title: atRA WT, set 4

city: New York

first: Kristian

middle: Bruun

last: Laursen

address: 1300 York Avenue

department: Pharmacology

institute: Weill Cornell Medical College

description:
Set4
Gene expression data from atRA treated WT cells

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix MG-430.2 expression array. The chips were washed and stained in the Affymetrix Fluidics stations FS450.

scan_protocol: GeneChips were scanned using the GeneChip scanner 3000-7G.

data_processing: The data were analyzed with GenespringGX version 7.0 using Affymetrix default analysis settings. The data sets were summarized using the GC-RMA algorithm, followed by a three-step normalization process consisting of: A) data transformation, converting values less than 0.01 to 0.01, B) chip normalization to the 50th percentile of total intensity and C) per gene normalization to median intensity. Genes were filtered by expression level to exclude genes with a raw signal below 100.

source_name: F9 WT treated 8hr with atRA

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: F9 Wt and RARaKO cells were propagated in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 5% calf serum and 5% fetal calf serum and maintained at 95% humidity in 37°C incubators equilibrated with 10% CO2. Prior to plating the tissue culture dishes were coated with 0.3% gelatin. For the microarray analysis 2 million cells were plated on 10 cm tissue culture dishes  were plated 16 hr prior to drug treatment.

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

treatment_protocol: All-trans retinoic acid (atRA) (Cat. #R2625, Sigma, MD) and cycloheximide (chx) (Cat. #C7698, Sigma, MD) were dissolved in 100% ethanol (EtOH). The cells were pretreated with 1 µg/ml chx for 30 min before 7.5hr treatment with RA (1 µM) or vehicle (EtOH, 0.1%).

tag: treatment

value: atRA + cycloheximide

value: WT


title: P1Tm_T

status: Public on Aug 10 2011

type: RNA

city: Heidelberg

first: Mohammed

last: Abba

address: Im Neuenheimer Feld 280

department: Molecular Oncology of Solid Tumors

country: Germany

institute: German Cancer Research Center (DKFZ)

hyb_protocol: Standard Illumina hybridzation protocol

scan_protocol: Beadstation array scanner, setting adjusted to a scaling factor of 1 and PMT settings at 430.

data_processing: Data extraction was done for all beads individually, and outliers with > 2.5 MAD (median absolute deviation) were removed. The data were normalised in BeadStudio using quantile normalisation without background subtraction

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: Patient no 1, Tumor whole tissue

label_protocol: Biotinylated cRNA were prepared with the TargetAmp 2-Round Biotin-aRNA amplification kit 3.0 (Epicentre Biotechnologies, Madison, USA)

extract_protocol: RNeasy mini and microkits(Qiagen) for whole tissue and laser microdissected samples, respectively according to the specified protocols. Microdissected samples were pooled prior to RNA isolation

tag: tissue

value: Colorectal cancer

tag: tissue sub-type

value: Tumor whole tissue

tag: patient no

value: Patient no 1


title: P26Tm_T

source_name: Patient no 26, Tumor whole tissue

value: Patient no 26


title: P2Nm_T_2

source_name: Patient no 2, Normal whole tissue

value: Normal whole tissue

value: Patient no 2


title: P102TS

source_name: Patient no 102, Tumor stroma

value: Tumor stroma

value: Patient no 102


title: P1Nm_T

source_name: Patient no 1, Normal whole tissue


title: P24Nm_T

source_name: Patient no 24, Normal whole tissue

value: Patient no 24


title: P28Nm_T

source_name: Patient no 28, Normal whole tissue

value: Patient no 28


title: P103NE

source_name: Patient no 103, Normal epithelium

value: Normal epithelium

value: Patient no 103


title: P103Nm_T

source_name: Patient no 103, Normal whole tissue


title: P26Nm_T

source_name: Patient no 26, Normal whole tissue


title: P103Tm_T

source_name: Patient no 103, Tumor whole tissue


title: P10Tm_T

source_name: Patient no 10, Tumor whole tissue

value: Patient no 10


title: P103TS_cRNA

source_name: Patient no 103, Tumor stroma


title: P16Nm_T

source_name: Patient no 16, Normal whole tissue

value: Patient no 16


title: P16Tm_T

source_name: Patient no 16, Tumor whole tissue


title: P102TE_cRNA

source_name: Patient no 102, Tumor epithelium

value: Tumor epithelium


title: P102Nm_T

source_name: Patient no 102, Normal whole tissue


title: P24Tm_T

source_name: Patient no 24, Tumor whole tissue


title: P102NS_cRNA

source_name: Patient no 102, Normal stroma

value: Normal stroma


title: EtOH, RARaKO, set 4

country: USA

description:
Set4
Gene expression data from EtOH treated RARaKO cells

label: biotin

organism: Mus musculus

source_name: F9 RARaKO treated 8hr with EtOH

value: EtOH + cycloheximide

tag: genotype

value: RARaKO

tag: cell line


title: P102NE

source_name: Patient no 102, Normal epithelium

value: Colorectal cancer


title: Mouse_sham_1

city: Rochester

first: Robert

middle: Christian

last: Huebert

state: MN

address: 200 1st Street SW

department: Gastroenterology and Hepatology

institute: Mayo Clinic

description: miRNA expression.

hyb_protocol: GeneChip® Hybridization.

scan_protocol: Affymetrix® GeneChip® Scanner.

data_processing:
Data were analyzed using the Affymetrix® miRNA QC Tool Software using the default analysis.

Probe-specific signal detection calls: Each probe on an array is assayed for detection. For miRNA probes, detection is based on a Wilcoxon Rank-Sum test of the miRNA probe set signals compared to the distribution of signals from GC-content-matched anti-genomic probes. If the resulting p-value for the probes is p=0.06, it is considered “detected above background”.

Background estimation and correction: The same set of anti-genomic probes used to determine detection calls are used to estimate GC-content-matched background signals. Each miRNA probe signal has a GC-content-matched background estimate subtracted from its value. This GC-specific background contribution is estimated by the median signal from the distribution of GC-matched anti-genomic probes. The resulting value may be negative at this stage, if the probe’s signal is less than the median value of the GC-matched anti-genomic probes. The same process can be applied using two other ways to match main content probes to background probes: a) by GC percent and b) by both GC content and probe length.

Constant Variance Stabilization on probes: Probe level constant variance stabilization is based on adding a small constant to all of the intensities. The default value of this constant is 16.

Normalization: Probe-level normalization is provided via quantile, mean array scaling, and mean array scaling (based on normalization probes) normalization algorithms.

Summarization: This process provides the quantification of probe intensities into probe set intensities (via mean, median or RMA methods).

source_name: whole liver RNA, control

label_protocol: GeneChip® One-Cycle Target Labeling.

growth_protocol: Standard mouse housing conditions.

extract_protocol: miR-VANA miRNA Isolation Kit (Ambion).

treatment_protocol: Common bile duct ligation or sham surgery.

tag: strain

value: liver

tag: cell type

value: endothelial cells

value: sham surgery

tag: phenoytpe

value: no cirrhosis


title: Mouse_BDL_1

description: miRNA expression.

source_name: whole liver RNA, BDL

value: bile duct ligation (BDL)

value: cirrhosis


title: EtOH, WT, set 2

description:
Set2
Gene expression data from EtOH treated WT cells

source_name: F9 WT treated 8hr with EtOH

value: WT


title: Patient 2, after Figitumumab

city: Brussels

first: Sandra

last: Schmitz

address: avenue Hippocrate 54

department: Medical Oncology

country: Belgium

institute: UCL

hyb_protocol: Following fragmentation, 12.5 ug of aRNA were hybridized for 16 hr at 45°C on GeneChip® Human Genome U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GCS3000 scanner

data_processing: The data were analyzed with Genechip expression console using the MAS5.0 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: Patient 2, after Figitumumab

label_protocol: Biotinylated aRNA were prepared according to the standard Affymetrix protocol from 100ng of total RNA (Gene Chip 3'IVT Express Kit User Manual, Affymetrix).

extract_protocol: Biopsies were stored in RNA later for up to one week at 4°C and than frozen by -80°C.Total RNA was extracted either using the TriPure Isolation reagent (Roche) and  the RNeasy mini kit (Qiagen) according to manufacturer's protocol. RNA quantity and quality was checked by a Nanodrop and Agilent Bioanalyzer 2100 respectivelly.

treatment_protocol: Patients with palliative SCCHN progressing after platinum-based therapy were treated with figitumumab IV 20 mg/kg, every 3 weeks. Biopsies were collected before inclusion in the trial and 2 hours after second infusion of figitumumab

value: head and neck squamous cell carcinoma (SCCHN)


title: EtOH, WT, set 4

description:
Set4
Gene expression data from EtOH treated WT cells


title: stromal

city: Beijing

first: wujiang

last: Liu

department: Urology

country: China

institute: Peking University

description:
by laser micro-dissection
Raw data file: 110119-11023A_1_(HG-U133_Plus_2).CEL

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip mouse 430 2.0 Genome Array in the Affymetrix Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the affymetrix scanner 3000 7G.The scanned images were first assessed by visual inspection then analyzed to generate raw data files saved as CEL files using the default setting of AGCC.

data_processing: The data were analyzed with Expression Console Software using GCRMA algorithm.

source_name: prostate stromal

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1ug total RNA (Expression Analysis Technical Manual, Affymetrix).

extract_protocol: extraction of total RNA was performed using Qiagen RNeasy kit according to the manufacturer's instructions.

tag: disease state

value: Benign Prostatic Hyperplasia


title: Patient 3, before Figitumumab

source_name: Patient 3, before Figitumumab


title: Patient 3, after Figitumumab

source_name: Patient 3, after Figitumumab


title: EtOH, RARaKO, set 2

description:
Set2
Gene expression data from EtOH treated RARaKO cells


title: atRA WT, set 2

description:
Set2
Gene expression data from atRA treated WT cells

source_name: F9 WT treated 8hr with atRA

value: atRA + cycloheximide


title: Patient 1, before Figitumumab

source_name: Patient 1, before Figitumumab


title: atRA RARaKO, set 2

description:
Set2
Gene expression data from atRA treated RARaKO cells

source_name: F9 RARaKO treated 8hr with atRA


title: atRA RARaKO, set 4

description:
Set4
Gene expression data from atRA treated RARaKO cells


title: Patient 2, before Figitumumab

source_name: Patient 2, before Figitumumab


title: EtOH, RARaKO, set 3

description:
Set3
Gene expression data from EtOH treated RARaKO cells


title: atRA RARaKO, set 3

description:
Set3
Gene expression data from atRA treated RARaKO cells


title: EtOH, WT, set 3

description:
Set3
Gene expression data from EtOH treated WT cells


title: epithelium

description:
by laser micro-dissection
Raw data file: 110119-11023A_2_(HG-U133_Plus_2).CEL

source_name: prostate epithelium


title: Patient 1, after Figitumulmab

source_name: Patient 1, after Figitumulmab


title: PC3

city: La Jolla

first: Daniel

last: Nomura

state: CA

address: 10550 North Torrey Pines Rd. SR107

institute: the Scripps Research Institute

description: gene expression data of cancer cell line

hyb_protocol: Following fragmentation, cRNA was hybridized for 16 hr at 45C on GeneChip Human HG-U133Plus2 Genome Array.

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

data_processing: RMA

source_name: cancer cell line

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

growth_protocol: MCF7, OVCAR3, SKOV3, C8161, MUM2C, and LNCaP cells were grown in RPMI medium with FCS and glutamine; 231MFP cells were grown in L-15 medium with FCS and glutamine; PC3 cells were grown in F12K medium with FCS and glutamine; DU145 cells were grown in DMEM medium with FCS and glutamine

extract_protocol: RNA was extracted using a Qiagen RNAeasy kit per manufactuerer's instructions

tag: cancer cell type

value: aggressive


title: DU145


title: atRA WT, set 3

description:
Set3
Gene expression data from atRA treated WT cells


title: pd4 testis Foxo1 null [5529237039_A]

city: Dallas

first: Diego

middle: H

last: Castrillon

state: TX

address: 6000 Harry Hines Blvd. NB6.126

department: Pathology

institute: U.T. Southwestern Medical Center

description:
5529237039A
replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

source_name: pd4 testis Foxo1 null

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

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

value: FVB

tag: genotype/variation

value: Foxo1 null

tag: age

value: postnatal day 4

value: testis


title: pd4 testis Foxo1 wild-type [5529237039_F]

description:
5529237039F
replicate 3

source_name: pd4 testis Foxo1 wild-type

value: wild type


title: pd4 testis Foxo1 null [5529237039_D]

description:
5529237039D
replicate 2


title: pd4 testis Foxo1 wild-type [5529237039_B]

description:
5529237039B
replicate 1


title: AVG_Signal-H24_2

city: Candiolo

first: Enzo

last: Medico

state: TO

address: Strada Prov. 142, km 3,95

department: Oncology

country: Italy

institute: Candiolo Cancer Institute, University of Torino

description:
H24_2
MDA-MB-435 treated with HGF for 24 hours.

hyb_protocol: 1500 ng of cRNA was hybridized for 20 hours. Array washing was performed using wash buffer. Arrays were stained with SA-Cy3.

scan_protocol: The hybridized BeadChips were scanned by an Illumina BeadScan scanner and analyzed by Illumina's BeadStudio version 1.5.1.3.

data_processing: Data were summarized and rank-invariant normalized using the Illumina Beadstudio software (ver. 1.5.1.3).

source_name: MDA-MB-435, 24 hour HGF treatment

label_protocol: cRNA synthesis and labeling were performed using the Illumina TotalPrep RNA Amplification kit.

growth_protocol: Standard growth conditions.

extract_protocol: RNA extraction was performed using Trizol plus RNA purification kit (Invitrogen). RNA qualitative and quantitative assessment was performed using the Bioanalyzer 2100 (Agilent Tecnologies).

treatment_protocol: Cells were treated with HGF for 1, 6 and 24 hours in a time-course experiment, or transduced with integrin Beta4.

value: melanoma

value: hepatocyte growth factor (HGF)

tag: treatment duration

value: 24 hrs


title: LNCaP

value: LNCaP

value: non-aggressive


title: MUM2C


title: CD4SP thymocytes, rep1

city: Saint Louis

first: Takeshi

last: Egawa

state: MO

address: 660 South Euclid

department: Pathology and Immunology

institute: Washington University School of Medicine

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: MAS 5.0

source_name: CD4+CD8-TCRb(hi) thymocytes

label_protocol: standard Affymetrix protocol

growth_protocol: RNA was extracted immediately after ex vivo isolation of cells without culture.

treatment_protocol: Cells were not treated.

value: CD4+CD8-TCRb(hi) thymocytes


title: pd4 testis Foxo1 wild-type [5529237039_C]

description:
5529237039C
replicate 2


title: pd4 testis Foxo1 null [5529237039_E]

description:
5529237039E
replicate 3


title: AVG_Signal-H1_2

description:
H1_2
MDA-MB-435 treated with HGF for 1 hour.

source_name: MDA-MB-435, 1 hour HGF treatment

value: 1 hr


title: CD8SP thymocytes, rep1

source_name: CD4-CD8+TCRb(hi) thymocytes

value: CD4-CD8+TCRb(hi) thymocytes


title: SKOV3


title: CD4SP thymocytes, rep2


title: CD8SP thymocytes, rep2


title: AVG_Signal-H1_1

description:
H1_1
MDA-MB-435 treated with HGF for 1 hour.


title: CD8SP thymocytes, rep3


title: AVG_Signal-H24_1

description:
H24_1
MDA-MB-435 treated with HGF for 24 hours.


title: OVCAR3


title: DP thymocytes, rep3

source_name: CD4+CD8+ thymocytes

value: CD4+CD8+ thymocytes


title: CD4SP thymocytes, rep3


title: AVG_Signal-H6_2

description:
H6_2
MDA-MB-435 treated with HGF for 6 hours.

source_name: MDA-MB-435, 6 hour HGF treatment

value: 6 hrs


title: AVG_Signal-H6_1

description:
H6_1
MDA-MB-435 treated with HGF for 6 hours.


title: C8161


title: AVG_Signal-B4_2

description:
B4_2
MDA-MB-435 transduced with integrin B4.

value: integrin Beta4


title: 231MFP

value: aggressive


title: AVG_Signal-WT_1

description:
WT_1
MDA-MB-435 untreated.

source_name: MDA-MB-435, WT


title: AVG_Signal-WT_2

description:
WT_2
MDA-MB-435 untreated.


title: DP thymocytes, rep2


title: MCF7


title: AVG_Signal-B4_1

description:
B4_1
MDA-MB-435 transduced with integrin B4.


title: H24_1

description:
4_sc2
MDA-MB-435 treated with HGF for 24 hours.

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol.

data_processing: RMA from Bioconductor affy package.

label_protocol: cRNA synthesis and labeling were performed using standard Affymetrix protocols.

extract_protocol: RNA extraction was performed using Trizol plus RNA purification kit (Invitrogen). RNA qualitative and quantitative assessment was performed using the Bioanalyzer 2100 (Agilent Technologies).


title: H24_2

description:
10_sc2
MDA-MB-435 treated with HGF for 24 hours.


title: PIK3CA.GDC0941.3

city: South San Francisco

first: Peter

last: Haverty

address: 1 DNA Way

department: Bioinformatics

institute: Genentech, Inc.

description: no additional information

hyb_protocol: Affymterix protocol for hyb and wash on Fludics 450

scan_protocol: Affymetrix protocol for GeneChip scanner 3000

data_processing: Data were processed using a program that implemented the recommendations of Choe, et al., Genome Biology, 2005 (PMID: 15693945). Background correction was performed as in the Affymetrix MAS 5.0 application. Probe-level normalization was performed using Quantile Normalization as in the RMA method. Perfect Match and Mismatch probes were contrasted as in the Affymetrix MAS 5.0 application. Multiple probes for each probeset were summarized using the median polish method from the RMA method. These summarized metrics where then normalized using LOESS.

label_protocol: Biotin labeled cRNA using an IVT kit

extract_protocol: RNA obtained using TrizolLS method.

tag: agent

value: GDC-0941 (PI3K inhibitor)


title: PIK3CA.DMSO.2

description: no additional information

value: DMSO


title: H6_1

description:
3_sc2
MDA-MB-435 treated with HGF for 6 hours.


title: DN thymocytes, rep3

source_name: CD4-CD8-TCRb- thymocytes

value: CD4-CD8-TCRb- thymocytes


title: DN thymocytes, rep2


title: PIK3CA.GDC0941.2

description: no additional information


title: B4_2

description:
Mock_B4_rep2_sc2
MDA-MB-435 transduced with integrin B4.


title: H1_1

description:
2_sc2
MDA-MB-435 treated with HGF for 1 hour.


title: PIK3CA.DMSO.3

description: no additional information


title: H6_2

description:
9_sc2
MDA-MB-435 treated with HGF for 6 hours.


title: right ventricle sham, rep4

city: Oslo

first: Ståle

last: Nygård

address: Institute for Experimental Medical Research, Oslo University Hospital - Ulleval

country: Norway

institute: University of Oslo

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

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

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

label: phycoerythrin

source_name: right ventricle sham, rep4

label_protocol: According to standard Affymetrix protocol (FS450_00007).

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

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

tag: gender

value: male

value: 6-8 weeks

value: right ventricle myocardium

tag: sample type

value: sham operated


title: DP thymocytes, rep1


title: DN thymocytes, rep1


title: WT_2

description:
7_sc2
MDA-MB-435 untreated.

value: melanoma

tag: treatment


title: B4_1

description:
Mock_B4_rep1_sc2
MDA-MB-435 transduced with integrin B4.


title: PIK3CA.GDC0941.1

description: no additional information


title: right ventricle sham, rep3

source_name: right ventricle sham, rep3

tag: tissue


title: Female ZDF rats vs male ZDFrats array 13

city: Stockholm

first: Carolina

last: Gustavsson

address: CMM L8:01

department: Molecular medicine and surgery

country: Sweden

institute: Karolinska institutet

description: Biological replicate 3 of 4.

hyb_protocol: Cy3- and Cy5 labelled samples were purifyed and mixed before addition of a hybridization buffer and added to respectively array for 18h of hybridization. After hybridization, the slides were washed multiple times, all according to the Pronto! Plus systems and the manufacturer´s instructions (Corning and Promega).

scan_protocol: Scanning was performed using a Genepix 4200A scanner (Axon). Images were quantified using Genepix 6.0 software (Axon).

data_processing: Background was subtracted using the in-house Easy Filter software. The data was normalized by the LOWESS method using the R language. The normalized data was finally statistically analyzed using SAM.

organism: Rattus norvegicus

source_name: Liver from female Zucker diabetic fatty rat

label_protocol: 5µg of total RNA was used for a first strand cDNA synthesis of each sample, labelled with either Cy3- or Cy5-dCTP (we used dye-swap technique wich was corrected after final result normalization). The microarray experiment was performed using the Pronto! Plus systems according to the manufacturer´s instructions (Corning and Promega).

extract_protocol: Total RNA was extracted from frozen livers using SV total RNA extraction kit (Promega) following manufacturer's instructions.

tag: sex

value: Female

value: 13-weeks old

value: Liver

value: Zucker diabetic fatty rat (ZDF/Gmi™-fa)

source_name: Liver from male ZDF rat


title: H1_2

description:
8_sc2
MDA-MB-435 treated with HGF for 1 hour.

value: hepatocyte growth factor (HGF)

value: 1 hr


title: WT_1

description:
1_sc2
MDA-MB-435 untreated.


title: right ventricle sham, rep2

source_name: right ventricle sham, rep2


title: WT.GDC0941.3

description: no additional information

value: WT


title: Control vs. Mybbp1a Knockdown C2C12 Cell Replicate 1

city: Kwei-San, Tao-Yuan

first: Bertrand

last: Tan

address: 259 Wen-Hwa 1st Road

department: Department of Biomedical Sciences

country: Taiwan

institute: Chang Gung University

description:
Biological replicate 1 of 2. Stable clones of C2C12 cells ectopically expressing either control or Mybbp1a-targeting shRNA. Comparative gene expression profiling of these two samples.
Ctrl vs knockdown-rep1
Raw data file: Mybbp1a-rep1.txt

hyb_protocol: Samples were applied to microarrays enclosed in Agilent microarray hybridization chambers. Hyrbidization protocol: Agilent Two-color Microarray-Based Gene Expression Analysis v5.

scan_protocol: Scanned on an Agilent Microarray Scanner. Images were quantified using Agilent Feature Extraction Software (version 9.5.3.1).

data_processing: Agilent Feature Extraction Software (v 9.5.3.1) was used for image analysis and quantitation. Background method: Spatial Detrend Surface Value. Signal measurement method: Density-Mean background. Normalization method: Rank consistency linear LOWESS normalization.

source_name: Mybbp1a Knockdown C2C12 Stable Clones

label_protocol: 0.5 µg of total RNA were labeled using the Agilent Quick Amp Labeling Kit, with Cy3-CTP or Cy5-CTP as the label.

growth_protocol: Mouse C2C12 myoblast cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM, Invitrogen) supplemented with 20% heat-inactivated fetal bovine serum (FBS, Invitrogen) and 100 U/ml penicillin and streptomycin solution (Invitrogen) (GM), at subconfluent densities.

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

tag: developmental stage

value: adult

value: leg muscle

source_name: Control Knockdown C2C12 Stable Clones


title: Female ZDF rats vs male ZDFrats array 10

description: Biological replicate 2 of 4.


title: Male ZDF rats vs Female ZDFrats array 9

description: Biological replicate 1 of 4.

source_name: Liver from male Zucker diabetic fatty rat rat

value: Male

source_name: Liver from female ZDF rat


title: right ventricle, pulmonary banding, rep5

tag: genotype

value: pulmonary banding


title: Male ZDF rats vs Female ZDFrats array 14

description: Biological replicate 4 of 4.


title: Control vs. Mybbp1a Knockdown C2C12 Cell Replicate 2

description:
Biological replicate 2 of 2. Stable clones of C2C12 cells ectopically expressing either control or Mybbp1a-targeting shRNA. Comparative gene expression profiling of these two samples.
Ctrl vs knockdown-rep2
Raw data file: Mybbp1a-rep2.txt

tag: cell line


title: WT.GDC0941.2

description: no additional information

value: GDC-0941 (PI3K inhibitor)


title: right ventricle, pulmonary banding, rep4

value: male


title: Female ZDF rats on HFD vs female ZDFrat on SDarray 15

description: Biological replicate 3 of 4.

tag: strain

tag: diet

value: HFD

source_name: Liver from female ZDF rat on SD

value: SD


title: maDCs

first: Xuebin

last: Qu

address: 5 Dongdansantiao

institute: Institute of Basic Medical Sciences & School of Basic Medicine

description: Gene expression of purified maDCs

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole mouse Genome Oligo Microarrays for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565AA) for array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: maDCs

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

growth_protocol: BM mononuclear cells were prepared from BALB/C mouse femur BM suspensions by depletion of red cells and then cultured  in PRMI-1640 medium supplemented with 10% FCS, 2 mM L-glutamine, 10 ng/mL GM-CSF, and 5 ng/mL IL-4. For imDCs, nonadherent cells were gently washed out on day 4, and the remaining loosely adherent cell clusters were collected and purified by anti-CD11c micromagnetic beads. Purified imDCs cultured for a further 4 to 5 days under the stimulation of 10 ng/mL bacterial lipopolysaccharide were used as maDCs. For sDCs, hematopoietic progenitor cells were enriched from bone marrow cells by depleting lineage-specific cells. In brief, an EasySep mouse hematopoietic progenitor enrichment kit was used to deplete lineage-specific cells. When the HPCs reached 50% confluence, they were seeded onto Sca-1+CD117-Lin- MSC monolayers. Lipopolysaccharide was added on day 4. SDCs were formed on day 9.

extract_protocol: RNA was prepared using Trizol (Invitrogen) and then purified with RNeasy® Mini Kit (Qiagen) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies).

value: BALB/C


title: sDCs

description: Gene expression of purified sDCs

source_name: sDCs


title: WT.DMSO.3

description: no additional information

value: DMSO


title: right ventricle, pulmonary banding, rep2

value: 6-8 weeks

value: right ventricle myocardium


title: Female ZDF rats on SD vs female ZDFrat on HFDarray 16

description: Biological replicate 4 of 4.

value: Female

value: 13-weeks old

value: Liver

source_name: Liver from female ZDF rat on HFD


title: Female ZDF rats on SD vs female ZDFrat on HFDarray 11

description: Biological replicate 1 of 4.

value: Zucker diabetic fatty rat (ZDF/Gmi™-fa)


title: WT.DMSO.2

description: no additional information

value: WT


description: Gene expression of purified neutralizing antibody-IL-10-treated sDCs

treatment_protocol: For neutralizing antibody-IL-10-treated sDCs, a neutralizing antibody for IL-10 (10 μg/ml) was added every two days into the coculture medium.


title: WT.GDC0941.1

description: no additional information


title: slide111_OPU4_Cy3vsMIV2_Cy5

status: Public on Aug 09 2011

city: Nouzilly

first: Svetlana

last: UZBEKOVA

address: PRC INRA

country: France

institute: INRA

description:
CC_VITROvsVIVO_sample7
Gene expression in cow cumulus cells that entouring the oocytes which have undergone maturation (metaphase II oocytes awaiting fertilization) and are developmpentally fully competent. In vivo matures (OPU) cumulus  were collected by ovum pick-up, in vitro matured cumuluscells  (MIV) were collected after 22h of in vitro culture in TCM199+EGF+LH+FSH

hyb_protocol: Slides (lot 290) were prehybridised in 3.5 X SSC, 0.1% SDS, and 1% BSA, for 30 minutes at 50°C and washed with water. 700 ng of each Cy3- and Cy5-labelled sample were hybridized on microarray. Hybridisation was performed at 60°C for 20 hours using Agilent’s DNA Microarray Hybridisation Oven and buffers (Agilent Technologies).  Slides were washed all at room temperature for 5 minutes under orbital agitation as follows: twice in [2× SSC, 0.1% SDS] solution, twice in [0.5× SSC, 0.1% SDS] solution, twice in [0.1× SSC, 0.1% SDS] solution, 3 times in [0.1X SSC] solution and finally 1 minute in ultra pure water. After the post-hybridisation washes slides were finally dried under neutral gas before scan.

scan_protocol: Microarrays were scanned at 10 µm pixel resolution using an Agilent scanner (Agilent Technologies).

data_processing: Quantitative data acquisition was realized using GenePix Pro 6.0 (Axon Molecular Devices, Sunnyvale, CA, USA). Lowess normalized log2 ratio (MIV/OPU) was calculated using Anapuce R package.

organism: Bos taurus

label_protocol: 200 ng of each RNA samples were labelled with Cy3 or Cy5 dyes (GE Healthcare Europe) using the SuperScript Indirect cDNA Amplification System (Invitrogen Life Technologies, France)03/08/2011  Labelled aRNA yield and frequencies of dye incorporation were estimated by measuring the absorbance at 260 nm, 550 nm and 650 nm on a Nanodrop spectrophotometer (Nyxor Biotech).

growth_protocol: Montbeliald adult non-lactating cows were used for sampling of mature COC (cumulus-oocyte complexes) after basic superovulation protocol. Adult cows of variable races at ages were used for recovery of immature COC, which were then matured during 22h in enriched TCM199 medium (Sigma).

extract_protocol: Total RNA was extracted using TRIzol reagent (Invitrogen, Cergy Pontoise, France). RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Cumulus cells were separated from the oocytes in TCM199 culture medium (Sigma), washed in PBS and kept in TriZol reagent at -80°C prior to extraction.

tag: breed

value: Montbeliald adult non-lactating cow

value: ovulatory follicles

tag: follicular maturation stage

value: mature metaphase-II oocyte

tag: cell type

value: Cumulus cells


title: PO4 T48 Kb1

city: Charleston

first: Frances

middle: M

last: Van Dolah

state: SC

address: 219 Fort Johnson Rd

institute: Marine Biotoxins Program, NOAA Center for Coastal Environmental Health and Biomolecular Research

hyb_protocol: 480 ng of Cy3 labeled targets were hybridized to the array for 17 hours at 60°C.  After hybridization, arrays were washed according to the manufacturer’s protocol (Agilent, Santa Clara, CA).

scan_protocol: Microarrays were imaged using an Agilent microarray scanner using extended dynamic range scanning

data_processing: Images and normalized intensity data are generated by Agilent Feature Extraction version 9.5.3.1

organism: Karenia brevis

source_name: Karenia brevis, deplete, 48 h post-P-addition

label_protocol: Total RNA (600 ng) was amplified and labeled with Cy3 dye using a low input linear amplification kit (Agilent, Santa Clara, CA).  The amplified, labeled RNA was quantified using a NanoDrop ND-1000.

growth_protocol: Karenia brevis, Wilson isolate, was grown in 1 L batch cultures in autoclaved, 20 µm filtered seawater at 36 ‰ enriched with f/2 medium (modified as noted in the treatment protocol), at 25 °C  on a 16 h:8 h light:dark cycle with illumination from cool white lights at 150 µE m-2 sec-1

extract_protocol: Three replicate cultures at each time point were independently harvested by centrifugation.  Three cultures grown in f/2 media and 3 cultures grown in 0.1 µM PO4 were also harvested at T0. Total RNA from each sample was prepared using TriReagent.  Following precipitation in isopropanol, the RNA was resuspended and purified using a Qiagen RNeasy column.  Total RNA was quantified using a NanoDrop ND-1000 and qualified on an Agilent 2100.

treatment_protocol: At time zero (T0) 168 µM PO4 was added to stationary phase (Day 12) cultures grown in 0.1 µM PO4 and RNA was extracted at 1, 4, 24, and 48 h post-addition.

tag: isolate

value: Wilson

tag: [po4] for growth

tag: [po4] added on day 12

tag: time  point (h post-p- addition sample was collected)


title: slide112_OPU4_Cy5vsMIV2_Cy3

description:
CC_VITROvsVIVO_sample8
Gene expression in cow cumulus cells that entouring the oocytes which have undergone maturation (metaphase II oocytes awaiting fertilization) and are developmpentally fully competent. In vivo matures (OPU) cumulus  were collected by ovum pick-up, in vitro matured cumuluscells  (MIV) were collected after 22h of in vitro culture in TCM199+EGF+LH+FSH


title: slide110_OPU1_Cy5vsMIV3_Cy3

description:
CC_VITROvsVIVO_sample6
Gene expression in cow cumulus cells that entouring the oocytes which have undergone maturation (metaphase II oocytes awaiting fertilization) and are developmpentally fully competent. In vivo matures (OPU) cumulus  were collected by ovum pick-up, in vitro matured cumuluscells  (MIV) were collected after 22h of in vitro culture in TCM199+EGF+LH+FSH


title: imDCs

description: Gene expression of purified imDCs

source_name: imDCs


title: right ventricle, pulmonary banding, rep3

tag: gender

value: male

tag: age

value: pulmonary banding


title: PO4 T24 Kb14

source_name: Karenia brevis, deplete, 24 h post-P-addition


title: WT.DMSO.1

description: no additional information

tag: agent


title: right ventricle sham, rep1

source_name: right ventricle sham, rep1

tag: tissue

tag: sample type

value: sham operated


title: Female ZDF rats on SD vs female ZDFrat on HFDarray 12

description: Biological replicate 2 of 4.

tag: sex

value: SD

value: HFD


title: slide88_OPU2_Cy5vsMIV4_Cy3

description:
CC_VITROvsVIVO_sample4
Gene expression in cow cumulus cells that entouring the oocytes which have undergone maturation (metaphase II oocytes awaiting fertilization) and are developmpentally fully competent. In vivo matures (OPU) cumulus  were collected by ovum pick-up, in vitro matured cumuluscells  (MIV) were collected after 22h of in vitro culture in TCM199+EGF+LH+FSH


title: PO4 T24 Kb11


title: PO4 T48 Kb20


title: PO4 T24 Kb34


title: slide109_OPU3_Cy3vsMIV1_Cy5

description:
CC_VITROvsVIVO_sample1
Gene expression in cow cumulus cells that entouring the oocytes which have undergone maturation (metaphase II oocytes awaiting fertilization) and are developmpentally fully competent. In vivo matures (OPU) cumulus  were collected by ovum pick-up, in vitro matured cumuluscells  (MIV) were collected after 22h of in vitro culture in TCM199+EGF+LH+FSH


title: slide347_OPU1_Cy3vsMIV3_Cy5

description:
CC_VITROvsVIVO_sample5
Gene expression in cow cumulus cells that entouring the oocytes which have undergone maturation (metaphase II oocytes awaiting fertilization) and are developmpentally fully competent. In vivo matures (OPU) cumulus  were collected by ovum pick-up, in vitro matured cumuluscells  (MIV) were collected after 22h of in vitro culture in TCM199+EGF+LH+FSH


title: slide107_OPU2_Cy3vsMIV4_Cy5

description:
CC_VITROvsVIVO_sample3
Gene expression in cow cumulus cells that entouring the oocytes which have undergone maturation (metaphase II oocytes awaiting fertilization) and are developmpentally fully competent. In vivo matures (OPU) cumulus  were collected by ovum pick-up, in vitro matured cumuluscells  (MIV) were collected after 22h of in vitro culture in TCM199+EGF+LH+FSH


title: PO4 T48 Kb23


title: slide106_OPU3_Cy5vsMIV1_Cy3

description:
CC_VITROvsVIVO_sample2
Gene expression in cow cumulus cells that entouring the oocytes which have undergone maturation (metaphase II oocytes awaiting fertilization) and are developmpentally fully competent. In vivo matures (OPU) cumulus  were collected by ovum pick-up, in vitro matured cumuluscells  (MIV) were collected after 22h of in vitro culture in TCM199+EGF+LH+FSH


title: PO4 T0 Kb30

source_name: Karenia brevis, deplete, 0 h

value: 0 µM


title: PIK3CA.DMSO.1

description: no additional information

tag: genotype

value: DMSO


title: PO4 T1 K13

source_name: Karenia brevis, deplete, 1 h post-P-addition


title: PO4 T1 Kb16


title: right ventricle, pulmonary banding, rep1

value: 6-8 weeks

value: right ventricle myocardium


title: PO4 T4 Kb36

source_name: Karenia brevis, deplete, 4 h post-P-addition


title: PO4 T4 Kb31


title: PO4 T0 Kb5


title: PO4 T0 Kb29


title: PO4 T1 Kb21


title: PO4 T4 Kb7


title: WT_uninduced_8h_groupB

city: Wageningen

first: Selahattin

last: Danisman

address: Droevendaalsesteeg 1

department: Business Unit Bioscience

country: Netherlands

institute: Plant Research International

hyb_protocol: WT double stranded target assay protocol (without amplification)

scan_protocol: Affymetrix GeneChip Scanner 3000G

data_processing: Data was analyzed according to Naouar et al. 2008 (DOI: 10.1111/j.1365-313X.2008.03662.x) using R and Affymetrix library files. Data was processed using global normalizatin (RMA).

organism: Arabidopsis thaliana

growth_protocol: plants were grown for 14 days at LD on 2.3g/L MS+6g/L Agar, then, plants were treated and above-ground material was harvestd for taret gene analysis

extract_protocol: QIAGEN RNeasy RNA isolation kit protocol

treatment_protocol: seedlings were grown on nylon meshes above a lowly concentrated MS-Agar medium. For Dexaemthasone treatment, nylon meshes with plants were transferred to liquid MS-medium containing 10µM Dexamethasone and 10µM Cycloheximide.

tag: genotype/variation

value: wild type

tag: ecotype

tag: induction time

value: 0 h


title: f/2 T0 Kb4

source_name: Karenia brevis, replete, 0 h

value: 36 µM


title: f/2 T0 Kb6


title: NO3 T48 Kb10

data_processing: Images were extracted with Agilent Feature Extraction version 9.5.3.1

source_name: Karenia brevis, deplete, 48 h post-N-addition

extract_protocol: Three replicate cultures at each time point were independently harvested by centrifugation.  Three cultures grown in f/2 media and 3 cultures grown in 10 µM NO3 were also harvested at T0. Total RNA from each sample was prepared using TriReagent.  Following precipitation in isopropanol, the RNA was resuspended and purified using a Qiagen RNeasy column.  Total RNA was quantified using a NanoDrop ND-1000 and qualified on an Agilent 2100.

treatment_protocol: At time zero (T0) 155 µM NO3 was added to stationary phase (Day 9) cultures grown in 10 µM NO3 and RNA was extracted at 4, 12, 24, and 48 h post-addition.

tag: [no3] for growth

value: 10 µM

tag: [no3] added on day 9

tag: h post-n- addition sample was collected


title: NO3 T48 Kb8


title: NO3 T24 Kb1

source_name: Karenia brevis, deplete, 24 h post-N-addition


title: NO3 T24 Kb13


title: NO3 T24 Kb5


title: NO3 T48 Kb6


title: NO3 T12 Kb4

source_name: Karenia brevis, deplete, 12 h post-N-addition


title: NO3 T12 Kb11


title: NO3 T12 Kb3


title: NO3 T4 Kb12

source_name: Karenia brevis, deplete, 4 h post-N-addition


title: NO3 T4 Kb14


title: WT_uninduced_8h_groupA

label_protocol: WT double stranded target assay protocol (without amplification)


title: f/2 T0 Kb5

tag: isolate


title: strain CJM569-Shake-flask 2% ethanol exponential phase

city: Delft

first: Jean-Marc

last: Daran

address: Julianalaan 67

department: Department of Biotechnology

institute: Delft University of Technology

hyb_protocol: Acquisition and quantification of the Affymetrix yeast S98 array images as well as primary data analysis were performed using the Affymetrix GeneChip Operating Software (GCOS) 2.1.

scan_protocol: Scanning of the Affymetrix Genechip® microarrays was performed with The Affymetrix scanner 3000 following Affymetrix instructions

data_processing: Data were processed with the GeneChip® Operating Software version 1.2 (GCOS 1.2) using Affymetrix default analysis settings and global scaling as normalization method

organism: Saccharomyces cerevisiae

source_name: Shake flask 2% ethanol time t 0

label_protocol: cDNA synthesis, cRNA synthesis and labelling, as well as array hybridization were performed as described (De Nicola et al 2007 AEM,73, 7680-7692 )

growth_protocol: CJM569 (MATa his3-11,15 ura3-1, 112 trp1-1 can1-100 tpk1::URA3 tpk2::HIS3 tpk3::TRP1 msn2::HIS3  msn4::TRP1) was grown at 30oC in minimal media (YNB with 0.1% sodium glutamate as nitrogen source) with 2% ethanol or 4% glucose + 2% ethanol as carbon sources and collected at the early exponential phase of growth. Samples were also taken after adding glucose (end concentration 4%) to cultures in 2% ethanol and incubating them at 30oC for 30min

extract_protocol: The RNA to be used for the microarrays was extracted using the hot-phenol method

treatment_protocol: Yeast cells were collected by rapid filtration (Belinchón et al 2004) and stored at  -70 oC until use

tag: time point

tag: treatment

value: Shake flask 2% ethanol time t 0

tag: strain


title: strain CJM569-Shake-flask 2% ethanol +4%glucose pulse 30 min

source_name: Shake flask 2% ethanol +4% glucose pulse  time t+ 30 min

value: 30 min


title: TCP20-GR_uninduced_8h_groupB

value: TCP20-GR in tcp20 mutant background


title: TCP20-GR_uninduced_8h_groupA


title: NO3 T4 Kb7


title: WT_induction_8h_groupB

value: 8 h


title: WT_induction_8h_groupA


title: TCP20-GR_induction_8h_groupB


title: TCP20-GR_induction_8h_groupA


title: NO3 T0 Kb15


title: strain CJM567-Shake-flask 2% ethanol +4%glucose pulse 30 min - 2

data_processing: Data were processed with the GeneChip® Operating Software version 1.2 (GCOS 1.2) using Affymetrix default analysis settings and global scaling as normalization method.

growth_protocol: Yeasts (CJM567 (MATa can1-100 TPK1 TPK2 TPK3), CJM569 (MATa his3-11,15 ura3-1, 112 trp1-1 can1-100 tpk1::URA3 tpk2::HIS3 tpk3::TRP1 msn2::HIS3  msn4::TRP1), CJM571 (MATa his3-11,15 leu2-3, 112 ura3-1 trp1-1 can1-100 tpk1::URA3 tpk2::HIS3 tpk3::TRP1 yak1::LEU2) were grown at 30oC in minimal media (YNB with 0.1% sodium glutamate as nitrogen source) with 2% ethanol or 4% glucose + 2% ethanol as carbon sources and collected at the early exponential phase of growth. Samples were also taken after adding glucose (end concentration 4%) to cultures in 2% ethanol and incubating them at 30oC for 30min

value: Shake flask 2% ethanol +4% glucose pulse  time t+ 30 min


title: strain CJM571-Shake-flask 2% ethanol +4%glucose pulse 30 min - 1


title: NO3 T0 Kb9


title: strain CJM571-Shake-flask 2% ethanol exponential phase - 2


title: strain CJM571-Shake-flask 2% ethanol exponential phase - 1


title: strain CJM567-Shake-flask 2% ethanol exponential phase - 2


title: NO3 T0 Kb2


title: f/2 T0 Kb2


title: strain CJM567-Shake-flask 2% ethanol +4%glucose pulse 30 min - 1


title: strain CJM567-Shake-flask 2% ethanol exponential phase - 1


title: f/2 T0 Kb1


title: f/2 T0 Kb3


title: Control Group Rep5

status: Public on Aug 08 2011

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

description: Control Group Rep5

hyb_protocol: After a two-hour reaction, 1.5 μg of purified, Cy3-labeled cRNA were hybridized to an oligonucleotide Whole Mouse Genome Microarray (4x44K, Agilent Technologies) for 17 hours at 65˚C. Post processing washes were done according to the Agilent Technologies SSPE protocol (v2.1), replacing wash solution 3 by acetonitril, followed by immediate scanning.

scan_protocol: Slides were scanned using an Agilent G2565BA scanner, and data were extracted using the Feature Extraction software version 9.5.3.1 (Agilent Technologies).

data_processing: Median signal intensities from the Feature Extraction Software were normalized using the VSN method from R package “limma”.

source_name: Naive #5

label_protocol: 600 ng of total RNA were reverse-transcribed and amplified, thereby incorporating Cyanine 3-CTP nucleotides, using the Low RNA Input Fluorescent Linear Amplification Kit according to the manufacturer's recommendations (Agilent One-Color Microarray-Based Gene Expression Analysis, protocol version 5.5, February 2007; Agilent Technologies).

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen, Gaithersburg, MD).  Nucleic acid quantity, quality and purity were determined using a spectrophotometer (Nanodrop, Rockland, DE) and a 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).  Only RNA samples with a RNA integrity number between 9.0 and 10.0 were considered for further analysis.

treatment_protocol: We employed mice to investigate fear extinction in the hippocampus-dependent contextual fear conditioning paradigm. To this end, male C57BL/6J mice were exposed to the fear conditioning box (context) followed by an electric foot-shock which elicits the acquisition of conditioned contextual fear. For extinction training animals were repeatedly reexposed to the conditioned context on consecutive days (24h interval) without receiving the footshockagain (extinction trial, E). This procedure eventually results in the decline of the aversive freezing behavior. Mice that were exposed to the conditioning context without receiving fear conditioning training served as control groups.

value: hippocampus

tag: experimentor

value: ENI Gö

value: Control Group


title: Control Group Rep3

description: Control Group Rep3

source_name: Naive #3


title: Control Group Rep2

description: Control Group Rep2

source_name: Naive #2


title: 1h after extinction trial low freezing Rep4

value: 1h after extinction trial low freezing


title: 1h after extinction trial low freezing Rep3


title: 1h after first extinction trial Rep5

description: 1h after first extinction trial Rep5

value: 1h after first extinction trial


title: 1h after extinction trial low freezing Rep5


title: 1h after extinction trial low freezing Rep2


title: 1h after first extinction trial Rep3

description: 1h after first extinction trial Rep3


title: Spyogenes_M49_ strain 591_BHI_0.4_repl2

status: Public on Aug 06 2011

city: Rostock

first: Nadja

last: Patenge

address: Schillingallee 70

department: Institute of Medical Microbiology, Virology and Hygiene

institute: University of Rostock

hyb_protocol: All hybridization and detection steps were done using the febit’s Geniom RT Analyzer (febit biomed, Heidelberg, Germany). Hybridizations were performed overnight (16 hours) at 42°C. Subsequently, biotin was detected with streptavidin-phycoerythrin (SAPE). A signal amplification step was added using biotinylated anti-streptavidin antibodies (Vector Laboratories, Burlingame, CA, USA) and a second incubation with SAPE (Invitrogen, Carlsbad, CA, USA).

scan_protocol: Signal detection using the appropriate filter set (570 nm) of the Geniom device employed the autoexposure function of the Geniom software.

data_processing: Genedata Expressionist software (version 5.3) was used for data processing. Raw data were Quantile normalized applying standard settings  (Averaging: Logarithmic Mean) of Expressionist Analyst.

organism: Streptococcus pyogenes M49 591

source_name: Spyogenes_M49_ strain 591_BHI_0.4

label_protocol: The RNA was pelleted by centrifugation, dissolved in nuclease-free water, and labelled using the Ambion mirVana labeling Kit (Applied Biosystems, Foster City, CA) following the manufacturer’s instructions.

growth_protocol: Cells cultured in Brain-Heart-Infusion medium (BHI, Invitrogen), at 37°C under a 5% CO2 20% O2 atmosphere, collected at described OD

extract_protocol: Total bacterial RNA from cultures grown to corresponding OD was isolated using the FastRNA ProBlue Kit from MP Biomedicals as outlined in the protocol provided by the manufacturer. The purified total RNA was digested with DNase to remove remaining traces of chromosomal DNA. The RNA preparation was treated with 10 U of DNase for 30 min at 37°C. The enzyme was subsequently heat inactivated at 72°C for 5 min. 5 µg of total RNA were fractionated using the Ambion FlashPAGE Fractionator, Ambion® FlashPAGE Precats Gels, and the Ambion® FlashPAGE™ Buffer Kit, following the manufacturer’s instructions. To collect a fraction of RNA molecules <200 nucleotides, the protocol was slightly modified: the running time was increased from 12 min to up to 45 min at 75 Volt. The fraction of small RNAs was ethanol-precipitated over night at -20°C.

treatment_protocol: Harvested by centrifugation

tag: growth phase

value: exponential


title: Control Group Rep4

description: Control Group Rep4

source_name: Naive #4


title: Control Group Rep1

description: Control Group Rep1

source_name: Naive #1


title: 1h after first extinction trial Rep2

description: 1h after first extinction trial Rep2


title: 1h after first extinction trial Rep4

description: 1h after first extinction trial Rep4


title: 1h after extinction trial low freezing Rep1


title: Spyogenes_M49_ strain 591_BHI_1.2_repl1

source_name: Spyogenes_M49_ strain 591_BHI_1.2

value: stationary


title: Spyogenes_M49_ strain 591_THY_1.2_repl2

source_name: Spyogenes_M49_ strain 591_THY_1.2

growth_protocol: Cells cultured in Todd-Hewitt broth supplemented with 0.5% yeast extract (THY; Invitrogen), at 37°C under a 5% CO2 20% O2 atmosphere, collected at described OD


title: Spyogenes_M49_ strain 591_BHI_0.4_repl1


title: Spyogenes_M49_ strain 591_THY_1.2_repl1


title: Spyogenes_M49_ strain 591_BHI_1.2_repl2


title: Spyogenes_M49_ strain 591_THY_0.4_repl2

source_name: Spyogenes_M49_ strain 591_THY_0.4


title: 1h after first extinction trial Rep1

description: 1h after first extinction trial Rep1


title: PLC5 AR ChIP-chip Slide 2

type: genomic

city: Hong Kong

first: Hai

last: Feng

address: The Chinese University of Hong Kong

country: Hong Kong

institute: The Chinese University of Hong Kong

description: Agilent ChIP-on-chip set 1 of 2

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent G2505B scanner.

data_processing: Agilent Feature Extraction Software (9.5.3.1) was used for background subtraction and LOWESS normalization log2 ratio (test/reference).

molecule: genomic DNA

source_name: PLC5 cells immunoprecipitated

label_protocol: DNA were amino-allyl labelled using randomly-primed, Klenow-based extension protocol. Cy5/3 dye was then incorporated into the DNA using in-direct labeling by incubating the dye with DNA for 3 hours.

growth_protocol: The 2 HCC cell lines were maintained in DMEM supplemented with 10% FBS.

extract_protocol: ChIP assays were performed as described previously (Lee et al. Nat Protoc 2006;1:729-748). IP and input DNA were then purified with standard phenol/chloroform method.

treatment_protocol: No treatment was performed. AR target genes in normal condition were identified.

tag: cell line

tag: antibody

value: anti-AR

tag: vendor

value: Millipore/Upstate

tag: catalogue #

source_name: PLC5 cells input


title: mLiver_1w_cont_rep1, 2 and 3

city: Tokyo

first: Takashi

last: Obama

address: 1-5-8, Hatanodai

department: Biological Chemistry

country: Japan

institute: Showa University, School of Pharmacy

description: Gene expression after 1 week in control diet-fed mouse liver

hyb_protocol: Cy3-labelled cRNA (0.5 ug; specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing Agilent fragmentation buffer and Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x GEx Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (G4122F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed for 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and for 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting for 4x44k array slides (Scan Area 71x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v5_91 or GE1-v5_95 and Grid: 014868_D_20060807).  Data were analyzed with GeneSpring GX 7.3 software. First, normalization was performed as follows: 1:Data transformation: Set measurement less than 0.01 to 0.01, 2:Per Chip; Normalize to median or percentile, 3:Per Gene; Normalize to specific samples (normal chow). Second, quality control was performed with Filter on Flags (chosing spots Present or Marginal” in minimum 75% of slides).

source_name: liver sample from apoE-KO mouse

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

extract_protocol: RNA was prepared using an RNeasy kit (QIAGEN, Valencia, CA) following the manufacturer's protocol. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Apo E-KO mice at 10 weeks of age were fed either normal chow (control) or the same chow containing 1.25% cholesterol ( high-Chol diet) for 1 week.

tag: genotype

value: apoE-KO

tag: tissue

value: liver

tag: gender

value: male

tag: diet

value: normal chow


title: mLiver_1w_HC_rep1, 2 and 3

description: Gene expression after 1 week in high-cholesterol diet-fed mouse liver

value: high-Chol diet


title: Spyogenes_M49_ strain 591_THY_0.4_repl1


title: Spyogenes_M49_ strain 591_CDM_1.2_repl2

source_name: Spyogenes_M49_ strain 591_CDM_1.2

growth_protocol: Cells cultured in chemical defined medium (CDM), at 37°C under a 5% CO2 20% O2 atmosphere, collected at described OD


title: PLC5 AR ChIP-chip Slide 1

description: Agilent ChIP-on-chip set 1 of 1


title: Huh7 AR ChIP-chip Slide 2

description: Agilent ChIP-on-chip set 1 of 2

source_name: Huh7 cells immunoprecipitated

source_name: Huh7 cells input


title: Spyogenes_M49_ strain 591_CDM_1.2_repl4


title: Spyogenes_M49_ strain 591_CDM_1.2_repl3


title: Spyogenes_M49_ strain 591_CDM_0.4_repl4

source_name: Spyogenes_M49_ strain 591_CDM_0.4


title: Spyogenes_M49_ strain 591_CDM_1.2_repl1


title: human thymus tissue, biological replicate 2

city: Brussels

first: Geert

middle: A.

last: Martens

address: Laarbeeklaan 103

department: Diabetes Research Center

institute: Vrije Universiteit Brussel

description:
Thymus_1b_A
primary human tissue w/o purification or subselection (Microarray Facility, Rigshospitalet, Copenhagen, Denmark)

hyb_protocol: After fragmentation at 94°C for 35 min in fragmentation buffer (40mM Tris, 30mM magnesium acetate, 10mM potassium acetate), the labelled cRNA was hybridized for 16h to the Affymetrix HG133A

scan_protocol: Arrays were stained with phycoerythrin-streptavidin with the Affymetrix Fluidics Station 400, and scanned in the Affymetrix GeneArray2500scanner.

data_processing: Scanned arrays were analyzed with dChip model-based expression analysis to the array with the median intensity. Using the PM-MM model with mismatch correction, a 90% confidence interval was calculated for the fold change in gene expression in each comparison, and the lower limit of this interval (LCB) was used as a measure of differential gene expression.

source_name: human thymus tissue

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

growth_protocol: For islet endocrine cells, 3 different pools of 6 µg RNA obtained from 10 human organs were collected: pool 1 (45% insulin+, from n=3 donor organs), pool 2 (65% ins+, from n=3 donor organs) and pool 3 (55% insulin+, from n=4 donor organs). Average donor age and BMI were 47±10 yrs and 26±4, respectively.  Pancreatic duct cells-enriched preparations contained 85±7% cytokeratin 19+ cells with 4±1% insulin+ cells and 6±4% glucagon+ cells and were isolated as described by Heimberg H. et al.( Diabetes 2001,49: 571-579 ).

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

treatment_protocol: Suspensions of human beta and duct cells were maintained 2-3w in culture as described ( Diabetes 2001,49: 571-579 ) with no specific treatment. Other human tissues taken post-mortem with no additional culture.

value: adult thymus


title: human thymus tissue, biological replicate 1

description:
Thymus_1a_A
primary human tissue w/o purification or subselection (Microarray Facility, Rigshospitalet, Copenhagen, Denmark)


title: human small intestine tissue, biological replicate 2

description:
Small_Instine_1b_A
primary human tissue w/o purification or subselection (Microarray Facility, Rigshospitalet, Copenhagen, Denmark)

source_name: human small intestine tissue

value: adult small intestine


title: human spleen tissue, biological replicate 1

description:
Spleen_1a_A
primary human tissue w/o purification or subselection (Microarray Facility, Rigshospitalet, Copenhagen, Denmark)

source_name: human spleen tissue

value: adult spleen


title: human spleen tissue, biological replicate 2

description:
Spleen_1b_A
primary human tissue w/o purification or subselection (Microarray Facility, Rigshospitalet, Copenhagen, Denmark)


title: human stomach tissue, biological replicate 2

description:
Stomach_1b
primary human tissue w/o purification or subselection (Microarray Facility, Rigshospitalet, Copenhagen, Denmark)

source_name: human stomach tissue

value: adult stomach


title: human stomach tissue, biological replicate 1

description:
Stomach_1a
primary human tissue w/o purification or subselection (Microarray Facility, Rigshospitalet, Copenhagen, Denmark)


title: Spyogenes_M49_ strain 591_CDM_0.4_repl3


title: Spyogenes_M49_ strain 591_CDM_0.4_repl2


title: human lung tissue, biological replicate 2

description:
Lung_1b_A
primary human tissue w/o purification or subselection (Microarray Facility, Rigshospitalet, Copenhagen, Denmark)

source_name: human lung tissue

value: adult lung


title: Huh7 AR ChIP-chip Slide 1

description: Agilent ChIP-on-chip set 1 of 1


title: human testis tissue, biological replicate 1

description:
Testis_1a_A
primary human tissue w/o purification or subselection (Microarray Facility, Rigshospitalet, Copenhagen, Denmark)

source_name: human testis tissue

value: adult testis


title: human liver tissue, biological replicate 2

description:
Liver_1b_A
primary human tissue w/o purification or subselection (Microarray Facility, Rigshospitalet, Copenhagen, Denmark)

source_name: human liver tissue

value: adult liver


title: human small intestine tissue, biological replicate 1

description:
Small_Instine_1a_A
primary human tissue w/o purification or subselection (Microarray Facility, Rigshospitalet, Copenhagen, Denmark)


title: human prostate tissue, biological replicate 1

description:
Prostata_1a_A
primary human tissue w/o purification or subselection (Microarray Facility, Rigshospitalet, Copenhagen, Denmark)

source_name: human prostate tissue

value: adult prostate


title: human testis tissue, biological replicate 2

description:
Testis_1b_A
primary human tissue w/o purification or subselection (Microarray Facility, Rigshospitalet, Copenhagen, Denmark)


title: human lung tissue, biological replicate 1

description:
Lung_1a_A
primary human tissue w/o purification or subselection (Microarray Facility, Rigshospitalet, Copenhagen, Denmark)


title: human myocardial tissue, biological replicate 1

description:
muscle heart_1a
primary human tissue w/o purification or subselection (Microarray Facility, Rigshospitalet, Copenhagen, Denmark)

source_name: human myocardial tissue

value: adult heart muscle


title: human skeletal muscle tissue, biological replicate 2

description:
muscle skeletal_1b_A
primary human tissue w/o purification or subselection (Microarray Facility, Rigshospitalet, Copenhagen, Denmark)

source_name: human skeletal muscle tissue

value: adult skeletal muscle


title: Spyogenes_M49_ strain 591_CDM_0.4_repl1

value: exponential


title: human skeletal muscle tissue, biological replicate 1

description:
muscle skeletal_1a_A
primary human tissue w/o purification or subselection (Microarray Facility, Rigshospitalet, Copenhagen, Denmark)


title: human kidney tissue, biological replicate 1

description:
Kidney_1a_A
primary human tissue w/o purification or subselection (Microarray Facility, Rigshospitalet, Copenhagen, Denmark)

source_name: human kidney tissue

value: adult kidney


title: human kidney tissue, biological replicate 2

description:
Kidney_1b_A
primary human tissue w/o purification or subselection (Microarray Facility, Rigshospitalet, Copenhagen, Denmark)


title: human liver tissue, biological replicate 1

description:
Liver_1a_A
primary human tissue w/o purification or subselection (Microarray Facility, Rigshospitalet, Copenhagen, Denmark)


title: human fetal brain tissue, biological replicate 1

description:
Fetal-Brain_1a_A
primary human tissue w/o purification or subselection (Microarray Facility, Rigshospitalet, Copenhagen, Denmark)

source_name: human fetal brain tissue

value: fetal brain


title: human fetal brain tissue, biological replicate 2

description:
Fetal-Brain_1b_A
primary human tissue w/o purification or subselection (Microarray Facility, Rigshospitalet, Copenhagen, Denmark)


title: human colon tissue, biological replicate 1

description:
Colon_1a_A
primary human tissue w/o purification or subselection (Microarray Facility, Rigshospitalet, Copenhagen, Denmark)

source_name: human colon tissue

value: adult colon


title: human colon tissue, biological replicate 2

description:
Colon_1b_A
primary human tissue w/o purification or subselection (Microarray Facility, Rigshospitalet, Copenhagen, Denmark)


title: strain CJM571-Shake-flask 2% ethanol +4%glucose pulse 30 min - 2

source_name: Shake flask 2% ethanol +4% glucose pulse  time t+ 30 min

value: 30 min


title: human cerebellum tissue, biological replicate 2

description:
Cerebellum_1b_A
primary human tissue w/o purification or subselection (Microarray Facility, Rigshospitalet, Copenhagen, Denmark)

source_name: human cerebellum tissue

value: adult cerebellum


title: PAO1, biological rep3

city: Lyngby

first: Liang

last: Yang

address: Building 301, Room 150

country: Denmark

institute: Technical University of Denmark

hyb_protocol: The labeled cDNA was hybridized on an Affymetrix P. aeruginosa PAO1 gene chip and stained on a GeneChip Fluidics Station 450.

scan_protocol: The probe arrays were finally scanned with a GeneChip Scanner 3000.

data_processing: The raw data (.cel files) were obtained using the Affymetrix GeneChip Operating System 1.4. The raw data files are preprocessed by Bioconductor using the RMA method.

label: biotin-ddUTP

organism: Pseudomonas aeruginosa

source_name: lab wild-type strain

label_protocol: The cDNA was synthezed from RNA, purified with a Qiagen PCR Purification Kit (Qiagen) and fragmented using DNase I (Promega). Fragmented cDNA was then labeled with biotinylated nucleotides at the 3' termini using labeling reagent (Affymetrix) and terminal deoxynucleotidyl transferase (Promega).

growth_protocol: P. aeruginosa strains were grown aerobically at 37 °C in LB medium starting from OD600 = 0.01 and harvested at OD600 = 0.5.

extract_protocol: RNA was extracted with an RNeasy Mini Kit (Qiagen) and transcribed to cDNA using a SuperScript III Reverse Transcriptase (Invitrogen).

treatment_protocol: Harvested cells were mixed immediately with RNAprotect Bacteria Reagent (Qiagen) and stored at −80 °C.

value: Gram-negative


title: PAO1, biological rep2


title: B38-6M isolate, biological rep3

source_name: B38 patient mucoid isolate at month 6


title: human cerebellum tissue, biological replicate 1

description:
Cerebellum_1a_A
primary human tissue w/o purification or subselection (Microarray Facility, Rigshospitalet, Copenhagen, Denmark)


title: B38-6M isolate, biological rep2


title: PAO1, biological rep1


title: B38-6M isolate, biological rep1


title: human cerebrum tissue, biological replicate 2

description:
Brain_1b_A
primary human tissue w/o purification or subselection (Microarray Facility, Rigshospitalet, Copenhagen, Denmark)

source_name: human cerebrum tissue

value: adult brain (telencephalon)


title: B38-2M isolate, biological rep3

source_name: B38 patient mucoid isolate at month 2


title: B38-2NM mutant, biological rep3

source_name: non-mucoid mutant derived from B38 patient mucoid isolate at month 2


title: B38-2NM mutant, biological rep1


title: B38-2M isolate, biological rep2


title: B38-1 isolate, biological rep3

source_name: B38 patient isolate at month 1


title: B38-2M isolate, biological rep1


title: Primary tumour region 5 PAXgene

city: Lyon cedex 08

first: Pierre

last: Martinez

address: 28 rue Laennec

institute: Cancer Research Centre of Lyon

description: Gene expression from a PAXgene primary tumour sample after 6 weeks everolimus treatment

hyb_protocol: Exon 1.0 ST Cocktail hybridization

scan_protocol: PICR scanner 3000

data_processing: The expression values of the samples were normalized using the oligo R package.

source_name: ccRCC patient1

label_protocol: Affymetrix protocol

extract_protocol: Each sample was taken from either the primary tumour or a metastatic site, divided in two pieces and one was preserved in Paxgene tissue preservative and RNA was extracted with a Paxgene kit, the second piece was snap frozen in liquid N2 and extracted with RNAeasy

tag: protocol

value: PAXgene

value: everolimus

value: primary

tag: age


title: B38-1 isolate, biological rep1


title: B38-1 isolate, biological rep2


title: Primary tumour region 4 Fresh Frozen

description: Gene expression from a fresh frozen primary tumour sample after 6 weeks everolimus treatment

value: Fresh Frozen


title: Pre-treatment kidney biopsy Fresh Frozen

description: Gene expression from a fresh frozen primary tumour sample before everolimus treatment

value: primary pre-treatment


title: B12-7 isolate, biological rep3

source_name: B12 patient isolate at month 7


title: Chestwall metastasis Fresh Frozen

description: Gene expression from a fresh frozen metastatic sample after 6 weeks everolimus treatment

value: metastasis


title: Primary tumour region 8 Fresh Frozen


title: Primary tumour region 4 PAXgene


title: human cerebrum tissue, biological replicate 1

description:
Brain_1a_A
primary human tissue w/o purification or subselection (Microarray Facility, Rigshospitalet, Copenhagen, Denmark)


title: Chestwall metastasis PAXgene

description: Gene expression from a PAXgene metastatic sample after 6 weeks everolimus treatment


title: Pre-treatment kidney biopsy PAXgene

description: Gene expression from a PAXgene primary tumour sample before everolimus treatment


title: B38-2NM mutant, biological rep2


title: Primary tumour region 8 PAXgene


title: Primary tumour region 5 Fresh Frozen


title: B12-7 isolate, biological rep1


title: B12-7 isolate, biological rep2


title: B12-4 isolate, biological rep3

source_name: B12 patient isolate at month 4


title: B12-4 isolate, biological rep2


title: B12-4 isolate, biological rep1


title: B12-0 isolate, biological rep2

source_name: B12 patient isolate at month 0


title: Colombiana

city: Athens

first: Todd

middle: A

last: Minning

state: GA

address: Rm 310 Coverdell

department: CTEGD

institute: University of Georgia

hyb_protocol: overnight at 42C using MAUI mixer, hyb buffer per Nimblegen protocol

scan_protocol: ScanArray 2000, 5 micron resolution

data_processing: Raw data generated by NimbleScan software, normalization by proprietary script ('get ratio').

organism: Trypanosoma cruzi

source_name: genomic DNA from Colombiana strain T. cruzi

label_protocol: Sonication and random-primed DNA synthesis per Nimblegen protocol

extract_protocol: DNA isolated by stardard cell lysis and phenol/chloroform extraction

value: Colombiana

source_name: genomic DNA from CL-Brener strain T. cruzi

value: CL Brener


title: Tu18 cl1

source_name: genomic DNA from Tu18 strain T. cruzi

value: Tu18 cl1


title: Tulahuen

source_name: genomic DNA from Tulahuen strain T. cruzi

value: Tulahuen


title: CL

source_name: genomic DNA from wtCL strain T. cruzi


title: B6-4 isolate, biological rep3

source_name: B6 patient isolate at month 4


title: B6-4 isolate, biological rep2


title: TEDa2 cl4

source_name: genomic DNA from TEDa2 strain T. cruzi

value: TEDa2 cl4


title: B6-4 isolate, biological rep1


title: CF333-2007 isolate, biological rep3

source_name: CF333 patient 2007 isolate


title: B12-0 isolate, biological rep1


title: B12-0 isolate, biological rep3


title: CF333-2007 isolate, biological rep2


title: B6-0 isolate, biological rep3

source_name: B6 patient isolate at month 0


title: CF333-2005 isolate, biological rep3

source_name: CF333 patient 2005 isolate


title: CF333-2007 isolate, biological rep1


title: B6-0 isolate, biological rep1


title: B6-0 isolate, biological rep2


title: TEP6 cl5

source_name: genomic DNA from TEP6 strain T. cruzi

value: TEP6 cl5


title: CF333-2003 isolate, biological rep1

source_name: CF333 patient 2003 isolate


title: CF333-2003 isolate, biological rep2


title: CF333-1997 isolate, biological rep2

source_name: CF333 patient 1997 isolate


title: CF333-2003 isolate, biological rep3


title: M78

source_name: genomic DNA from M78 strain T. cruzi


title: M5631

source_name: genomic DNA from M5631 strain T. cruzi


title: Y

source_name: genomic DNA from Y strain T. cruzi

value: Y


title: Esmeraldo

source_name: genomic DNA from Esmeraldo strain T. cruzi

value: Esmeraldo


title: CF333-1991 isolate, biological rep3

source_name: CF333 patient 1991 isolate


title: TCC

source_name: genomic DNA from TCC strain T. cruzi

value: TCC

source_name: genomic DNA from CL-Brener strain T. cruzi


title: CF333-1997 isolate, biological rep1

value: Gram-negative


title: Brazil

source_name: genomic DNA from Brazil strain T. cruzi

value: Brazil


title: CF333-2005 isolate, biological rep2


title: Montalvania

source_name: genomic DNA from Montalvania strain T. cruzi

value: Montalvania


title: PalDa cl9

source_name: genomic DNA from PalDa strain T. cruzi

value: PalDa cl9


title: CF333-2005 isolate, biological rep1


title: Sylvio X10/4

source_name: genomic DNA from Sylvio strain T. cruzi

value: Sylvio X10/4


title: CF333-1991 isolate, biological rep2


title: Chinata

source_name: genomic DNA from Chinata strain T. cruzi

value: Chinata


title: CF333-1997 isolate, biological rep3


title: CF333-1991 isolate, biological rep1


title: CF243-2002 isolate, biological rep3

source_name: CF243 patient 2002 isolate


title: CF243-2002 isolate, biological rep2


title: CF243-2002 isolate, biological rep1


title: CF173-2002 isolate, biological rep2

source_name: CF173 patient 2002 isolate


title: CF173-2002 isolate, biological rep1


title: CF173-2002 isolate, biological rep3


title: CF173-2005 isolate, biological rep1

source_name: CF173 patient 2005 isolate


title: CF173-2005 isolate, biological rep3


title: CF173-2005 isolate, biological rep2


title: CF173-1984 isolate, biological rep2

source_name: CF173 patient 1984 isolate


title: CF105-1973 isolate, biological rep1

source_name: CF105 patient 1973 isolate


title: CF114-1973 isolate, biological rep2

source_name: CF114 patient 1973 isolate


title: CF66-2008 isolate, biological rep3

source_name: CF66 patient 2008 isolate


title: CF114-1973 isolate, biological rep3


title: CF173-1984 isolate, biological rep1


title: CF105-1973 isolate, biological rep2


title: CF66-1992 isolate, biological rep2

source_name: CF66 patient 1992 isolate


title: CF105-1973 isolate, biological rep3


title: CF66-1992 isolate, biological rep3


title: CF173-1984 isolate, biological rep3


title: CF66-2008 isolate, biological rep2


title: CF66-2008 isolate, biological rep1


title: CF114-1973 isolate, biological rep1


title: CF66-1992 isolate, biological rep1


title: CF66-1973 isolate, biological rep1

source_name: CF66 patient 1973 isolate


title: CF66-1973 isolate, biological rep3


title: CF66-1973 isolate, biological rep2


title: Inflorescence_rdr2mutant_replicate3

city: No.12 Zhongguancun South Street, Haidian

first: Jun

last: Liu

state: Beijing

address: 1230 York Avenue

department: Chinese Academy of Agricultural Sciences

institute: Institute of Crop Science

description: Expression profiling of lincRNA in rdr2-1

hyb_protocol: 1.5 ug of Cy3-labelled cRNA was fragmented at 60C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to ATH lincRNA v1 array for 17 hours at 65C 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 37C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 8x15k array slides.

data_processing: Raw data of processed signal intensities are obtained by analysis using Feature Extraction Software (Agilent) with default parameters. Standard QC analysis, background normalization and quantile normalization were performed using GeneSpring GX Software (Agilent) with default parameters.

label_protocol: We performed RNA labeling, hybridization and scaning using protocols according to the Agilent's instructions. Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent).

growth_protocol: Plants of Arabidopsis thaliana were grown on sterile solid half-strength Murashige-Skoog (MS) medium or in a greenhouse under similar conditions (22°C, 16/8h photoperiod cycles).  Inflorescences with open flowers, flowers buds and some very young siliques were collected from 4 week-old WT(Col-0) and rdr2-1 plants.

extract_protocol: Total RNA was extracted and treated with DNase I using RNeasy Plant mini kit (Qiagen).

tag: ecotype

tag: genotype/variation

value: 4 weeks

tag: organ

value: Inflorescence


title: CF43-1973 isolate, biological rep3

source_name: CF43 patient 1973 isolate


title: CF43-1973 isolate, biological rep2


title: Inflorescence_rdr2mutant_replicate2


title: CF43-1973 isolate, biological rep1


title: Inflorescence_rdr2mutant_replicate1


title: Inflorescence_WT_replicate2

description: Expression profiling of lincRNA in WT

value: wild type


title: Root_replicate3

description: Expression profiling of lincRNA in roots

source_name: Root

growth_protocol: Plants of Arabidopsis thaliana were grown on sterile solid half-strength Murashige-Skoog (MS) medium or in a greenhouse under similar conditions (22°C, 16/8h photoperiod cycles).  Inflorescences with open flowers, flowers buds and some very young siliques were collected from 4 week-old WT(Col-0) plants. Root and leaf samples were collected from 30 day-old WT (Col-0) grown hydroponically in full-strength MGRL medium.

value: 30 days

value: Root


title: Root_replicate2


title: GM06990_Exp

city: Bronx

first: John

last: Greally

state: NY

address: 1301 Morris Park Avenue

department: Genetics

institute: Albert Einstein College of Medicine

hyb_protocol: see manufacturer's web site www.nimblegen.com

data_processing: The raw data (.pair file) was analyzed the NimbleScan software package (Roche NimbleGen, Inc.).

source_name: Total RNA

growth_protocol: The GM06990 cells were cultured as recommended by the Coriell repository. The fibroblast cells were grown in Dulbecco’s modified Eagle medium (DMEM) supplemented with 10% Fetal Bovine Serum, 2 mM Glutamine and Penicillin-Streptomycin (Invitrogen) in a 37°C incubator with 5% CO2.

extract_protocol: The  mRNA was converted to dsDNA using SuperScript Double-Strand cDNA Synthesis kit (Invitrogen) with T7-Oligo(dT)24 (5’- GGCCAGTGAATTGTAATACGACTCACTATAGGGAGGCGGTTTTTTTTTTTTTTTTTTTTTTTT -3’).  DNA labeling and hybridization to the microarrays were performed using a published technique (Selzer, Richmond, Pofahl, Green, Eis, Nair, Brothman and Stallings 2005).

tag: cell type

value: Foreskin fibroblast


title: Inflorescence_WT_replicate1

description: Expression profiling of lincRNA in WT


title: Root_replicate1


title: Fibroblast_Exp

scan_protocol: see manufacturer's web site www.nimblegen.com

value: Lymphoblastoid


title: Leaf_replicate3

description: Expression profiling of lincRNA in leaves

source_name: Leaf

value: Leaf


title: CF30-1979 isolate, biological rep3

source_name: CF30 patient 1979 isolate

tag: strain


title: Inflorescence_WT_replicate3

description: Expression profiling of lincRNA in WT


title: Leaf_replicate2


title: WT_hypoxia_90min

city: Cambridge

first: David

last: Lando

address: Tennis Court Road

department: Gurdon Institute

country: United Kingdom

institute: Cambridge University

description: This sample is wild type strain grown under low oxygen conditions

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

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

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

organism: Schizosaccharomyces pombe 972h-

source_name: S. pombe wild type, hypoxia, 90 min

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

growth_protocol: Strains were grown at 30˚C with shaking to exponential phase (OD=0.5) in yeast extract media containing 2% glucose (YES) plus supplements (225µg/ml each of histidine, leucine, adenine, lysine and uracil)

extract_protocol: Cells were harvested at 4˚C and total RNA was isolated and purified using the RNeasy Mini Kit (Qiagen) in-conjunction with the RNase-Free DNase Set (Qiagen) to remove genomic DNA as per manufacturer’s instructions.

treatment_protocol: For hypoxia growth conditions  (<1% oxygen) cells were cultured for 90 minutes in the AnaeroGen system (Oxoid), as per the manufacturer’s instructions. For normoxia (20% oxygen) cells were grown in conical flasks exposed to normal room level oxygen conditions.


title: WT_normoxia_90min

description: This sample is wild type strain grown under normal oxygen conditions

source_name: S. pombe wild type, normoxia, 90 min


title: deltaOfd2_hypoxia_90min

description: This sample is deletion strain of Ofd2 grown under low oxygen conditions

source_name: S. pombe delta-Ofd2 (SPAP8A3.02c), hypoxia, 90 min

value: deletion strain Ofd2 (SPAP8A3.02c)


title: deltaOfd2_normoxia_90min

description: This sample is deletion strain of Ofd2 grown under normal oxygen conditions

source_name: S. pombe delta-Ofd2 (SPAP8A3.02c), normoxia, 90 min


title: Inflorescence_replicate3

description: Expression profiling of lincRNA in inflorescences

source_name: Inflorescence


title: CF30-1979 isolate, biological rep1


title: Leaf_replicate1


title: CF30-1979 isolate, biological rep2


title: Inflorescence_replicate1


title: PC346Flu2_16h_Flutamide_Average_DyeSwap

status: Public on Aug 05 2011

city: Rotterdam

first: Rute

last: Marques

address: Dr Molewaterplein 50

institute: Erasmus MC

description: Label OH-Flutamide samples: EHF080=Cy3, EHF053=Cy5

hyb_protocol: Before the hybridization, microarray slides were prehybridized in 5x SSC, 0.05% SDS, 4% BSA solution for 30 min at 45°C, washed twice with RNAse-free water for 2 min, rinsed with isopropanol and spin-dried for 3 min at 1500g. Microarray hybridizations were performed overnight at 45°C, with continuous agitation, in a HS4800 Hybridization Station (Tecan Benelux BV). Finally, the arrays were washed automatically in the Hybridization Station using: 2x SSC/0.05% SDS (at 45°C), 1x SSC and 0.2x SSC (at room temperature), and dried under a stream of N2, before scanning.

scan_protocol: Arrays were scanned in a ScanArray Express HT scanner (Perkin Elmer, Nederland BV) and spot intensities were quantified using Imagene software (Bio Discovery Inc, El Sequndo, CA, USA).

data_processing: Loewess normalization per subarray was performed using limma-package (http://bioinf.wehi.edu.au/limma/) from Bioconductor (http://www.bioconductor.org), followed by background substraction. To scale between arrays, the global median intensity per array was set at 1000. Dye intensities below 200 were then thresholded at 200, to minimize noise and make fold-change on the low-intensity range more robust against outliers. Spots with intensities below the threshold (200) for both Cy3 and Cy5 channels in more than 50% (>3/6) of the arrays for each time-course, were excluded from the analysis. Sample to vehicle-control ratios were then calculated and 2log transformed. Spots that showed opposite effects for the dye-swap/biological replicates were excluded from further analysis. Following normalization and all the above-mentioned quality controls, the 2log intensity ratios from both replicates were averaged for each time point.

source_name: 16h stimulation with 1 uM OH-Flutamide

label_protocol: Cy3- or Cy5-labelled RNA probes were produced by incorporating amino-allyl UTP during RNA amplification, followed by coupling to N-hydroxysuccinimide modified dye. Finally, 2 µg of the contra-labelled RNA probes were combined and purified/concentrated using Microcon-YM 30. Probe was collected in 5-15 ml final volume and resuspended in 80 µl Ambion hybridization buffer number 1.

growth_protocol: The basic culture medium used in the maintenance of PC346 cell lines consisted of DMEM-F12 medium (Cambrex BioWhitaker, Belgium) supplemented with 2% fetal calf serum (FCS; PAN Biotech GmbH, Aidenbach, Germany), 1% insulin-transferrin-selenium (Gibco BRL), 0.01% bovine serum albumin (Boehringer Mannheim, Germany), 10 ng/ml epidermal growth factor (Sigma-Aldrich), penicillin/streptomycin antibiotics (100 U/ml penicillin, 100 mg/ml streptomycin; BioWhitaker, Belgium); plus the following additions: 100 ng/ml fibronectin (Harbor Bio-Products, Tebu-bio, The Netherlands), 20 mg/ml fetuine (ICN Biomedicals, The Netherlands), 50 ng/ml choleratoxin, 0.1 mM phosphoethanolamine, 0.6 ng/ml triiodothyronine and 500 ng/ml dexametason (all from Sigma). Cells were grown in T25 PrimariaTM tissue culture flasks (BD Biosciences Benelux N.V, The Netherlands) at 37oC under 5% CO2 humidified atmosphere.

extract_protocol: Total RNA was isolated with RNAzol B reagent (Campro Scientific, Veenendaal, The Netherlands) and further purified through RNeasy columns (Qiagen) with on-column DNA digestion, according to the manufacturer’s protocol.

treatment_protocol: Prior to the stimulations, cells were starved in dextran-coated charcoal treated FCS supplemented in the DMEM-F12 basic medium, without the above mentioned additions. Cells were treated for 4, 8 and 16h with 0.1 nM 17-methyltrienolone (R1881; NEN, Boston MA, USA),  1 μM of hydroxyflutamide (OH-flutamide, Schering-Plough Research Institute, New Jersey, USA) or vehicle control. PC346DCC was only treated with R1881 and not hydroxyflutamide.

tag: treatment

value: 16h stimulation with 1 uM OH-Flutamide

source_name: 16h incubation with vehicle

value: 16h incubation with vehicle


title: PC346Flu1_8h_Flutamide_Average_DyeSwap

description: Label OH-Flutamide samples: EHF055=Cy3, EHF042=Cy5

source_name: 8h stimulation with 1 uM OH-Flutamide

value: 8h stimulation with 1 uM OH-Flutamide

source_name: 8h incubation with vehicle

value: 8h incubation with vehicle


title: Inflorescence_replicate2


title: PC346Flu2_4h_R1881_Average_DyeSwap

description: Label R1881 samples: EHF048=Cy3, EHF044=Cy5

source_name: 4h stimulation with 1 nM R1881

value: 4h stimulation with 1 nM R1881

source_name: 4h incubation with vehicle

value: 4h incubation with vehicle


title: PC346Flu1_16h_Flutamide_Average_DyeSwap

description: Label OH-Flutamide samples: EHF062=Cy3, EHF043=Cy5


title: PC346Flu2_4h_Flutamide_Average_DyeSwap

description: Label OH-Flutamide samples: EHF078=Cy3, EHF051=Cy5

source_name: 4h stimulation with 1 uM OH-Flutamide

value: 4h stimulation with 1 uM OH-Flutamide


title: PC346Flu2_8h_Flutamide_Average_DyeSwap

description: Label OH-Flutamide samples: EHF079=Cy3, EHF052=Cy5


title: PC346Flu2_16h_R1881_Average_DyeSwap

description: Label R1881 samples: EHF050=Cy3, EHF047=Cy5

source_name: 16h stimulation with 1 nM R1881

value: 16h stimulation with 1 nM R1881


title: PC346Flu1_16h_R1881_Average_DyeSwap

description: Label R1881 samples: EHF038=Cy3, EHF035=Cy5


title: PC346Flu1_4h_R1881_Average_DyeSwap

description: Label R1881 samples: EHF041=Cy3, EHF040=Cy5


title: PC346DCC_16h_R1881_Average_DyeSwap

description: Label R1881 samples: EHF029=Cy3, EHF026=Cy5


title: PC346Flu1_4h_Flutamide_Average_DyeSwap

description: Label OH-Flutamide samples: EHF054=Cy3, EHF082=Cy5


title: WT genomic DNA as a reference

first: Hideo

last: Iwasaki

address: TWIns 1F 2-2 Wakamatsu-cho, Shinjuku

department: Electrical Engineering & Bioscience

institute: Waseda University

description: Genomic DNA signals for better quantification of RNA signals

hyb_protocol: Following fragmentation, 1.5 ug of cDNA were hybridized for 16 hr at 45C on GeneChip Synechococcus Custom Arrays (Syel6301a520114F). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with GeneChip Operating Software (GCOS) ver 1.2.1.001 using Affymetrix default analysis settings, divided by corresponding genomic DNA signals (genomic DNA sample), and global scaling as normalization method except for samples under DD conditions. The trimmed average target intensity of each array was arbitrarily set to 1000. For data under DD, genomic-DNA-divided value is shown.

organism: Synechococcus elongatus PCC 7942 = FACHB-805

source_name: wild type genomic DNA was partially digested with DNaseI as a reference

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix prokaryotic protocol from 10 ug total RNA (Expression Analysis Technical Manual)

growth_protocol: Synechococcus cells were grown in continuous culture systems in any conditions at 30C under the light (46 micromol/m^2/sec) or the dark

extract_protocol: Total RNAs were extracted with a modified hot-phenol extraction method

treatment_protocol: Cells were collected at indicated times and stored at -80C until use


title: PC346Flu2_8h_R1881_Average_DyeSwap

description: Label R1881 samples: EHF049=Cy3, EHF046=Cy5

source_name: 8h stimulation with 1 nM R1881

value: 8h stimulation with 1 nM R1881


title: PC346C_8h_Flutamide_Average_DyeSwap

description: Label OH-Flutamide samples: EHF022=Cy3, EHF021=Cy5


title: PC346C_4h_Flutamide_Average_DyeSwap

description: Label OH-Flutamide samples: EHF024=Cy3, EHF070=Cy5


title: PC346DCC_8h_R1881_Average_DyeSwap

description: Label R1881 samples: EHF032=Cy3, EHF031=Cy5


title: PC346C_16h_R1881_Average_DyeSwap

description: Label R1881 samples: EHF069=Cy3, EHF066=Cy5


title: PC346C_8h_R1881_Average_DyeSwap

description: Label R1881 samples: EHF068=Cy3, EHF065=Cy5


title: PC346C_4h_R1881_Average_DyeSwap

description: Label R1881 samples: EHF067=Cy3, EHF064=Cy5


title: PC346C_16h_Flutamide_Average_DyeSwap

description: Label OH-Flutamide samples: EHF018=Cy3, EHF017=Cy5


title: PC346DCC_4h_R1881_Average_DyeSwap

description: Label R1881 samples: EHF027=Cy3, EHF030=Cy5


title: PC346Flu1_8h_R1881_Average_DyeSwap

description: Label R1881 samples: EHF037=Cy3, EHF033=Cy5


title: constitutive MLL-AF9, KrasG12D AML, line 3, 6 days doxycycline

city: Vienna

first: Johannes

last: Zuber

state: Vienna

address: Dr. Bohr-Gasse 7

country: Austria

institute: Research Institute for Molecular Pathology (IMP)

hyb_protocol: Samples were hybridized using the Affymetrix Hybridization, Wash and Scan kit (P/N 900720) according to Affymetrix GeneChip Expression Analysis Technical Manual (P/N 702232 Rev 2), using fluidics protocol FS450_0004 in a GeneChip Fluidics Station 450

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Command Console Software on a 3000 7G Affymetrix GeneChip Scanner (P/N GCS 3000)

data_processing: Raw data were processed in two ways: (1) A probeset-based analysis was performed using the RMA algorithm in GenePattern. (2) A gene-based analysis was performed by processing raw data using FARMS method (Hochreiter et al.  2006) with an up-to-date probe set definition based on Entrez gene sequences (Dai et al. 2005).

source_name: constitutive MLL-AF9;KrasG12D AML, line 3, 6 days doxycycline

label_protocol: Samples were Amplified by a Modified T7 IVT, with Ambion's Message Amp II Biotin Enhanced kit according to Manufacturer's instruction.

growth_protocol: Cells were cultured in RPMI1640 + 10% FBS.

extract_protocol: Trizol extraction of total RNA was performed according to manufacturers instructions.

treatment_protocol: Cells were either left untreated or treated with doxycycline (1.0 ug/mL) for 6 days.

value: murine AML cell line

tag: transgene

value: constitutive MLL-AF9;KrasG12D

value: doxycycline

tag: genetic background


title: constitutive MLL-AF9, KrasG12D AML, line 1, untreated

source_name: constitutive MLL-AF9;KrasG12D AML, line 1, untreated

value: untreated


title: constitutive MLL-AF9, KrasG12D AML, line 2, 6 days doxycycline

source_name: constitutive MLL-AF9;KrasG12D AML, line 2, 6 days doxycycline


title: constitutive MLL-AF9, KrasG12D AML, line 3, untreated

source_name: constitutive MLL-AF9;KrasG12D AML, line 3, untreated


title: constitutive MLL-AF9, KrasG12D AML, line 1, 6 days doxycycline

source_name: constitutive MLL-AF9;KrasG12D AML, line 1, 6 days doxycycline


title: inducible MLL-AF9, NrasG12D AML, line 5, 6 days doxycycline

source_name: inducible MLL-AF9;NrasG12D AML, line 5, 6 days doxycycline

value: inducible MLL-AF9;NrasG12D


title: constitutive MLL-AF9, KrasG12D AML, line 2, untreated

source_name: constitutive MLL-AF9;KrasG12D AML, line 2, untreated


title: shMyb.2652 biol repl 3, 3 d dox, sorted

data_processing: Raw data were processed in two ways: (1) A probeset-based analysis was performed using the RMA algorithm in GenePattern. (2) A gene-based analysis was performed by processing raw data using FARMS method (Hochreiter et al., 2006) with an up-to-date probe set definition based on Entrez gene sequences (Dai et al. 2005).

source_name: TRMPV-Neo.shMyb.2652 expressing MLL-AF9/NrasG12D AML cells, 3 d dox, sorted

treatment_protocol: shRNA expression was induced by doxycycline treatment (1.0 ug/mL for 3 days).

tag: knockdown


title: shMyb.2572 biol repl 2, 3 d dox, sorted

source_name: TRMPV-Neo.shMyb.2572 expressing MLL-AF9/NrasG12D AML cells, 3 d dox, sorted


title: inducible MLL-AF9, KrasG12D AML, line 3, 6 days doxycycline

source_name: inducible MLL-AF9;KrasG12D AML, line 3, 6 days doxycycline

value: inducible MLL-AF9;KrasG12D


title: inducible MLL-AF9, NrasG12D AML, line 5, untreated

source_name: inducible MLL-AF9;NrasG12D AML, line 5, untreated


title: shMyb.2652 biol repl 1, 3 d dox, sorted


title: inducible MLL-AF9, KrasG12D AML, line 2, untreated

source_name: inducible MLL-AF9;KrasG12D AML, line 2, untreated


title: Rec vector biol repl 1, 3 d dox, sorted

source_name: TRMPV-Neo.Rec vector expressing MLL-AF9/NrasG12D AML cells,  3 d dox, sorted

value: empty vector


title: shRen.713 biol repl 3, 3 d dox, sorted

source_name: TRMPV-Neo.shRen.713 expressing MLL-AF9/NrasG12D AML cells, 3 d dox, sorted

value: luciferase


title: shRen.713 biol repl 1, 3 d dox, sorted


title: shMyb.2572 biol repl 3, 3 d dox, sorted


title: inducible MLL-AF9, KrasG12D AML, line 1, 6 days doxycycline

source_name: inducible MLL-AF9;KrasG12D AML, line 1, 6 days doxycycline


title: inducible MLL-AF9, KrasG12D AML, line 1, untreated

source_name: inducible MLL-AF9;KrasG12D AML, line 1, untreated


title: inducible MLL-AF9, KrasG12D AML, line 2, 6 days doxycycline

source_name: inducible MLL-AF9;KrasG12D AML, line 2, 6 days doxycycline


title: Rec vector biol repl 3, 3 d dox, sorted

source_name: TRMPV-Neo.Rec vector expressing MLL-AF9/NrasG12D AML cells, 3 d dox, sorted


title: inducible MLL-AF9, NrasG12D AML, line 4, 6 days doxycycline

source_name: inducible MLL-AF9;NrasG12D AML, line 4, 6 days doxycycline


title: shMyb.2652 biol repl 2, 3 d dox, sorted


title: shRen.713 biol repl 2, 3 d dox, sorted


title: inducible MLL-AF9, KrasG12D AML, line 3, untreated

source_name: inducible MLL-AF9;KrasG12D AML, line 3, untreated


title: Rec vector biol repl 2, 3 d dox, sorted


title: inducible MLL-AF9, NrasG12D AML, line 4, untreated

source_name: inducible MLL-AF9;NrasG12D AML, line 4, untreated


title: hpMSCs, empty vector, rep4

city: Torino

first: Paolo

last: Provero

address: Via Nizza 52

department: Molecular Biotechnology and Health Sciences

institute: University of Turin

hyb_protocol: Manufacturer's protocol.

scan_protocol: Manufacturer's protocol.

data_processing: Gene expression data were obtained with the RMA method using the Affymetrix Power Tools suite.

source_name: hpMSCs infected with empty vector

label_protocol: Manufacturer's protocol.

growth_protocol: hpMSCs were obtained from femoral head bone marrow of four pediatric patients undergoing limb axis correction surgery and cultured as described previously (PMIDs: 14584050, 17786951, 18381423).

extract_protocol: Total RNA was extracted 12 days after infection and selection using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s recommendations. RNA quality was verified by an Agilent RNA 600 nanoassay and by measuring the 260/280 absorbance ratio.

treatment_protocol: hpMSCs were infected as previously described (PMIDs: 14584050, 17786951, 18381423).

value: human pediatric mesenchymal stem cells (hpMSCs)


title: shMyb.2572 biol repl 1, 3 d dox, sorted