title: 35S:VuDREB2A (full length) line vs. wild type Replicate 2

city: Guwahati

first: Ayan

last: Sadhukhan

state: Assam

address: IIT GUwahati, Amingaon, North Guwahati

department: Biotechnology

country: India

institute: Indian Institute of Technology Guwahati

description: Biological replicate 2 of 2. 21 day-old seedlings of VuDREB2A (full length)-overexpressing line and wild type whole plants were harvested.

hyb_protocol: 0.825 μg of Cy3- and Cy5-labelled cRNA (specific activity >10.0 pmol Cy3 or Cy5 per μg cRNA) were fragmented with Gene Expression Hybridization Kit (5188-5242, Agilent) following the manufacturer's instructions. On completion of the fragmentation reaction, 55 ul of 2x GE hybridization buffer HI-PRM was added to the fragmentation mixture and hybridized to Agilent Arabidopsis 4 Oligo Microarray (G2519F) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Scanned on an Agilent G2505C scanner

data_processing: Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction and LOWESS normalization.

organism: Arabidopsis thaliana

source_name: 35S:VuDREB2A (full length) line

label_protocol: Cyanine-3 (Cy3) and Cyanine-5 (Cy5) labeled cRNA were prepared from 200 ng of total RNA using the Low Input Quick Amp Labeling kit (5190-2306, Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).

growth_protocol: VuDREB2A overexpressing  and wild type Arabidopsis were grown in 1/2 MS agar media with 1% sucrose in vertically oriented plates for 21 days. All seedlings were kept under 12 h illuminations per day (30 µmol m–2 s–1) at 25°C .

extract_protocol: Total RNA was isolated by the method of Suzuki et al. (2004).

treatment_protocol: No treatment

tag: background

value: whole plants

source_name: wild type Col-0


title: DHL6_48h_JQ1_C

status: Public on Dec 10 2013

type: RNA

city: Boston

first: Björn

last: Chapuy

state: MA

address: 450 Brookline Ave.

department: Medical Onology

country: USA

institute: Dana-Farber Cancer Institute

description: Cell line DHL6 treated with JQ1 at 48h (replicateC)

hyb_protocol: Following fragmentation, cRNA was hybridized overnight according to the Affymetrix protocol.

scan_protocol: GCS3000 (Affymetrix)

data_processing: The raw cel files were converted into probeset-specific expression values using Affymetrix RMA summarization method and alternative probe set definitions (HuGene10stv1_Hs_ENTREZ, Brainarray v15) as implemented in the BioConductor package simpleaffy (Gentleman et al., 2004). All samples were scaled to have a mean expression level of 100.

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: Cell line DHL6 treated with JQ1 at 48h

label_protocol: cRNA was biotinylated according to the standard Affymetrix protocol.

growth_protocol: Five lymphoma cell lines, SU-DHL6, OCI-Ly1, OCI-Ly4, Toledo and HBL-1, were propagated in their appropriate growth media under standard conditions.

extract_protocol: For total RNA, cells were homogenized in Trizol and RNA was extracted according to standard protocols.

treatment_protocol: Each lymphoma cell line was profiled in triplicate at baseline (0h) and at four additional time points (2h, 6h, 24h and 48h) after treatment with 500nM of JQ1 or vehcile (DMSO) control.

tag: cell line

tag: cell type

value: diffuse large B-cell lymphoma (DLBCL)

tag: time

tag: treatment

tag: replicate

value: C


title: DHL6_48h_JQ1_B

description: Cell line DHL6 treated with JQ1 at 48h (replicateB)

value: B


title: HSC flox/flox 18 day post pIC rep3

city: Copenhagen N

first: Marie

middle: S

last: Hasemann

address: Ole Maaløes Vej 5

department: Finsen Laboratory

country: Denmark

institute: Rigshospitalet

hyb_protocol: Affymetrix EukGE-WS2v4_450 Hybridization protocol, according to manufacturers specifications

scan_protocol: standard Affymetrix protocol

data_processing: Cell intesity files (CEL files) were generated in the Genechip Command Console Software (AGCC), (Affymetrix, Santa Clara, CA, USA). The data was normalized using the RMA function from the Bioconductor package affy in R.

label: biotin

organism: Mus musculus

source_name: Sorted HSCs (LSKCD150+CD48-) from bone marrow samples, 18 days post conditional gene knock out

label_protocol: 2.5ug of amplified cDNA was fragmentated and labeled using Encore Biotin Module V2 according to manufactures instructions. www.nugeninc.com/nugen/index.cfm/products/pl/target-preparation/encore-biotin-module/

growth_protocol: Murine bone marrow cells were enriched for cKit+ and hematopoietic stem cells were sorted by FACS.

extract_protocol: Total RNA from sorted cells were isolated with RNeasy Micro Kit (Qiagen). Samples were prepared in triplicates for each genotype. 20 ng of total RNA was amplified using Ovation Pico WTA system V2 (Nugene)according to manufactures instructions. www.nugeninc.com/nugen/index.cfm/products/cs/microarrays-and-qpcr/ovation-pico-wta-system-v2/manufacturers instructions.

treatment_protocol: Female mice were injected with pIC, at day 18 they were sacrifized and bones were dissected, bone marrow cells were isolated by crushing and HSCs were sorted by FACS.

tag: Sex

value: female

tag: strain

tag: tissue

value: Bone marrow cells, HSCs

tag: genotype

value: Cebpa flox/flox

tag: cell population

value: HSC:Lin-, Sca1+, cKit+, CD150+, CD48-


title: Liver from control mice, biological replicate 4

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum Muenchen

description:
Ctrl_04
Gene expression data from liver of control mice.

hyb_protocol: According to the Affymetrix expression protocol (HWS kit).

scan_protocol: According to the Affymetrix expression protocol.

data_processing: RMA probeset summary with standard settings of the Affymetrix Expression Console software (v.1.2) including median polish and Sketch-Quantile normalisation.

source_name: liver, ctrl mice

label_protocol: WT Expression Kit (Ambion) and the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Animals were housed under spf conditions.

extract_protocol: miRNeasy Mini Kit (Qiagen) including DNase treatment.

treatment_protocol: To induce type 1 diabetes, 65 mg/kg of streptozotocin (STZ) was injected i.p. into 10- to 16-week-old mice on 5 consecutive days while respective controls were mock-injected with citrate buffer. Animals were sacrificed 9-11 weeks after this treatment.

value: wildtype

value: liver

tag: age

value: 5-6 months

tag: gender

value: male

value: mock


title: Liver from control mice, biological replicate 2

description:
Ctrl_02
Gene expression data from liver of control mice.


title: 35S:VuDREB2A (truncated) line vs. wild type Replicate 2

description: Biological replicate 2 of 2. 21 day-old seedlings of VuDREB2A (truncated)-overexpressing line and wild type whole plants were harvested.

source_name: 35S:VuDREB2A (truncated) line


title: DHL6_48h_JQ1_A

description: Cell line DHL6 treated with JQ1 at 48h (replicateA)

value: A


title: DHL6_24h_JQ1_B

description: Cell line DHL6 treated with JQ1 at 24h (replicateB)

source_name: Cell line DHL6 treated with JQ1 at 24h


title: DHL6_48h_DMSO_A

description: Cell line DHL6 treated with DMSO at 48h (replicateA)

source_name: Cell line DHL6 treated with DMSO at 48h

value: DMSO


title: 35S:VuDREB2A (truncated) line vs. wild type Replicate 1

description: Biological replicate 1 of 2. 21 day-old seedlings of VuDREB2A (truncated)-overexpressing line and wild type whole plants were harvested.


title: DHL6_24h_DMSO_B

description: Cell line DHL6 treated with DMSO at 24h (replicateB)

source_name: Cell line DHL6 treated with DMSO at 24h


title: colorectal cancer with liver metastasis_16

city: Guangzhou

first: Dong-liang

last: Chen

address: No.651 Dong Feng East Road

country: China

institute: Sun Yat-sen University Cancer Center

description:
Gene expression data from human colorectal cancer tissue with liver metastasis
614T

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

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000G.

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.

source_name: colorectal cancer with liver metastasis

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

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

treatment_protocol: Their primary CRC tissues (n = 99), adjacent normal tissues (n = 99) and corresponding matched liver metastatic tissues (n = 44) were obtained immediately after surgery and stored at -80 ºC until use

tag: disease state

value: CRC

tag: liver metastasis

value: with


title: DHL6_48h_DMSO_B

description: Cell line DHL6 treated with DMSO at 48h (replicateB)


title: colorectal cancer with liver metastasis_15

description:
Gene expression data from human colorectal cancer tissue with liver metastasis
595T


title: Liver from control mice, biological replicate 3

description:
Ctrl_03
Gene expression data from liver of control mice.


title: DHL6_12h_JQ1_B

description: Cell line DHL6 treated with JQ1 at 12h (replicateB)

source_name: Cell line DHL6 treated with JQ1 at 12h


title: chick forebrains, 16h DMSO

city: Rennes

first: Valérie

last: Dupé

address: 2 av leon Bernard

country: France

description: Gene expression after 16hr in culture medium with DMSO

hyb_protocol: Hybridization was accomplished on the agilent 4x44K whole chicken genome in situ oligonucleotide microarray.

scan_protocol: Image acquisition was performed using the Agilent Scanner (Biogenouest, Rennes).

data_processing: Signals were extracted by Agilent Feature Extraction software. Data normalization was performed by a per-chip 50th percentile method by the GeneSpring Agilent GX12.

organism: Gallus gallus

source_name: chick forebrains, 16h DMSO

label_protocol: Total RNA (50µg) from each sample was reverse transcripted and cRNA were prepared according to the Agilent recommendations and following the one color protocol to be labelled with Cy3-CTP.

extract_protocol: Total RNA was immediately extracted. The RNA quality had been controlled by 2100 Bioanalyser.

treatment_protocol: Chick embryonic anterior head was dissected after 16hours roller culture with DMSP or DAPT.

value: forebrain

value: embryo HH13


title: DHL6_12h_DMSO_C

description: Cell line DHL6 treated with DMSO at 12h (replicateC)

source_name: Cell line DHL6 treated with DMSO at 12h

value: diffuse large B-cell lymphoma (DLBCL)

value: C


title: DHL6_24h_JQ1_A

description: Cell line DHL6 treated with JQ1 at 24h (replicateA)


title: chick forebrains, 16h DAPT

description: Gene expression after 16hr in culture medium with DAPT

source_name: chick forebrains, 16h DAPT


title: DHL6_12h_JQ1_C

description: Cell line DHL6 treated with JQ1 at 12h (replicateC)


title: DHL6_48h_DMSO_C

description: Cell line DHL6 treated with DMSO at 48h (replicateC)


title: DHL6_12h_DMSO_B

description: Cell line DHL6 treated with DMSO at 12h (replicateB)

value: B


title: DHL6_12h_DMSO_A

description: Cell line DHL6 treated with DMSO at 12h (replicateA)


title: DHL6_6h_DMSO_C

description: Cell line DHL6 treated with DMSO at 6h (replicateC)

source_name: Cell line DHL6 treated with DMSO at 6h


title: 35S:VuDREB2A (full length) line vs. wild type Replicate 1

description: Biological replicate 1 of 2. 21 day-old seedlings of VuDREB2A (full length)-overexpressing line and wild type whole plants were harvested.

value: whole plants


title: DHL6_6h_JQ1_C

description: Cell line DHL6 treated with JQ1 at 6h (replicateC)

source_name: Cell line DHL6 treated with JQ1 at 6h


title: DHL6_6h_JQ1_A

description: Cell line DHL6 treated with JQ1 at 6h (replicateA)


title: DHL6_6h_DMSO_B

description: Cell line DHL6 treated with DMSO at 6h (replicateB)


title: DHL6_6h_JQ1_B

description: Cell line DHL6 treated with JQ1 at 6h (replicateB)


title: DHL6_2h_JQ1_A

description: Cell line DHL6 treated with JQ1 at 2h (replicateA)

source_name: Cell line DHL6 treated with JQ1 at 2h


title: DHL6_0h_nothing_A

description: Cell line DHL6 treated with nothing at 0h (replicateA)

value: nothing


title: DHL6_0h_nothing_C

description: Cell line DHL6 treated with nothing at 0h (replicateC)


title: Ly1_0h_nothing_A_1_9

description: Cell line Ly1 treated with nothing at 0h (replicateA)


title: DHL6_2h_JQ1_C

description: Cell line DHL6 treated with JQ1 at 2h (replicateC)


title: Toledo_48h_DMSO_C

description: Cell line Toledo treated with DMSO at 48h (replicateC)

value: Toledo


title: DHL6_2h_JQ1_B

description: Cell line DHL6 treated with JQ1 at 2h (replicateB)


title: DHL6_2h_DMSO_B

description: Cell line DHL6 treated with DMSO at 2h (replicateB)

source_name: Cell line DHL6 treated with DMSO at 2h


title: Toledo_24h_JQ1_C

description: Cell line Toledo treated with JQ1 at 24h (replicateC)


title: DHL6_2h_DMSO_A

description: Cell line DHL6 treated with DMSO at 2h (replicateA)


title: Toledo_48h_JQ1_B

description: Cell line Toledo treated with JQ1 at 48h (replicateB)


title: Toledo_48h_JQ1_A

description: Cell line Toledo treated with JQ1 at 48h (replicateA)


title: Ly1_0h_nothing_A_1_7

source_name: Cell line Ly1 treated with nothing at 0h


title: DHL6_6h_DMSO_A

description: Cell line DHL6 treated with DMSO at 6h (replicateA)


title: DHL6_0h_nothing_B

description: Cell line DHL6 treated with nothing at 0h (replicateB)


title: Toledo_48h_JQ1_C

description: Cell line Toledo treated with JQ1 at 48h (replicateC)


title: Toledo_24h_JQ1_B

description: Cell line Toledo treated with JQ1 at 24h (replicateB)


title: Toledo_24h_DMSO_C

description: Cell line Toledo treated with DMSO at 24h (replicateC)


title: Toledo_48h_DMSO_B

description: Cell line Toledo treated with DMSO at 48h (replicateB)


title: DHL6_2h_DMSO_C

description: Cell line DHL6 treated with DMSO at 2h (replicateC)


title: Toledo_24h_DMSO_B

description: Cell line Toledo treated with DMSO at 24h (replicateB)


title: Toledo_24h_JQ1_A

description: Cell line Toledo treated with JQ1 at 24h (replicateA)


title: Toledo_12h_JQ1_C

description: Cell line Toledo treated with JQ1 at 12h (replicateC)


title: Toledo_12h_JQ1_B

description: Cell line Toledo treated with JQ1 at 12h (replicateB)


title: Toledo_24h_DMSO_A

description: Cell line Toledo treated with DMSO at 24h (replicateA)


title: Toledo_12h_JQ1_A

description: Cell line Toledo treated with JQ1 at 12h (replicateA)


title: at 60 mins during the LHOT condition

city: Esch-sur-Alzette

first: Feng

middle: Q.

last: Hefeng

address: 29, rue Henri Koch

department: Department of Infection and Immunity

country: Luxembourg

institute: Luxembourg Institute of Health

description:
LHOT60
time-series gene expression data from Pseudomonas aeruginosa PAO1

hyb_protocol: The cDNA was loaded onto Affymetrix PA GeneChip. Target hybridization was performed at 37 °C for 16 hours by using a GeneChip Hybridization Oven 640. Chip washing and staining were performed with an Affymetrix GeneChip Fluidics Station 400

scan_protocol: The chips were scanned with Agilent Genearray Scanner. The scanned images were analyzed using the Affymetrix GCOS program 1.2.

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 set to 150.
MAS5.0 signal intensity, detection call (ABS_CALL), and detection P-value by MAS5.0 method (default setting) are reported.

organism: Pseudomonas aeruginosa PAO1

source_name: at 60 mins during the LHOT condition

label_protocol: The Enzo BioArray terminal labeling kit (Affymetrix) was used for labeling the fragmented cDNA with a size range from 50-200 bp. The fragmentation and labeling effect were checked by gel electrophoresis.

growth_protocol: Pseudomonas aeruginosa PAO1 (PA) was grown in a continuous cultivation system during the transition from high oxygen tension to low oxygen tension (HLOT) and the reversed transition from low to high oxygen tension (LHOT).

extract_protocol: The total RNA was extracted by using the RNeasy mini kit including an on-column DNase treatment according to the manufacturer’s instructions (Qiagen). The RNA concentration and purity were determined using the 2100 Bioanalyser (Agilent). A total of 10 μg of each experimental RNA sample was used for cDNA synthesis with Superscript II reverse transcriptase (Invitrogen, Carlsbad, CA). DNaseI (Pierce) and 10-fold One-Phor-All Buffer (GE healthcare) were used for cDNA fragmentation.

treatment_protocol: In order to stabilize RNA immediately, the samples from chemostat culture of PA were directly flushed into pre-cooled RNAprotect Bacteria Reagent (Qiagen) and treated instantly as suggested by the supplier before stored at -80°C for later RNA isolation.

value: 60 mins

value: the oxygen-availability transition from oxygen deplete (low oxygen tension, 0.5%) to oxygen replete condition (high oxygen tension, 100%).


title: at 80 mins during the LHOT condition

description:
LHOT80
time-series gene expression data from Pseudomonas aeruginosa PAO1

source_name: at 80 mins during the LHOT condition

value: 80 mins


title: at 35 mins during the LHOT condition

description:
LHOT35
time-series gene expression data from Pseudomonas aeruginosa PAO1

source_name: at 35 mins during the LHOT condition

value: 35 mins


title: at 70 mins during the LHOT condition

description:
LHOT70
time-series gene expression data from Pseudomonas aeruginosa PAO1

source_name: at 70 mins during the LHOT condition

value: 70 mins


title: at 40 mins during the LHOT condition

description:
LHOT40
time-series gene expression data from Pseudomonas aeruginosa PAO1

source_name: at 40 mins during the LHOT condition

value: 40 mins


title: Toledo_12h_DMSO_B

description: Cell line Toledo treated with DMSO at 12h (replicateB)

value: DMSO


title: Toledo_12h_DMSO_C

description: Cell line Toledo treated with DMSO at 12h (replicateC)


title: at 90 mins during the LHOT condition

description:
LHOT90
time-series gene expression data from Pseudomonas aeruginosa PAO1

source_name: at 90 mins during the LHOT condition

value: 90 mins


title: Toledo_6h_JQ1_C

description: Cell line Toledo treated with JQ1 at 6h (replicateC)

source_name: Cell line Toledo treated with JQ1 at 6h


title: at 50 mins during the LHOT condition

description:
LHOT50
time-series gene expression data from Pseudomonas aeruginosa PAO1

source_name: at 50 mins during the LHOT condition

value: 50 mins


title: Toledo_12h_DMSO_A

description: Cell line Toledo treated with DMSO at 12h (replicateA)

value: A


title: Toledo_6h_JQ1_B

description: Cell line Toledo treated with JQ1 at 6h (replicateB)


title: at 30 mins during the LHOT condition

description:
LHOT30
time-series gene expression data from Pseudomonas aeruginosa PAO1

source_name: at 30 mins during the LHOT condition

value: 30 mins


title: Toledo_6h_JQ1_A

description: Cell line Toledo treated with JQ1 at 6h (replicateA)

value: diffuse large B-cell lymphoma (DLBCL)


title: at 20 mins during the LHOT condition

description:
LHOT20
time-series gene expression data from Pseudomonas aeruginosa PAO1

source_name: at 20 mins during the LHOT condition

value: 20 mins


title: at 25 mins during the LHOT condition

description:
LHOT25
time-series gene expression data from Pseudomonas aeruginosa PAO1

source_name: at 25 mins during the LHOT condition

value: 25 mins


title: at 0 min during the LHOT condition

description:
LHOT0
time-series gene expression data from Pseudomonas aeruginosa PAO1

source_name: at 0 min during the LHOT condition

value: 0 min


title: at 5 mins during the LHOT condition

description:
LHOT5
time-series gene expression data from Pseudomonas aeruginosa PAO1

source_name: at 5 mins during the LHOT condition

value: 5 mins


title: DHL6_24h_DMSO_C

description: Cell line DHL6 treated with DMSO at 24h (replicateC)

source_name: Cell line DHL6 treated with DMSO at 24h

value: C


title: at 10 mins during the LHOT condition

description:
LHOT10
time-series gene expression data from Pseudomonas aeruginosa PAO1

source_name: at 10 mins during the LHOT condition

value: 10 mins


title: Toledo_6h_DMSO_C

description: Cell line Toledo treated with DMSO at 6h (replicateC)

value: Toledo


title: at 50 mins during the HLOT condition

description:
HLOT50
time-series gene expression data from Pseudomonas aeruginosa PAO1

source_name: at 50 mins during the HLOT condition

value: the oxygen-availability transition from oxygen replete (high oxygen tension, 100%) to oxygen deplete condition (low oxygen tension, 0.5%).


title: Toledo_6h_DMSO_B

description: Cell line Toledo treated with DMSO at 6h (replicateB)

value: B


title: at 15 mins during the LHOT condition

description:
LHOT15
time-series gene expression data from Pseudomonas aeruginosa PAO1

source_name: at 15 mins during the LHOT condition

value: 15 mins

value: the oxygen-availability transition from oxygen deplete (low oxygen tension, 0.5%) to oxygen replete condition (high oxygen tension, 100%).


title: at 90 mins during the HLOT condition

description:
HLOT90
time-series gene expression data from Pseudomonas aeruginosa PAO1

source_name: at 90 mins during the HLOT condition


title: at 60 mins during the HLOT condition

description:
HLOT60
time-series gene expression data from Pseudomonas aeruginosa PAO1

source_name: at 60 mins during the HLOT condition

value: 60 mins


title: at 80 mins during the HLOT condition

description:
HLOT80
time-series gene expression data from Pseudomonas aeruginosa PAO1

source_name: at 80 mins during the HLOT condition

value: 80 mins


title: at 70 mins during the HLOT condition

description:
HLOT70
time-series gene expression data from Pseudomonas aeruginosa PAO1

source_name: at 70 mins during the HLOT condition

value: 70 mins


title: at 30 mins during the HLOT condition

description:
HLOT30
time-series gene expression data from Pseudomonas aeruginosa PAO1

source_name: at 30 mins during the HLOT condition


title: at 40 mins during the HLOT condition

description:
HLOT40
time-series gene expression data from Pseudomonas aeruginosa PAO1

source_name: at 40 mins during the HLOT condition

value: 40 mins


title: DHL6_2h_DMSO_B_2

description: Cell line DHL6 treated with DMSO at 2h (replicateB)

source_name: Cell line DHL6 treated with DMSO at 2h

value: DMSO


title: Toledo_6h_DMSO_A

description: Cell line Toledo treated with DMSO at 6h (replicateA)

value: diffuse large B-cell lymphoma (DLBCL)

value: A


title: Toledo_2h_JQ1_B

description: Cell line Toledo treated with JQ1 at 2h (replicateB)

source_name: Cell line Toledo treated with JQ1 at 2h


title: DHL6_12h_JQ1_A

description: Cell line DHL6 treated with JQ1 at 12h (replicateA)

source_name: Cell line DHL6 treated with JQ1 at 12h


title: at 20 mins during the HLOT condition

description:
HLOT20
time-series gene expression data from Pseudomonas aeruginosa PAO1

source_name: at 20 mins during the HLOT condition

value: 20 mins


title: Toledo_2h_JQ1_A

description: Cell line Toledo treated with JQ1 at 2h (replicateA)


title: Toledo_2h_DMSO_C

description: Cell line Toledo treated with DMSO at 2h (replicateC)


title: at 25 mins during the HLOT condition

description:
HLOT25
time-series gene expression data from Pseudomonas aeruginosa PAO1

source_name: at 25 mins during the HLOT condition

value: 25 mins


title: DHL6_24h_JQ1_C

description: Cell line DHL6 treated with JQ1 at 24h (replicateC)

source_name: Cell line DHL6 treated with JQ1 at 24h


title: DHL6_24h_DMSO_A

description: Cell line DHL6 treated with DMSO at 24h (replicateA)


title: at 10 mins during the HLOT condition

description:
HLOT10
time-series gene expression data from Pseudomonas aeruginosa PAO1

source_name: at 10 mins during the HLOT condition


title: at 5 mins during the HLOT condition

description:
HLOT5
time-series gene expression data from Pseudomonas aeruginosa PAO1

source_name: at 5 mins during the HLOT condition

value: 5 mins


title: Toledo_2h_JQ1_C

description: Cell line Toledo treated with JQ1 at 2h (replicateC)

value: C


title: at 0 min during the HLOT condition

description:
HLOT0
time-series gene expression data from Pseudomonas aeruginosa PAO1

source_name: at 0 min during the HLOT condition

value: 0 min


title: at 15 mins during the HLOT condition

description:
HLOT15
time-series gene expression data from Pseudomonas aeruginosa PAO1

source_name: at 15 mins during the HLOT condition


title: WT in lung surfactant, replicate 2

city: Burlington

first: Matthew

middle: J

last: Wargo

state: VT

address: 95 Carrigan Dr

department: Department of Microbiology and Molecular Genetics

institute: University of Vermont

hyb_protocol: Following fragmentation, 2.4 ug of cRNA were hybridized on the Pseudomonas aeruginosa PAO1 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Probe intensities were first generated using the AGCC program (Affymetrix). Probe-level intensities were background-corrected, normalized, and summarized, and Robust Multichip Average (RMA) statistics were calculated for each probe set and sample as is implemented in Partek Genomic Suites®, version 6.6

organism: Pseudomonas aeruginosa

source_name: Pseudomonas aeruginosa WT in MOPS pyruvate plus lung surfactant

label_protocol: Biotinylated cDNA was prepared from 50 ng of whole RNA using the NuGen Ovation Pico system and the Encore Biotin Module according to manufacturer's instructions.

growth_protocol: Cells were pregrown for 18 h in MOPS with 25 mM pyruvate and 5 mM glucose and then resuspended in MOPS pyruvate or MOPS pyruvate + 1:50 dilution of Survanta

extract_protocol: RNA was extracted from RNA Protect-treated pellets using the Qiagen RNeasy kit using lysozyme-aided lysis. RNA from the first round of columns was treated with DNase I and another round of RNeasy conducted including the on-column DNase step.

treatment_protocol: Cell suspension was treated with two volumes of RNA Protect Bacterial Reagent (Qiagen) and processed to a wet pellet as per manufacturer's instructions

value: PAO1 wild type

value: lung surfactant


title: Toledo_2h_DMSO_B

description: Cell line Toledo treated with DMSO at 2h (replicateB)

value: Toledo

value: B


title: WT in lung surfactant, replicate 1


title: at 35 mins during the HLOT condition

description:
HLOT35
time-series gene expression data from Pseudomonas aeruginosa PAO1

source_name: at 35 mins during the HLOT condition

value: 35 mins

value: the oxygen-availability transition from oxygen replete (high oxygen tension, 100%) to oxygen deplete condition (low oxygen tension, 0.5%).


title: WT in pyruvate, replicate 2

source_name: Pseudomonas aeruginosa WT in MOPS pyruvate

value: pyruvate control


title: sphR mutant in lung surfactant, replicate 1

source_name: Pseudomonas aeruginosa sphR mutant in MOPS pyruvate plus lung surfactant

value: PAO1 sphR deletion


title: sphR mutant in pyruvate, replicate 2

source_name: Pseudomonas aeruginosa sphR mutant in MOPS pyruvate


title: Toledo_0h_nothing_C

description: Cell line Toledo treated with nothing at 0h (replicateC)

value: nothing


title: Toledo_0h_nothing_B

description: Cell line Toledo treated with nothing at 0h (replicateB)


title: Toledo_0h_nothing_A

description: Cell line Toledo treated with nothing at 0h (replicateA)


title: WT in pyruvate, replicate 1


title: Toledo_2h_DMSO_A

description: Cell line Toledo treated with DMSO at 2h (replicateA)

value: DMSO


title: Ly1_0h_nothing_A_1_15

description: Cell line Ly1 treated with nothing at 0h (replicateA)

value: diffuse large B-cell lymphoma (DLBCL)


title: sphR mutant in lung surfactant, replicate 2


title: Normal thyroid, commercial RNA pool

city: Lisboa

first: Branca

middle: Maria

last: Cavaco

address: Rua Prof. Lima Basto

department: Unidade de Investigação de Patobiologia Molecular (UIPM)

country: Portugal

institute: Instituto Português de Oncologia de Lisboa Francisco Gentil (IPOLFG)

hyb_protocol: Labelling, hybridization and scanning protocols were done in a certified Affymetrix Core Facility at Instituto Gulbenkian de Ciência (Oeiras, Portugal)

data_processing: The data were analyzed with DNA-Chip Analyzer (dChip) 2006 software. Arrays were normalized with the invariant set normalization method and gene-level expression was determined by using model-based expression analysis with perfect match-only model.

source_name: Commercial total RNA pool of normal thyroid tissues

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA

extract_protocol: Total RNA was extracted and purified using the RNeasy Mini kit (Quiagen) according to the manufacturer’s instructions.

value: Female/Male

tag: age at diagnosis

value: pool of normal thyroid tissues (commercial source)

tag: mutational status


title: sphR mutant in pyruvate, replicate 1


title: Ly1_0h_nothing_A_1_14

source_name: Cell line Ly1 treated with nothing at 0h

value: A


title: Ly4_48h_JQ1_B

description: Cell line Ly4 treated with JQ1 at 48h (replicateB)

source_name: Cell line Ly4 treated with JQ1 at 48h


title: Ly4_48h_JQ1_C

description: Cell line Ly4 treated with JQ1 at 48h (replicateC)


title: Ly4_48h_JQ1_A

description: Cell line Ly4 treated with JQ1 at 48h (replicateA)


title: Normal thyroid, biological rep1

scan_protocol: Labelling, hybridization and scanning protocols were done in a certified Affymetrix Core Facility at Instituto Gulbenkian de Ciência (Oeiras, Portugal)

source_name: fresh-frozen normal thyroid tissue from contralateral lobe of thyroid tumor

value: Female


title: PTC, biological rep7

source_name: fresh-frozen PTC

value: PTC

value: BRAF -


title: Ly1_0h_nothing_A_1_8


title: Normal thyroid, biological rep2

value: normal thyroid tissue from contralateral lobe of thyroid tumor


title: PTC, biological rep6

value: Male

value: BRAF +


title: Ly4_48h_DMSO_C

description: Cell line Ly4 treated with DMSO at 48h (replicateC)

source_name: Cell line Ly4 treated with DMSO at 48h

value: C


title: PTC, biological rep2


title: PDTC, biological rep5

source_name: fresh-frozen PDTC

value: PDTC

value: RAS -


title: Toledo_48h_DMSO_A

description: Cell line Toledo treated with DMSO at 48h (replicateA)

value: Toledo


title: PTC, biological rep5


title: Ly1_0h_nothing_A_1_13


title: PDTC, biological rep2


title: PDTC, biological rep4


title: PDTC, biological rep1

value: RAS+


title: Ly4_48h_DMSO_A

description: Cell line Ly4 treated with DMSO at 48h (replicateA)


title: Ly4_48h_DMSO_B

description: Cell line Ly4 treated with DMSO at 48h (replicateB)

value: B


title: PTC, biological rep3


title: FVPTC, biological rep6

source_name: fresh-frozen FVPTC

value: FVPTC


title: FVPTC, biological rep8


title: PDTC, biological rep3


title: Ly4_24h_JQ1_C

description: Cell line Ly4 treated with JQ1 at 24h (replicateC)

source_name: Cell line Ly4 treated with JQ1 at 24h

value: diffuse large B-cell lymphoma (DLBCL)


title: FVPTC, biological rep5


title: FVPTC, biological rep7


title: PTC, biological rep4


title: Ly4_24h_JQ1_B

description: Cell line Ly4 treated with JQ1 at 24h (replicateB)


title: Ly4_24h_DMSO_A

description: Cell line Ly4 treated with DMSO at 24h (replicateA)

source_name: Cell line Ly4 treated with DMSO at 24h

value: DMSO


title: PTC, biological rep1


title: Ly4_24h_JQ1_A

description: Cell line Ly4 treated with JQ1 at 24h (replicateA)


title: FVPTC, biological rep4


title: Ly4_12h_JQ1_A

description: Cell line Ly4 treated with JQ1 at 12h (replicateA)

source_name: Cell line Ly4 treated with JQ1 at 12h


title: FVPTC, biological rep3


title: FVPTC, biological rep1


title: Ly4_12h_DMSO_B

description: Cell line Ly4 treated with DMSO at 12h (replicateB)

source_name: Cell line Ly4 treated with DMSO at 12h


title: FTC, biological rep4

source_name: fresh-frozen FTC

value: FTC


title: FVPTC, biological rep2


title: FTC, biological rep2


title: FTC, biological rep3


title: Ly4_24h_DMSO_C

description: Cell line Ly4 treated with DMSO at 24h (replicateC)


title: Ly4_12h_DMSO_A

description: Cell line Ly4 treated with DMSO at 12h (replicateA)

value: A


title: Ly4_12h_JQ1_C

description: Cell line Ly4 treated with JQ1 at 12h (replicateC)


title: Gudjohnsson_008_8470_PN

first: William

middle: R

last: Swindell

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard University

description: uninvolved skin biopsy

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix U133 Human Genome Plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray TM Scanner 3000.

data_processing: Robust Multichip Average (RMA)

source_name: skin

extract_protocol: RNA was extracted using QIAGEN RNEasy mini kits

treatment_protocol: At baseline, two biopsies were taken from each patient; one 6mm punch biopsy was obtained from lesional skin of each patient (involved sample) and the other from non-lesional skin (uninvolved sample). Non-lesional biopsies were taken from the buttocks or upper thighs. Biopsies were snap-frozen in liquid nitrogen, stored at -80°C. At processing the biopsy samples were homogenized while still frozen and total RNA isolation was performed using RNeasy kit protocol (Qiagen, Chatsworth, Ca, USA).

tag: patient

tag: phenotype

value: uninvolved

value: uninvolved skin biopsy


title: Ly4_12h_DMSO_C

description: Cell line Ly4 treated with DMSO at 12h (replicateC)

tag: cell line

tag: cell type


title: Ly4_12h_JQ1_B

description: Cell line Ly4 treated with JQ1 at 12h (replicateB)

tag: time

tag: treatment


title: Ly4_24h_DMSO_B

description: Cell line Ly4 treated with DMSO at 24h (replicateB)

tag: replicate


title: Ly4_6h_JQ1_B

description: Cell line Ly4 treated with JQ1 at 6h (replicateB)

source_name: Cell line Ly4 treated with JQ1 at 6h


title: Gudjohnsson_005_7912_PP

description: lesional skin biopsy

value: lesional

value: lesional skin biopsy


title: Gudjohnsson_006_7912_PN

description: uninvolved skin biopsy


title: FTC, biological rep1

value: Female


title: Ly4_6h_DMSO_B

description: Cell line Ly4 treated with DMSO at 6h (replicateB)

source_name: Cell line Ly4 treated with DMSO at 6h


title: Ly4_6h_DMSO_C

description: Cell line Ly4 treated with DMSO at 6h (replicateC)


title: Ly4_6h_JQ1_C

description: Cell line Ly4 treated with JQ1 at 6h (replicateC)


title: Ly4_6h_DMSO_A

description: Cell line Ly4 treated with DMSO at 6h (replicateA)


title: Gudjohnsson_001_6690_PP

description: lesional skin biopsy


title: Ly4_6h_JQ1_A

description: Cell line Ly4 treated with JQ1 at 6h (replicateA)


title: Ly4_2h_JQ1_C

description: Cell line Ly4 treated with JQ1 at 2h (replicateC)

source_name: Cell line Ly4 treated with JQ1 at 2h


title: Ly4_2h_JQ1_B

description: Cell line Ly4 treated with JQ1 at 2h (replicateB)


title: human radioresistant NPC, biological rep2

city: Changsha

first: Jia-Quan

last: QU

state: Hunan

address: Xiangya street No.87

department: Xiangya Hospital

institute: Central South University

description: Gene expression data from radioresistant NPC cell line.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000.

data_processing: Expression data were subsequently background corrected, normalized, and polished using robust multichip average (RMA)using Affymetrix default analysis settings and global scaling as normalization method.

source_name: human radioresistant NPC cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Radioresistant NPC cell line CNE2-IR and its control cell line CNE2 were culture with 10 % FCS (Invitrogen, USA) and 1 % antibiotics in an incubator at 37 C with humidified 5 % CO2.

extract_protocol: Trizol extraction of total RNAof 10^7 CNE2-IR and CNE2 cells was performed according to the manufacturer's instructions.

treatment_protocol: Radioresistant subclone of nasopharyngeal carcinoma CNE2-IR cell line was cultured and produced according to the experienment schedule to undergo five rounds of sublethal dose of irradiation (11 Gy),and the parent cell line CNE2 sensitive to radiotherapy as the control.

value: radioresistance


title: Gudjohnsson_004_7450_PP

description: lesional skin biopsy


title: human radiosensitive NPC, biological rep2

description: Gene expression data from radiosenative NPC cell line.

source_name: human radiosensitive NPC cell line

value: radiosensitive


title: Gudjohnsson_007_8470_PP

description: lesional skin bioposy


title: human radiosensitive NPC, biological rep1


title: Gudjohnsson_002_6690_PN

description: uninvolved skin biopsy


title: Ly4_2h_DMSO_C

description: Cell line Ly4 treated with DMSO at 2h (replicateC)

source_name: Cell line Ly4 treated with DMSO at 2h

value: C


title: Gudjohnsson_003_7450_PN

description: uninvolved skin biopsy


title: Ly4_2h_JQ1_A

description: Cell line Ly4 treated with JQ1 at 2h (replicateA)


title: Ly4_2h_DMSO_B

description: Cell line Ly4 treated with DMSO at 2h (replicateB)


title: human radioresistant NPC, biological rep1


title: Ly4_0h_nothing_A

description: Cell line Ly4 treated with nothing at 0h (replicateA)

value: nothing


title: Ly4_0h_nothing_B

description: Cell line Ly4 treated with nothing at 0h (replicateB)


title: Ly1_0h_nothing_A_1_6

description: Cell line Ly1 treated with nothing at 0h (replicateA)


title: Ly1_0h_nothing_A_1_5

source_name: Cell line Ly1 treated with nothing at 0h


title: Ly4_2h_DMSO_A

description: Cell line Ly4 treated with DMSO at 2h (replicateA)


title: Ly4_0h_nothing_C

description: Cell line Ly4 treated with nothing at 0h (replicateC)


title: HBL1_48h_JQ1_C

description: Cell line HBL1 treated with JQ1 at 48h (replicateC)

source_name: Cell line HBL1 treated with JQ1 at 48h


title: siHMGA1.exp4

city: Trieste

first: Silvano

last: Piazza

address: localita' Padriciano 99

country: Italy

institute: ICGEB

description: MDA-MB-231 siRNA-HMGA1, biological replicate D.

hyb_protocol: Affymetrix Eukaryotic Target Hybridization protocol (GeneChip Expression Analysis Technical Manual).

scan_protocol: Standard Affymetrix protocol.

data_processing: Probe set summarization and normalization was performed by robust multi-array averaging (RMA, including background subtraction) using the R/Bioconductor package affy.

source_name: Breast cancer cell line, HMGA1 siRNA

label_protocol: Affymetrix GeneChip IVT Labeling Kit, according to the manufacturer's protocol (GeneChip Expression Analysis Technical Manual).

extract_protocol: TRIzol (Invitrogen) followed by RNeasy column cleanup (Qiagen) using the manufacturers' protocols.

value: breast cancer cells

tag: sirna


title: siHMGA1.exp2

description: MDA-MB-231 siRNA-HMGA1, biological replicate B.


title: Ly1_0h_nothing_A_1_4


title: HBL1_48h_JQ1_B

description: Cell line HBL1 treated with JQ1 at 48h (replicateB)


title: siCTRL.exp2

description: MDA-MB-231 siRNA-Control, biological replicate B.

source_name: Breast cancer cell line, control siRNA

value: control


title: HBL1_48h_JQ1_A

description: Cell line HBL1 treated with JQ1 at 48h (replicateA)


title: siHMGA1.exp3

description: MDA-MB-231 siRNA-HMGA1, biological replicate C.


title: siCTRL.exp4

description: MDA-MB-231 siRNA-Control, biological replicate D.


title: HBL1_48h_DMSO_C

description: Cell line HBL1 treated with DMSO at 48h (replicateC)

source_name: Cell line HBL1 treated with DMSO at 48h


title: 7040272

city: Madrid

first: Gema

last: Moreno-Bueno

state: Madrid

address: Arturo Duperier

department: Biochemistry

country: Spain

institute: IIB

hyb_protocol: The arrays hybridization was performed using In Situ Hybridization Kit Plus (Agilent technologies) according to Peinado et al, Cancer Research 2008.

scan_protocol: After hybridization and washing, the slides were scanned in an Axon GenePix Scanner (Axon Instruments), according to manufacturer´s protocol.

data_processing: The slides were analyzed using Feature Extraction Software 10.0 (Agilent technologies), following manufacturer’s protocol. A hierarchical clustering method was applied to group the genes and samples on the basis of the similarities in expression and the unsupervised analyses were visualized using the SOTA and TreeView software assuming euclidean distances between genes (http://bioinfo.cnio.es/cgi-bin/tools/clustering/sotarray). Genes with potentially significant changes in expression were identified using the POMELO program (http://www.genoma.wi.mit.edu/MPR/software). We tested the null hypothesis of equal means among groups using T-test, computing p-values using a permutation test. To select differentially expressed genes, we adjusted for multiple testing using the False Discovery Rate (FDR) method (Chung et al, 2004)

source_name: Total RNA from lung tumor biopsies

label_protocol: 1mg from tRNA was labelled and array hybridized using the Low RNA Linear Amplification Kit (Agilent) following manufacturer’s protocol.

extract_protocol: Total RNA was obtained using TRIZOL method following to RNAesy Extraction Kit (QIAGen, Germany,  both methods were performed according to the manufacturers´protocol. One mg of total RNA from each independent tumours were labelled with Cy5-dUTP and as control a pooled RNA obtained from equal concentration of each RNA tumor sample labelled with Cy3-dUTP was used. The amplification and labelling of mRNA were performed using   Low RNA Linear Amplification Kit (Agilent technologies).

tag: tissue

value: lung adenocarcinoma

source_name: Pool from the analysed samples

tag: reference

value: Pool from the analysed samples


title: siCTRL.exp3

description: MDA-MB-231 siRNA-Control, biological replicate C.


title: siHMGA1.exp1

description: MDA-MB-231 siRNA-HMGA1, biological replicate A.


title: HBL1_48h_DMSO_B

description: Cell line HBL1 treated with DMSO at 48h (replicateB)

value: diffuse large B-cell lymphoma (DLBCL)

value: B


title: siCTRL.exp1

description: MDA-MB-231 siRNA-Control, biological replicate A.


title: 7040337


title: 7040176

value: squamous lung cell carcinoma


title: 7040162


title: HBL1_48h_DMSO_A

description: Cell line HBL1 treated with DMSO at 48h (replicateA)

value: DMSO

value: A


title: 7040625


title: HBL1_24h_JQ1_C

description: Cell line HBL1 treated with JQ1 at 24h (replicateC)

source_name: Cell line HBL1 treated with JQ1 at 24h


title: HBL1_24h_JQ1_B

description: Cell line HBL1 treated with JQ1 at 24h (replicateB)


title: HBL1_24h_DMSO_C

description: Cell line HBL1 treated with DMSO at 24h (replicateC)

source_name: Cell line HBL1 treated with DMSO at 24h


title: 7040627


title: 7040139


title: HBL1_12h_JQ1_C

description: Cell line HBL1 treated with JQ1 at 12h (replicateC)

source_name: Cell line HBL1 treated with JQ1 at 12h


title: 7060358


title: 7060051


title: HBL1_24h_DMSO_A

description: Cell line HBL1 treated with DMSO at 24h (replicateA)


title: HBL1_12h_JQ1_A

description: Cell line HBL1 treated with JQ1 at 12h (replicateA)


title: HBL1_24h_DMSO_B

description: Cell line HBL1 treated with DMSO at 24h (replicateB)


title: HBL1_24h_JQ1_A

description: Cell line HBL1 treated with JQ1 at 24h (replicateA)


title: 7050059


title: HBL1_12h_JQ1_B

description: Cell line HBL1 treated with JQ1 at 12h (replicateB)


title: 7040532


title: wildtype BMDMs  infected with Listeria monocytogenes for 2 hours, biological replicate 3

city: Worcester

first: Daniel

last: Caffrey

address: 364 Plantation St

institute: UMASS Medical School

hyb_protocol: Following fragmentation, cRNA was hybridized on genechip mouse 430 2.0 genome Array (Affymetrix) . GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: The arrays were scanned using an Affymetrix GeneChip Scanner 3000

data_processing: Affymetrix CEL files were normalized in Bioconductor using the GCRMA method.  Differentially regulated genes were identified using a moderated t-test.  False discovery rate adjusted P-values were calculated using the method of Benjamini and Hochberg.

source_name: Bone marrow derived macrophages from wildtype mouse

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

extract_protocol: RNA was purified using the RNeasy mini kit from Qiagen.

value: Bone marrow derived macrophages

tag: strain

tag: genotype

value: wildtype


title: HBL1_12h_DMSO_C

description: Cell line HBL1 treated with DMSO at 12h (replicateC)

source_name: Cell line HBL1 treated with DMSO at 12h


title: 7060447


title: 7041009


title: 7041015


title: 7040422


title: 7040778


title: 7060414


title: wildtype BMDMs uninfected, biological replicate 2


title: 7050338


title: HBL1_6h_JQ1_B

description: Cell line HBL1 treated with JQ1 at 6h (replicateB)

source_name: Cell line HBL1 treated with JQ1 at 6h


title: HBL1_6h_JQ1_A

description: Cell line HBL1 treated with JQ1 at 6h (replicateA)


title: wildtype BMDMs  infected with Listeria monocytogenes for 2 hours, biological replicate 1


title: 7050762


title: 7050475


title: HBL1_12h_DMSO_B

description: Cell line HBL1 treated with DMSO at 12h (replicateB)


title: HBL1_12h_DMSO_A

description: Cell line HBL1 treated with DMSO at 12h (replicateA)


title: wildtype BMDMs uninfected, biological replicate 3


title: BLIMP1 conditional knockout BMDMs infected with Listeria monocytogenes for 2 hours, biological replicate 3

source_name: Bone marrow derived macrophages from BLIMP1 conditional knockout mouse

value: BLIMP conditional knockout


title: 7050192


title: HBL1_6h_DMSO_B

description: Cell line HBL1 treated with DMSO at 6h (replicateB)

source_name: Cell line HBL1 treated with DMSO at 6h


title: BLIMP1 conditional knockout BMDMs uninfected, biological replicate 1


title: BLIMP1 conditional knockout BMDMs uninfected, biological replicate 2


title: BLIMP1 conditional knockout BMDMs infected with Listeria monocytogenes for 2 hours, biological replicate 2


title: 7050289


title: 7050265


title: wildtype BMDMs uninfected, biological replicate 1


title: BLIMP1 conditional knockout BMDMs infected with Listeria monocytogenes for 2 hours, biological replicate 1


title: HBL1_6h_DMSO_A

description: Cell line HBL1 treated with DMSO at 6h (replicateA)


title: 7060502


title: 7040531


title: HBL1_6h_DMSO_C

description: Cell line HBL1 treated with DMSO at 6h (replicateC)


title: HBL1_6h_JQ1_C

description: Cell line HBL1 treated with JQ1 at 6h (replicateC)


title: HBL1_2h_JQ1_C

description: Cell line HBL1 treated with JQ1 at 2h (replicateC)

source_name: Cell line HBL1 treated with JQ1 at 2h


title: BLIMP1 conditional knockout BMDMs uninfected, biological replicate 3


title: liver of mouse fed a high-fat diet containing 2 % unroasted green coffee 2

city: Tokyo

first: Shoko

last: Takahashi

address: 1-1-1 Yayoi, Bunkyo-ku

department: aDepartment of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences

country: Japan

institute: The University of Tokyo

description: Hepatic gene expression data from mouse fed a high-fat diet containing 2 % unroasted green coffee 2

hyb_protocol: Hybridization mixtures were boiled at 99C for 5 min, loaded on an Affymetrix GeneChip Mouse Genome 430 2.0 array, and hybridized at 45C for 16 h. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using Affymetrix Gene Array Scanner 3000.

data_processing: After normalisation of the intensity files was performed with robust multi-array average (RMA) normalising, and then a clustering analysis was done with hclust (hierarchical clustering, average linkage). Rank products were used for intergroup comparison. The expression change was taken as informative when the false discovery rate (FDR) value was <0.1.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA.

growth_protocol: Seven-week-old male C57BL/6J mice had ad libitum access to each diet and drinking water for 9 weeks, then mice were sacrificed and the livers were subjected to the Affymrtix DNA microarray experiment.

treatment_protocol: Livers were immediately frozen in liquid nitrogen and stored at -80C until RNA extraction.

tag: gender

value: male

value: liver


title: 7060353


title: HBL1_2h_JQ1_A

description: Cell line HBL1 treated with JQ1 at 2h (replicateA)


title: HBL1_2h_DMSO_C

description: Cell line HBL1 treated with DMSO at 2h (replicateC)

source_name: Cell line HBL1 treated with DMSO at 2h


title: HBL1_2h_JQ1_B

description: Cell line HBL1 treated with JQ1 at 2h (replicateB)


title: liver of mouse fed a high-fat diet containing 2 % decaffeinated coffee 3

description: Hepatic gene expression data from mouse fed a high-fat diet containing 2 % decaffeinated coffee 3


title: liver of mouse fed a high-fat diet containing 2 % unroasted green coffee 3

description: Hepatic gene expression data from mouse fed a high-fat diet containing 2 % unroasted green coffee 3


title: 7040343


title: liver of mouse fed a high-fat diet containing 2 % caffeinated coffee 3

description: Hepatic gene expression data from mouse fed a high-fat diet containing 2 % caffeinated coffee 3


title: HBL1_2h_DMSO_A

description: Cell line HBL1 treated with DMSO at 2h (replicateA)


title: 7040404


title: liver of mouse fed a high-fat diet containing 2 % caffeinated coffee 2

description: Hepatic gene expression data from mouse fed a high-fat diet containing 2 % caffeinated coffee 2


title: 7040288


title: liver of mouse fed a high-fat diet containing 2 % decaffeinated coffee 2

description: Hepatic gene expression data from mouse fed a high-fat diet containing 2 % decaffeinated coffee 2


title: liver of mouse fed a high-fat diet 3

description: Hepatic gene expression data from mouse fed a high-fat diet 3

source_name: liver of mouse fed a high-fat diet 3

value: fed a high-fat diet


title: liver of mouse fed a high-fat diet containing 2 % unroasted green coffee 1

description: Hepatic gene expression data from mouse fed a high-fat diet containing 2 % unroasted green coffee 1


title: 7060455


title: 7040015


title: 7040375


title: HBL1_2h_DMSO_B

description: Cell line HBL1 treated with DMSO at 2h (replicateB)


title: HBL1_0h_nothing_B

description: Cell line HBL1 treated with nothing at 0h (replicateB)


title: 7060446


title: liver of mouse fed a high-fat diet 2

description: Hepatic gene expression data from mouse fed a high-fat diet 2

source_name: liver of mouse fed a high-fat diet 2


title: HBL1_0h_nothing_A

description: Cell line HBL1 treated with nothing at 0h (replicateA)


title: liver of mouse fed a high-fat diet containing 2 % caffeinated coffee 1

description: Hepatic gene expression data from mouse fed a high-fat diet containing 2 % caffeinated coffee 1


title: 7050315


title: Ly1_0h_nothing_A_1_11

description: Cell line Ly1 treated with nothing at 0h (replicateA)


title: liver of mouse fed a high-fat diet containing 2 % decaffeinated coffee 1

description: Hepatic gene expression data from mouse fed a high-fat diet containing 2 % decaffeinated coffee 1


title: Ly1_0h_nothing_A_1_12

source_name: Cell line Ly1 treated with nothing at 0h


title: HBL1_0h_nothing_C

description: Cell line HBL1 treated with nothing at 0h (replicateC)

value: C


title: liver of mouse fed a normal diet 3

description: Hepatic gene expression data from mouse fed a normal diet 3

source_name: liver of mouse fed a normal diet 3

value: fed a normal diet


title: Ly1_48h_JQ1_C

description: Cell line Ly1 treated with JQ1 at 48h (replicateC)

source_name: Cell line Ly1 treated with JQ1 at 48h


title: Ly1_0h_nothing_A_1_10

value: nothing


title: Ly1_48h_JQ1_A

description: Cell line Ly1 treated with JQ1 at 48h (replicateA)


title: 7050288

source_name: Total RNA from lung tumor biopsies


title: 7050359

source_name: Pool from the analysed samples


title: liver of mouse fed a normal diet 1

description: Hepatic gene expression data from mouse fed a normal diet 1

source_name: liver of mouse fed a normal diet 1


title: liver of mouse fed a normal diet 2

description: Hepatic gene expression data from mouse fed a normal diet 2

source_name: liver of mouse fed a normal diet 2


title: Ly1_48h_JQ1_B

description: Cell line Ly1 treated with JQ1 at 48h (replicateB)


title: 7060037


title: 7050377


title: 7060311


title: liver of mouse fed a high-fat diet 1

description: Hepatic gene expression data from mouse fed a high-fat diet 1

source_name: liver of mouse fed a high-fat diet 1


title: wildtype BMDMs  infected with Listeria monocytogenes for 2 hours, biological replicate 2

source_name: Bone marrow derived macrophages from wildtype mouse


title: 7060270


title: Ly1_48h_DMSO_B

description: Cell line Ly1 treated with DMSO at 48h (replicateB)

source_name: Cell line Ly1 treated with DMSO at 48h


title: Ly1_48h_DMSO_C

description: Cell line Ly1 treated with DMSO at 48h (replicateC)


title: OT-I CD8 T cells from vLM-OVA infected mice, biological rep2

city: Iowa City

first: John

middle: T

last: Harty

state: Iowa

address: 3-501 Bowen Science Building, 51 Newton Road

department: Microbiology

institute: University of Iowa

description: vLM-OVA 2

hyb_protocol: The resulting biotin-labeled cDNA was mixed with Affymetrix eukaryotic hybridization buffer (Affymetrix, Inc., Santa Clara, CA), placed onto Affymetrix Mouse EXON 1.0 ST Arrays, and incubated at 45º C for 18 hr with 60 rpm rotation in an Affymetrix Model 640 Genechip Hybridization Oven. The Mouse EXON 1.0 ST Array interrogates over 1 million exon clusters within the known and predicted transcribed regions of the entire genome. Following hybridization, the arrays will be washed, stained with streptavidin-phycoerythrin (Molecular Probes, Inc., Eugene, OR), signal amplified with antistreptavidin antibody (Vector Laboratories, Inc., Burlingame, CA) using the Affymetrix Model 450 Fluidics Station.

scan_protocol: Arrays were scanned with the Affymetrix Model 3000 scanner with 7G upgrade and data collected using the using the GeneChip operating software (GCOS) v1.4.

data_processing:
The microarray data will be analyzed for significant changes in expression profiles using the Partek Genomics Suite Software (Partek, Inc.).  Three arrays each for each treatment were processed and analyzed.  Briefly, the expression values estimates generated by the microarray scanners will first be normalized using the RMA (robust multi-array averaging) algorithm.  An ANOVA, followed by a multiple testing correction using the false-discovery rate (FDR), was used to assess significant changes in expression profiles between the strains.  The gene targets identified to be significantly differentially expressed (FDR<0.01) were subjected to DAVID functional cluster/KEGG analysis or whole transcriptomes with GSEA analysis by comparing significantly regulated genes between DC and DC+CpG.
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: spleen

label_protocol: Microarray hybridizations were performed at the University of Iowa DNA Facility.  Briefly, 25 nanograms total RNA was converted to SPIA amplified cDNA using the WT-Ovation Pico RNA Amplification System, v1 (NuGEN Technologies, San Carlos, CA, Cat. #3300) according to the manufacturer’s recommended protocol. The amplified SPIA cDNA product was purified through a QIAGEN MinElute Reaction Cleanup column (QIAGEN Cat #28204) according to modifications from NuGEN.  3.3 ug of SPIA amplified DNA was then used to generate ST-cDNA using the WT-Ovation EXON Module v1 (NuGEN Technologies, Cat #2000) and again cleaned up with the Qiagen column as above.  Five micrograms of this product was fragmented (average fragment size = 85 bases) and biotin labeled using the NuGEN FL-Ovation cDNA Biotin Module, v2 (NuGEN Technologies, Cat. #4200) per the manufacturer’s recommended protocol.

growth_protocol: Mouse spleens were dissected from mice at day 7 post-immunization/infection or from naïve mice between 6-8 weeks of age

extract_protocol: Rneasy (Qiagen) kit - as desribed by the manufacturer

treatment_protocol: Cells were stained with anti-Thy1.1-PE Ab and then incubated with anti-PE beads in 10% FCS/PBS.  These cells were enriched with AutoMACS selection before FACS sort on PE+ cells.

value: female

tag: age

value: 6-8 weeks

value: vLM-OVA infected mice

value: OT-I CD8 T cells


title: 7060047

value: Pool from the analysed samples


title: 7050866

value: squamous lung cell carcinoma


title: Ly1_24h_JQ1_C

description: Cell line Ly1 treated with JQ1 at 24h (replicateC)

source_name: Cell line Ly1 treated with JQ1 at 24h

value: diffuse large B-cell lymphoma (DLBCL)


title: F/F.ES. rep1

city: Bethesda

first: Yongshun

last: Lin

state: MD

address: 10 Center Dr.

institute: National Heart, Lung, and Blood Institute

description: Gene expression from control ESCs, biological rep1

hyb_protocol: Following fragmentation, 16 ug of aRNA were hybridized for 16 hr at 45C on GeneChip Mouse 430 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Data was analyzed using the limma and affy bioconductor packages implemented in the R-statistical environment version 2.12.2. RMA was used to normalize the data and fit log2 transformed expression values.

source_name: Control knock out ESCs

label_protocol: Biotinylated aRNA were prepared according to the Affymetrix GeneChip 3’ IVT Express kit protocol from 250 ng total RNA (Affymetrix GeneChip 3’ IVT Express kit Instruction Manual, P/N 702646 Rev. 5)

growth_protocol: control and Snai1 knockout ESCs were cultured in standard ESC culture condition with LIF and feeder.

extract_protocol: Total RNA of ESCs was collected and purified using RNeasy Mini Kits (QIAGEN)

treatment_protocol: no special treatment for ESC standard culture

value: ESC

tag: genotype/variation

value: control


title: OT-I CD8 T cells from vLM-OVA infected mice, biological rep3

description: vLM-OVA 3


title: OT-I CD8 T cells from vLM-OVA infected mice, biological rep1

description: vLM-OVA 1


title: OT-I CD8 T cells from DC-OVA +CpG immunized mice, biological rep3

description: CD+CpG 3

value: DC-OVA +CpG immunized mice


title: KO.TM

description: Gene expression from 6 weeks Snai1 knockout teratoma

hyb_protocol: Following fragmentation, 16 ug of aRNA were hybridized for 16 hr at 45C on GeneChip Mouse 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

data_processing: Data was analyzed using the affy Bioconductor package implemented in the R-statistical environment version 2.12. RMA was used to normalize the data and fit log2 transformed expression values.

source_name: Snai1 knokcout teratoma

label_protocol: Biotinylated aRNA were prepared according to the Ambion Premier kit protocol from 250 ng total RNA (MessageAmp Premier RNA Amplification Kit Instruction Manual, 2008, Ambion).

growth_protocol: For EBs, control and Snai1 knockout ESCs were cultured as hanging drops to form embryoid bodies and then suspension cultured in spotaneous differentiation media. For teratomas, 1 millioncontrol and Snai1 knockout ESCs were injected subcutaneously into the hind limbs of 6 wk-old male nude mice to form teratomas.

extract_protocol: Total RNA of EBs was collected and purified using RNeasy Mini Kits (QIAGEN); total RNA of teratomas was collected using Trizol extraction.

treatment_protocol: 5 day EBs and 6 weeks teratomas were collected for RNA extraction.

value: Teratoma

value: Snai1 knockout


title: F/F.ES. rep2

description: Gene expression from control ESCs, biological rep2


title: Ly1_48h_DMSO_A

description: Cell line Ly1 treated with DMSO at 48h (replicateA)

hyb_protocol: Following fragmentation, cRNA was hybridized overnight according to the Affymetrix protocol.

data_processing: The raw cel files were converted into probeset-specific expression values using Affymetrix RMA summarization method and alternative probe set definitions (HuGene10stv1_Hs_ENTREZ, Brainarray v15) as implemented in the BioConductor package simpleaffy (Gentleman et al., 2004). All samples were scaled to have a mean expression level of 100.

value: DMSO

value: A


title: Ly1_24h_JQ1_B

description: Cell line Ly1 treated with JQ1 at 24h (replicateB)

value: B


title: KO.5d embryoid body

description: Gene expression from 5 days Snai1 knockout embryoid body

source_name: 5 day Snai1 knockout embryoid body

value: embryoid body


title: KO.ES. rep1

description: Gene expression from Snai1 knockout ESCs, biological rep1

source_name: Snai1 knock out ESCs


title: Polysome ratio 8 day

type: mixed

city: Ikoma

first: Kiyotaka

last: Ueda

state: Nara

department: Graduate School of Biological Science

institute: Nara Institute of Science and Technology

description:
polysomal RNA
harvested on 8 day after inoculation

hyb_protocol: Polysomal RNAs were labeled with Cy3, and total RNAs were labeled with Cy5. Mixtures of 0.85 μg of Cy3-labeled and Cy5-labeled cRNAs were co-hybridized at 65 ° C for 17 h on an Agilent Technologies 4 × 44K Arabidopsis 4 60mer oligo microarray.

scan_protocol: Microarray slides were scanned using a Agilent Microarray Scanner

data_processing:
Data were normalized via a Linear and LOWESS method followed by spike-in normalization utilizing a Two-Color RNA Spike-InKit (Agilent Technologies).
The ratio of signal intensities (Cy3 : Cy5) of each spot provides the relative abundance of a given mRNA in polysomal over all fractions. We used this ratio as an indicator of the translation state for each transcript and termed it the ‘polysome ratio’ (PR1day and PR 8day for 1 day and 8 day cells, respectively). We also calculated the change in PR from 1 day to 8 day after inoculation(i.e. DeltaPR) for each transcript.

source_name: T87, 8 day after inoculation

label_protocol: Fluorescent cRNA was generated from polysomal and total RNAs from cells using a Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies). A 500 ng aliquot of RNA was subjected to reverse transcription using MMLV reverse transcriptase and an oligo(dT) primer containing the T7 promoter, and subsequently in vitro transcribed using T7 RNA polymerase, resulting in Cy3-labeled and Cy5-labeled cRNAs. The cRNA was purifi ed using RNeasy mini spin columns (Qiagen).

growth_protocol: Arabidopsis thaliana suspension cell strain T87 was cultured in modifi ed LS medium with constant agitation at 120 r.p.m. at 22 ° C under a 16 h light/8 h dark photoperiod. An aliquot of cell suspensions (4 ml) was transferred into 95 ml of fresh medium every week.

extract_protocol: Approximately 0.2 g of cells were pulverized in liquid nitrogen with a mortar and pestle. The resulting frozen powder was homogenized in 1.5 ml of buffer U (200 mM Tris-HCl, pH 8.5, 50 mM KCl, 25 mM MgCl2, 2 mM EGTA, 100 ?g/ml heparin, 2% polyoxyethylene 10-tridecyl ether, and 1% sodium deoxycholate) and centrifuged at 15,000 x g for 10 min at 4°C.  Aliquots of the supernatant were layered on 4.6 ml of 15-60% sucrose density gradient in buffer B (50 mM Tris-HCl, pH 8.5, 25 mM KCl, and 10 mM MgCl2) and centrifuged at 55,000 rpm for 50 min at 4°C in a SW55 rotor (Beckman Coulter, Fullerton, CA, USA).  The gradient was collected from the bottom using a peristaltic pump into 8 fractions of approximately 650 μl, with simultaneous recording of absorbance profiles at 254 nm using a UV monitor (Monitor UV-1; GE Healthcare, Little Chalfont, UK). Fraction 1 to 3 (polysome fraction) and 1 to 8 (all fraction) were individually collected into tubes containing 8 M guanidine hydrochloride (final concentration, 5.5 M) and mixed. Direction of sedimentation is from fraction 8 to fraction 1. Concomitantly with the collection, known amounts of spike-in RNAs (Two-Color RNA Spike-In Kit; Agilent Technologies, Palo Alto, CA, USA) were added to both fractions as an external control. Equal volumes of Spike A and Spike B Mix were added to polysome and nonpolysome fractions, respectively. RNA was precipitated by addition of an equal volume of ethanol to the sucrose mixture, overnight incubation at -20°C, and centrifugation at 10,000 rpm for 45 min in a JA-20 rotor (Beckman Coulter). The resulting RNA precipitation was washed with 80% ethanol and purified using an RNeasy kit (Qiagen, Hilden, Germany) with on-column DNaseI treatment. RNA solution was further subjected to LiCl precipitation by the addition of LiCl at a final concentration of 1.5 M, followed by centrifugation. After ethanol precipitation, RNA pellet was resuspended in RNase-free water. RNA integrity was examined with an Agilent Bioanalyzer 2100.

tag: culture

value: suspension cell cultures

value: 8 day

molecule: other

source_name: fraction 1-3 of the solution after sucrose ultracentrifugation


title: Ly1_24h_JQ1_A

first: Björn

last: Chapuy

description: Cell line Ly1 treated with JQ1 at 24h (replicateA)

scan_protocol: GCS3000 (Affymetrix)

label_protocol: cRNA was biotinylated according to the standard Affymetrix protocol.

extract_protocol: For total RNA, cells were homogenized in Trizol and RNA was extracted according to standard protocols.


title: F/F.TM

description: Gene expression from 6 weeks control teratoma

source_name: control teratoma

value: F/F


title: OT-I CD8 T cells from DC-OVA +CpG immunized mice, biological rep1

description: CD+CpG 1

value: female

value: 6-8 weeks


title: OT-I CD8 T cells from DC-OVA +CpG immunized mice, biological rep2

description: CD+CpG 2

value: OT-I CD8 T cells


title: Ly1_24h_DMSO_C

description: Cell line Ly1 treated with DMSO at 24h (replicateC)

source_name: Cell line Ly1 treated with DMSO at 24h

value: C


title: OT-I CD8 T cells from DC-OVA alone immunized mice, biological rep3

description: DC 3

value: DC-OVA alone immunized mice


title: F/F.5d embryoid body

description: Gene expression from 5 days control embryoid body

source_name: 5 day control embryoid body


title: cp8_Lame13492375

city: Nouzilly

first: Joel

last: Gautron

address: UR83 Recherches avicoles

institute: INRA

description: Scraped uterine tissue of chicken (Normal vs Expelled).

hyb_protocol: Samples were hybridized at 42°C for 16 h using the Slide-Booster (Olympus Advalytix, Germany), and PRONTO buffer (Corning, Life Sciences).

scan_protocol: Microarray slides were scanned at 532 nm for Alexa® 555 and 635 nm for Alexa® 647 using a GenePix 4000B microarray scanner (Axon Molecular Devices, Sunnyvale, CA, USA).

data_processing: GenePix Pro 6.0 software was used to acquire the fluorescent images, align the spots, quantify their intensity and finally export GenePix report (GPR) files containing spot intensity raw data. Gene expression was compared between uterine tissues in normal (N) and expelled conditions (E). Differentially expressed genes were determined using Limma package developed for R (http://www.bioconductor.org/packages/2.1/bioc/html/limma.html) allowing standardization and data analysis of differential expression, according dye-swap procedure, between different biological conditions.

label: Alexa 555

label_protocol: Sixty micrograms of total RNA were used for labeling the cDNA with Alexa 555 fluorophore using Superscript indirect cDNA labeling system.

extract_protocol: Total RNA was extracted from uterus using Macherey Nagel Nucleospin RNA-L kit according to manufacturer instructions.

treatment_protocol: Uterine tissue was scraped and 100-300 mg were weighed in individual replicates before to be immersed in RNA preservatives (RNAlater) and stored at -80 ° C until total RNA extraction.

value: uterine

tag: condition

value: expelled

value: 42 weeks

tag: Stage

value: 160.8 hours post-ovulation

tag: collection date

tag: tissue weight

tag: extraction date

tag: rna

tag: total rna

tag: ratio 28s/18s

tag: foi (dye/1000 bases)

tag: alexa 555 dye

tag: labeled cdna

label: Alexa 647

label_protocol: Sixty micrograms of total RNA were used for labeling the cDNA with Alexa 647 fluorophore using Superscript indirect cDNA labeling system.

value: normal

value: 43 weeks

value: 15.53 hours post-ovulation

tag: alexa 647 dye


title: 7050276

source_name: Total RNA from lung tumor biopsies

tag: tissue

value: squamous lung cell carcinoma

source_name: Pool from the analysed samples

tag: reference

value: Pool from the analysed samples


title: Ly1_24h_DMSO_B

city: Boston

address: 450 Brookline Ave.

institute: Dana-Farber Cancer Institute

description: Cell line Ly1 treated with DMSO at 24h (replicateB)

tag: cell line

tag: cell type

value: diffuse large B-cell lymphoma (DLBCL)

tag: time

tag: treatment

value: DMSO

tag: replicate

value: B


title: cp8_Lame13492372

tag: condition

tag: age

tag: Stage

tag: collection date

value: 53 pmol

value: 16.08 hours post-ovulation


title: Ly1_12h_JQ1_C

description: Cell line Ly1 treated with JQ1 at 12h (replicateC)

source_name: Cell line Ly1 treated with JQ1 at 12h


title: OT-I CD8 T cells from DC-OVA alone immunized mice, biological rep2

description: DC 2

tag: strain

tag: gender

value: female

value: 6-8 weeks

value: OT-I CD8 T cells


title: Ly1_12h_DMSO_C

description: Cell line Ly1 treated with DMSO at 12h (replicateC)

source_name: Cell line Ly1 treated with DMSO at 12h

value: C


title: Naïve OT-I CD8 T cells, biological rep2

description: Naïve 2

value: Naïve


title: Ly1_12h_JQ1_A

description: Cell line Ly1 treated with JQ1 at 12h (replicateA)

value: A


title: Naïve OT-I CD8 T cells, biological rep3

description: Naïve 3


title: Ly1_24h_DMSO_A

description: Cell line Ly1 treated with DMSO at 24h (replicateA)


title: Ly1_12h_DMSO_B

description: Cell line Ly1 treated with DMSO at 12h (replicateB)


title: cp7_Lame13492379

value: uterine

value: expelled

value: 42 weeks

value: 16.06 hours post-ovulation

tag: tissue weight

tag: extraction date

tag: rna

tag: total rna

tag: ratio 28s/18s

tag: foi (dye/1000 bases)

value: 95 pmol

value: 15.43 hours post-ovulation


title: cp6_Lame13527018

tag: tissue

value: normal

value: 43 weeks

value: 16 hours post-ovulation

value: 2.6 µg/µl

tag: alexa 555 dye

tag: labeled cdna

value: 16.34 hours post-ovulation

tag: alexa 647 dye


title: cp7_Lame13492395

value: 67 pmol


title: cp4_Lame13527013

value: 16.09 hours post-ovulation

value: 81 pmol

value: 16.25 hours post-ovulation


title: Ly1_12h_DMSO_A

description: Cell line Ly1 treated with DMSO at 12h (replicateA)

tag: cell line

tag: cell type

value: diffuse large B-cell lymphoma (DLBCL)

tag: time

tag: treatment

value: DMSO

tag: replicate


title: OT-I CD8 T cells from DC-OVA alone immunized mice, biological rep1

description: DC 1

tag: strain

value: female

tag: age

value: 6-8 weeks

value: DC-OVA alone immunized mice

value: OT-I CD8 T cells


title: cp5_Lame13527001

value: uterine

tag: condition

value: expelled

value: 42 weeks

tag: Stage

tag: collection date

tag: tissue weight

value: 89 pmol

value: 16.39 hours post-ovulation


title: Polysome ratio 1 day

description:
polysomal RNA
harvested on 1 day after inoculation

source_name: T87, 1 day after inoculation

tag: culture

value: suspension cell cultures

value: 1 day


title: Ly1_12h_JQ1_B

description: Cell line Ly1 treated with JQ1 at 12h (replicateB)

value: B


title: cp6_Lame13492391

value: 43 weeks

value: 16.34 hours post-ovulation

tag: extraction date

tag: rna

tag: total rna

tag: ratio 28s/18s

tag: foi (dye/1000 bases)

value: normal

value: 16 hours post-ovulation

value: 2.6 µg/µl


title: cp4_Lame13492373

tag: tissue

value: 16.25 hours post-ovulation

tag: alexa 555 dye

tag: labeled cdna

value: 16.09 hours post-ovulation

tag: alexa 647 dye


title: Ly1_6h_JQ1_A

description: Cell line Ly1 treated with JQ1 at 6h (replicateA)

source_name: Cell line Ly1 treated with JQ1 at 6h

tag: cell line

tag: cell type

value: diffuse large B-cell lymphoma (DLBCL)

tag: time

tag: treatment

tag: replicate

value: A


title: cp3_Lame13492390

value: uterine

tag: condition

tag: age

tag: Stage

value: 16.37 hours post-ovulation

tag: collection date

value: 16.16 hours post-ovulation


title: Ly1_6h_JQ1_C

description: Cell line Ly1 treated with JQ1 at 6h (replicateC)

value: C


title: Ly1_6h_JQ1_B

description: Cell line Ly1 treated with JQ1 at 6h (replicateB)


title: cp3_Lame13492387

tag: tissue weight

tag: extraction date

tag: rna

value: 50 pmol

value: expelled

value: 42 weeks


title: Ly1_6h_DMSO_C

description: Cell line Ly1 treated with DMSO at 6h (replicateC)

source_name: Cell line Ly1 treated with DMSO at 6h

value: DMSO


title: Ly1_6h_DMSO_B

description: Cell line Ly1 treated with DMSO at 6h (replicateB)

value: B


title: Ly1_6h_DMSO_A

description: Cell line Ly1 treated with DMSO at 6h (replicateA)


title: cp2_Lame13492394

tag: total rna

tag: ratio 28s/18s

tag: foi (dye/1000 bases)

value: 43 weeks

value: 16.46 hours post-ovulation


title: cp1_Lame13527012

tag: tissue

value: normal

value: 17.24 hours post-ovulation

tag: alexa 555 dye

tag: labeled cdna

value: 18 hours post-ovulation


title: cp2_Lame13527009

value: 93 pmol

tag: alexa 647 dye

value: 160 pmol


title: cp5_Lame134923767

value: 16.39 hours post-ovulation

value: 16.34 hours post-ovulation


title: Ly1_2h_JQ1_C

description: Cell line Ly1 treated with JQ1 at 2h (replicateC)

source_name: Cell line Ly1 treated with JQ1 at 2h

tag: cell line

tag: cell type

value: diffuse large B-cell lymphoma (DLBCL)

tag: time


title: Ly1_2h_JQ1_B

description: Cell line Ly1 treated with JQ1 at 2h (replicateB)

tag: treatment

tag: replicate


title: isopentenol_3_2.5hr

city: Emeryville

first: Robert

last: Dahl

state: CA

address: 5885 Hollis St, JBEI

department: Chemical Engineering

institute: University of California-Berkeley

description: Biological replicate 3 of 3

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.).

label: Alexa Fluor 555

organism: Escherichia coli

source_name: E. coli 0.2% isopentenol 2.5 hr

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: E. coli DH1 containing 3 plasmids: pMevT(C159A), pMevB, pC9b, was inoculated to an OD of 0.1 into 250 ml flasks containing 60 ml M9 media and grown at 30 C.

extract_protocol: Samples were snap frozen in liquid nitrogen and 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)

treatment_protocol: When the OD reached 0.3, 0.5 mM IPTG was added to all flasks to induce the pathway protein expression.  Also at this point, 0.2% v/v isopentenol was added to the 3 test flasks.  2.5 hr later the samples were extracted.

tag: genotype

value: E. coli DH1 containing 3 plasmids pMevT(C159A), pMevB, pC9b

value: 0.2% isopentenol addition


title: cp1_Lame13492376

description: Scraped uterine tissue of chicken (Normal vs Expelled).

value: uterine

tag: condition

tag: age

tag: Stage

tag: collection date


title: PLCb3 KO AD-induced

city: La Jolla

first: Tomoaki

last: Ando

address: 9420 Athena Circle

institute: La Jolla Institute for Allergy and Immunology

description: back skin, Der f/SEB-induced AD model

hyb_protocol: Standard hybridization

scan_protocol: Agilent Technologies Scanner G2505C

data_processing: 75 percentile shift normalization using GeneSpring

source_name: PLCb3 KO AD-induced

growth_protocol: Whole skin was homogenized and total RNA was extracted.

extract_protocol: TRIzol-extracted total RNA was cleaned using RNeasy Total RNA Mini Kit (Qiagen)

treatment_protocol: Der f/SEB-induced atopic dermatitis model (Kawakami Y et al., Allergol Int., 2007)

value: back skin


title: isopentenol_1_2.5hr

description: Biological replicate 1 of 3


title: 7050880

value: lung adenocarcinoma

tag: reference

value: Pool from the analysed samples


title: human radiosensitive NPC, biological rep3 [miRNA]

description: miRNA expression data from radioresistant NPC cell line.

hyb_protocol: 100 ng of Cy3 labelled RNA were hybridized to Human miRNA V2 Microarray 8 × 15K (G4470B, Agilent Technologies) according to manufacturer's instructions (miRNA Microarray System Protocol, Agilent Technologies). Arrays were scanned at 5 um resolution on an Agilent DNA Microarray Scanner (G2565BA, Agilent Technologies) using the default settings for miRNA Microarray v2.0 (miRNA Microarray System Protocol, Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the Agilent Feature Extraction(v10.7) using one color scan setting for array slides (Agilent Technologies Scanner G2505C).

data_processing:
Images provided by the scanner were analyzed using Agilent's software Feature Extraction version10.7 using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
The raw data were normalized and analyzed by GeneSpring GX software version 7.3 (Percentile shift, normalizing to the 75th percentile)

source_name: human radiosensitive NPC cell line

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using Agilent miRNA Complete Labeling and Hybridization Kit according to the manufacturer's instructions, followed by .

treatment_protocol: Radioresistant subclone of nasopharyngeal carcinoma CNE2-IR cell line was cultured and produced according to the experienment schedule to undergo five rounds of sublethal dose of irradiation (11 Gy),and the parent cell line CNE2 cell line sensitive to radiotherapy as the control.

value: radiosensitive


title: PLCb3 KO healthy control

description: back skin, healthy control

source_name: PLCb3 KO healthy control


title: Naïve OT-I CD8 T cells, biological rep1

description: Naïve 1

source_name: spleen

tag: strain

tag: gender

value: female

value: 6-8 weeks

value: Naïve

value: OT-I CD8 T cells


title: Ly1_2h_DMSO_B

description: Cell line Ly1 treated with DMSO at 2h (replicateB)

source_name: Cell line Ly1 treated with DMSO at 2h

treatment_protocol: Each lymphoma cell line was profiled in triplicate at baseline (0h) and at four additional time points (2h, 6h, 24h and 48h) after treatment with 500nM of JQ1 or vehcile (DMSO) control.

value: DMSO

value: B


title: C57BL/6 AD-induced

description: back skin, Der f/SEB-induced AD model

source_name: C57BL/6 AD-induced

tag: tissue


title: control_2_2.5hr

description: Biological replicate 2 of 3

source_name: E. coli control 2.5 hr

value: control


title: KO Flk1+

description: Gene expression of Snai1 knockout Flk1+ cells from 4 day EBs

hyb_protocol: Following fragmentation, 3.7 ug of cDNA were hybridized for 16 hr at 45C on HT MG-430 PM array strips using the Affymetrix Gene Atlas system (software version 1.0.4.267).

scan_protocol: Arrays were scanned using the Affymetrix Gene Atlas system

data_processing: Data was analyzed using the limma and affy bioconductor packages implemented in the R-statistical environment version 2.15.1. RMA was used to normalize the data and fit log2 transformed expression values.

source_name: 4 day snai1 knockout Flk1+

label_protocol: cDNA were prepared according to the NuGen WT-Pico V2 kit protocol from 50 ng total RNA (Ovation PicoSL WTA System V2 P/N 3312). Biotinylated single-stranded cDNA were prepared from 3ug of cDNA (Encore Biotin Module P/N 4200-12, 4200-60, 4200-A01)

growth_protocol: Control and Snai1 knockout ESCs were cultured as hanging drops to form embryoid bodies and then suspension cultured in spotaneous differentiation media.

extract_protocol: Total RNA of EBs was collected and purified using RNeasy Mini Kits (QIAGEN)

treatment_protocol: 4 day EBs were dissociated and sorted with anti-Flk1 antibody to separated Flk1+ and Flk1- cells

tag: genotype/varitaion

value: Snai1 knockout


title: human radiosensitive NPC, biological rep2 [miRNA]


title: control_1_2.5hr

description: Biological replicate 1 of 3


title: control_3_2.5hr

description: Biological replicate 3 of 3


title: C57BL/6 healthy control

description: back skin, healthy control

source_name: C57BL/6 healthy control


title: Ly1_2h_JQ1_A

description: Cell line Ly1 treated with JQ1 at 2h (replicateA)

value: A


title: NC/Nga AD-induced

description: back skin, Der f/SEB-induced AD model

source_name: NC/Nga AD-induced


title: human radiosensitive NPC, biological rep1 [miRNA]


title: Ly1_2h_DMSO_A

description: Cell line Ly1 treated with DMSO at 2h (replicateA)

value: diffuse large B-cell lymphoma (DLBCL)


title: human radioresistant NPC, biological rep3 [miRNA]

source_name: human radioresistant NPC cell line

value: radioresistance


title: F/F Flk1-

description: Gene expression of control Flk1- cells from 4 day EBs

source_name: 4 day control Flk1-

value: F/F


title: isopentenol_2_2.5hr

description: Biological replicate 2 of 3

value: E. coli DH1 containing 3 plasmids pMevT(C159A), pMevB, pC9b

value: 0.2% isopentenol addition


title: Ly1_2h_DMSO_C

description: Cell line Ly1 treated with DMSO at 2h (replicateC)

value: C


title: Ly1_0h_nothing_B

description: Cell line Ly1 treated with nothing at 0h (replicateB)

value: nothing


title: NC/Nga healthy control

description: back skin, healthy control

source_name: NC/Nga healthy control

value: back skin


title: human radioresistant NPC, biological rep2 [miRNA]


title: F/F Flk1+

description: Gene expression of control Flk1+ cells from 4 day EBs

source_name: 4 day control Flk1+


title: human radioresistant NPC, biological rep1 [miRNA]


title: Ly1_0h_nothing_A_1_3

description: Cell line Ly1 treated with nothing at 0h (replicateA)


title: Ly1_0h_nothing_A_1_1

source_name: Cell line Ly1 treated with nothing at 0h


title: Ly1_0h_nothing_A_1_2


title: Ly1_0h_nothing_C

description: Cell line Ly1 treated with nothing at 0h (replicateC)


title: eMCAo 5day

status: Public on Dec 09 2013

city: Singapore

first: Kandiah

last: Jeyaseelan

address: 8 Medical Drive

country: Singapore

institute: National University of Singapore

description: around 3000 microRNAs capture probes cover human, mouse and rat microRNAs and present a global miRNA profiling for the specific species

hyb_protocol: hybridization for 16-18hrs on miRCURY LNA™ Arrays, using MAUI® hybridization system according to manufacturer’s protocol (Exiqon, Denmark).

scan_protocol: The microarray chips were then washed and scanned using InnoScan700, microarray scanner (Innopsys, Carbonne, France) and analysed on Mapix® Ver4.5 software.

data_processing: Microarray analysis involved multiple sample analysis including background subtraction, t-Test/One-way ANOVA analysis, hierarchical clustering (PMID: 21829658). Normalization was performed using 5S rRNA. t-Test was performed between ‘‘control’’ and ‘‘test’’ sample groups and the t values were calculated for each mRNA. p-values were computed from the theoretical t-distribution. The clustering using hierarchical method was performed with average linkage and Euclidean distance metric. The clustering was generated using TIGR MeV (Multiple Experimental Viewer) software and statistical analysis was performed using Partek® Genomics Suite™ 6.6 (Partek Inc, USA).  Only the microRNA presented in Rattus norvegicus (rno-miR-) were included for our analysis, while our raw data include the entire  probe that was on  the chip (hsa+mmu+rno).

organism: Rattus norvegicus

source_name: eMCAo 5day

label_protocol: miRNA array was performed (PMID: 21829658) using total RNA (500 ng) which was 3′-end-labelled with Hy3 dye using the miRCURY LNA™ Power Labeling Kit (Exiqon, Denmark)

growth_protocol: All animals were handled according to the Council for International Organisation of Medical Sciences on Animal Experimentation (World Health Organisation, Geneva, Switzerland) and the National University of Singapore (IACUC/NUS) guidelines for laboratory animals. The protocol was approved by the Committee on the Ethics of Animal Experiments of the National University of Singapore (Protocol Number: 081/09 and 025/11). All surgery was performed using ketamine/xylazine as anesthesia, and all efforts were made to minimize suffering.

extract_protocol: Total RNA (+ miRNA) was extracted from brain tissues by a single-step method using Trizol reagent (Invitrogen, Life Technologies, USA) according to manufacturers’ protocol.

treatment_protocol: no treatment

value: Wistar

tag: weight

value: male

value: ischemic brain


title: eMCAo 7day

source_name: eMCAo 7day


title: ZF4 fibroblastic cell line rep 2

first: Steven

last: Weicksel

state: Massachusetts

address: 55 Lake Ave

department: BMP

institute: UMass Medical School

hyb_protocol: Followed standard Affymetric protocols for chip type

data_processing: CEL files were normalized using invariant set and background corrected by mas5 using expresso from the R affy package (v.2.15.2).

organism: Danio rerio

source_name: ZF4 fibroblastic cell line

extract_protocol: Trizol - following manufactor protocols

value: fibroblastic cells


title: Retinoic acid treated six hour post fertilization embryo rep 1

scan_protocol: Followed standard Affymetric protocols for chip type

source_name: Retinoic acid treated_6 hr post fertilization embryo

value: whole embryo

tag: developmental stage

value: 6 hr post fertilization

tag: treated with

value: Retinoic acid


title: KO Flk1-

description: Gene expression of Snai1 knockout Flk1- cells from 4 day EBs

source_name: 5 day snai1 knockout Flk1-

tag: cell type

value: Snai1 knockout


title: ZF4 fibroblastic cell line rep 1

label_protocol: Followed standard Affymetric protocols for chip type

tag: cell line


title: eMCAo 48hrs

source_name: eMCAo 48hrs


title: Retinoic acid treated nine hour post fertilization embryo rep 1

source_name: Retinoic acid treated_9 hr post fertilization embryo

value: 9 hr post fertilization


title: Retinoic acid treated nine hour post fertilization embryo rep 2


title: Retinoic acid treated six hour post fertilization embryo rep 2


title: eMCAo 24hrs2

source_name: eMCAo 24hrs


title: Retinoic acid treated four hour post fertilization embryo rep 2

source_name: Retinoic acid treated_4 hr post fertilization embryo

value: 4 hr post fertilization


title: Untreated nine hour post fertilization embryo rep 2

source_name: Untreated_9 hr post fertilization embryo

value: none (untreated)


title: Retinoic acid treated four hour post fertilization embryo rep 1


title: eMCAo 3day

source_name: eMCAo 3day


title: KO.ES. rep2

description: Gene expression from Snai1 knockout ESCs, biological rep2

source_name: Snai1 knock out ESCs

value: ESC

tag: genotype/variation


title: eMCAo 24hrs1


title: Untreated nine hour post fertilization embryo rep 1


title: Untreated six hour post fertilization embryo rep 2

source_name: Untreated_6 hr post fertilization embryo


title: eMCAo 12hrs2

source_name: eMCAo 12hrs


title: Untreated six hour post fertilization embryo rep 1


title: eMCAo 12hrs1


title: eMCAo 6hrs

source_name: eMCAo 6hrs


title: Asymptomatic HBV carriers group rep2

type: genomic

city: Wuhan

first: Lin

last: Ju-Sheng

state: Hubei

address: 1095 Jiefang Road

department: Gastroenterology

institute: Tongji Hospital

description: Hybridized to Affymetrix SNP6.0 Array

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations 450, and scanned using the Gene Chip Scanner 3000 7G.

data_processing: CEL files and TXT files were analyzed using Birdseed algorithm, an evolution of the RLMM genotype-calling algorithm (Rabbee and Speed, 2006) by Affymetrix Genotyping Console software, which makes genotype calls by fitting a Gaussian mixture model in the two-dimensional A-signal vs. B-signal space, using SNP-specific models to increase performance.

molecule: genomic DNA

source_name: Asymptomatic HBV carriers

label_protocol: standard Affymetrix protocol

extract_protocol: Genomic DNA was extracted from EDTA-anticoagulated peripheral blood using a QuickGene DNA whole blood kit S (DB-S) as instruction. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, PicoGreen and agarose gel electrophoresis.

value: peripheral blood

tag: pools

value: 66 patients

tag: group

value: control

tag: disease state

value: Asymptomatic HBV carriers


title: eMCAo 0hrs

source_name: eMCAo 0hrs


title: HBV - related liver cirrhosis group rep3

description: Hybridized to Affymetrix SNP6.0 Array

source_name: HBV - related liver cirrhosis patients

value: 88 patients

value: case 2

value: HBV - related liver cirrhosis patients


title: eMCAo normal3

source_name: eMCAo normal

value: Wistar

value: male

value: ischemic brain


title: eMCAo normal1

description: around 3000 microRNAs capture probes cover  human, mouse and rat microRNAs and present a global miRNA profiling


title: eMCAo normal2


title: eMCAo normal4


title: Untreated four hour post fertilization embryo rep 2

source_name: Untreated_4 hr post fertilization embryo

value: whole embryo


title: Untreated four hour post fertilization embryo rep 1


title: HBV - related hepatocellular carcinoma group rep2

description: Hybridized to Affymetrix SNP6.0 Array

source_name: HBV - related hepatolecullar carcinoma patients

value: 90 patients

value: case 3

value: HBV - related hepatocellularcarcinoma patients


title: ZF4 cell line replicate 2

description:
ZF4 biological replicate 2 of 2
ZF4-2

hyb_protocol: Adapted from Yuan et al 2005 Science

scan_protocol: Scanned on an Agilent High-Resolution C Scanner or an Axon 4000B. Images were quantified and background subtraction was done using Agilent Feature Extraction Software.

data_processing: Mean singals of the background subtracted data from two replicates for each sample was assigned to each probe location.  Signals were then taillied using a 30bp sliding window with a 10bp step. A Lowess fitting line (f=.05) then plotted to show the trend of the aggregated signals.

source_name: ZF4 cell line_untreated

label_protocol: Adapted from Yuan et al 2005 Science

extract_protocol: Adapted from Dennis et al 2007 Genome Research

value: fibroblast cells derived from 24hpf embryos

tag: dna fragmentation

value: Micrococcal Nuclease

source_name: pooled whole zebrafish embryo 24hpf

value: Sonication


title: Asymptomatic HBV carriers group rep3

description: Hybridized to Affymetrix SNP6.0 Array

value: peripheral blood


title: HBV - related hepatocellular carcinoma group rep3

description: Hybridized to Affymetrix SNP6.0 Array


title: eMCAo 3hrs

source_name: eMCAo 3hrs


title: DEAB treated 6hpf embryo replicate 2

description:
6hpf biological replicate 2 of 2
DEAB6h-2

source_name: pooled whole zebrafish embryo 6hpf_DEAB treated

value: 6 hr post fertilization

value: Diethylaminobenzaldehyde (DEAB)

source_name: pooled whole zebrafish embryo 6hpf

value: none (untreated)


title: RA treated 6hpf embryo replicate 2

description:
6hpf biological replicate 2 of 2
RA6h-2

source_name: pooled whole zebrafish embryo 6hpf_RA treated

value: Retinoic acid (RA)


title: ZF4 cell line replicate 1

description:
ZF4 biological replicate 1 of 2
ZF4-1


title: X6042316131_R05C01_genomic DNA from whole blood_array

city: London

first: Jordana

last: Bell

address: St Thomas' Hospital, Westminster Bridge Rd

department: Department of Twin Research and Genetic Epidemiology

country: United Kingdom

institute: King's College London

description: Family 25 monozygotic twin 2

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: BeadStudio software for 450k data.

label: Cy5 and Cy3

source_name: whole blood

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted and purified from whole blood samples

tag: individual

value: Family 25 monozygotic twin 2

value: Female

tag: pain temperature

tag: age

tag: medip-seq id

tag: 450k chip

tag: order on 450k chip


title: RA treated 9hpf embryo replicate 1

description:
9hpf biological replicate 1 of 2
RA9h-1

source_name: pooled whole zebrafish embryo 9hpf_RA treated

tag: tissue

value: 9 hr post fertilization

source_name: pooled whole zebrafish embryo 9hpf


title: DEAB treated 9hpf embryo replicate 1

description:
9hpf biological replicate 1 of 2
DEAB9h-1

source_name: pooled whole zebrafish embryo 9hpf_DEAB treated


title: DEAB treated 6hpf embryo replicate 1

description:
6hpf biological replicate 1 of 2
DEAB6h-1


title: RA treated 4hpf embryo replicate 2

description:
4hpf biological replicate 2 of 2
RA4h-2

source_name: pooled whole zebrafish embryo 4hpf_RA treated

value: 4 hr post fertilization

source_name: pooled whole zebrafish embryo 4hpf


title: HBV - related hepatocellular carcinoma group rep1

description: Hybridized to Affymetrix SNP6.0 Array


title: Asymptomatic HBV carriers group rep1

description: Hybridized to Affymetrix SNP6.0 Array

source_name: Asymptomatic HBV carriers

value: 66 patients

value: control

value: Asymptomatic HBV carriers


title: DEAB treated 9hpf embryo replicate 2

description:
9hpf biological replicate 2 of 2
DEAB9h-2

value: whole embryo


title: RA treated 6hpf embryo replicate 1

description:
6hpf biological replicate 1 of 2
RA6h-1


title: RA treated 9hpf embryo replicate 2

description:
9hpf biological replicate 2 of 2
RA9h-2


title: Stat5 flox/cKO OC

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

description: osteoclasts from Stat5 flox/cKO mice

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: S635 Median column as Red signal and S532 Median column as Green signal. Global normalized, background subtracted data obtained from log2 of processed Green signal/processed Red signal.

source_name: flox R4

label_protocol: cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: Osteoclasts were generated by stimulating bone marrow cells with 10 ng/ml M-CSF and 100 ng/ml RANKL

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

tag: genotype

value: Stat5 flox

value: osteoclasts derived from Stat5 flox bone marrow cells

tag: strain

source_name: CKO R4

value: osteoclasts derived from Stat5 cKO bone marrow cells

value: Stat5 cKO


title: X6042308068_R06C02_genomic DNA from whole blood_array

description: Family 24 monozygotic twin 2

value: Family 24 monozygotic twin 2

tag: gender


title: X6055432099_R01C01_genomic DNA from whole blood_array

description: Family 22 monozygotic twin 2

value: Family 22 monozygotic twin 2


title: HBV - related liver cirrhosis group rep1

description: Hybridized to Affymetrix SNP6.0 Array

source_name: HBV - related liver cirrhosis patients

value: peripheral blood

value: 88 patients

value: case 2

value: HBV - related liver cirrhosis patients


title: eMCAo 7day

description:
5320724053_G.AVG_Signal
400ng of total RNA was detected by beadchip

hyb_protocol: Hybridization was performed in 15ul volume by using illumina hybridization kit.

scan_protocol: Data were scanned and analysed with the BeadStudio software (v.1.8.0).

data_processing: Differentially expressed genes were selected based on p value < 0.05, differential score > 20, average signal intensity > 100, and normalize to endo-control and baseline (Illumina Inc. GenomeStudio Version 1.8.0).

source_name: ischemic brain

label_protocol: Biotin-labelled complementary RNA probes were synthesized with the Illumina TotalPrep RNA Amplification kit (Ambion).

tag: species

value: Wistar rat

value: male

tag: weight

value: ischemic brain


title: RA treated 2hpf embryo replicate 1

description:
2hpf biological replicate 1 of 2
RA2h-1

source_name: pooled whole zebrafish embryo 2hpf_RA treated

tag: developmental stage

value: 2 hr post fertilization

tag: treated with

value: Retinoic acid (RA)

value: Micrococcal Nuclease

source_name: pooled whole zebrafish embryo 2hpf

value: none (untreated)

value: Sonication


title: HBV - related liver cirrhosis group rep2

description: Hybridized to Affymetrix SNP6.0 Array

tag: pools

tag: group


title: X6055432092_R04C02_genomic DNA from whole blood_array

description: Family 22 monozygotic twin 1

value: Family 22 monozygotic twin 1

value: Female


title: eMCAo 5day

description:
5320724053_F.AVG_Signal
400ng of total RNA was detected by beadchip