µg/ml hydrocortisone and 10µg/ml insulin. HMEC cells were either cultured on standard coated dishes or plated 24h in Ultra-Low Adherence dishes (Corning). MCF-10A cells were obtained from ATCC (Manassas, Virginia) and cultured in DMEM/F12 (Invitrogen) supplemented with 5% donor horse serum, 20 ng/ml epidermal growth factor (EGF), 10 μg/ml insulin, 100 μg/ml hydrocortisone, 1 ng/ml cholera toxin, 50 U/ml penicillin, and 50 mg/ml streptomycin.

extract_protocol: Total RNAs were extract with the Qiagen RNeasy minikit (Qiagen) in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: transducer


title: MCF10A-SNAIL3

description: MCF10A cells transduced with SNAIL3

value: express SNAIL3


title: MCF10A-SNAIL2

description: MCF10A cells transduced with SNAIL2

value: express SNAIL2


title: HMEC-hTERT-MOCK LA #B

description: human mammary epithelial cells, immortalized with hTERT, plated 24h in low-adherent condition.

source_name: HMEC

value: HMEC

tag: treatment

value: immortalized with hTERT and cultured in low-adherence (LA)


title: HMEC-hTERT-SNAIL1 LA #A

description: human mammary epithelial cells, immortalized with hTERT and transduced with SNAIL1, plated 24h in low-adherent condition.

value: express SNAIL1


title: MCF10A-SNAIL1

description: MCF10A cells transduced with SNAIL1


title: HMEC-hTERT-SNAIL3 #A

description: human mammary epithelial cells, immortalized with hTERT and transduced with SNAIL3

value: immortalized with hTERT


title: HMEC-hTERT-SNAIL2 #C

description: human mammary epithelial cells, immortalized with hTERT and transduced with SNAIL2


title: HMEC-hTERT-MOCK LA #A


title: HMEC-hTERT-SNAIL2 #B


title: MCF-7_pcDNA3.1-PinX1

city: Guangzhou

first: Rong

last: Shi

address: 7th Floor, Building of Life Science, 1023 Sha Tai Nan Road

department: Institute of Genetic Engineering

institute: Southern Medical University

description: Gene expression

hyb_protocol: The hybridization solution for each sample was prepared using a Gene Expression Hybridization Kit (Agilent, USA) and 1.5 µg of the labeled cRNAs. The hybridization solution was applied on the Human LncRNA Array V2.0 (Arraystar, USA) in a SureHyb chamber (Agilent, USA), and the hybridization was conducted in a hybridization oven (Agilent, USA) at 65°C for 17 hours. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: the slide was scanned using a G2505C Scanner (Agilent, USA)

data_processing: Raw signal intensities were normalized in quantile method by GeneSpring GX v11.5.1, and low intensity mRNAs and LncRNAs were filtered (mRNA or LncRNAs that at least 2 out of 2 samples have flags in Present or Marginal were chosen for further analysis).

source_name: MCF-7 cells stably overexpression of pcDNA3.1-PinX1

label_protocol: mRNA was purified using a mRNA-ONLY Eukaryotic mRNA Isolation Kit (Epicentre, USA); subsequently, Cyanine-3-CTP (NEB, USA) was incorporated and the fluorescent cRNA  was linearly amplified using a Quick Amp Labeling Kit, One-Color (Agilent, USA). The labeled cRNA were then purified using a RNeasy Mini Kit (Qiagen, Germany)

growth_protocol: MCF-7 breast cancer cells were grown in DMEM high glucose medium supplemented with 10% fetal bovine serum and 1% Penicillin-Streptomycin.

extract_protocol: Total RNA was extracted from the pcDNA3.1-PinX1 group and empty vector group of MCF-7 cells using a Takara RNAiso plus kit

treatment_protocol: The plasmid pcDNA3.1-PinX1 and pcDNA3.1 empty vector were  transfected separately into MCF-7 cells by Lipofectamine 2000 , a fresh cell culture medium containing 700 µg/mL of G418 was applied for screening, the cell clones were harvested and those with a high expression level were selected for microarray analysis.

tag: cell

value: breast cancer cell


title: HMEC-hTERT-SNAIL2 LA #B


title: HMEC-hTERT-SNAIL1 #C

description: human mammary epithelial cells, immortalized with hTERT and transduced with SNAIL1


title: MCF7_BRCA1_unstimulated rep1

description: BRCA1 0h_rep1

value: BRCA1 shRNAs

value: BRCA1 depleted cells

value: none (unstimulated)


title: HMEC-hTERT-SNAIL1 #A


title: HMEC-hTERT-SNAIL1 #B


title: HMEC-hTERT-SNAIL3 #C


title: HMEC-hTERT MOCK #A

description: human mammary epithelial cells, immortalized with hTERT


title: MCF-7_pcDNA3.1 empty vector

description: Gene expression

source_name: MCF-7 cells stably overexpression of pcDNA3.1 empty vector


title: HMEC-hTERT MOCK #B


title: HMEC-hTERT MOCK #C


title: HMEC-hTERT-SNAIL2 #A


title: Normal RCC H1H2 3110_12158_22B

city: philadelphia

first: lijoy

last: mathew

state: pa

address: 438 brb II/III, curie blvd

institute: university of pennsylvania

description: miRNA expression from adjacent renal tissue

hyb_protocol: 10 ug of cRNA were hybridized for 16-18 hr at 48C on Affymetrix miRNA_v1 Array. Ran FS450_0003 fluidics script

scan_protocol: GeneChip 3000 7G scanner was used for the arrays

data_processing: Raw data was processed using Partek Genomic Suite version 6.3. Data was normalized using default RMA settings. A 1-way-ANOVA analysis between tumor and adjacent normal tissue of the human probesets was carried out. miRNAs that changed at least 2-fold in either direction at false discovery rate of 5% were considered differentially expressed.

source_name: Normal

label_protocol: 1ug needed per sample for Affymetrix miRNA and FlashTag labeling

growth_protocol: Frozen human tissue samples

extract_protocol: RNA was isolated with Qiagen's miRNEasy with on Column DNAse treatment

treatment_protocol: Frozen human tissue samples

tag: disease state

value: adjacent normal tissue

tag: tissue

value: adjacent renal tissue

tag: subject


title: Tumor RCC H1H2 3110_12161_25A

description: miRNA expression from H1H2 tumor tissue

source_name: Tumor

value: renal cancer

value: H1H2 tumor tissue


title: Tumor RCC H1H2 3110_12159_23A

description: miRNA expression from H1H2 tumor tissue


title: Normal RCC H1H2 3110_12162_26B


title: Normal RCC H1H2 3110_12156_20B


title: Tumor RCC H1H2 3110_12157_21A

description: miRNA expression from H1H2 tumor tissue


title: Normal RCC H2only 3110_12152_16B


title: Normal RCC H1H2 3110_12153_17A


title: Tumor RCC H1H2 3110_12154_18B

description: miRNA expression from H1H2 tumor tissue


title: Tumor RCC H2only 3110_12151_15A

description: miRNA expression from H2 tumor tissue

value: H2 tumor tissue


title: Tumor RCC H2only 3110_12149_13A

description: miRNA expression from H2 tumor tissue


title: Tumor RCC H2only 3110_12147_11A

description: miRNA expression from H2 tumor tissue


title: Normal RCC H2only 3110_12150_14B


title: HMEC-hTERT-SNAIL3 #B


title: Tumor RCC H2only 3110_12143_7A

description: miRNA expression from H2 tumor tissue


title: Normal RCC H2only 3110_12142_6B


title: Tumor RCC H2only 3110_12145_9A

description: miRNA expression from H2 tumor tissue


title: Normal RCC H2only 3110_12144_8B


title: Tumor RCC H2only 3110_12141_5A

description: miRNA expression from H2 tumor tissue


title: Normal RCC H2only 3110_12138_2B


title: Normal RCC H2only 3110_12146_10B


title: Normal RCC H2only 3110_12140_4B


title: Normal RCC H1H2 3110_12160_24B


title: Tumor RCC H2only 3110_12139_3A

description: miRNA expression from H2 tumor tissue


title: Tumor RCC H1H2 3110_12155_19A

description: miRNA expression from H1H2 tumor tissue


title: Runx2_pDC

city: New York

first: Catherine

last: Sawai

state: New York

address: 701 W. 168th Street - HHSC 9-906

institute: Columbia University Medical Center

hyb_protocol: Biotinylated DNA probe was made according to the standard Affymetrix protocol.

scan_protocol: Arrays were scanned according to the Affymetrix protocol.

data_processing: Gene level RMA

source_name: Bone marrow pDCs from Runx2-/- fetal liver chimeras

label_protocol: We used the Ambion WT Labelling Kit as per manufacturer's instructions. We used 250 ng/sample of starting total RNA.

extract_protocol: Total RNA was extracted from Trizol LS according to manufacturer's instructions.

treatment_protocol: Total BM cells were stained with antibodies to CD11b, CD11c, BST2, and B220. CD11b- BST2+ B220+ pDCs were FACS sorted on BD FACS Aria.

tag: genotype

value: Bone marrow pDCs from fetal liver chimeras


title: Wildtype_pDC

source_name: Bone marrow pDCs from fetal liver chimeras

value: wild type


title: Tumor RCC H2only 3110_12137_1A

description: miRNA expression from H2 tumor tissue


title: H19 siRNA (simH19) tranfected into C2C12 myoblasts rep2

city: ct

first: haifeng

last: zhang

address: new haven

department: pathology

institute: yale

description: C2C12 cells were seeded in same numbers and cultured in same condition.

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C (GeneChip® WT Terminal Labeling and Hybridization User Manual, P/N 702808 Rev.5, Affymetrix). GeneChips were washed and stained according to the standard Affymetrix protocol(GeneChip® Expression Wash, Stain and Scan User Manual For Cartridge Arrays,P/N 702731 Rev.3,Affymetrix).

scan_protocol: The stained chips were read and analyzed with GeneChip Scanner 3000 (Affymetrix).

data_processing:
RMA signal estimates from Expression Console software
probe group file: MoGene-1_0-st-v1.r2.pgf

source_name: Wild type C2C12 cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (GeneChip® WT Terminal Labeling and Hybridization User Manual, P/N 702808 Rev.5, Affymetrix).

growth_protocol: C2C12(ATCC, CRL-1772) cells were cultured using standard protocols provided by the ATCC

extract_protocol: Total RNA was isolated using RNeasy mini kits(QIAGEN) according to the manufacturer's protocol

treatment_protocol: C2C12 myoblast cells were maintained in growth medium(DMEM containing 10% fetal bovine serum). To induce differentiation, cells were reseeded in 12-well dishes and after reaching ~90% desity, the medium was changed to DMEM containing 2% horse serum(differentiation medium)

tag: transfection

value: H19 siRNA (simH19)


title: control siRNA (siCon) tranfected into C2C12 myoblasts rep2

value: control siRNA (siCon)


title: MCF7_PALB2_unstimuated_rep3

description: PALB2 0_rep3

value: breast adenocarcinoma cells

tag: infected with

value: PALB2 shRNAs

value: PALB2 depleted cells


title: PCOS Endometrium Endothelial Cell_140.UC271+-

city: San Francisco

first: Linda

last: Giudice

state: CA

address: 513 Parnassus Ave. HSE 1619

department: OBGYN and RS

institute: University of California, San Francisco

hyb_protocol: Microarrays were hybridized, washed, stained, and scanned according to the protocol described in the WT sense target labeling assay manual from Affymetrix (version 4; FS450_0007).

scan_protocol: Microarrays were hybridized, washed, stained, and scanned according to the protocol described in WT Sense Target Labeling Assay Manual from Affymetrix (Version 4; FS450_0007) at the UCSF Gladstone Genomics Core Facility.

data_processing:
GeneSpringGX 11, Microarray Technology: Affymetrix.ExonExprChip.HuGene-1_0-st-v1, Summarization Algorithm: ExonRMA16, Normalization: Quantile, Baseline Transformation: median of all samples
Summarization Algorithm: RMA16. Transcript Level: Core. Baseline to median of all samples

label: Biotin

source_name: PCOS Endometrial Biopsy

label_protocol: Reverse transcription and amplification of isolated RNA into cDNA was performed using NuGEN WT-Ovation Exon FFPE System V2 (NuGen, San Carlos, CA). The integrity of resultant cDNA was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies), and individual samples meeting yield and quality standards were further processed and hybridized to Affymetrix Human Gene 1.0 ST arrays (Affymetrix, Cleveland, OH), probing 36,079 genes.

growth_protocol:
Tissue Processing and Fluorescence Activated Cell Sorting (FACS) of Endometrial Cell Populations:
Tissue biopsies were divided into two fresh tissue samples processed separately for fluorescence activated cell sorting (FACS) and for histological examination in formalin-fixed, paraffin embedded tissue. Tissue processing for viable cell isolation and FACS analysis were performed as previously described (15). Briefly, enzymatically dissociated endometrial cells were incubated in blocking buffer (PBS with 40% human serum [HS] and 1% bovine serum albumin [BSA]) for 30min then labeled with the following fluorochrome-conjugated antibodies (BD Biosciences, San Jose, CA) in PBS containing 10% HS and 1% BSA: cluster of differentiation 45 (CD45, PE-Cy7 anti-CD45) at 1:20 dilution to label contaminating leukocytes for their removal; epithelial cell adhesion molecule (EPCAM, allophycocyanin anti-EPCAM) at 1:20 dilution to label eEP; cluster of differentiation 146 (CD146 or melanoma cell adhesion molecule [MCAM], CD146, fluorescein isothiocyanate anti-MCAM) at 1:5 dilution to label eEN/perivascular cells; beta-type platelet-derived growth factor receptor (PDGFRB, phycoerythrin (PE) anti-PDGFRB) at 1:5 dilution to label eSF. eMSCs were sorted using double labeling for CD146 and PDGFRB antibodies respectively, both at 1:5 dilutions. The cell suspension was sorted using a FACS Aria II with FACS Diva software (BD Biosciences). The FACS-sorted cell pellets were stored at -80C until RNA extraction.
FACS analyzed sorted cell populations were subject to RNA isolation and purification, with DNAse treatment, using Pico Pure RNA Isolation Kit

extract_protocol: Total RNA was isolated form FACS-sorted cell populations and purified using the Arcturus PicoPure RNA Isolation Kit (Applied Biosystems, Life Technologies Corporation, Carlsbad, CA) following manufacturer´s instructions. An additional DNase treatment was performed using the RNase-Free DNase Set (Qiagen, Valencia, CA).

tag: gender

value: female

value: endometrium

tag: phase

value: PCOS

value: Endothelial Cell


title: H19 siRNA (simH19) tranfected into C2C12 myoblasts rep1


title: H19 siRNA (simH19) tranfected into C2C12 myoblasts rep3


title: PCOS Endometrium Mesenchymal Cell_120.PC11++

value: Mesenchymal Cell


title: PCOS Endometrium Stromal Cell_134.UC271-+

value: Stromal Cell


title: control siRNA (siCon) tranfected into C2C12 myoblasts rep3


title: control siRNA (siCon) tranfected into C2C12 myoblasts rep1


title: Normal RCC H2only 3110_12148_12B

value: adjacent normal tissue

value: adjacent renal tissue


title: PCOS Endometrium Epithelial Cell_109.PC08_EpCAM

value: Epithelial Cell


title: PCOS Endometrium Endothelial Cell_103.PC01+-


title: PCOS Endometrium Stromal Cell_118.PC11-+


title: PCOS Endometrium Stromal Cell_104.PC07-+


title: PCOS Endometrium Endothelial Cell_107.PC07+-


title: PCOS Endometrium Epithelial Cell_119.PC11_EpCAM


title: PCOS Endometrium Mesenchymal Cell_106.PC07++


title: PCOS Endometrium Epithelial Cell_105.PC07_EpCAM


title: PCOS Endometrium Epithelial Cell_138.UC271 EpCAM


title: PCOS Endometrium Stromal Cell_101.PC01-+


title: PCOS Endometrium Mesenchymal Cell_102.PC01++


title: Control Endometrium Endothelial Cell_036.UC209+-

source_name: Proliferative Stage Endometrial Biopsy

value: Proliferative Stage


title: Control Endometrium Stromal Cell_033.UC-209-+


title: Control Endometrium Epithelial Cell_034.UC209_EpCAM


title: Control Endometrium Mesenchymal Cell_031.UC208++


title: Control Endometrium Stromal Cell_029.UC208-+


title: Control Endometrium Stromal Cell_ETB65 -+


title: Control Endometrium Epithelial Cell_030.UC208_EpCAM


title: Control Endometrium Mesenchymal Cell_035.UC209++)


title: Control Endometrium Endothelial Cell_032.UC208+-


title: Control Endometrium Epithelial Cell_014.UC182_EpCAM


title: Control Endometrium Endothelial Cell_016.UC182+-new


title: Control Endometrium Mesenchymal Cell_015.UC182++new


title: Control Endometrium Stromal Cell_013.UC182-+


title: Control Endometrium Mesenchymal Cell_ETB65 ++


title: Control Endometrium Endothelial Cell_ETB65 +-


title: T cell medip moderate aggressivity.12

type: genomic

city: Montreal

first: Moshe

last: Szyf

state: Quebec

address: McIntyre Medical Building, 3655 Promenade Sir William Osler, Room 1309

department: Pharmacology

country: Canada

institute: McGill University

description: comparison of T cell DNA methylation in individuals with different aggressivity trajectories

hyb_protocol: All the steps of hybridization and washing were performed following the Agilent protocol for chip-on-chip analysis.

scan_protocol: Scanning was performed using the Agilent Technologies Scanner G2505B.

data_processing: The value is background subtracted and log2-quantile normalized using the limma Bioconductor package.

molecule: genomic DNA

source_name: T cell meDIP moderate aggressivity

label_protocol: 2ug of each of the input and bound fractions were labeled for the microarray hybridization. Cy3-dUTP and Cy5-dUTP (Perkin Elmer) were used to label the input and the bound fractions respectively. Cot-1 DNA was added to the hybridization mix to minimize cross-hybridization between repetitive elements.

extract_protocol: 20 ml of blood were drawn in EDTA coated-tubes for each subjects. PBMC (whole mononuclear cells from peripheral blood) andT cell isolation procedures were adapted from Current Protocols in Immunology (1997, sections 7.1 and 7.5.1-7.5.11). Briefly, PBMC isolation was done by centrifugation with Ficoll-Paque (GE healthcare) and washed twice with HBSS (Hanks balanced salt solution, GIBCO). T cells were isolated from the PBMCs by immunomagnetic isolation using CD3 dynabeads (Dynal). The beads were washed 3 times and incubated with the PBMCs for 45 min on a rotator at 4°C. Coated CD3+ cells with the dynabeads were isolated using a strong magnet (Steam Cell Technology) and washed 5 times with PBS/FBS. CD3+ cells coated with the dynabeads were then frozen at -80°C until DNA extraction. T cells DNA was extracted with Wizard® Genomic DNA Purification kit (Promega) following the manufacturer's protocol. For MeDIP analysis, 2 µg of T cell DNA was sonicated and methylated DNA was immunoprecipitated with 10 µg of anti-5methylCytosine (Calbiochem). Prior to sonication, two control plasmids were added to the DNA (6ug each), an unmethylated GFP plasmid and an in vitro methylated Luciferase plasmid. The DNA-antibody complex was immunoprecipitated with 5 mg protein A and the methylated DNA was eluted with 150 µl of TE at 1.5% SDS. The input and bound fractions were then purified and validated by PCR analysis for two control genes, H19 (methylated control) and ²-actin (unmethylated control) and the two added plasmid, GFP (unmethylated control) and Luciferase (in vitro methylated control) using the following primers: H19: forward (5'-TTGGTGGAACACGCTGTGATCA-3'), reverse (5'-GAGCCGCACCAGGTCTTCAG-3'); ²-actin: forward (5'-AGCCATAAAAGGCAACTTTCG-3'), reverse (5'-CCAACGCCAAAACTCTCCC-3'); GFP: forward (CCAACGCCAAAACTCTCCC), reverse (AGCCATAAAAGGCAACTTTCG); Luciferase: forward (5'-AGAGATACGCCCTGGTTCC-3'), reverse (5'-CCAACACCGGCATAAAGAA-3'). The input and bound fractions were then amplified in triplicate using the Whole Genome Amplification kit (Sigma). The amplified input and bound fractions were labeled for microarray hybridization with either Cy3-dUTP or Cy5-dUTP (Perkin Elmer) respectively using the CGH labeling kit (Invitrogen) following the manufacturer's instructions.

value: T cell

tag: phenotype

value: moderate aggressivity

tag: chip antibody

value: anti-5 methylcytosine antibody (Calbiochem, Cat. # NA81, Lot:D00048001)

source_name: T cell input DNA moderate aggressivity


title: T cell medip high aggressivity.13

source_name: T cell meDIP high aggressivity

tag: cell type

value: high aggressivity

source_name: T cell input DNA high aggressivity


title: T cell medip moderate aggressivity.10


title: T cell medip high aggressivity.11


title: T cell medip moderate aggressivity.11


title: T cell medip low aggressivity.12

source_name: T cell meDIP low aggressivity

value: low aggressivity

source_name: T cell input DNA low aggressivity


title: T cell medip moderate aggressivity.9


title: 0.3 nM ORC + genomic DNA

city: Madison

middle: Anne

last: Fox

state: WI

address: 420 Henry Mall

department: Biomolecular Chemistry

institute: University of Wisconsin - Madison

hyb_protocol: Hybing upon tiled arrays were performed by Nimblegen.

scan_protocol: Scanning and imaging of arrays were performed by Nimblegen.

data_processing: Log2 ratios for each array were spatially normalized so that the histograms were centered at zero.

organism: Saccharomyces cerevisiae

source_name: 0.3 nM ORC shifted genomic DNA

label_protocol: Labeling performed by Nimblegen.

extract_protocol: ORC shifted genomic DNA was extracted from acrylamide gels through a NaOAC crush/soak protocol.

tag: sample composition

value: genomic DNA, recombinant ORC

tag: orc concentration

value: 0.3 nM ORC

tag: molecule composition

value: ORC shifted sheared, genomic DNA

source_name: 0.3 nM unshifted genomic DNA

value: genomic DNA, no ORC

value: unshifted sheared, genomic DNA


title: 3 nM ORC + genomic DNA

source_name: 3 nM ORC shifted genomic DNA

value: 3 nM ORC

source_name: 3 nM unshifted genomic DNA


title: 30 nM ORC + genomic DNA

source_name: 30 nM ORC shifted genomic DNA

value: 30 nM ORC

source_name: 30 nM unshifted genomic DNA


title: T cell medip moderate aggressivity.7


title: T cell medip high aggressivity.7


title: T cell medip high aggressivity.10


title: T cell medip moderate aggressivity.8


title: T cell medip high aggressivity.12


title: T cell medip moderate aggressivity.4


title: T cell medip chronic aggressivity.18

source_name: T cell meDIP chronic aggressivity

value: chronic aggressivity

source_name: T cell input DNA chronic aggressivity


title: T cell medip moderate aggressivity.5


title: T cell medip low aggressivity.13


title: T cell medip high aggressivity.8


title: T cell medip high aggressivity.9


title: T cell medip moderate aggressivity.6


title: T cell medip chronic aggressivity.22


title: T cell medip chronic aggressivity.17


title: T cell medip low aggressivity.10


title: T cell medip chronic aggressivity.23


title: T cell medip chronic aggressivity.19


title: T cell medip low aggressivity.11


title: T cell medip chronic aggressivity.16


title: T cell medip chronic aggressivity.21


title: Lp-WT-2, liver, biological replicate 2

city: seattle

first: Joseph

last: Nadeau

state: WA

address: 720 Broadway

institute: Pacific Northwest Research Institute

description: wild-type control for Lp-Het

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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.
To identify differentially expressed genes for each test mutant and its wild-type control, we used Variance-Modeled Posterior Inference with Regional Exponentials (VAMPIRE) with FDR=0.05. Each of the gene lists identified with VAMPIRE for each of the five mutants was interpreted biologically by associating them with canonical pathways using Ingenuity Pathways Analysis (IPA) software.

source_name: liver from female mouse 6-8 weeks of age, Lp-WT

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Approximately 0.5 cm3 of liver was excised from each of the experimental female mice and placed in RNA-Later solution (Ambion) at 4ºC overnight for RNA stabilization. The Qiagen RNeasy Mini Kit was used to isolate total RNA from liver. This method included a DNAse treatment to digest genomic DNA.

tag: strain

tag: genotype/variation

value: wild-type

value: female

value: liver


title: Lp-WT-1, liver, biological replicate 1

description: wild-type control for Lp-Het


title: T cell medip low aggressivity.7


title: Lp-WT-4, liver, biological replicate 4

description: wild-type control for Lp-Het


title: Lp-Het-2, liver, biological replicate 2

description:
Resistant
mutant: Lp-Het-2
control: Lp-WT-2

source_name: liver from female mouse 6-8 weeks of age, Lp-Het

value: Heterozygote

tag: response to dietary fa

value: Resistant


title: T cell medip low aggressivity.8

value: T cell


title: Lp-Het-4, liver, biological replicate 4

description:
Resistant
mutant: Lp-Het-4
control: Lp-WT-4


title: Lp-Het-1, liver, biological replicate 1

description:
Resistant
mutant: Lp-Het-1
control: Lp-WT-1


title: T cell medip moderate aggressivity.3

value: moderate aggressivity

value: anti-5 methylcytosine antibody (Calbiochem, Cat. # NA81, Lot:D00048001)


title: Lp-Het-3, liver, biological replicate 3

description:
Resistant
mutant: Lp-Het-3
control: Lp-WT-3


title: T cell medip chronic aggressivity.14


title: T cell medip chronic aggressivity.15


title: Lp-WT-3, liver, biological replicate 3

description: wild-type control for Lp-Het


title: T cell medip moderate aggressivity.2


title: CBA-2, liver, biological replicate 2

description: wild-type control for Ct

source_name: liver from female mouse 6-8 weeks of age, CBA

value: CBA/CaJ


title: CBA-4, liver, biological replicate 4

description: wild-type control for Ct


title: CBA-3, liver, biological replicate 3

description: wild-type control for Ct


title: Ct-4, liver, biological replicate 4

description:
Resistant
mutant: Ct-4
control: CBA-4

source_name: liver from female mouse 6-8 weeks of age, Ct

value: ct

value: random bred closed colony; all individuals considered to be ct/ct homozygotes


title: T cell medip moderate aggressivity.1

source_name: T cell meDIP moderate aggressivity

source_name: T cell input DNA moderate aggressivity


title: T cell medip chronic aggressivity.13


title: Ct-3, liver, biological replicate 3

description:
Resistant
mutant: Ct-3
control: CBA-3


title: ER5_cy3_s17b

first: Marjorie

middle: F.

last: Oleksiak

address: 4600 Rickenbacker Causeway

department: Marine Biology and Fisheries

hyb_protocol: Labeled aRNA samples (2 pmol dye/µl) were hybridized to slides in 10 µl of hybridization buffer [50% formamide buffer, 5x SSPE, 1% sodium dodecyl sulfate, 0.2 mg/ml bovine serum albumin, 1 mg/ml denatured salmon sperm DNA (Sigma), and 1 mg/ml RNase free poly(A) RNA (Sigma)] for 44 hours at 42° C.  Slides were prepared for hybridization by blocking in 5% ethanolamine, 100 mM Tris pH 7.8, and 0.1% SDS added just before use for 30 minutes at room temperature, washed for one hour in 4x SSC, 0.1% SDS at 50° C, and then boiled for 2 minutes in distilled water to denature the cDNAs.

scan_protocol: Arrays were scanned using  a ScanArray Express 4000 (Perkin Elmer).  Resulting 16 bit Tiff Images were quantified using ImaGene® (Biodiscovery, Inc.) spotfinding software.

data_processing: Log2 measures of loess normalized gene expression data were normalized using a linear mixed model in JMP Genomics 3.2 (SAS, Cary, NC, USA) to remove the effects of dye (fixed effect) and array (random effect) following a joint regional and spatial Lowess transformation in MAANOVA version 0.98.8 for R to account for both intensity and spatial bias.  The model was of the form yij = μ  + Ai + Dj + (AxD)ij + εij where, yij is the signal from the ith array with dye j, μ is the sample mean, Ai and Dj are the overall variation in arrays (arrays 1-80) and dyes (Cy3 and Cy5), (AxD)ij is the array x dye interaction and εij is the stochastic error.  Because we were not interested in differences due to developmental stage, we analyzed residuals from the above model separately by time (e.g., separately for times 5, 10 and 15 dpf).  Thus, residuals from this model were used for gene-by-gene analyses by time of population and treatment effects, using population, treatment and dye as fixed effects, and array as a random effect.  The model was rijn = μ  + Ai + Dj + Pn + Tk + PnxTk + εijn where Pn is the nth population and Tk is the kth treatment (DMSO or PCB-126).  For all mixed model analyses, we used a false discovery rate (FDR) p-value of < 0.01 to control for multiple testing

organism: Fundulus heteroclitus

source_name: ER5_1 ug/L BNF + 100 ug/L ANF_cy3

label_protocol: RNA for hybridization was prepared by one round of amplification (aRNA) using Ambion’s Amino Allyl MessageAmp aRNA Kit to form copy template RNA by T7 amplification.  Amino-allyl UTP was incorporated into targets during T7 transcription, and resulting amino-allyl aRNA was coupled to Cy3 and Cy5 dyes (GE Healthcare, Piscataway, NJ, USA).

growth_protocol: Adult Fundulus were collected from both a reference site at King’s Creek, near the mouth of the York River in Gloucester County, Virginia (37°17’52.4”N, 76°25’31.4”W) and from a contaminated site on the Elizabeth River in Portsmouth, Virginia (36°48’27.48”N, 76°17’35.77”W).  Adult fish were depurated for 12 months in a recirculating system containing artificial seawater (ASW 25 ppt) prepared from Instant Ocean® (Mentor, OH).  Fish were kept at 23-25° C on a photoperiod of 14:10 L:D and fed a daily diet of Tetramin® Tropical Fish Food (Tetra Systems, Blacksburg VA, USA) and newly hatched brine shrimp (Artemia, Brine Shrimp Direct, Ogden, UT).  Killifish embryos were obtained from in vitro fertilization of pooled oocytes mixed with pooled milt from multiple males.  Embryos were examined 24 hours post fertilization (hpf) for viability and placed individually into 20 mL glass scintillation vials with 10 mL of treatment solution.

extract_protocol: Individual embryo RNA was extracted using a TRIzol buffer (Invitrogen, Carlsbad, CA, USA) followed by purification using the Qiagen RNeasy Mini Kit (Qiagen Inc., Valencia, CA, USA).

treatment_protocol: Dimethyl sulfoxide (DMSO), ANF, BNF and ethoxyresorufin were purchased from Sigma-Aldrich (St. Louis, MO).  Killifish embryos were exposed to ANF (0, 50 or 100 µg/L) with or without 1 µg/L BNF.  Individual embryos of parents from both populations were exposed to the treatment solution or to the DMSO vehicle control from 24 to 120 hpf  (n = 20).  In all of the treatment groups, DMSO concentration was maintained at less than 0.03%.  At 120 hpf, embryos were removed from the dosing solution and placed into vials containing clean ASW.

tag: population

value: Elizabeth River, VA

tag: pollutant sensitivity

value: Whole embryo

tag: treatment

value: 1 ug/L BNF + 100 ug/L ANF

tag: Stage


title: T cell medip chronic aggressivity.20


title: ERC_cy5_s17b

tag: tissue

value: vehicle control (DMSO)


title: ER5_cy5_s46a

source_name: ER5_1 ug/L BNF + 100 ug/L ANF_cy5


title: ER4_cy3_s46a

source_name: ER4_1 ug/L BNF + 50 ug/L ANF_cy3

value: 1 ug/L BNF + 50 ug/L ANF


title: T cell medip chronic aggressivity.12

value: chronic aggressivity


title: Ct-2, liver, biological replicate 2

description:
Resistant
mutant: Ct-2
control: CBA-2


title: CBA-1, liver, biological replicate 1

description: wild-type control for Ct

value: wild-type


title: T cell medip low aggressivity.2

source_name: T cell meDIP low aggressivity

value: low aggressivity

source_name: T cell input DNA low aggressivity


title: T cell medip low aggressivity.5


title: ER4_cy5_s17a

source_name: ER4_1 ug/L BNF + 50 ug/L ANF_cy5


title: T cell medip low aggressivity.6


title: Ct-1, liver, biological replicate 1

description:
Resistant
mutant: Ct-1
control: CBA-1

value: female

value: liver


title: T cell medip low aggressivity.3


title: ER3_cy3_s17a

source_name: ER3_100 ug/L ANF_cy3

value: Resistant

value: 100 ug/L ANF


title: Apob-3, liver, biological replicate 3

description:
Resistant
mutant: Apob-3
control: B6-3

source_name: liver from female mouse 6-8 weeks of age, Apob

value: Heterozygote


title: Apob-4, liver, biological replicate 4

description:
Resistant
mutant: Apob-4
control: B6-4


title: T cell medip chronic aggressivity.11

value: T cell

value: anti-5 methylcytosine antibody (Calbiochem, Cat. # NA81, Lot:D00048001)


title: T cell medip low aggressivity.1


title: T cell medip low aggressivity.4


title: T cell medip low aggressivity.9


title: Apob-1, liver, biological replicate 1

description:
Resistant
mutant: Apob-1
control: B6-1


title: ER2_cy3_s4c

source_name: ER2_50 ug/L ANF_cy3

value: 50 ug/L ANF


title: ER2_cy5_s5b

source_name: ER2_50 ug/L ANF_cy5


title: ER1_cy3_s5b

source_name: ER1_1 ug/L BNF_cy3

value: 1 ug/L BNF


title: Apob-2, liver, biological replicate 2

description:
Resistant
mutant: Apob-2
control: B6-2


title: T cell medip chronic aggressivity.9

source_name: T cell meDIP chronic aggressivity

source_name: T cell input DNA chronic aggressivity


title: ER1_cy5_s5c

source_name: ER1_1 ug/L BNF_cy5

value: Elizabeth River, VA


title: Cd-WT-4, liver, biological replicate 4

description: wild-type control for Cd-Het

source_name: liver from female mouse 6-8 weeks of age, Cd-WT


title: Erc_cy3_s5c

value: Whole embryo


title: T cell medip chronic aggressivity.10


title: Cd-WT-3, liver, biological replicate 3

description: wild-type control for Cd-Het


title: ER3_cy5_s4c

source_name: ER3_100 ug/L ANF_cy5


title: Cd-WT-2, liver, biological replicate 2

description: wild-type control for Cd-Het


title: T cell medip chronic aggressivity.8


title: KCc_cy5_s41d

value: King's Creek, VA

value: Sensitive


title: T cell medip chronic aggressivity.5


title: Cd-WT-1, liver, biological replicate 1

description: wild-type control for Cd-Het


title: T cell medip chronic aggressivity.6


title: KC5_cy3_s41d

source_name: KC5_1 ug/L BNF + 100 ug/L ANF_cy3

value: 1 ug/L BNF + 100 ug/L ANF


title: Cd-Het-3, liver, biological replicate 3

description:
Responsive
mutant: Cd-Het-3
control: Cd-WT-3

source_name: liver from female mouse 6-8 weeks of age, Cd-Het

value: Responsive


title: Cd-Het-1, liver, biological replicate 1

description:
Responsive
mutant: Cd-Het-1
control: Cd-WT-1


title: KC5_cy5_s2a

source_name: KC5_1 ug/L BNF + 100 ug/L ANF_cy5


title: KC4_cy3_s2a

source_name: KC4_1 ug/L BNF + 50 ug/L ANF_cy3

value: 1 ug/L BNF + 50 ug/L ANF


title: KC4_cy5_s6d

source_name: KC4_1 ug/L BNF + 50 ug/L ANF_cy5


title: T cell medip chronic aggressivity.7

value: chronic aggressivity


title: T cell medip chronic aggressivity.4


title: Cd-Het-4, liver, biological replicate 4

description:
Responsive
mutant: Cd-Het-4
control: Cd-WT-4

value: female


title: T cell medip chronic aggressivity.2


title: T cell medip chronic aggressivity.1


title: KC3_cy3_s6d

source_name: KC3_100 ug/L ANF_cy3


title: B6-4, liver, biological replicate 4

description: wild-type control for both Pax3Sp2H and Apobtm1Unc heterozygous mice

source_name: liver from female mouse 6-8 weeks of age, B6

value: wild-type

value: liver


title: B6-3, liver, biological replicate 3


title: KC3_cy5_s3d

source_name: KC3_100 ug/L ANF_cy5

value: 100 ug/L ANF


title: KC2_cy3_s3d

source_name: KC2_50 ug/L ANF_cy3


title: KC2_cy5_s17c

source_name: KC2_50 ug/L ANF_cy5


title: T cell medip chronic aggressivity.3


title: B6-2, liver, biological replicate 2


title: DBA/2_0w_rep2

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

description: Gene expression of leukocyte derived from DBA/2 after 0 week CAWS administration

hyb_protocol: Before hybridization, 825ng labeled cRNA of each product was fragmented and mixed with hybridization buffer according to the manufacturer's protocol (Agilent Technologies). Hybridizations were done for approximately 17h at 65°C. The slides were washed according to the manufacturer's manual, and scanning of microarrays was performed with 5µm resolution using a DNA microarray laser scanner (Agilent Technologies).

scan_protocol: The array was scanned using Agilent G2505B DNA microarray scanner.

data_processing: The image files were extracted using Agilent Feature Extraction software version 9.5.3.1.

label_protocol: RNA labeling was performed with a Fluorescent Linear Amplification Kit (Agilent Technologies). In brief, cDNA was reverse transcribed from 500ng of total RNA (pooled sample from 16 healthy control patients) with an oligo-dT-T7 promoter primer and MMLV-RT. Second strand synthesis was carried out with random hexamers. Fluorescent antisense cRNA was synthesized with cyanine 3-CTP (Cy3-CTP) and T7 polymerase. The fluorescent-labeled antisense cRNA was purified with RNeasy columns (Qiagen) according to manufacturer's protocols and resuspended in water. The purified products were quantified at A552nm for Cy3-CTP with Agilent 2100 Bioanalyzer (Agilent Technologies).

extract_protocol: Total RNA of leukocytes from whole blood of B6 and DBA/2mice was stabilized by RNAlater (Ambion), and then isolated using the LeukoLOCK, a total RNA Isolation System (Ambion, Austin, TX, USA), according to the manufacturer’s instructions.

treatment_protocol: At 2, 4, 8 or 9 weeks after CAWS injection, we sacrificed the survived mice for preparation of mRNA from PBMC.

value: leukocyte

value: male

tag: after administration

value: 0 week

tag: replicate

value: biological replicate 2


title: T cell medip high aggressivity.5

source_name: T cell meDIP high aggressivity

value: T cell

value: high aggressivity

value: anti-5 methylcytosine antibody (Calbiochem, Cat. # NA81, Lot:D00048001)

source_name: T cell input DNA high aggressivity


title: KC1_cy3_s17c

source_name: KC1_1 ug/L BNF_cy3

value: King's Creek, VA

value: Whole embryo

value: 1 ug/L BNF


title: T cell medip high aggressivity.6


title: T cell medip high aggressivity.1


title: Pax3-3, liver, biological replicate 3

description:
Responsive
mutant: Pax3-3
control: B6-3

source_name: liver from female mouse 6-8 weeks of age, Pax3

value: Heterozygote

tag: gender

value: Responsive


title: T cell medip high aggressivity.3

tag: phenotype


title: T cell medip high aggressivity.4

tag: chip antibody


title: B6-1, liver, biological replicate 1


title: KCc_cy3_s2d

value: Sensitive

value: vehicle control (DMSO)


title: Pax3-4, liver, biological replicate 4

description:
Responsive
mutant: Pax3-4
control: B6-4

value: female


title: DBA/2_4w_rep2

description: Gene expression of leukocyte derived from DBA/2 after 4 weeks CAWS administration

value: 4 weeks


title: ER5_cy5_s16c

source_name: ER5_1 ug/L BNF + 100 ug/L ANF_cy5

value: Elizabeth River, VA

value: Resistant

value: 1 ug/L BNF + 100 ug/L ANF


title: Pax3-2, liver, biological replicate 2

description:
Responsive
mutant: Pax3-2
control: B6-2

value: liver


title: ER5_cy3_s6b

source_name: ER5_1 ug/L BNF + 100 ug/L ANF_cy3


title: KCc_cy5_s6b


title: T cell medip high aggressivity.2

tag: cell type


title: JH_101019_TweakCaki_17_Vehicle_Mouse

city: Watertown

first: Mary

last: Simcox

address: 500 Arsenal St

institute: Forma Therapeutics

description:
Human cells were implanted as xenografts.  Treated xenografts were removed and processed for hybridization to mouse chips to investigate mouse stromal infiltration.
Kidney, carcinoma_kidney_CC, Caucasian, Male

hyb_protocol: Hybridization followed manufacturer's recommendations

scan_protocol: GC_scanner3000 Affymetrix scanner was utilized with AGCC

data_processing: Statistical analysis was done by simple linear modeling using Partek Genomics Suite software.  A model containing fixed effects for treatment and time and their interaction was calculated, and contrasts were constructed for the overall TWEAK vs. vehicle treatment comparison and for each individual time point.  Relevant gene lists of interesting genes and patterns of genes were created.  Lists were generated for probesets where treatment induced changes had significance p values of <0.05 and which change at least 1.8-fold at 2 time points.

source_name: CAKI-1 cells, treated with Vehicle_Control for 24hours

label_protocol: 5'IVT Express kit was followed according to manufacturer's recommendations

growth_protocol: Human cancer cell lines used in tumor xenograft studies were obtained from the ATCC.  These cells were cultured according to instructions provided by the ATCC.  Cell numbers for implantation were determined in previous tumor growth kinetic studies.  Matrigel (BD Biosciences, Bedford, MA) was added 1:1 to cold sterile PBS for cells requiring this supplement for growth in a final cell inoculum volume of 0.2 ml per mouse.  Cells were implanted subcutaneously (sc) in the right hind flank of each mouse using a 1 cc syringe and 26 gauge needle.  All tumor cell lines tested negative for mycoplasma within 1 week of tumor implantation.  After implantation mice were randomized according to tumor volume so that all groups had similar starting mean tumor volumes of 100 – 200 mm3.

extract_protocol: total RNA was extracted using Qiagen Rneasy Minikit.

treatment_protocol: Anti-TWEAK antibodies were stored at -80° C, thawed and diluted immediately prior to use with Histidine buffer (10 mM Histidine, 140 mM NaCl, pH 6.0) and administered intraperitoneally (ip) to tumor-bearing mice.  The anti-VEGF antibody, B20.4.1, was obtained from Roche Diagnostics GmbH (Penzberg, Germany).  All stock antibodies were kept frozen at -80° C, thawed prior to use and diluted to the desired concentration for in vivo administration.

tag: cell line

tag: tissue type

value: xenograft

value: kidney carcinoma

tag: implant host

value: Athymic, Nu/Nu nude mice


title: DBA/2_2w_rep2

description: Gene expression of leukocyte derived from DBA/2 after 2 weeks CAWS administration

value: leukocyte

value: male

value: 2 weeks

tag: strain

value: biological replicate 2_technical replicate2


title: DBA/2_9w_rep2

description: Gene expression of leukocyte derived from DBA/2 after 9 weeks CAWS administration

value: 9 weeks

value: biological replicate 2


title: JH_101019_TweakCaki_11_Vehicle_Mouse


title: JH_101019_TweakCaki_15_Vehicle_Mouse


title: B6_9w_rep2

description: Gene expression of leukocyte derived from B6 after 9 weeks CAWS administration


title: JH_101019_TweakCaki_16_Vehicle_Mouse


title: Pax3-1, liver, biological replicate 1

description:
Responsive
mutant: Pax3-1
control: B6-1

tag: genotype/variation

value: Heterozygote

value: Responsive


title: B6_0w_rep2_tech2

description: Gene expression of leukocyte derived from B6 after 0 week CAWS administration

value: 0 week

value: biological replicate 2_technical replicate1


title: KC5_cy3_s16c

source_name: KC5_1 ug/L BNF + 100 ug/L ANF_cy3

value: King's Creek, VA

value: Sensitive

value: Whole embryo


title: JH_101019_TweakCaki_19_TW212_Mouse

source_name: CAKI-1 cells, treated with TW212 for 24hours


title: B6_8w_rep2

description: Gene expression of leukocyte derived from B6 after 8 weeks CAWS administration

value: 8 weeks


title: Cd-Het-2, liver, biological replicate 2

description:
Responsive
mutant: Cd-Het-2
control: Cd-WT-2

source_name: liver from female mouse 6-8 weeks of age, Cd-Het

value: female

tag: response to dietary fa

value: liver


title: DBA/2_8w_rep2

description: Gene expression of leukocyte derived from DBA/2 after 8 weeks CAWS administration


title: KC5_cy5_s6c

source_name: KC5_1 ug/L BNF + 100 ug/L ANF_cy5

tag: population

value: 1 ug/L BNF + 100 ug/L ANF


title: KC1_cy5_s2d

source_name: KC1_1 ug/L BNF_cy5

tag: pollutant sensitivity

value: 1 ug/L BNF


title: JH_101019_TweakCaki_14_TW212_Mouse

value: xenograft

value: kidney carcinoma

value: Athymic, Nu/Nu nude mice


title: DBA/2_0w_rep1

source_name: leukocyte derived from DBA/2 after 0 week CAWS administration

value: leukocyte

value: male

value: biological replicate 1


title: ER4_cy3_s6c

source_name: ER4_1 ug/L BNF + 50 ug/L ANF_cy3

value: Elizabeth River, VA

value: Resistant

tag: treatment

value: 1 ug/L BNF + 50 ug/L ANF


title: JH_101019_TweakCaki_12_TW212_Mouse


title: JH_101019_TweakCaki_18_TW212_Mouse


title: JH_120319_Tweak_Cell_Lines_072

description: Pancreas, carcinoma_pancreas_ADC, Unspecified sex, C57BL/6  cells grown orthotopically.

source_name: Pan02 cells, treated with 100ng_per_ml for 24hours

growth_protocol: Cells were seeded in appropriate media with 2% heat-inactivated FBS in humidified 95% air, 5% CO2 overnight in 6-well plates at 37oC.

treatment_protocol: 100 ng/ml TWEAK or media control was added on day 2 to subconfluent cells. For each time point and treatment, five replicates were generated.  One replicate from each treatment group was used for QC as assessed with immunoblotting for Fn14 expression. Samples were collected in all cell lines after 4 h, 8 h or 24 h of stimulation or control treatment with five replicates. For the U2OS and MDA-MB-436 arrays, 15 min and 1 h time points were also collected.

value: pancreatic carcinoma


title: B6_4w_rep2

description: Gene expression of leukocyte derived from B6 after 4 weeks CAWS administration

value: 4 weeks

value: biological replicate 2


title: DBA/2_8w_rep1

source_name: leukocyte derived from DBA/2 after 8 weeks CAWS administration

value: 8 weeks


title: KC3_cy3_s5d

source_name: KC3_100 ug/L ANF_cy3

value: King's Creek, VA

value: Sensitive

value: Whole embryo

value: 100 ug/L ANF

tag: Stage


title: ER3_cy3_s4b

source_name: ER3_100 ug/L ANF_cy3

tag: tissue


title: KC4_cy5_s4b

source_name: KC4_1 ug/L BNF + 50 ug/L ANF_cy5


title: ER3_cy5_s5d

source_name: ER3_100 ug/L ANF_cy5


title: ER4_cy5_s4d

source_name: ER4_1 ug/L BNF + 50 ug/L ANF_cy5


title: DBA/2_4w_rep1

source_name: leukocyte derived from DBA/2 after 4 weeks CAWS administration

tag: after administration


title: DBA/2_9w_rep1

source_name: leukocyte derived from DBA/2 after 9 weeks CAWS administration

value: 9 weeks

tag: replicate


title: JH_120319_Tweak_Cell_Lines_070

source_name: Pan02 cells, treated with 100ng_per_ml for 8hours


title: DBA/2_2w_rep1

source_name: leukocyte derived from DBA/2 after 2 weeks CAWS administration

tag: gender

value: 2 weeks


title: JH_120319_Tweak_Cell_Lines_071


title: JH_120319_Tweak_Cell_Lines_069

source_name: Pan02 cells, treated with 0ng_per_ml for 4hours


title: B6_0w_rep1

source_name: leukocyte derived from B6 after 0 week CAWS administration

value: 0 week


title: KC4_cy3_s4d

source_name: KC4_1 ug/L BNF + 50 ug/L ANF_cy3


title: JH_120319_Tweak_Cell_Lines_065

source_name: Pan02 cells, treated with 100ng_per_ml for 4hours


title: ER2_cy3_s3c

source_name: ER2_50 ug/L ANF_cy3

value: 50 ug/L ANF


title: JH_120319_Tweak_Cell_Lines_063


title: ER2_cy5_s2c

source_name: ER2_50 ug/L ANF_cy5


title: KC3_cy5_s3c

source_name: KC3_100 ug/L ANF_cy5


title: KC2_cy3_s2c

source_name: KC2_50 ug/L ANF_cy3


title: JH_120319_Tweak_Cell_Lines_066

source_name: Pan02 cells, treated with 0ng_per_ml for 8hours


title: KC2_cy5_s6a

source_name: KC2_50 ug/L ANF_cy5


title: ER1_cy3_s6a

source_name: ER1_1 ug/L BNF_cy3

value: 1 ug/L BNF


title: JH_120319_Tweak_Cell_Lines_062


title: B6_4w_rep1

source_name: leukocyte derived from B6 after 4 weeks CAWS administration

value: leukocyte

value: male

value: biological replicate 1