title: Tg(αMHC-MerCreMer), left ventricle, 4 TAM injection, rep1

description: left ventricle, 4 TAM injection, rep1


title: LNCaP-R1881-24h-rep2

status: Public on Sep 01 2010

type: RNA

city: Cambridge

first: Charlie

middle: Edward

last: Massie

state: CAMBS

address: CRUK CRI, Robinson Way

department: Oncology

country: United Kingdom

institute: Cambridge University and Cancer Research UK

description:
replicate 2
4117151102_F_1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The Illumina HumanWG v2 BeadArrays consist of two replicate sections that we treat as technical replicate arrays for the purposes of this analysis due to small but systematic shifts between sections that need to be addressed in the normalization. Data were analysed from the raw bead-level using the beadarray software, with spatial artefacts identified and removed automatically (BASH) and curated manually (Cairns et al., 2008; Dunning et al., 2007)

label: biotin

molecule: total RNA

organism: Homo sapiens

label_protocol: cRNA was generated and biotin labelled using the Illumina TotalPrep RNA Amplification Kit, according to the manufacturers instructions.

growth_protocol: LNCaP cells grown in phenolred-free RPMI supplemented with 10% charcaol dextran stripped FBS for 72h prior to treatement.

extract_protocol: Total RNA was extracted using Trizol and isopropanol precipitation, according to the manufacturers instructions. Quality control was performed with an Agilent Bioanalyser.

treatment_protocol: 1nM R1881 (synthetic androgen) or 0.1% ethanol (vehicle control) were added and RNA samples harvested at time points between 0.5h and 24h, as indicated.

tag: cell type

value: prostate cancer

tag: agent

tag: time point

tag: growth media

value: RPMI + 10% charcoal stripped FBS for 72h before treatment


title: Tg(αMHC-MerCreMer), left ventricle, 1 ctrl injection, rep1

city: Oslo

first: Karina

last: Hougen

address: Kirkeveien 166

country: Norway

institute: University of Oslo

description: left ventricle, 1 ctrl injection, rep1

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 h at 450C in the hybridization oven at 60 rpm, as described by manufacturer (Affymetrix).

scan_protocol: Gene Chips were scanned using the Hewlett Packard GeneArray Scanner 3000 7G.

data_processing: The data were preprocessed using the robust multi-array average (RMA) package in R with default settings, i.e. quantile normalization and RMA background correction

organism: Mus musculus

source_name: left ventricle, 1 ctrl injection

label_protocol: According to standard Affymetrix protocol (FS450_00007).

extract_protocol: Total RNA was isolated with an RNeasy mini kit according to the manufacturer's instructions.

treatment_protocol: Mice were anesthetized with isoflurane and sacrificed by cervical dislocation. Left ventricle was quickly excised and immediately frozen in liquid nitrogen.

value: 1 day

value: control

tag: gender

value: male

tag: genotype

value: Tg(αMHC-MerCreMer)

tag: age

value: 9-13 weeks

tag: tissue

value: left ventricle myocardium


title: Tg(αMHC-MerCreMer), left ventricle, 4 TAM injection, rep3

description: left ventricle, 4 TAM injection, rep3

source_name: left ventricle, 4 TAM injection

value: 4 days

value: tamoxifen

value: female


title: Tg(αMHC-MerCreMer), left ventricle, 4 ctrl injection, rep1

description: left ventricle, 4 ctrl injection, rep1

source_name: left ventricle, 4 ctrl injection


title: Tg(αMHC-MerCreMer), left ventricle, 4 ctrl injection, rep2

description: left ventricle, 4 ctrl injection, rep2


title: LNCaP-R1881-24h-rep1

description:
replicate 1
4117151201_E_1


title: LNCaP-R1881-24h-rep2, replicate section

description:
replicate 2
4117151102_F_2


title: LNCaP-R1881-23h-rep1

description:
replicate 1
4117151167_D_1


title: Tg(αMHC-MerCreMer), left ventricle, 1 TAM injection, rep3

description: left ventricle, 1 TAM injection, rep3

source_name: left ventricle, 1 TAM injection


title: LNCaP-R1881-22h-rep1, replicate section

description:
replicate 1
4117151142_C_2


title: Tg(αMHC-MerCreMer), left ventricle, 1 TAM injection, rep1

description: left ventricle, 1 TAM injection, rep1


title: LNCaP-R1881-24h-rep1, replicate section

description:
replicate 1
4117151201_E_2


title: LNCaP-R1881-20h-rep2, replicate section

description:
replicate 2
4117151033_B_2


title: H siJMJD2B#1

city: Oxford

first: Francesca

last: Buffa

address: The Weatherall Institute of Molecular Medicine

institute: University of Oxford

description: H siJMJD2B#1: Hypoxia (1% O2) with siRNA#1 against JMJD2B

hyb_protocol: Biotin labelled, amplified cRNA (1500 ng per array) was hybridized to the Illumina HumanWG-6_V3 BeadChip according to the Manufacturer's instructions (Illumina, Inc., San Diego, CA).

scan_protocol: Arrays were scanned with an Illumina BeadArray Reader using BeadScan 3.5.49.29917 software and direct hybridization assay, according to the Manufacturer's instructions.

data_processing: Array data processing and analysis was performed using Illumina BeadStudio 3.2.6 software using the average chip normalization method.

label_protocol: Biotinylated cRNA were generated following manufacturer protocols using the Illumina TotalPrep96 Amplification Kit from Ambion # 4393543

growth_protocol: Cells were grown in DMEM with 10% fetal bovine serum, penicillin (50 IU/ml) and streptomycin sulphate (50 μg/ml).

extract_protocol: Total RNA was extracted using RNAeasy kit from Qiagen

treatment_protocol: 1% oxygen treatment for 16 hours

tag: cell line


title: Tg(αMHC-MerCreMer), left ventricle, 1 ctrl injection, rep3

description: left ventricle, 1 ctrl injection, rep3


title: Tg(αMHC-MerCreMer), left ventricle, 1 ctrl injection, rep2

description: left ventricle, 1 ctrl injection, rep2


title: LNCaP-R1881-22h-rep1

description:
replicate 1
4117151142_C_1


title: H siJMJD2B#2

description: H siJMJD2B#2: Hypoxia (1% O2) with siRNA#2 against JMJD2B


title: LNCaP-R1881-23h-rep1, replicate section

description:
replicate 1
4117151167_D_2


title: LNCaP-R1881-16h-rep2

description:
replicate 2
4117151201_C_1


title: LNCaP-R1881-20h-rep1

description:
replicate 1
4117151199_A_1


title: LNCaP-R1881-20h-rep1, replicate section

description:
replicate 1
4117151199_A_2


title: LNCaP-R1881-13h-rep1

description:
replicate 1
4117151199_E_1


title: LNCaP-R1881-16h-rep2, replicate section

description:
replicate 2
4117151201_C_2


title: LNCaP-R1881-20h-rep2

description:
replicate 2
4117151033_B_1


title: LNCaP-R1881-13h-rep1, replicate section

description:
replicate 1
4117151199_E_2


title: LNCaP-R1881-18h-rep1, replicate section

description:
replicate 1
4117151142_E_2


title: LNCaP-R1881-14h-rep1

description:
replicate 1
4117151033_F_1


title: N siJMJD2B#1

description: N siJMJD2B#1: Normoxic conditions with siRNA#1 against JMJD2B


title: LNCaP-R1881-12h-rep2, replicate section

description:
replicate 2
4117151168_D_2


title: LNCaP-R1881-17h-rep1

description:
replicate 1
4117151033_D_1


title: H Control#1

description: H Control#1: Hypoxia (1% O2) with siRNA control replicate 1


title: LNCaP-R1881-12h-rep2

description:
replicate 2
4117151168_D_1


title: LNCaP-R1881-10h-rep1, replicate section

description:
replicate 1
4117151201_A_2


title: LNCaP-R1881-16h-rep1

description:
replicate 1
4117151168_B_1


title: LNCaP-R1881-19h-rep1, replicate section

description:
replicate 1
4117151167_F_2


title: LNCaP-R1881-16h-rep1, replicate section

description:
replicate 1
4117151168_B_2


title: LNCaP-R1881-12h-rep1

description:
replicate 1
4117151144_C_1


title: LNCaP-R1881-11h-rep1

description:
replicate 1
4117151102_B_1


title: LNCaP-R1881-10h-rep1

description:
replicate 1
4117151201_A_1


title: LNCaP-R1881-8h-rep2

description:
replicate 2
4117151144_E_1


title: N Control#1

description: N Control#1: Normoxic conditions with siRNA control replicate 1


title: LNCaP-R1881-15h-rep1, replicate section

description:
replicate 1
4117151144_A_2


title: N Control#2

description: N Control#2: Normoxic conditions with siRNA control replicate 2


title: LNCaP-R1881-12h-rep1, replicate section

description:
replicate 1
4117151144_C_2


title: LNCaP-R1881-9h-rep1

description:
replicate 1
4117151168_F_1


title: LNCaP-R1881-19h-rep1

description:
replicate 1
4117151167_F_1


title: LNCaP-R1881-7h-rep1, replicate section

description:
replicate 1
4117151199_C_2


title: LNCaP-R1881-8h-rep2, replicate section

description:
replicate 2
4117151144_E_2


title: LNCaP-R1881-9h-rep1, replicate section

description:
replicate 1
4117151168_F_2


title: LNCaP-R1881-8h-rep1, replicate section

description:
replicate 1
4117151102_D_2


title: LNCaP-R1881-4h-rep2, replicate section

description:
replicate 2
4117151201_F_2


title: LNCaP-R1881-5h-rep1, replicate section

description:
replicate 1
4117151142_A_2


title: H Control#2

description: H Control#2: Hypoxia (1% O2) with siRNA control replicate 2


title: LNCaP-R1881-17h-rep1, replicate section

description:
replicate 1
4117151033_D_2


title: LNCaP-R1881-4h-rep1, replicate section

description:
replicate 1
4117151168_E_2


title: DEHP 50ug/ml, rep2

city: Washington

first: Nikki

middle: Gillum

last: Posnack

state: Please select a region, state or province.

address: 111 Michigan Ave, NW

country: USA

institute: Childrens National Hospital

description: Gene expression data from cardiomyocyte monolayers treated with 50 ug/mL DEHP, 3 days.

hyb_protocol: Following fragmentation, 15 ug of cRNA was hybridized for 16 hr at 45C on the Rat 1.0 ST arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Data was exported from Affymetrix software (CEL files). Analysis was conducted using GeneSpring GX10. The GeneSpring software performed a baseline transformation, which takes the median of all samples. Quantile normalization (RMA) and summarization were then performed.

organism: Rattus norvegicus

source_name: 2-day-old rat hearts, 50 ug/ml DEHP

label_protocol: Biotinylated cRNA was generated according to the standard Affymetrix protocol from 5 ug of total RNA (GeneChip Expression Analysis Technical Manual; Affymetrix).

growth_protocol: Cardiomyocytes isolated from 2-day-old Sprague-Dawley rat pups using an enzymatic digestion protocol. Cells were plated on laminated coverslips. Cells were cultured for 3 days prior to treatment.

extract_protocol: RNA was extracted from cell monolayers using TRIzol reagent (Invitrogen) and total RNA was purified using RNeasy columns (Qiagen) according to manufacturer's protocols.

treatment_protocol: Cells were treated for 3 days with 1, 10, 50ug/mL DEHP (in 0.1% DMSO) or with vehicle control (0.1% DMSO).

tag: strain

value: Sprague-Dawley

value: heart

value: 2 days

tag: treatment

value: DEHP

tag: treatment dosage

value: 50 ug/ml

tag: treatment time

value: 3 days


title: LNCaP-R1881-14h-rep1, replicate section

description:
replicate 1
4117151033_F_2

value: prostate cancer


title: DEHP 50ug/ml, rep1


title: N siJMJD2B#2

description: N siJMJD2B#2: Normoxic conditions with siRNA#2 against JMJD2B


title: DEHP 50ug/ml, rep3


title: LNCaP-R1881-6h-rep1

description:
replicate 1
4117151167_B_1

value: RPMI + 10% charcoal stripped FBS for 72h before treatment


title: LNCaP-R1881-5h-rep1

description:
replicate 1
4117151142_A_1


title: LNCaP-R1881-3.5h-rep1

description:
replicate 1
4117151144_D_1


title: LNCaP-R1881-11h-rep1, replicate section

description:
replicate 1
4117151102_B_2


title: LNCaP-R1881-15h-rep1

description:
replicate 1
4117151144_A_1


title: LNCaP-R1881-6h-rep1, replicate section

description:
replicate 1
4117151167_B_2


title: LNCaP-R1881-4h-rep1

description:
replicate 1
4117151168_E_1


title: LNCaP-R1881-4h-rep2

description:
replicate 2
4117151201_F_1


title: LNCaP-R1881-18h-rep1

description:
replicate 1
4117151142_E_1


title: LNCaP-R1881-3.5h-rep1, replicate section

description:
replicate 1
4117151144_D_2


title: LNCaP-R1881-2.5h-rep1, replicate section

description:
replicate 1
4117151199_B_2


title: DEHP 10ug/ml, rep3

description: Gene expression data from cardiomyocyte monolayers treated with 10 ug/mL DEHP, 3 days.

source_name: 2-day-old rat hearts, 10 ug/ml DEHP

value: 10 ug/ml


title: LNCaP-R1881-3h-rep1, replicate section

description:
replicate 1
4117151102_C_2


title: LNCaP-R1881-7h-rep1

description:
replicate 1
4117151199_C_1


title: LNCaP-R1881-8h-rep1

description:
replicate 1
4117151102_D_1


title: DEHP 10ug/ml, rep1


title: LNCaP-R1881-2h-rep2

description:
replicate 2
4117151167_A_1


title: LNCaP-R1881-1.5h-rep1, replicate section

description:
replicate 1
4117151033_E_2


title: LNCaP-R1881-2h-rep1

description:
replicate 1
4117151142_F_1


title: LNCaP-R1881-2h-rep2, replicate section

description:
replicate 2
4117151167_A_2


title: DEHP 1ug/ml, rep3

description: Gene expression data from cardiomyocyte monolayers treated with 1 ug/mL DEHP, 3 days.

source_name: 2-day-old rat hearts, 1 ug/ml DEHP

value: 1 ug/ml


title: LNCaP-R1881-2.5h-rep1

description:
replicate 1
4117151199_B_1


title: DEHP 1ug/ml, rep1


title: LNCaP-R1881-1h-rep2

description:
replicate 2
4117151201_D_1


title: LNCaP-R1881-2h-rep1, replicate section

description:
replicate 1
4117151142_F_2


title: DEHP 1ug/ml, rep2


title: LNCaP-R1881-1.5h-rep1

description:
replicate 1
4117151033_E_1


title: LNCaP-R1881-1h-rep2, replicate section

description:
replicate 2
4117151201_D_2


title: LNCaP-R1881-3h-rep1

description:
replicate 1
4117151102_C_1


title: Control 0ug/ml, rep2

description: Gene expression data from cardiomyocyte monolayers treated with vehicle control (DMSO), 3 days.

source_name: 2-day-old rat hearts, control

value: DMSO


title: LNCaP-R1881-0.5h-rep1

description:
replicate 1
4117151144_B_1


title: DEHP, rep6

description: Gene expression data from cardiomyocyte monolayers treated with DEHP, 3 days.

source_name: 2-day-old rat hearts, DEHP

treatment_protocol: Cells were treated for 3 days with either 50ug/mL DEHP (in 0.1% DMSO) or with vehicle control (0.1% DMSO).


title: LNCaP-ethanol-24h-rep2, replicate section

description:
replicate 2
4117151102_A_2

source_name: 0.1% ethanol 24h

value: 0.1% ethanol


title: DEHP, rep5


title: LNCaP-ethanol-24h-rep1, replicate section

description:
replicate 1
4117151199_F_2


title: DEHP 10ug/ml, rep2


title: LNCaP-R1881-0.5h-rep1, replicate section

description:
replicate 1
4117151144_B_2


title: LNCaP-R1881-1h-rep1

description:
replicate 1
4117151168_C_1


title: Control 0ug/ml, rep1


title: LNCaP-ethanol-12h-rep2, replicate section

description:
replicate 2
4117151167_E_2

source_name: 0.1% ethanol 12h


title: Control 0ug/ml, rep3


title: LNCaP-ethanol-24h-rep2

description:
replicate 2
4117151102_A_1


title: LNCaP-ethanol-12h-rep2

description:
replicate 2
4117151167_E_1


title: DEHP, rep4


title: LNCaP-R1881-1h-rep1, replicate section

description:
replicate 1
4117151168_C_2


title: LNCaP-ethanol-8h-rep1

description:
replicate 1
4117151201_B_1

source_name: 0.1% ethanol 8h


title: LNCaP-ethanol-8h-rep2

description:
replicate 2
4117151033_C_1


title: LNCaP-ethanol-8h-rep1, replicate section

description:
replicate 1
4117151201_B_2


title: LNCaP-ethanol-8h-rep2, replicate section

description:
replicate 2
4117151033_C_2


title: Control, rep4


title: DEHP, rep3


title: Control, rep5


title: LNCaP-ethanol-2h-rep2

description:
replicate 2
4117151144_F_1

source_name: 0.1% ethanol 2h


title: LNCaP-ethanol-12h-rep1, replicate section

description:
replicate 1
4117151142_D_2


title: LNCaP-ethanol-4h-rep1

description:
replicate 1
4117151102_E_1

source_name: 0.1% ethanol 4h


title: LNCaP-ethanol-12h-rep1

description:
replicate 1
4117151142_D_1


title: DEHP, rep1


title: LNCaP-ethanol-4h-rep1, replicate section

description:
replicate 1
4117151102_E_2


title: Control, rep6


title: LNCaP-ethanol-2h-rep1

description:
replicate 1
4117151168_A_1


title: LNCaP-time0-rep3, replicate section

description:
replicate 3
4117151167_C_2

source_name: LNCaP no treatment

value: no treatment


title: DEHP, rep2


title: LNCaP-ethanol-4h-rep2, replicate section

description:
replicate 2
4117151199_D_2


title: LNCaP-ethanol-4h-rep2

description:
replicate 2
4117151199_D_1


title: LNCaP-time0-rep2, replicate section

description:
replicate 2
4117151142_B_2


title: Control, rep1


title: LNCaP-ethanol-2h-rep1, replicate section

description:
replicate 1
4117151168_A_2


title: LNCaP-time0-rep3

description:
replicate 3
4117151167_C_1


title: Control, rep2


title: LNCaP-time0-rep1, replicate section

description:
replicate 1
4117151033_A_2


title: LNCaP-ethanol-24h-rep1

description:
replicate 1
4117151199_F_1


title: LNCaP-ethanol-2h-rep2, replicate section

description:
replicate 2
4117151144_F_2


title: LNCaP-time0-rep2

description:
replicate 2
4117151142_B_1


title: LNCaP-time0-rep1

description:
replicate 1
4117151033_A_1


title: Control, rep3


title: wildtype, tumor 254, mouse 72

city: Lausanne

first: Michel

last: Aguet

address: Rue du Bugnon 25

department: Life Sciences

country: Switzerland

institute: EPFL/ISREC

hyb_protocol: cDNA was hybridized to Affymetrix Mouse Genome 430 2.0 arrays (Affymetrix, Santa Clara, USA).

scan_protocol: scanner GCS 3000, software was GCOS (GeneChip Operating Software 1.4)

data_processing: Robust multi-array averaging and quantile normalization were used to quantify gene expression (R, Bioconductor, RMA package).

source_name: laser dissected tumor tissue

label_protocol: 30 ng of total RNA were amplified using the NuGEN WT-Ovation pico kit (NuGEN Inc., San Carlos, USA).

growth_protocol: 6-8- Week-old mice were exposed first to a single dose dimethylhydrazine (DMH, 44 mg/kg body weight), which is metabolized in the liver to carcinogenic azoxymethane (AOM), followed by 7 days oral administration of 2 % dextrane sulfate sodium (DSS) in the drinking water

extract_protocol: Microdissected samples from one mouse were pooled and total RNA extracted in 20µL using the PicoPure RNA Isolation Kit (MDS Analytical Technologies).

treatment_protocol: Segments of one cm length of colon were cut, washed in chilled PBS, embedded in OCT and frozen immediately. 14 µm frozen sections were mounted on Leica membranes (Leica Microsystems, Wetzlar, Germany) for laser dissection microscopy, fixed in ethanol and colored with Mayer’s hematoxylin. Membranes were rinsed in water and ethanol and air-dried. Samples were prepared using a laser-dissecting microscope (Leica Microsystems, MMI-Nikon).

value: 129SvEv/C57BL/6/DBA/2 mixed background

value: wildtype

tag: sample id


title: wildtype, tumor 216, mouse 72


title: vil-Cre-Bcl9-/-/Bcl9l-/- tumor 256, mouse 02


title: wildtype, tumor 191, mouse 72


title: wildtype healthy colon epithelium 6

scan_protocol: Affymetrix M10 version 1.0, Software version 4.0.0.16

source_name: EDTA_dissociated healthy colon epithelial tissue

growth_protocol: 12- Week-old mice were used.

extract_protocol: Samples from two or three mice were pooled and total RNA extracted in 20µL using the PicoPure RNA Isolation Kit (MDS Analytical Technologies).

treatment_protocol: The intestine was cut open longitudinally, washed well in PBS and incubated in 3mM EDTA, 0.05mM DTT in PBS for 1.5 to 2 hours at RT. The tubes were shaked vigorously for ca. 30sec, such that the epithelium came off the muscle (solution became cloudy). The muscle was removed and the tube centrifuged at high speed for 1 min to pellet the epithelial cells. The supernatant was removed and the pellet frozen.

value: 12-week old


title: vil-Cre-Bcl9-/-/Bcl9l-/- tumor 257, mouse 02


title: vil-Cre-Bcl9-/-/Bcl9l-/- healthy colon epithelium 2


title: vil-Cre-Bcl9-/-/Bcl9l-/- tumor 258, mouse 04


title: vil-Cre-Bcl9-/-/Bcl9l-/- tumor 255, mouse 04


title: vil-Cre-Bcl9-/-/Bcl9l-/- tumor 195, mouse 99


title: wildtype, tumor 215, mouse 72


title: vil-Cre-Bcl9-/-/Bcl9l-/- healthy colon epithelium 1


title: wildtype, tumor 229, mouse 82


title: vil-Cre-Bcl9-/-/Bcl9l-/- healthy colon epithelium 3


title: Antibiotic_liver_animal #14

status: Public on Aug 31 2010

city: Macclesfield

first: James

last: Sidaway

address: Mereside, Alderely Park

department: Safety Assessment

institute: AstraZeneca

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip

scan_protocol: Affymetrix GeneChip Scanner 3000; GCOS 1.4

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: Biotin

source_name: antibiotic dosed

label_protocol: 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Qiagen RNeasy miniprep  (according to manufacturer's protocol)

treatment_protocol: The antibiotic was provided as a pre-prepared solution in water, made up of 4 mg/ml Streptomycin and 2 mg/ml Penicillin.  The antibiotic solution was supplied as a 10X stock (stored at approximately +4ºC) in 30 mL pre-prepared aliquots which was then be diluted by adding into 270 mL of the animals’ drinking water to make up to 300 mL.  Light-protective water bottles (amber) were used throughout the study.  The animals  had free access to the antibiotic for 8 days, until necropsy.

value: Han Wistar

value: liver

value: antibiotic dosed


title: Antibiotic_liver_animal #13


title: Normal_not-germ-free_liver_animal #8

source_name: normal

value: Sprague Dawley

value: normal


title: Normal_not-germ-free_liver_animal #7


title: Antibiotic_liver_animal #15


title: Control_no-antibiotic_liver_animal #2

source_name: control

value: control


title: wildtype healthy colon epithelium 5


title: Control_no-antibiotic_liver_animal #3


title: Control_no-antibiotic_liver_animal #1


title: wildtype healthy colon epithelium 4


title: Germ_free_liver_animal #4

source_name: germ free

value: germ free


title: Germ_free_liver_animal #3


title: Germ_free_liver_animal #1


title: Normal_not-germ-free_liver_animal #6


title: Rosa26-BMPR2-R899X lung (1)

status: Public on Aug 25 2010

city: Nashville

last: West

state: TN

address: 4200 E 9TH Ave, Box B133

department: Medicine

institute: Vanderbilt University

description: Pooled RNA from whole lung homogenate from three female FVB/N mouse heterozygous for Rosa26-rtTA2 and TetO7-Bmpr2-R899X transgenes, fed doxycycline for 6 weeks starting at average age 5 months, with vehicle control in osmotic pumps infused for the final 2 weeks. Mice had near normal right ventricular systolic pressure (RVSP) at time of sacrifice. These transgenics often develop pulmonary arterial hypertension.

hyb_protocol: Standard Affymteric protocol (Affymetrix GeneChip Expression Analysis Manual).

data_processing: Raw Affymetrix CHP and CEL files. Data processed using MAS5.0.

source_name: Whole lung homogenate, -ACE2, +BMPR2

extract_protocol: Heparin was injected into the jugular 5 minutes before sacrifice; right lung was flushed with PBS immediately after sacrifice, removed, and immediately converted to RNA using Qiagen rnEasy columns

value: FVB/N

value: female

value: whole lung


title: GMP from IRF4/8DKO, rep2

status: Public on Aug 22 2010

city: Waltham

first: Ruibao

last: Ren

state: MA

address: 415 South St.

institute: Brandeis University

description: Gene expression data from granulocyte/macrophage progenitor cells in a IRF4/8 DKO mouse

hyb_protocol: cRNA were hybridized for 18 hr at 45C on GeneChip Murine Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned with the Affymetrix GeneArray Scanner G3000

data_processing: Hybridization data were normalized and expression values were determined using the PM/MM difference model by dChip 1.3 (DNA-Chip analyzer). After filtering genes (1.05<SD/mean<10, P call % in the array >= 20%) to identify genes with a large variation across samples, we performed hierarchical clustering from filter genes and selected out genes that show large variations within each group.

source_name: granulocyte/macrophage progenitors from a IRF4/8 DKO mouse

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ng total RNA

extract_protocol: Qiagen RNAeasy Micro kit was used according to the manufacturer's instructions.

tag: genotype/variation

value: Bone marrow

value: granulocyte/macrophage progenitor (GMP)

value: 16 weeks


title: Control mouse + chronic ACE2 lung (1)

description: Pooled RNA from whole lung homogenate from three female FVB/N mouse heterozygous for Rosa26-rtTA2 transgene, fed doxycycline for 6 weeks starting at average age 5 months, with recombinant human ACE2 in osmotic pumps infused for the final 2 weeks. Mice had near normal right ventricular systolic pressure (RVSP) at time of sacrifice.

scan_protocol: Standard Affymteric protocol (Affymetrix GeneChip Expression Analysis Manual).

source_name: Whole lung homogenate, +ACE2, -BMPR2

value: heterozygous for Rosa26-rtTA2 transgene


title: Rosa26-BMPR2-R899X mouse + chronic ACE2 lung (1)

description: Pooled RNA from whole lung homogenate from three female FVB/N mouse heterozygous for Rosa26-rtTA2 and TetO7-Bmpr2-R899X transgenes, fed doxycycline for 6 weeks starting at average age 5 months, with recombinant human ACE2 in osmotic pumps infused for the final 2 weeks. Mice had near normal right ventricular systolic pressure (RVSP) at time of sacrifice. These transgenics often develop pulmonary arterial hypertension.

source_name: Whole lung homogenate, +ACE2, +BMPR2

label_protocol: Standard Affymteric protocol (Affymetrix GeneChip Expression Analysis Manual).


title: Control mouse lung (2)

description: Pooled RNA from whole lung homogenate from three female FVB/N mouse heterozygous for Rosa26-rtTA2 transgene, fed doxycycline for 6 weeks starting at average age 5 months. Mice had near normal right ventricular systolic pressure (RVSP) at time of sacrifice. The Rosa26-rtTA2 transgene drives universal expression of a transactivator, which has no phenotype in the absence of other transgenes - this is thus a control group.

source_name: Whole lung homogenate, -ACE2, -BMPR2


title: GMP from IRF4/8DKO, rep1

value: male


title: Control mouse + chronic ACE2 lung (2)


title: Endo-str_SP_rep4

status: Public on Aug 15 2010

city: Valencia

first: Jose

middle: Antonio

last: Martinez-Conejero

address: C/ Guadassuar 1, bajo

country: Spain

institute: iGenomix

description: No comments

hyb_protocol: The protocols for sample preparation and the hybridization of the endometrial samples were adapted from the Agilent Technical Manual.

scan_protocol: Hybridized microarrays were scanned in an Axon 4100A scanner (Molecular Devices, Sunnyvale, CA, USA), and the data were extracted with the GenePix Pro 6.0 software (Molecular  Devices, Sunnyvale, CA, USA).

data_processing: In order to remove all the possible sources of variation of a non biological origin between the arrays, densitometry values were normalized using the quantitative normalization function and were further transformed to the logarithmic scale (log2). Statistically significant differences between groups (SP epithelial versus total epithelial fractions, and SP stromal versus total stromal fraction) were carried out using the rank products (35) method performed using the Bioconductor http://www.bioconductor.org/) package RankProd, which was run using the R software (http://www.r-project.org/). Venn diagrams were drawn with Venny (36), and functional annotations were carried out using Ingenuity (http://www.ingenuity.com/), where the gene symbols and the fold changes of the up- and down-regulated probes were imported.

source_name: Endometrial stroma SP fraction

label_protocol: All the samples were hybridized in the Whole Human Genome Oligo Microarray (Agilent Technologies, Madrid, Spain) which encompassed more than 44000 human DNA probes.

extract_protocol: Total RNA was extracted using the ‘TRIzol method’ according to the protocol recommended by the manufacturer

tag: sample type

value: stromal endometrial SP fraction


title: Rosa26-BMPR2-R899X mouse + chronic ACE2 lung (2)

value: heterozygous for Rosa26-rtTA2 and TetO7-Bmpr2-R899X transgenes


title: Control mouse lung (1)


title: GMP from IRF8KO, rep2

description: Gene expression data from granulocyte/macrophage progenitor cells in a IRF8 KO mouse

source_name: granulocyte/macrophage progenitors from a IRF8 KO mouse

value: 22 weeks


title: GMP from wild type, rep2

description: Gene expression data from granulocyte/macrophage progenitor cells in a wild type mouse

source_name: granulocyte/macrophage progenitors from a wild type mouse

value: wild type

value: 19 weeks


title: GMP from IRF8KO, rep1

value: 12 weeks


title: Endo-str_SP_rep3

description: No comments


title: Endo-str_SP_rep2

description: No comments


title: 15hr Biological Replicate 02

city: Seattle

first: Dhileep

last: Sivam

state: WA

address: 307 Westlake Ave N

department: Bioinformatics Core

institute: Seattle Biomedical Research Institute

description: Total RNA from in vitro differentiating (by concomitant exposure to 37 degrees C and pH 5.5) Leishmania donovani 1S.

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

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

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

organism: Leishmania donovani

source_name: Leishmania donovani 1S +24 hr differentiating

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

growth_protocol: 26°C in Medium 199 (Sigma Ltd.) supplemented with 10% fetal calf serum

extract_protocol: RNA was harvested at 0 (promastigotes), 2.5, 5, 7.5, 10, 15, and 24 hrs during differentiation and from fully-formed (2 weeks) axenic amastigotes using Trizol reagent (Gibco BRL)

treatment_protocol: In vitro differentiation induced by concomitant exposure to 37 degrees C and pH 5.5.

tag: life cycle

value: 15 hour differentiating

tag: biological replicate


title: 24hr Biological Replicate 02

source_name: Leishmania donovani 1S +15 hr differentiating

value: 24 hour differentiating


title: GMP from wild type, rep1

tag: cell type


title: Endo-str_SP_rep1

description: No comments


title: Endo-str_NonSP_rep2

description: No comments

source_name: Endometrial stroma fraction

value: stromal endometrial cell suspensions


title: 144hr Biological Replicate 02

source_name: Leishmania donovani 1S amastigote

value: amastigote (144 hour)


title: 5.0hr Biological Replicate 02

source_name: Leishmania donovani 1S +5 hr differentiating

value: 5.0 hour differentiating


title: Endo-epi_NonSP_rep1

description: No comments

source_name: Endometrial epithelium fraction

value: epithelial endometrial cell suspensions


title: Endo-str_NonSP_rep3

description: No comments


title: Endo-epi_SP_rep4

description: No comments

source_name: Endometrial epithelium SP fraction

value: epithelium endometrial SP fraction


title: Endo-epi_SP_rep1

description: No comments


title: 10hr Biological Replicate 02

source_name: Leishmania donovani 1S +7.5 hr differentiating

value: 10 hour differentiating


title: Endo-epi_SP_rep3

description: No comments


title: Endo-epi_SP_rep2

description: No comments


title: 10hr Biological Replicate 01


title: Endo-str_NonSP_rep1

description: No comments


title: 0.0hr Biological Replicate 02

description: Total RNA from promastigote stage Leishmania donovani 1S.

source_name: Leishmania donovani 1S promastigote

value: promastigote (0 hour)


title: 2.5hr Biological Replicate 02

source_name: Leishmania donovani 1S +2.5 hr differentiating

value: 2.5 hour differentiating


title: 144hr Biological Replicate 01


title: 7.5hr Biological Replicate 02

source_name: Leishmania donovani 1S +10 hr differentiating

value: 7.5 hour differentiating


title: 24hr Biological Replicate 01


title: Endo-epi_NonSP_rep4

description: No comments


title: 15hr Biological Replicate 01


title: 2.5hr Biological Replicate 01


title: Endo-epi_NonSP_rep2

description: No comments


title: 7.5hr Biological Replicate 01


title: Rosa26-BMPR2-R899X lung (2)

source_name: Whole lung homogenate, -ACE2, +BMPR2

value: FVB/N

value: female

value: whole lung


title: 5.0hr Biological Replicate 01


title: Endo-epi_NonSP_rep3

description: No comments


title: 0.0hr Biological Replicate 01


title: Endo-str_NonSP_rep4

description: No comments


title: gd T cells from calf 303 stimulated with vehicle only control.

status: Public on Aug 10 2010

city: Bozeman

first: Jodi

middle: Fern

last: Hedges

state: MT

address: 960 Technology Blvd.

department: Veterinary Molecular Biology

institute: Montana State University

description:
Gene expression data stimulated bovine gamma delta T cells
303_PBS

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Bovine Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using an Affymetrix 7G scanner

data_processing: The data were imported into Genespring using RMA preprocessing for analysis.

organism: Bos taurus

source_name: Bovine gamma delta T cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 15ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Peripheral blood was collected from  1 to 6 month old calves and gamma delta T cells were sorted to >97% purity.

extract_protocol: Rneasy (Qiagen)  extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Sorted cells were rested overnight then stimulated for 4 hours with either PBS or APP.

tag: gamma delta T cells

tag: from bovine calves


title: PC-3 AKR1C3 transfected, Rep 3

city: Oklahoma City

first: Hsueh-Kung

last: Lin

state: OK

address: Room 462, 800 Research Parkway

department: Urology

institute: University of Oklahoma Health Sciences Center

description: AKR1C3 replicate 3

hyb_protocol: Biotinylated cRNA was hybridized to Illumina HumanWG 6 v2 BeadChips containing a total of 48,702 probes.

scan_protocol: Microarray chips were labeled with streptavidin -Cy3 (Amersham Biosciences, Piscataway, NJ) and scanned on an Illumina BeadArray Reader.

data_processing: The functions used for normalization were implemented in Matlab and in Bioconductor package diffGeneAnalysis. Raw expression values were first normalized based on normal distribution of genes with low expression levels as previously described [25, 26].  Briefly, normalization was performed for each array by first plotting a frequency histogram of the raw expression data for all genes.  The histograms showed a right-skewed unimodal distribution curve with the mode around zero.  Normal distribution curve representing random variability of the genes with low expression values was then fitted around the mode, mirroring Gaussian profile of the left part of the histogram.  Two parameters [mean and standard deviation (SD)] were defined.  The expression values then were normalized to the SD of the normal distribution after subtraction of the mean and log10-transformed.  The arrays were than adjusted to each other by robust linear regression [27, 28].  Genes with expression value less than 3.0 (or 0.477 in log10 scale) were considered to be not expressed; this is equivalent of setting a threshold at 3 SD above noise level. 25. Dozmorov I, Knowlton N, Tang Y, Centola M: Statistical monitoring of weak spots for improvement of normalization and ratio estimates in microarrays. BMC Bioinformatics 2004, 5:53.  26. Knowlton N, Dozmorov IM, Centola M: Microarray Data Analysis Toolbox (MDAT): for normalization, adjustment and analysis of gene expression data. Bioinformatics 2004, 20:3687-3690.  27. Hua J, Balagurunathan Y, Chen Y, Lowey J, Bittner ML, Xiong Z, Suh E, Dougherty ER: Normalization benefits microarray-based classification. EURASIP journal on bioinformatics & systems biology 2006:43056.  28. Gusnanto A, Calza S, Pawitan Y: Identification of differentially expressed genes and false discovery rate in microarray studies. Curr Opin Lipidol 2007, 18:187-193.

source_name: PC-3 cultured cells

label_protocol: A total of 250 ng of total RNA from each clone was labeled using the Illumina Total Prep RNA Amplification kit (Ambion, Austin. TX).  cDNA was reverse transcribed from the total RNA after priming with T7-oligo(dT); and cRNA was synthesized from the T7 promoter in the presence of biotinylated UTP.

growth_protocol: PC-3 cells were maintained in a complete growth medium consisting of F-12 nutrient mixture supplemented with 7% FBS and 1% penicillin-streptomycin in a humidified cell incubator at 37 oC and 5% CO2.

extract_protocol: Total RNA was isolated from 2 independent PC3-mock clones and 3 independent PC3-AKR1C3 clones for gene expression analysis.  Briefly, following PC-3 transfectants (5x105) seeding and adherence, total RNA was isolated from these clones using RNeasy® Mini total RNA isolation kit (Qiagen, Valencia, CA).  The concentration of the isolated total RNA was determined with a Nanodrop scanning spectrophotometer, and then qualitatively assessed using the ratio of 28:18s rRNA by Agilent 2100 Bioanalyzer capillary gel electrophoresis system (Agilent Technologies, Santa Clara CA).

treatment_protocol: AKR1C3 expression construct (pcDNA3-AKR1C3) was established as previously described [24].  Transfection of PC-3 cells with either pcDNA3 empty vector or pcDNA3-AKR1C3 construct was achieved using Lipofectamine 2000; and stable transfectants were established in the presence of G418 selection (600 μg/ml).  Multiple independent clones were isolated and expanded in the complete growth medium containing G418.  PC-3 stable transfectants were designated as PC3-mock or PC3-AKR1C3 for cells stably transfected with pcDNA3 or pcDNA3-AKR1C3 plasmids, respectively.  Three independent PC3-AKR1C3 clones confirmed with elevated AKR1C3 expression as compared to PC3-mock transfectants were used for bioinformatics and biological analyses [24]. 24. Wang S, Yang Q, Fung KM, Lin HK: AKR1C2 and AKR1C3 mediated prostaglandin D2 metabolism augments the PI3K/Akt proliferative signaling pathway in human prostate cancer cells. Mol Cell Endocrinol 2008, 289:60-66.

tag: transfection


title: PC-3 AKR1C3 transfected, Rep 1

description: AKR1C3 replicate 1


title: PC-3 AKR1C3 transfected, Rep 2

description: AKR1C3 replicate 2


title: gd T cells from calf 303 stimulated with apple polyphenol (APP).

description:
Gene expression data stimulated bovine gamma delta T cells
303_APP


title: gd T cells from calf 301 stimulated with apple polyphenol (APP).

description:
Gene expression data stimulated bovine gamma delta T cells
301_APP


title: gd T cells from calf 301 stimulated with vehicle only control.

description:
Gene expression data stimulated bovine gamma delta T cells
301_PBS


title: 3rd 24 hrs (DMNQ)

status: Public on Aug 06 2010

city: Leicester

first: Amy

last: Pointon

address: Lancaster Road

department: Systems Toxicology Group

institute: MRC Toxicology Unit

hyb_protocol: 4µg tRNA and 2x enhanced hybridization buffer (Genesiphere) were added, samples heated to 95oC for 2 minutes then 42oC for 30 minutes.  Samples applied to microarrays enclosed in a Genetix humidified chamber.  After hybridization overnight, slides were washed sequential.

scan_protocol: Scanned on a Axon 4200A scanner Images were quantified using Genepix 6.0 software

data_processing: LOWESS normalized, log2 of processed red signal / green signal, A and B files combined and files combined when reverse labelling conducted, resulting in 1 file per time point per biological replicate

label: Alexa 555

source_name: Cardiac tissue treated with 10ml/kg arachis oil

label_protocol: 7µg of total RNA were primed with 1µl of 8µg/µl oligo dT25N2 and 1µl 10nM/µl random pentadecamers at 95oC for 5 minutes and then 70oC for 10 minutes, then reverse ttranscribed at 50oC for 3 hours in the presence of 0.5mM each dATP, dGTP, dCTP, 0.2mM dTTP, 0.3mM aadUTP, and 1µl Superscript III (Invitrogen).  Remaining RNA hydrolysised with 0.5M EDTA and 1M NaOH and heated to 65oC for 15 minutes.  Resultant cDNA purfied using Microcon YM-30 filters (Millipore).  cDNA labeled with Alexa fluorophore 555 or 647 (Molecular probes, Invitrogen) for 1 hour and quenched with 4.5µl 4M hydroxylamine, samples purfied with Qiagen PCR purification kit.

growth_protocol: Mice housed with free assess to food and water, with a 12 hour light dark cycle

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

treatment_protocol: Mice randomly assigned to control or treatment group and treated with 10ml/kg arachis oil (control) or 25mg/kg DMNQ in 10ml/kg arachis oil (treatment) as sacrificed at 0.5, 1, 2, 12, 24, 120 hours following dosing, hearts quickly removed and snap frozen in liquid nitrogen

tag: gender

value: Male

value: 8 weeks

value: Heart

label: Alexa 647

source_name: Cardiac tissue treated with 25mg/kg DMNQ in 10ml/kg arachis oil


title: PC-3 mock transfected, Rep 2

description: Mock replicate 2

value: mock


title: 2nd 24 hrs DMNQ

tag: age


title: PC-3 mock transfected, Rep 1

description: Mock replicate 1


title: 3rd 120 hrs (DMNQ)

tag: tissue


title: 2nd 5 hrs

description: Samples normalized and condensed into 1 file


title: 2nd 120 hrs (DMNQ)


title: 3rd 5 hrs


title: 2nd 12 hrs (DMNQ)


title: 3rd 12 hrs (DMNQ)


title: 1st 2 hrs (DMNQ)


title: 5th 2 hrs


title: 3rd 2 hrs (DMNQ)


title: 4th 2 hrs (DMNQ)


title: 4th 5 hrs


title: 1st 5 hrs


title: 5th 5 hrs


title: 2nd 2 hrs (DMNQ)


title: 3rd 1.5 hrs


title: 4th 1.5 hrs


title: 5th 1.5 hrs


title: 2nd 1 hr DMNQ


title: 3rd 1 hr


title: 2nd 1.5 hrs


title: 4th 1 hr DMNQ


title: 1st 1 hr DMNQ


title: 1st 1.5 hrs


title: 4th 45 mins


title: 5th 1 hr


title: 5th 45 mins


title: 2nd 45 mins


title: 3rd 45 mins


title: 5th 30 mins


title: 2nd 30 mins


title: 1st 30 mins


title: 4th 30 mins


title: 1st 45 mins


title: 3rd 30 mins


title: 2nd 20 mins


title: 4th 15 mins


title: 5th 20 mins


title: 5th 15 mins


title: 3rd 15 mins


title: 4th 20 mins


title: 2nd 15 mins


title: 3rd 20 mins


title: 1st 15 mins


title: 3rd 10 mins


title: 4th 10 mins


title: 2nd 10 mins


title: 1st 10 mins


title: 2nd 5 mins


title: 3rd 120 hrs monosomes DMNQ

type: other

description: Samples normalized and A and B and reverse labeling condensed into 2 files (monosome and polysome)

hyb_protocol: 4µg tRNA and 2x enhanced hybridization buffer (Genesiphere) were added, samples heated to 95oC for 2 minutes then 42oC for 30 minutes. Samples applied to microarrays enclosed in a Genetix humidified chamber. After hybridization overnight, slides were washed sequential.

data_processing: LOWESS normalized, log2 of processed red signal / green signal, A and B files combined, the Log2 for the monosome arrays for each gene was subtracted from that of the polysome array, the resultant Log2 represents differential translation. These data are present on the Series record.

molecule: other

source_name: Monosomal RNA extracted from cardiac tissue treated with 10ml/kg arachis oil

label_protocol: Upto 10µg monosome or polysome RNA were primed with 1µl of 8µg/µl oligo dT25N2 at 70 oC for 10 minutes, then reverse transcribed at 50oC for 2 hours in the presence of 1µl Superscript III (Invitrogen) and 100µM each dATP, dTTP, dGTP with 25 µM dCTP and 25µM cy-3 or cy-5

extract_protocol: Cardiac tissue lysated and subjected to centrifugation on a 0-65% sucrose gradient allowing separation of RNA species, gradients fractionated into 1ml fractions directly into Trizol, RNA extracted according to the manufactures instructions. Equal volumes of polysome or monosome fractions combined. Control monosome and treated monosome were assayed on one microarray slide and control polysome and treated polysomes assayed on another microarray

source_name: Monosomal RNA extracted from cardiac tissue treated with 25 mg/kg DMNQ in 10ml/kg arachis oil


title: 1st 120 hrs polysomes DMNQ

description: Samples normalized and A and B condensed into 1 file

source_name: Polysomal RNA extracted from cardiac tissue treated with 10ml/kg arachis oil

source_name: Polysomal RNA extracted from cardiac tissue treated with 25 mg/kg DMNQ in 10ml/kg arachis oil


title: 1st 5 mins


title: 4th 5 mins


title: 3rd 120 hrs polysomes DMNQ


title: 3rd 24 hrs polysomes DMNQ


title: 1st 120 hrs monosomes DMNQ


title: 2nd 120 hrs monosomes DMNQ


title: 3rd 24 hrs monosomes DMNQ


title: 2nd 120 hrs polysomes DMNQ


title: 2nd 2 hrs polysomes DMNQ


title: 3rd 12 hrs monosomes DMNQ


title: 3rd 5 mins


title: 3rd 2 hrs monosomes DMNQ


title: 1st 24 hrs polysomes DMNQ


title: 2nd 12 hrs monosomes DMNQ


title: 1st 24 hrs monosomes DMNQ


title: 3rd 2 hrs polysomes DMNQ


title: 1st 2 hrs monosomes DMNQ


title: 3rd 12 hrs polysomes DMNQ


title: 3rd 1 hr polysomes DMNQ


title: 1st 2 hrs polysomes DMNQ


title: 2nd 12 hrs polysomes DMNQ


title: 1st 1 hr monosomes DMNQ


title: 2nd 1 hr monosomes DMNQ


title: 2nd 1 hr polysomes DMNQ


title: 1st 1 hr polysomes DMNQ


title: 3rd 1 hr monosomes DMNQ


title: 3rd 0.5 hrs monosomes DMNQ


title: 2nd 24 hrs

source_name: Cardiac tissue treated with 10ml/kg saline

treatment_protocol: Mice randomly assigned to control or treatment group and treated with 10ml/kg saline (control) or 15mg/kg doxorubicin in 10ml/kg(treatment) as sacrificed at 0.5, 1, 2, 12, 24, 120 hours following dosing, hearts quickly removed and snap frozen in liquid nitrogen

source_name: Cardiac tissue treated with 15mg/kg doxorubicin in 10ml/kg saline


title: 2nd 0.5 hrs polysomes DMNQ


title: 2nd 0.5 hrs monosomes DMNQ


title: 1st 0.5 hrs polysomes DMNQ


title: 2nd 120 hrs


title: 1st 120 hrs


title: 1st 0.5 hrs monosomes DMNQ


title: 3rd 0.5 hrs polysomes DMNQ


title: 3rd 120 hrs


title: 3rd 12 hrs


title: 4th 2 hrs


title: 3rd 24 hrs


title: 2nd 12 hrs


title: 1st 24 hrs


title: 2nd 1 hr


title: 2nd 2 hrs


title: 3rd 2 hrs


title: 1st 2 hrs


title: 1st 12 hrs


title: 4th 0.5 hrs


title: 4th 1 hr


title: 3rd 1hr


title: 2nd 0.5 hrs


title: 1st 1 hr


title: 3rd 120 hrs polysomes

source_name: Polysomal RNA extracted from cardiac tissue treated with 10ml/kg saline

extract_protocol: Cardiac tissue lysated and subjected to centrifugation on a 0-65% sucrose gradient allowing separation of RNA species, gradients fractionated into 1ml fractions directly into Trizol, RNA extracted according to the manufactures instructions.  Equal volumes of polysome or monosome fractions combined.  Control monosome and treated monosome were assayed on one microarray slide and control polysome and treated polysomes assayed on another microarray

source_name: Polysomal RNA extracted from cardiac tissue treated with 15mg/kg doxorubcin in 10ml/kg saline


title: 3rd 0.5 hrs


title: 3rd 120 hrs monosomes

source_name: Monosomal RNA extracted from cardiac tissue treated with 10ml/kg saline

source_name: Monosomal RNA extracted from cardiac tissue treated with 15mg/kg doxorubicin in 10ml/kg saline


title: 1st 0.5 hrs


title: 1st 120 hrs polysomes


title: 1st 120 hrs monosomes

description:
Samples normalized and A and B condensed into 1 file
none


title: 2nd 120 hrs monosomes


title: 3rd 24 hrs monosomes


title: 3rd 24 hrs polysomes


title: 3rd 2 hrs monosomes


title: 2nd 24 hrs polysomes


title: 2nd 12 hrs polysomes


title: 3rd 12 hrs monosomes


title: 2nd 24 hrs monosomes


title: 1st 12 hrs monosomes


title: 3rd 1 hr polysomes


title: 3rd 12 hrs polysomes


title: 3rd 2 hrs polysomes


title: 1st 2 hrs monosomes


title: 1st 24 hrs monosomes


title: 2nd 120 hrs polysomes


title: 1st 24 hrs polysomes


title: 3rd 1 hr monosomes


title: 2nd 12 hrs monosomes


title: 1st 2 hrs polysomes


title: 1st 1 hr polysomes


title: 1st 12 hrs polysomes


title: 2nd 2 hrs polysomes


title: 1st 1 hr monosomes


title: 2nd 0.5 hrs polysomes


title: 2nd 2 hrs monosomes


title: 2nd 1 hr monosomes


title: 2nd 1 hr polysomes


title: 1d exposed to S.mansoni miricidia (3) BS-90

status: Public on Aug 01 2010

city: Albuquerque

first: Patrick

middle: C

last: Hanington

state: NM

address: 1 University of New Mexico

department: Department of Biology, University of New Mexico

institute: Center for Evolutionary and Theoretical Immunology

description: Reference sample RNA consisted of a mixture of RNA from snails

hyb_protocol: Purified Cy3 and Cy5 labeled products were then pooled, ethanol precipitated, resuspended in 100 µL hybridization buffer (40 % formamide, 5x Denhardt’s, 5x SSC, 1 mM sodium pyrophosphate, 50 mM Tris (pH 7.4) and 0.1 % SDS) and incubated at 95°C for 5 min followed by 50°C for 5 min. Arrays were pre-hybridized for 3.0 h at 42°C in hybridization buffer prior to hybridization with labeled probes.  Labeled cDNA was hybridized overnight at 42°C.

scan_protocol: Microarray slides were scanned with a GenePix® 4000B scanner (Axon Instruments) with GenePix® Pro 6.0 (Axon Instruments) software using a modified protocol as described by Aragon and colleagues.

data_processing: A preloaded grid was used to align and identify array spots. Alignment diameter minimum and maximums were set at 50% and 200%, respectively. Nearest negative control spots were selected for background subtraction. Acuity version 4.0 (Axon Instruments) software was used in array analyses and arrays were normalized using a ratio of medians to Alien control spots. SAM was used to determine significiantly differentially regulated genes with a cut of of 2-fold and a false positive rate of less then 10%

organism: Biomphalaria glabrata

source_name: 8-12 mm Biomphalaria glabrata BS-90 strain

label_protocol: Complementary DNA was synthesized, amplified, labeled and hybridized using the modified SMART (Clontech) cDNA labeling protocol described by Petalidis and colleagues. Briefly, 300 ng total RNA were mixed with 3 µL of 10 μM 3′ SMART CDS primer IIA (5′-AAGCAGTGGTATCAACGCAGAGTACT30VN-3′) and 3 µL 10 μM template switching primer (5′-d(AAGCAGTGGTATCAACGCAGAGTACGC)r(GGG)-3′) and brought to a final volume of 15 µL with RNase free dH2O. The template switching primer is a DNA:RNA hybrid where the last 3 bases are RNA. The reaction was then incubated at 72°C for 2 min and then placed on ice. Six microliters of 5x first-strand buffer (Clontech), 3 µL DTT (20 mM), 3 µL dNTPs (10 mM), and 3 µL and PowerScriptTM reverse transcriptase (Clontech) were then added to the reaction and the mixture incubated at 42°C for 1.0 h to generate first strand cDNA. Second-strand cDNA was then amplified by mixing 15 µL of the first-strand cDNA reaction with 57 µL dH2O, 10 µL 10x PCR buffer II (Applied Biosystems), 10 µL 25 mM MgCl2, 2 µL 10 mM dNTPs, 4 µL 10 μM 5’ PCR primer (5′-AAGCAGTGGTATCAACGCAGAGT-3′) and 2 µl AmpliTaq® (40 U/µL). Amplification conditions were 95°C for 1 min for one cycle followed by 95°C for 5 s, 65°C for 5 s, and 68°C for 6 min for 15 cycles. Second strand cDNA was then purified using a QIAquick® PCR Purification Kit (Qiagen), quantified using a NanoDrop® ND-1000 spectrophotometer and labeled with Cy3/Cy5 d-CTPs (GE Healthcare-Amersham) using BioPrime® DNA Labeling System (Invitrogen). For labeling, 200 ng of second-strand cDNA suspended in 21 µL dH2O was mixed with 20 μL of 2.5x random primer reaction buffer (Invitrogen) and incubated at 95°C for 5 min, then placed on ice. While on ice, 2 µL dH2O, 5 μL low-C dNTP mix (5 mM dATP, 5 mM dGTP, 5 mM dTTP, 2 mM dCTP), 1 µL Cy3 or Cy5 dCTP and 1 μL Klenow enzyme (40 U/µL; Invitrogen) were mixed and incubated at 37°C for 2.0 h. The labeling reaction was stopped by adding 5 μL stop buffer (Invitrogen). For all experiments, reference samples were labeled with Cy3 and experimental samples with Cy5. Cy3 and Cy5 labeled probes were purified separately using an AutoSeqTM G-50 Dye Terminator Removal Kit (GE Healthcare) and labeling efficiency quantified using a NanoDrop® ND-1000 spectrophotometer.

growth_protocol: Snails and trematodes used in this study were maintained at the University of New Mexico

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

treatment_protocol: The trematode infected experimental groups and one control group examined this study were non-infected M line (control), Echinostoma paraensei infected and Schistosoma mansoni infected B. glabrata.  For each treatment three pools of 5 snails were used as the biological replicates to reduce individual variability. Individual juvenile snails (shell diameter 4-8mm) B. glabrata were exposed to 15-20 S. mansoni or E. paraensei miracidia in artificial spring water (ASW), (Loker and Hertel, 1987) and kept alive before RNA extraction which was performed on days 0.5, 1, 2, 4, 8, 16 and 32 post infection.  Control snails were placed into 24-well plates with ASW for 12 hours to mimic the conditions of infection protocol, afterwards RNA was extraction at the same time points as in the experimental groups.

tag: line

value: M-line

value: BS-90 strain

tag: developmental stage

tag: experimental variable

value: 1 day exposed to S. mansoni miricidia

source_name: Reference


title: 2d exposed to S.mansoni miricidia (1) BS-90

tag: strain

value: 2 day exposed to S. mansoni miricidia

value: Reference sample RNA consisted of a mixture of RNA from snails


title: 2d exposed to S.mansoni miricidia  (1) BS-90


title: 32d exposed to S.mansoni miracidia (2) BS-90

value: 32 day exposed to S. mansoni miricidia


title: 16d exposed to S.mansoni miracidia (3) BS-90

value: 16 day exposed to S. mansoni miricidia


title: 32d exposed to S.mansoni miracidia (3) BS-90


title: 32d exposed to S.mansoni miracidia (1) BS-90


title: 16d exposed to S.mansoni miracidia (2) BS-90


title: 8d exposed to S.mansoni miracidia (1) BS-90

value: 8 day exposed to S. mansoni miricidia


title: 1st 0.5 hrs polysomes


title: 4d exposed to S.mansoni miricidia (3) BS-90

value: 4 day exposed to S. mansoni miricidia


title: 1st 0.5 hrs monosomes


title: 4d exposed to S.mansoni miricidia (1) BS-90


title: 4d exposed to S.mansoni miricidia (2) BS-90


title: 2d exposed to S.mansoni miricidia (2) BS-90


title: 8d exposed to S.mansoni miracidia (2) BS-90


title: 16d exposed to S.mansoni miracidia (1) BS-90


title: 1d exposed to S.mansoni miricidia (1) BS-90


title: 2nd 0.5 hrs monosomes


title: 12h exposed to S.mansoni miricidia  (3) BS-90

value: 12 hr exposed to S. mansoni miricidia


title: 1d exposed to S.mansoni miricidia (2) BS-90


title: 8d exposed to S.mansoni miracidia (3) BS-90


title: fily3y5_2

city: Rehovot

first: Idan

middle: D.

last: Efroni

address: Weizmann

country: Israel

institute: Weizmann Institute

hyb_protocol: Standard affymetrix protocol

scan_protocol: Arrays were scanned using Affymetrix GeneChip Scanner 3000 7G using standard affymetrix protocol.

data_processing: Signal values were obtained and normalized with the GC-RMA protocol using R 2.7.2 and Bioconductor 2.2. Genes with expression value lower than log2(10) were removed.

organism: Arabidopsis thaliana

source_name: Apices of fil-8 yab3-2 yab5-1 14 DAS seedlines

label_protocol: Standard affymetrix protocol

growth_protocol: Plants were grown for 14 days under short days conditions

extract_protocol: Total RNA (10-7 μg) was extracted with the RNeasy RNA isolation kit (Qiagen)

tag: ecotype

value: Ler

value: 14 DAS

value: Apices

value: fil-8 yab3-2 yab5-1


title: fily3_2

source_name: Apices of fil-8 yab3-2 14 DAS seedlines

value: fil-8 yab3-2


title: 4d exposed to E. paraensei miricidia (2) BS-90

value: 4 day exposed to E. paraensei miricidia


title: 2d exposed to E. paraensei miricidia  (1) BS-90

value: 2 day exposed to E. paraensei miricidia


title: 4d exposed to E. paraensei miricidia (3) BS-90

value: M-line


title: 8d exposed to E. paraensei miracidia (2) BS-90

value: BS-90 strain

value: 8 day exposed to E. paraensei miricidia


title: 12h exposed to E. paraensei miricidia  (3) BS-90

value: 12 hr exposed to E. paraensei miricidia


title: 8d exposed to E. paraensei miracidia (1) BS-90

value: Reference sample RNA consisted of a mixture of RNA from snails


title: fily3_1


title: 2d exposed to E. paraensei miricidia (2) BS-90


title: 2d exposed to E. paraensei miricidia (3) BS-90


title: 12h exposed to S.mansoni miricidia  (1) BS-90


title: 12h exposed to S.mansoni miricidia  (2) BS-90


title: 12h exposed to E. paraensei miricidia  (2) BS-90


title: wt_3

source_name: Apices of Ler 14 DAS seedlines

value: wt


title: 16d exposed to E. paraensei miracidia (2) BS-90

value: 16 day exposed to E. paraensei miricidia


title: 4d exposed to E. paraensei miricidia (1) BS-90


title: 32d exposed to E. paraensei miracidia (3) BS-90

value: 32 day exposed to E. paraensei miricidia


title: 8d exposed to E. paraensei miracidia (3) BS-90


title: fily3y5_1


title: 16d exposed to E. paraensei miracidia (3) BS-90


title: 32d exposed to E. paraensei miracidia (1) BS-90


title: 16d exposed to E. paraensei miracidia (1) BS-90


title: 32d exposed to E. paraensei miracidia (2) BS-90


title: 1d exposed to E. paraensei miricidia (2) BS-90

value: 1 day exposed to E. paraensei miricidia


title: 1d exposed to E. paraensei miricidia (3) BS-90


title: wt_2


title: wt_1


title: wt_4


title: 12h exposed to E. paraensei miricidia  (1) BS-90


title: 1d exposed to E. paraensei miricidia (1) BS-90


title: control unexposed  (3) BS-90

value: control


title: control unexposed  (2) BS-90


title: control unexposed  (1) BS-90


title: 2d exposed to E. paraensei miricidia (4)

hyb_protocol: Purified Cy3 and Cy5 labeled products were then pooled, ethanol precipitated, resuspended in 100 µL hybridization buffer (40 % formamide, 5x Denhardt’s, 5x SSC, 1 mM sodium pyrophosphate, 50 mM Tris (pH 7.4) and 0.1 % SDS) and incubated at 95°C for 5 min followed by 50°C for 5 min. Arrays were pre-hybridized for 3.0 h at 42°C in hybridization buffer prior to hybridization with labeled probes. Labeled cDNA was hybridized overnight at 42°C.

source_name: 12-20 mm Biomphalaria glabrata

treatment_protocol: The trematode infected experimental groups and one control group examined this study were non-infected M line (control), Echinostoma paraensei infected and Schistosoma mansoni infected B. glabrata. For each treatment three pools of 5 snails were used as the biological replicates to reduce individual variability. Individual juvenile snails (shell diameter 4-8mm) B. glabrata were exposed to 15-20 S. mansoni or E. paraensei miracidia in artificial spring water (ASW), (Loker and Hertel, 1987) and kept alive before RNA extraction which was performed on days 0.5, 1, 2, 4, 8, 16 and 32 post infection. Control snails were placed into 24-well plates with ASW for 12 hours to mimic the conditions of infection protocol, afterwards RNA was extraction at the same time points as in the experimental groups.


title: 4d exposed to E. paraensei miricidia (1)


title: 4d exposed to E. paraensei miricidia (2)


title: 8d exposed to E. paraensei miracidia (4)


title: 16d exposed to E. paraensei miracidia (2)


title: 8d exposed to E. paraensei miracidia (1)


title: 16d exposed to E. paraensei miracidia (4)


title: 4d exposed to E. paraensei miricidia (5)


title: 8d exposed to E. paraensei miracidia (2)


title: 8d exposed to E. paraensei miracidia (3)


title: 2d exposed to E. paraensei miricidia (3)


title: 2d exposed to E. paraensei miricidia (2)


title: 4d exposed to E. paraensei miricidia (3)


title: 1d exposed to E. paraensei miricidia (2)


title: 2d exposed to E. paraensei miricidia (1)


title: 1d exposed to E. paraensei miricidia (3)


title: 1d exposed to E. paraensei miricidia (5)


title: 4d exposed to E. paraensei miricidia (4)


title: 16d exposed to E. paraensei miracidia (1)


title: 16d exposed to E. paraensei miracidia (3)


title: 2d exposed to E. paraensei miricidia (5)


title: 12h exposed to E. paraensei miricidia (5)


title: 12h exposed to E. paraensei miricidia (2)


title: 1d exposed to E. paraensei miricidia (4)


title: 1d exposed to E. paraensei miricidia (1)


title: 12h exposed to E. paraensei miricidia (4)


title: 12h exposed to E. paraensei miricidia (3)


title: control unexposed (5)


title: 12h exposed to E. paraensei miricidia (1)


title: control unexposed (3)


title: control unexposed (4)


title: 8d challenged with viable miricidia (2)

source_name: 8-10 mm Biomphalaria glabrata

value: 8 day challenged with viable miricidia


title: 8d challenged with viable miricidia (3)


title: 2d challenged with viable miricidia (3)

value: 2 day challenged with viable miricidia


title: 1d challenged with viable miricidia (3)

value: 1 day challenged with viable miricidia


title: 2d challenged with viable miricidia (2)


title: 1d challenged with viable miricidia (1)


title: 1d challenged with viable miricidia (2)


title: 12h challenged with viable miricidia (3)

value: 12 hr challenged with viable miricidia


title: 8d exposed to irradiated miricidia (1)

value: sensitized (8 day)


title: 8d exposed to irradiated miricidia (3)


title: 12h challenged with viable miricidia (1)


title: 8d exposed to irradiated miricidia (2)


title: control unexposed (1)


title: 12h challenged with viable miricidia (2)


title: 4d challenged with viable miricidia (2)

value: 4 day challenged with viable miricidia


title: 4d exposed to irradiated miricidia (1)

value: sensitized (4 day)


title: 1d exposed to irradiated miricidia (3)

value: M-line

value: sensitized (1 day)


title: 4d exposed to irradiated miricidia (2)


title: 2d challenged with viable miricidia (1)


title: 4d challenged with viable miricidia (1)


title: 8d challenged with viable miricidia (1)


title: 4d exposed to irradiated miricidia (3)


title: 4d challenged with viable miricidia (3)


title: 2d exposed to irradiated miricidia (2)

value: sensitized (2 day)


title: 2d exposed to irradiated miricidia (1)


title: 2d exposed to irradiated miricidia (3)


title: 1d exposed to irradiated miricidia (1)


title: 1d exposed to irradiated miricidia (2)


title: control unexposed (2)


title: 12h exposed to irradiated miricidia (2)

value: sensitized (12 hr)


title: 8d exposed to irradiated miricidia and then challenged with viable miricidia 8 days later (3)

value: sensitized (8 day) then challenged with viable miricidia 8 days later

value: Reference sample RNA consisted of a mixture of RNA from snails


title: 1d exposed to irradiated miricidia and then challenged with viable miricidia 8 days later (2)

value: sensitized (1 day) then challenged with viable miricidia 8 days later


title: 2d exposed to irradiated miricidia and then challenged with viable miricidia 8 days later (3)

value: sensitized (2 day) then challenged with viable miricidia 8 days later


title: 12h exposed to irradiated miricidia and then challenged with viable miricidia 8 days later (2)

value: sensitized (12 hr) then challenged with viable miricidia 8 days later


title: 12h exposed to irradiated miricidia and then challenged with viable miricidia 8 days later (3)


title: 8d exposed to irradiated miricidia and then challenged with viable miricidia 8 days later (2)


title: 1d exposed to irradiated miricidia and then challenged with viable miricidia 8 days later (1)


title: 12h exposed to irradiated miricidia and then challenged with viable miricidia 8 days later (1)

value: sensitized (12 hr) then challenged with viable miricidia 8 days later then challenged with viable miricidia 8 days later


title: 12h exposed to irradiated miricidia (1)


title: 2d exposed to irradiated miricidia and then challenged with viable miricidia 8 days later (2)


title: 2d exposed to irradiated miricidia and then challenged with viable miricidia 8 days later (1)


title: 1d exposed to irradiated miricidia and then challenged with viable miricidia 8 days later (3)


title: 12h exposed to irradiated miricidia (3)


title: Control 3

value: control


title: Control 2


title: 8d exposed to irradiated miricidia and then challenged with viable miricidia 8 days later (1)


title: 4d exposed to irradiated miricidia and then challenged with viable miricidia 8 days later (2)

value: sensitized (4 day) then challenged with viable miricidia 8 days later


title: 4d exposed to irradiated miricidia and then challenged with viable miricidia 8 days later (1)


title: 4d exposed to irradiated miricidia and then challenged with viable miricidia 8 days later (3)


title: Control 1


title: 0.2% glucose and 0.2% xylose sample 1

status: Public on Jul 31 2010

city: Emeryville

first: Robert

last: Dahl

state: CA

address: 5885 Hollis St, JBEI

department: Chemical Engineering

institute: University of California-Berkeley

description: Biological Replicate 1 of 3

label: Alexa Fluor 555

organism: Sulfolobus acidocaldarius DSM 639

source_name: Sulfolobus acidocaldarius DSM 639, glucose 0.2% and xylose 0.2%

label_protocol: 20 ug of total RNA was converted to cDNA and labeled with Alexa Fluor 555 with the Superscript Plus Indirect cDNA labeling kit (Invitrogen)

growth_protocol: S. acidocaldarius was grown in NYT medium supplemented with 0.4% xylose, 0.4% glucose, or 0.2% xylose and 0.2% glucose to mid-exponential phase (OD=0.2-0.4).

extract_protocol: At mid-exponential phase, 50 ml of cells were pelleted at 8000g for 5 min and then re-suspended in 0.5 ml of NYT medium and 1.0 ml of RNAlater (Qiagen). The cells were lysed with 15 mg/ml lysozyme and total RNA was extracted with the Rneasy Mini Kit. DNA was removed with an on-column DNase treatment. RNA integrity was verified with a 2100 Bioanalyzer (Agilent)

tag: growth condition

value: glucose 0.2% and xylose 0.2%


title: 0.2% glucose and 0.2% xylose sample 2

description: Biological Replicate 2 of 3


title: 0.2% glucose and 0.2% xylose sample 3

description: Biological Replicate 3 of 3


title: 0.4% xylose sample 2

description: Biological Replicate 2 of 3

source_name: Sulfolobus acidocaldarius DSM 639, xylose 0.4%

value: xylose 0.4%


title: 0.4% xylose sample 1

description: Biological Replicate 1 of 3


title: 0.4% xylose sample 3

description: Biological Replicate 3 of 3


title: 0.4% glucose sample 3

description: Biological Replicate 3 of 3

source_name: Sulfolobus acidocaldarius DSM 639, glucose 0.4%

value: glucose 0.4%


title: 0.4% glucose sample 2

description: Biological Replicate 2 of 3


title: Spermatogonial Stem Cell -F+S Replicate 4

city: Beijing

first: Chunsheng

last: Han

address: 1 Beichen West Road, Chaoyang District

country: China

institute: Institute of Zoology, CAS

hyb_protocol: see manufacturer's instructions

scan_protocol: see manufacturer's instructions

data_processing: Agilent Feature Extraction version 10.5.1.1 to normalize the data. We used the lowess algorithm to normalize our data.

source_name: SSCs -F+S 12 hr

label_protocol: see manufacturer's instructions

growth_protocol: Normal SSCs were maintained in serum free medium mainly composed of MEMa, 40 ng/ml GDNF, 5 ng/ml FGF2 and other factors. Upon passage, the control SSCs were maitained in the normal medium while the test SSCs were maintained in medium with FGF2 withdrawn and the FGFR inhibitor SU5402 supplemented, a condition referred to as -F+S.

extract_protocol: Total RNA was isolated and purified using QIGEN RNeasy mini RNA kit according to the manufacturer's instructions.

value: day 5

value: C57/BL6 x DBA/2 F1

source_name: SSCs normal culture


title: 0.4% glucose sample 1

description: Biological Replicate 1 of 3


title: Spermatogonial Stem Cell -F+S Replicate 3


title: Li65738

city: Jyväskylä

first: Heikki

last: Kainulainen

address: Seminaarinmäki

department: Department of Biology of Physical Activity

country: Finland

institute: University of Jyväskylä

description: Pair: Li65738, Li65739

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing:
The data were normalised using quantile normalisation with Affy package of Bioconductor.

Non-normalized data is available in 'GSE20536_non-normalized.txt', which is linked to the Series GSE20536 record as a supplementary file.

source_name: Biopsy, subcutaneous adipose tissue

label_protocol: Illumina RNA amplification kit (Ambion, Austin, TX) was used according to the manufacturer´s instructions to obtain biotin-labeled cRNA from 500 ng of total RNA.

extract_protocol: Total RNA was isolated from subcutaneous abdominal adipose tissue (after needle suspension) with Ambion’s RNAqueous -Micro Kit (AM 1931, Applied Biosystems) according to manufacturer's instructions.

tag: discordance for physical activity

value: non-active

tag: zygosity

value: DZ

value: male

value: subcutaneous abdominal adipose tissue


title: Spermatogonial Stem Cell -F+S Replicate 1


title: Li65739

description: Pair: Li65738, Li65739

value: active


title: Li73579

description: Pair: Li73578, Li73579

value: MZ

value: female


title: pair9_d0_Mu73579

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with affy package of Bioconductor

source_name: biopsy of m. vastus lateralis

label_protocol: Illumina RNA amplification kit (Ambion, Austin, TX) was used according to the manufacturer´s instructions to obtain biotinlabeled cRNA from 500 ng of total RNA.

extract_protocol: Trizol-reagent (Invitrogen, Carlsbad, CA) was used to isolate total RNA from muscle biopsy samples of m. vastus lateralis homogenized on FastPrep FP120 apparatus (MP Biomedicals, Illkirch, France).

value: musculus vastus lateralis


title: Li73578

description: Pair: Li73578, Li73579


title: pair9_d1_Mu73578


title: Li82602u

description: Pair: Li82601u, Li82602u


title: Li62928

description: Pair: Li62928, Li62929


title: Li60257

description: Pair: Li60256, Li60257


title: pair10_d0_Mu82601


title: Li62929

description: Pair: Li62928, Li62929


title: pair10_d1_Mu82602


title: Li60256

description: Pair: Li60256, Li60257


title: Li56757

description: Pair: Li56756, Li56757


title: Li56756

description: Pair: Li56756, Li56757


title: Spermatogonial Stem Cell -F+S Replicate 2


title: pair7_d1_Mu75001u


title: pair8_d0_Mu76816


title: pair6_d0_Mu65738


title: pair7_d0_Mu75002u


title: pair6_d1_Mu65739


title: pair5_d0_Mu60256


title: Li82601u

description: Pair: Li82601u, Li82602u


title: pair4_d0_Mu56756


title: pair5_d1_Mu60257


title: pair4_d1_Mu56757


title: pair8_d1_Mu76817


title: pair2_d0_Mu76665


title: pair3_d1_Mu62929


title: pair2_d1_Mu76664


title: Liver HQ11-CAST hyb66

status: Public on Jul 30 2010

city: Bar Harbor

first: Ricardo

middle: Alejandro

last: Verdugo

state: ME

address: 600 Main Street

department: Research

institute: The Jackson Laboratory

data_processing: Quantiles normalization with the affy package from Bioconductor. Log2 transformation. No background correction.

source_name: Liver from 9wk HQ11 female

label_protocol: cDNA was labeled with Biotin-16-UTP.

growth_protocol: Mice were weaned at 3 weeks old, housed in age and sex matching cages with five or less animals per cage. All animals were fed a standard Purina Formulab Chow 5008 diet and euthanized at 9 weeks old.

extract_protocol: Total RNA was extracted with TRIzol (Invitrogen), DNase treated (TurboDNA, Ambion) and cDNA was generated by reverse transcription using Total Prep RNA Amplification Kit (Illumina).

treatment_protocol: Congenic genotypes for chromosomes 2, 11, and 17 were created by backcrossing CAST/EiJ males to C57BL/6J-HG females. Non-recombinant F2s from three Congenic x Background crosses were profiled.

tag: array

tag: strain details

tag: sample id

tag: animal tube id

tag: genotype

value: CAST

tag: sex

value: F

value: Liver

tag: beadchip slot

value: B

tag: beadchip id

tag: animal id


title: pair3_d0_Mu62928

tag: tissue


title: pair1_d1_Mu56553


title: pair1_d0_Mu56552


title: Liver HQ11-CAST hyb71

value: A


title: Adipose HQ11-C57 hyb69

source_name: Adipose from 9wk HG female

value: Adipose


title: Brain HQ11-C57 hyb67

source_name: Brain from 9wk HG female

value: Brain

value: D


title: Adipose HQ11-C57 hyb63

value: C


title: Liver HQ11-CAST hyb54


title: Liver HQ11-C57 hyb65

source_name: Liver from 9wk HG female


title: Adipose HQ11-CAST hyb70

source_name: Adipose from 9wk HQ11 female


title: Adipose HQ11-CAST hyb64


title: Brain HQ11-CAST hyb62

source_name: Brain from 9wk HQ11 female


title: Brain HQ11-C57 hyb61

value: E


title: Liver HQ11-CAST hyb60


title: Adipose HQ11-C57 hyb57


title: Liver HQ11-C57 hyb72


title: Adipose HQ11-C57 hyb51


title: Adipose HQ11-CAST hyb58


title: Brain HQ11-CAST hyb55


title: Brain HQ11-CAST hyb50


title: Brain HQ11-C57 hyb49


title: Brain HQ11-CAST hyb68


title: Adipose HQ11-CAST hyb52


title: Liver HQ17-CAST hyb48

source_name: Liver from 9wk HQ17 female


title: Liver HQ11-C57 hyb53


title: Liver HQ11-C57 hyb59


title: Brain HQ11-C57 hyb56


title: Brain HQ17-C57 hyb44


title: Adipose HQ17-C57 hyb45


title: Adipose HQ17-CAST hyb46

source_name: Adipose from 9wk HQ17 female


title: Brain HQ17-CAST hyb43

source_name: Brain from 9wk HQ17 female


title: Liver HQ17-C57 hyb41


title: Liver HQ17-C57 hyb30


title: Adipose HQ17-CAST hyb40


title: Liver HQ17-CAST hyb36


title: Adipose HQ17-C57 hyb39


title: Liver HQ17-CAST hyb42


title: Brain HQ17-CAST hyb37


title: Adipose HQ17-CAST hyb33


title: Brain HQ17-C57 hyb31


title: Adipose HQ17-C57 hyb27


title: Liver HQ2D-CAST hyb18

source_name: Liver from 9wk HQ2D female


title: Brain HQ17-C57 hyb38


title: Liver HQ2D-C57 hyb24


title: Liver HQ17-C57 hyb35


title: Adipose HQ17-CAST hyb28


title: Liver HQ17-CAST hyb29


title: Brain HQ17-CAST hyb32


title: Adipose HQ17-C57 hyb34


title: Brain HQ17-C57 hyb25


title: Brain HQ17-CAST hyb26


title: Brain HQ2D-C57 hyb20


title: Adipose HQ2D-CAST hyb23

source_name: Adipose from 9wk HQ2D male

value: M


title: Brain HQ2D-C57 hyb22


title: Brain HQ2D-CAST hyb19

source_name: Brain from 9wk HQ2D female


title: Adipose HQ2D-C57 hyb17

source_name: Adipose from 9wk HG male


title: Brain HQ2D-CAST hyb13


title: Brain HQ2D-CAST hyb16


title: Adipose HQ2D-CAST hyb10


title: Adipose HQ2D-C57 hyb7


title: Brain HQ2D-C57 hyb15


title: Brain HQ2D-C57 hyb14


title: Adipose HQ2D-CAST hyb11


title: Adipose HQ2D-CAST hyb12


title: Adipose HQ2D-C57 hyb8


title: Liver HQ17-C57 hyb47


title: Liver HQ2D-C57 hyb3


title: Liver HQ2D-CAST hyb4


title: Adipose HQ2D-C57 hyb9


title: Liver HQ2D-CAST hyb6


title: P19 Setx wild type transfected no retinoic acid 2

status: Public on Jul 10 2010

city: brescia

first: andrea

last: bozzato

address: viale europa 11

country: Italy

institute: university of brescia

description: P19 Setx wild type transfected no retinoic acid  technical replicate of biological replicate 1

hyb_protocol: Following the Affymetrix GeneChip WT Terminal Labeling and Hybridization protocol RNA samples were hybridized at 45C for 17hrs

scan_protocol: The arrays were scanned using the Affymetrix GeneChip® Scanner 3000 7G

data_processing: The data were analyzed with Affymetrix GeneChip Expression Console and using Bioconductor limma inside of onechannelGUI package

source_name: P19 cells

label_protocol: 200 ng of total RNA were used for the preparation of targets for Affymetrix  Mouse GeneChip Gene 1.0 ST arrays according to the Ambion WT Expression Kit protocol

extract_protocol: RNA was extracted with RNeasy mini kit (Qiagen) according to the manufacturer’s protocol

tag: cell type


title: P19 cells shRNA setx transfected no retinoic acid 4

description: P19 cells shRNA setx transfected no retinoic acid  technical replicate biological replicate 2


title: P19 cells shRNA setx transfected +retinoic acid 2

description: P19 cells shRNA setx transfected +retinoic acid  technical replicate of biological replicate 1


title: P19 cells shRNA setx transfected no retinoic acid 3

description: P19 cells shRNA setx transfected no retinoic acid biological replicate 2


title: P19 Setx wild type transfected +retinoic acid 1

description: P19 Setx wild type transfected +retinoic acid biological replicate 1


title: Liver HQ2D-C57 hyb1


title: P19 cells shRNA setx transfected no retinoic acid 2

description: P19 cells shRNA setx transfected no retinoic acid  technical replicate of biological replicate 1


title: P19 Setx wild type transfected no retinoic acid 3

description: P19 Setx wild type transfected no retinoic acid  technical replicate of biological replicate 2


title: P19 Setx wild type transfected +retinoic acid 2

description: P19 Setx wild type transfected +retinoic acid  technical replicate of biological replicate 1


title: P19 cells shRNA setx transfected +retinoic acid 1

description: P19 cells shRNA setx transfected +retinoic acid biological replicate 1


title: P19 cells shRNA setx transfected +retinoic acid 4

description: P19 cells shRNA setx transfected +retinoic acid  technical replicate biological replicate 2


title: P19 Setx wild type transfected no retinoic acid 4

description: P19 Setx wild type transfected no retinoic acid  biological replicate 2


title: P19 Setx wild type transfected +retinoic acid 4

description: P19 Setx wild type transfected +retinoic acid  technical replicate of biological replicate 2


title: P19 Setx wild type transfected +retinoic acid 3

description: P19 Setx wild type transfected +retinoic acid biological replicate 2


title: P19 control no retinoic acid 4

description: P19 control no retinoic acid technical replicate of biological replicate 2


title: P19 Setx wild type transfected no retinoic acid 1

description: P19 Setx wild type transfected no retinoic acid  biological replicate 1


title: Liver HQ2D-CAST hyb5


title: P19 cells shRNA setx transfected +retinoic acid 3

description: P19 cells shRNA setx transfected +retinoic acid  biological replicate 2


title: P19 control no retinoic acid 3

description: P19 control no retinoic acid biological replicate 2


title: P19 control no retinoic acid 2

description: P19 control no retinoic acid technical replicate of biological replicate 1


title: Liver HQ2D-C57 hyb2


title: P19 cells shRNA setx transfected no retinoic acid 1

description: P19 cells shRNA setx transfected no retinoic acid biological replicate 1


title: P19 control no retinoic acid 1

description: P19 control no retinoic acid biological replicate 1


title: P19 control +retinoic acid 4

description: P19 control +retinoic acid technical replicate of biological replicate 2


title: P19 control +retinoic acid 3

description: P19 control +retinoic acid biological replicate 2


title: P19 control +retinoic acid 1

description: P19 control +retinoic acid biological replicate 1


title: P19 control +retinoic acid 2

description: P19 control +retinoic acid technical replicate of biological replicate 1


title: 6C-Secondary - iPS

status: Public on Jul 01 2010

city: Toronto

first: Payman

last: Samavarchi-Tehrani

state: Ontario

address: 600 University Ave

country: Canada

institute: Samuel Lunenfeld Research Institute

description:
6C-secondary - Dox Independent iPS
MoEx1_040709H_AN5_DOX#1.13Dataset_ALL_.rma-gene-core-Signal

hyb_protocol: Samples were hybridized and washed using FS450_0001 protocol

scan_protocol: Affymetrix Gene ChIP Scanner 3000

data_processing:
Data was processed using Affymetrix Expression Console at Gene Level of the exon Core probes using RMA normalization.
Gene-level analysis:
probe group file = MoEx-1_0-st-v1.r2.pgf
meta-probeset file = MoEx-1_0-st-v1.r2.dt1.mm9.core.mps

source_name: 6C-secondary - iPS

label_protocol: cDNA synthesis was done using Affymetrix WT Kit and in vitro transcription was done using Affymetrix WT IVT Kit

growth_protocol: Culture of MEFs in standard mouse ES media throughout reprogramming. Cells were split every2-3 days based on density and colony size.

extract_protocol: QIAGEN RNAeasy kit

treatment_protocol: 1.5ug/ml of Dox treatment, if applicable.

value: 6C secondary MEFs (converted into Dox-independent, 6C-secondary - iPS)

tag: agent

value: Dox

tag: time

value: day 30


title: 6C-Secondary - day5

description:
6C-secondary - 5days of Dox
MoEx1_020309L_AN04_1 Day5+Dox.13Dataset_ALL_.rma-gene-core-Signal

source_name: 6C-secondary cells

value: 6C-secondary MEFs

value: day 5


title: 1B-Secondary - day0

description:
1B-secondary MEFs without Dox
MoEx1_022609H_AN1_NO DOX.13Dataset_ALL_.rma-gene-core-Signal

source_name: 1B-secondary cells

value: 1B-secondary MEFs

value: untreated

value: day 0


title: 1B-Secondary - day5

description:
1B-secondary - 5days of Dox
MoEx1_022609H_AN2_5D DOX.13Dataset_ALL_.rma-gene-core-Signal


title: 6C-Secondary - day21

description:
6C-secondary - 21days of Dox
MoEx1_012709L_AN02_1 day21 + Dox.13Dataset_ALL_.rma-gene-core-Signal

value: day 21


title: 6C-Secondary - day16

description:
6C-secondary - 16days of Dox
MoEx1_020309L_AN06_1-2 Day16+Dox.13Dataset_ALL_.rma-gene-core-Signal

value: day 16


title: Brain HQ2D-CAST hyb21

tag: strain

value: CAST

value: F


title: Parental MEF cells

description:
Parental MEF cells
MoEx1_020309L_AN08_1 Primary mef.13Dataset_ALL_.rma-gene-core-Signal

source_name: Parental MEF

value: Parental MEFs

value: control


title: Caco-2 at T4

city: Horsholm

first: Ondrej

last: Valina

address: Boge alle 10-12

department: H&N Divison

country: Denmark

institute: Chr. Hansen A/S

description: Gene expression data from Caco-2 cells after 4 hours of the incubation with B. animalis subsp. lactis BB-12

hyb_protocol: 15 µg of cRNA was fragmented at 94°C for 35 min in a fragmentation buffer containing 40 mM Tris-acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc. Prior to hybridization, the fragmented cRNA in a 6xSSPE-T hybridization buffer (1 M NaCl, 10 mM Tris pH 7.6, 0.005% Triton), was heated to 95°C for 5 min and subsequently to 45°C for 5 min before loading onto the Affymetrix Human Genome U133 Plus 2.0 array cartridge (Affymatrix, Santa Clara, CA). The probe array was then incubated for 16 h at 45°C at constant rotation (60 rpm). The washing and staining procedure was performed in the Affymetrix Fluidics Station 450. The probe array was exposed to 10 washes in 6xSSPE-T at 25°C followed by 4 washes in 0.5xSSPE-T at 50°C. The biotinylated cRNA was stained with a streptavidin-phycoerythrin conjugate, final concentration 2 mg/ml (Molecular Probes, Eugene, OR) in 6xSSPE-T for 30 min at 25°C followed by 10 washes in 6xSSPE-T at 25°C. An antibody amplification step followed using normal goat IgG as blocking reagent (Sigma, Brøndby, Denmark), final concentration 0.1 mg/ml and biotinylated anti-streptavidin antibody (Vector Laboratories, Burlingame, CA), final concentration 3 mg/ml. This was followed by a staining step with a streptavidin-phycoerythrin conjugate (Molecular Probes, Eugene, OR), final concentration 2 mg/ml in 6xSSPE-T for 30 min at 250C and 10 washes in 6xSSPE-T at 250C.

scan_protocol: The probe arrays were scanned at 560 nm using a confocal laser-scanning microscope (GeneChip® Scanner 3000). The readings from the quantitative scanning were analyzed by the Affymetrix Gene Expression Analysis Software.

data_processing: The data were analyzed with R/Bioconductor and GC-RMA as normalization method. affylmGUI used. Expresso() function for preprocessing chips, limma package was used for differential exprression - fold change and standard errors by fitting a linear model (using the lmFit function) moderated t-statistics of differential expression by applying empirical Bayes shrinkage of the standard errors towards a common value (using the eBayes function).

source_name: Caco-2 cells (4 hours)

label_protocol: Biotinylated cRNA were prepared using standard Affymetrix protocol.

growth_protocol: Caco-2 intestinal enterocyte cells (ACC 169, Deutsche Sammlung von Mikroorganismen und Zellkulturen, Germany) were routinely grown in Dulbecco modified Eagle minimal (DMEM) medium Glutamax (Invitrogen, Carlsbad, CA) supplemented with 20% fetal bovine serum (FBS) (HyClone, Cramlington, UK) and 1% nonessential amino acids (NEAA) (Invitrogen, Carlsbad, CA) and 0.2% antibiotics gentamicin/amphotericin (Cascade Biologics, Portland, OR). Cells were cultured at 37°C in a 5% CO2 - 95% air atmosphere. The culture medium was changed every 2 days. Differentiated cells were used after 21 days of culturing for expression and enzyme-linked immunosorbent assay experiments were done in 0.4 μm polyester transwell permeable insert chambers (Corning B.V., Schiphol-Rijk, The Netherlands); trans-epithelial electrical resistance measurement (TEER) was used as a measure of cell differentiation - TEER between 500-700 Ohm/cm2 - after 21 days of culturing.

extract_protocol: The thawed cell pellets were resuspended in RLT buffer (Qiagen, Hilden, Germany) and total RNA was extracted using the RNeasy kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.

treatment_protocol: BB-12 was grown to stationary phase. Then the bacterial culture of OD600 = 1.0 (5×10e8 CFU/ml) was co-cultured in the cell culture medium without antibiotics together with differentiated 21 days Caco-2 cells in transwell inserts. The same experimental set-up without BB-12 in the upper compartment of the insert was used as a control for the transcriptomic experiments.   The Caco-2 cells were harvested from the transwell inserts after 4 hours of co-cultivation. The entire medium was carefully removed from the wells and 500 μl of RTL buffer from RNeasy Plus Mini Kit (Qiagen, Hilden, Germany) was added to the transwell. The cells were scraped off the membrane surface, collected in to the new vial and vortexed for 5 s. Samples from 3 independent wells (for experiment as well as control) were pooled together and then were stored at -80°C until further use. The medium used in experiment as well as in the control was freshly made cell culture medium. DNA microarrays were produced for the Caco-2 cells co-cultured with bacteria versus Caco-2 cells cultured without bacteria.

value: intestinal enterocyte cell line

tag: cell line


title: 6C-Secondary - day0

description:
6C-secondary MEFs without Dox
MoEx1_012709L_AN01_1 day2 No Dox.13Dataset_ALL_.rma-gene-core-Signal


title: 1B-Secondary - day5w, day5w/o

description:
1B-secondary - 5days of Dox followed by 5days without Dox
MoEx1_022609H_AN3_+DOX-DOX.13Dataset_ALL_.rma-gene-core-Signal

value: Dox (5days), followed by no Dox (5days)

value: day 10


title: Caco-2 at T0 rep2

description: Gene expression data from Caco-2 cells before the incubation with B. animalis subsp. lactis BB-12

source_name: Caco-2 cells (control)


title: 6C-Secondary - day11

description:
6C-secondary - 11days of Dox
MoEx1_020309L_AN05_1 Day11+Dox.13Dataset_ALL_.rma-gene-core-Signal

value: day 11


title: 6C-Primary - iPS

description:
6C-primary - Dox Independent iPS
MoEx1_020309L_AN07_1 Primary ips+Dox.13Dataset_ALL_.rma-gene-core-Signal

source_name: 6C-primary - iPS

value: 6C-primary - iPS

value: Dox


title: Caco-2 at T0 rep1


title: Tlr2-/- to WT_90n/Tlr4 [mRNA]

city: Houston

first: Richard

last: Kellermayer

state: TX

address: One Baylor Plaza

institute: Baylor College of Medicine

hyb_protocol: Hybridization of the arrays was carried out  according to the Agilent Chip-on-chipmammalian protocol (version 9.1, 2006)

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization. Probe ratios were calculated for Tlr2-/- to WT comparisons in each of the 4 arrays separately.

source_name: P90 WT

label_protocol: RNA (0.4ug) samples were processed and labelled with Cy3 and Cy5 (Quick Amp labelling kit, two color, Agilent technologies)

extract_protocol:
tissue isolation protocol: Colonic mucosa was sheared by microscope slide and flash frozen on dry ice.
Total RNA was extracted by Quiagen Rneasy mini kit (Cat.no.74106)

tag: genotype/variation

value: wild type

tag: age

value: 90 postnatal days

value: colonic mucosa

value: Tlr2 knockout


title: 6C-Secondary - day2

description:
6C-secondary - 2days of Dox
MoEx1_020309L_AN03_1 Day2+Dox.13Dataset_ALL_.rma-gene-core-Signal

value: 6C-secondary MEFs

value: day 2


title: Tlr2-/- to WT_90o/Tlr5 [mRNA]


title: hydro_vs_saline_rep5

city: Salt Lake City

first: Kelley

last: Deren

state: UT

address: 175 N Medical Drive East CNC 3305

department: Neurosurgery

institute: University of Utah

hyb_protocol: Agilent Two-color Gene Expression Hyb/Wash Protocol.

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505C Microarray Scanner at 5 um resolution.

data_processing: Images processed with Agilent Feature Extraction softtware version 10.1.1.1. Intensities were log2 transformed and quantile normalized.

source_name: parietal cortex tissue, kaolin

label_protocol: Agilent Two-Color LRILAK Labeling Protocol.

growth_protocol: At birth (approximately 21 days of gestation), pups were divided into two groups: sham control and hydrocephalic.  All pups remained with the dam until sacrifice on post-kaolin day 21.

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

treatment_protocol: On postnatal day 1, rats were injected with either kaolin or saline.

value: postnatal day 22

value: brain

tag: brain region

value: parietal cortex

tag: treatment

value: kaolin

source_name: parietal cortex tissue, saline

value: saline


title: 6C-Secondary - day8

description:
6C-secondary - 8days of Dox
MoEx1_040709H_AN4_Day9+ DOX.13Dataset_ALL_.rma-gene-core-Signal

value: day 8


title: Tlr2-/- to WT_Tlr1/90f [mRNA]


title: hydro_vs_saline_rep4


title: hydro_vs_saline_rep3


title: Tlr2-/- to WT_Tlr2/90k [mRNA]


title: hydro_vs_saline_rep2


title: Stomach_Car9ko_rep4

city: Tampere

first: Heini

last: Kallio

address: Biokatu 6

department: Institute of Medical Technology and School of Medicine

institute: University of Tampere

description: Replicate 4 of 6.

hyb_protocol: Standard Illumina hybridization protocol. 18h at 58 degrees.

scan_protocol: Standard scan factor in Illumina BeadArray reader.

data_processing: Array data were normalized with Chipster version 1.3.0 using the quantile normalization method.

source_name: Mouse stomach, Car9 knockout

label_protocol: Using Illumina TotalPrep RNA Amplification kit (#AMIL1791, Ambion), following the manufacturer's protocol. Input amount: 400ng of total RNA. Incubation of labeling reaction: 14.5h.

extract_protocol: RNA was extracted with Rneasy RNA isolation kit including Rnase-free Dnase treatment (Qiagen) according to the manufacturer's protocol. Concentration and purity were measured with Nanodrop.

tag: gender

value: male

value: stomach

value: 12 months


title: hydro_vs_saline_rep1


title: Stomach_Car9ko_rep5

description: Replicate 5 of 6.

value: female

value: 10 months


title: Stomach_Car9ko_rep6

description: Replicate 6 of 6.


title: Stomach_wt_rep4

description: Replicate 4 of 6.

source_name: Mouse stomach

value: wildtype


title: Stomach_wt_rep5

description: Replicate 5 of 6.


title: Stomach_wt_rep1

description: Replicate 1 of 6.


title: Stomach_Car9ko_rep3

description: Replicate 3 of 6.


title: Stomach_Car9ko_rep2

description: Replicate 2 of 6.


title: Stomach_wt_rep3

description: Replicate 3 of 6.

value: 8 months


title: Stomach_wt_rep6

description: Replicate 6 of 6.


title: Stomach_wt_rep2

description: Replicate 2 of 6.


title: Beta'_rep 2

type: genomic

city: Madison

first: Yann

middle: S

last: Dufour

state: WI

address: 1550 Linden Drive

department: Bacteriology

institute: University of Wisconsin - Madison

description: ChIP-chip Beta' in wild-type cells

hyb_protocol: 4 ug of labelled DNA were hybridized on 385K NimbleGen custom arrays according to NimbleGen's protocol.

scan_protocol: Arrays were scanned on an Axon 4000B scanner according to the manufacturer's protocol.

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction. The signal from Beta' ChIP was subtracted from the signals from FnrL and Sigma70 ChIP using loess normalization to remove background signal.

molecule: genomic DNA

organism: Cereibacter sphaeroides 2.4.1

source_name: Beta' ChIP DNA

label_protocol: Before labelling, the ChIP DNA was amplified using ligation mediated PCR. 1 ug of DNA was labelled using the NimbleGen Dual-color DNA labelling Kit (05223547001) according to the manufacturer's protocol.

growth_protocol: cells were cultured in minimal succinate based medium under anaerobic photosynthetic conditions until mid-exponential growth phase

extract_protocol: cells were fixed with 1% formaldehyde in culture medium for 5 minutes at 30°C followed by quenching with 0.125 M clycine for 30 minutes on ice. The cells were washed twice with ice cold PBS, frozen in dry/ethanol bath and stored at -80°C. Cells were resuspended in 500uL IP buffer (100 mM Tris pH 8, 300 mM NaCl, 2% TritinX-100), and sonicated (50% output, level 6) for 20 seconds 8 times to shear the DNA to fragments of 1 kbp in average. 50 units of micrococcal DNase and 0.5ug of RNaseA were added to the lysate and incubated for 1 hour at 4°C to reduce fragment size to 500 bp in avergage and degrade RNA. To stop the nucleases EDTA was added to 10mM final concentration. The lysate was cenrtrifuged to remove cell debris and 100 uL was saved for Input DNA. The lysate was was incubated with polyclonal antibodies against RpoE or Beta' at 4°C over night. Then, ProteinA coated sepharose beads were added to the lysate, which was incubated for another 3 hours to capture antibodies. Beads were washed once with LiCl buffer (125 mM LiCL, 50 mM Tris pH 8, 1 % TritonX-100), twice with 600 mM NaCl Tris buffer, twice with 300mM NaCl Tris buffer and twive with TE buffer (10 mM Tris ph 8, 1 mM EDTA). Beads were ressupended in 200 uL Elution buffer (50 mM Tris pH 8, 10 nM EDTA, 1% SDS) and incubated at 65°C for 15 hours to reverse cross linking. DNA was cleaned using QIAGen DNA purification kit.

value: Wild-type

tag: antibody

value: Beta

source_name: Input DNA


title: Sigma70_rep_3

description: ChIP-chip sigma70 in Wild-type cells

source_name: Sigma70 ChIP DNA


title: Sigma70_rep_2

description: ChIP-chip sigma70 in Wild-type cells


title: Beta'_rep 1

description: ChIP-chip Beta' in wild-type cells


title: Stomach_Car9ko_rep1

description: Replicate 1 of 6.

tag: genotype


title: Beta'_rep 3

description: ChIP-chip Beta' in wild-type cells


title: Sigma70_rep_1

description: ChIP-chip sigma70 in Wild-type cells


title: aCML #160 SNP6.0

status: Public on Jun 30 2010

city: Salisbury

first: Andy

last: Chase

address: Salisbury District Hospital

institute: Wessex Regional Genetics Laboratory

description: hybridised to Affymetrix SNP 6.0 array

hyb_protocol: Processed by Almac Diagnostic (Craigavon, UK).  Hybridisation according to Affymetrix protocols. Array washed and stained on the GeneChip® fluidics station 450 .

scan_protocol: Processed by Almac Diagnostic (Craigavon, UK).  Array scanned using a GeneChip® Scanner 3000 7G.

data_processing:
Chp files were produced using Affymetrix Genotyping Console version 3.0.2 (birdseed-v2 algorithm); data was analysed using Partek Genomic Suite 6.5 and CNAG version 3.2 using Hapmap normal references
Affymetrix SNP 6.0 CEL and CHP files

source_name: hematopoietic

label_protocol: Processed by Almac Diagnostic (Craigavon, UK). Biotin labeled according to Affymetrix protocols.

extract_protocol: Qiagen QIAamp DNA extraction kit

value: blood

tag: disease state

value: aCML

tag: patient gender


title: CMML #169 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array

value: CMML


title: MDS/MPN #167 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array

value: MDS/MPN


title: aCML #064 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: MDS/MPN #157 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: aCML #060 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: CMML #161 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: MDS/MPN #156 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: CMML #055 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: CMML #162 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: MDS/MPN #049 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: MDS/MPN #159 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: MDS/MPN #166 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: CMML #164 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: aMPD #168 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array

value: aMPD


title: MDS/MPN #155 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: CMML #163 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: CMML #067 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: CMML #006 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: CMML #041 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: MDS/MPN #158 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: MDS/MPN #059 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: MDS/MPN #154 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: CMML #070 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: CMML #152 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: MDS/MPN #153 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: MDS/MPN #007 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: MDS/MPN #012 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: CMML #165 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: CMML #043 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: aCML #148 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: CMML #065 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: aCML #147 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array


title: CMML #146 SNP6.0

description: hybridised to Affymetrix SNP 6.0 array