title: NM-2C5-2-1

status: Public on May 03 2012

city: Lund

first: Rolf

last: Søkilde

address: Scheelevägen 2

department: Department of Oncology

country: Sweden

institute: Lund University, Sweden

hyb_protocol: Global miRNA expression analysis was performed using the miRCURY LNA (Locked Nucleic Acid) microRNA Arrays (Exiqon, A/S, Vedbaek, Denmark) version 10.0 extended version, which in addition to 1200 probes that target all human, mouse and rat miRNA sequences annotated in miRBase 10.0, also include 66 probes that target proprietary microRNAs identified by deep sequencing (Nygaard et al., 2009) (Griffiths-Jones et al., 2008).

scan_protocol: The arrays were scanned in an Agilent G2565BA Microarray Scanner System (Agilent Technologies, Santa Clara, CA, USA).

data_processing: The fluorescence images produced from the scans were analyzed using ImaGeneTM software (BioDiscovery, CA, USA). A grid was placed on the array and the image signal intensities and background intensities were measured for each spot for both dye channels. Poor quality spots were removed and spots were background corrected using the Normexp method (with an offset of 50) in the statistical programming language R with the Bioconductor (Gentleman et al., 2004) software package LIMMA (Linear Models for Microarray Data) (Ritchie et al., 2006). All fluorescence intensities were log2 transformed, and normalization was performed using LOESS (Locally weighted scatterplot smoothing) (Smyth and Speed, 2003) in the statistical programming language R with the Bioconductor (Gentleman et al., 2004) software package LIMMA.

source_name: Cell line NM-2C5-GFP

label_protocol: Two independent purifications were made from each cell line and miRNA expression was measured for each of the RNA purifications on two different arrays relative to one of the other cell lines, using dual color labeling (Exiqon).

growth_protocol: The human cancer cell lines NM-2C5-GFP (NM-2C5), M-4A4-GFP (M-4A4) and M-4A4-LM3-GFP (LM3) (American Type Culture Collection (ATCC), derived from the cell line MDA-MB-435 Manassas, VA, USA) were cultured in Dulbecco's Modified Eagle's Medium (DMEM) with GlutamaxTM-I, glucose and sodium pyrovate (Gibco, Invitrogen, Carlsbad, California, USA) supplemented with 10% fetal bovine serum (FBS) (Gibco, Invitrogen), 1% Non-essential amino acids (Gibco, Invitrogen) and 1% Penicillin/Streptomycin (100 Units/ml Penicillin, 100 μg/ml Streptomycin) (Gibco, Invitrogen).

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) from cell lines NM-2C5-GFP, M-4A4-GFP and M- 4A4-LM3-GFP according to the manufacturer’s instructions.

tag: cell line

tag: metastatic status

value: non-metastatic


title: MDA-MB-435-3-1

type: RNA

molecule: total RNA

organism: Homo sapiens

source_name: Cell line MDA-MB-435

value: parental


title: NM-2C5-3-2


title: MDA-MB-435-2-2


title: NM-2C5-2-2


title: MDA-MB-435-2-1


title: M4A4-3-1

source_name: Cell line M4A4-GFP

value: metastatic


title: MDA-MB-435-3-2


title: M4A4-3-2


title: LM3-3-3

source_name: Cell line LM3-GFP


title: M4A4-2-1


title: M4A4-2-2


title: LM3-2-2


title: LM3-3-1


title: LM3-2-1


title: NM-2C5-3-1


title: Cells obtained from the bottom 50 µm of the biofilm, replicate 3

city: Bozeman

first: Kate

last: McInnerney

state: MT

address: 109 Lewis Hall

department: Microbiology

country: USA

institute: Montana State University

hyb_protocol: Fragmented and biotin-end labeled cDNA was hybridized for 16 hr at 50C to the Affymetrix P. aeruginosa genome array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using an Affymetrix 7G scanner and GCOS version 1.4.

data_processing:
Microarray data were analyzed using FlexArray version 1.4.  Using the just RMA option, background was corrected and probes summarized.  For this analysis, however, the arrays were not normalized.

Unscaled GCOS (MAS5.0) signal intensities and calls are available in the supplementary CHP file.

label: biotin

organism: Pseudomonas aeruginosa

source_name: Pseudomonas aeruginosa PA01 from the bottom 50 µm of the biofilm

label_protocol: RNA was poly(A) tailed (Epicentre kit) and amplified with the Quantitect Whole Transcriptome Amplification kit (Qiagen).  After fragmentation, it was end-labeled with GeneChip DNA labeling reagent (Affymetrix).

growth_protocol: Pseudomonas aeruginosa was grown in colony biofilms on tryptic soy agar (TSA) plates for 52 hours at 37C with transfer to fresh media occurring every 12 hours.

extract_protocol: The RNeasy Micro kit was used according to the manufacturer's microdissected cryosection protocol.

treatment_protocol: Cells were captured from the top 50 µm or bottom 50 µm of thin-sectioned biofilms using the laser catapult parameter of the Zeiss/P.A.L.M. Laser-MicroBeam microscope. From each independent biofilm, 9 samples, catapulted from the top or bottom of the biofilm into buffer in the lids of microcentrifuge tubes, were pooled.

tag: strain

tag: subpopulation

value: bottom 50 µm of the biofilm


title: siRNA-Scrambled HUVEC for 48h (exon level) rep3

status: Public on May 04 2012

city: Frankfurt

first: niels

last: boeckel

address: Theodor-Stern-Kai 7

department: Institut for Cardiovascular Regenration

country: Germany

institute: University Frankfurt

description: Huvec treated with control (SCR) siRNA for 48h

hyb_protocol: cDNA synthesis, labeling, hybridization and scanning was performed by ATLAS Biolabs using standard Affymetrix protocols.

data_processing:
Data were processed using the EAA (exon array analyzer, Version 2.2); RMA normalized; gene and exon expression levels from Affymetrix Power Tools
HuEx-1_0-st-v2.r2.pgf
HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

source_name: HUVEC

growth_protocol: HUVECs (Lonza) were grown in EBM medium (Lonza) suppelement with EGM single quots (Lonza) and 10% FCS (Gibco). After the third passage, 300000  cells were seeded into 6 cm dishes.

extract_protocol: Total RNA was isolated using the miRNeasy Mini kit (Qiagen) according to the manufacturer's protocol. The optional on-column DNA digestion was performed, using the RNase-free DNase Set (Qiagen).

treatment_protocol: After 24 h attchement, cells were transfected with siRNA targeting Jmjd6 or a scrambled siRNA (all Sigma Aldrich) using GeneTrans II (MobiTec), all in a final concentration of 60 nM for 48 h

tag: cell type

value: HUVEC

tag: treatment

value: control siRNA


title: Cells obtained from the top 50 µm of the biofilm, replicate 4

source_name: Pseudomonas aeruginosa PA01 from the top 50 µm of the biofilm

value: top 50 µm of the biofilm


title: Cells obtained from the bottom 50 µm of the biofilm, replicate 5


title: siRNA-Jmjd6 HUVEC for 48h (exon level) rep1

description: Huvec treated with siRNA targeting Jmjd6 for 48h

scan_protocol: cDNA synthesis, labeling, hybridization and scanning was performed by ATLAS Biolabs using standard Affymetrix protocols.

value: siRNA targeting Jmjd6


title: siRNA-Scrambled HUVEC for 48h (exon level) rep2

label_protocol: cDNA synthesis, labeling, hybridization and scanning was performed by ATLAS Biolabs using standard Affymetrix protocols.


title: Cells obtained from the bottom 50 µm of the biofilm, replicate 4


title: Cells obtained from the top 50 µm of the biofilm, replicate 3


title: Cells obtained from the bottom 50 µm of the biofilm, replicate 2


title: Cells obtained from the top 50 µm of the biofilm, replicate 5


title: Cells obtained from the top 50 µm of the biofilm, replicate 1


title: Cells obtained from the top 50 µm of the biofilm, replicate 2


title: Cells obtained from the bottom 50 µm of the biofilm, replicate 1


title: siRNA-Scrambled HUVEC for 48h (exon level) rep1


title: With both HCV infection and IFN treatment_Mouse#1

city: Hiroshima

first: Masataka

last: Tsuge

address: 1-2-3, Kasumi, Minami-ku

country: Japan

institute: Hiroshima university

description:
GroupD#1
Gene expression data from human hepatocytes.

hyb_protocol: Biotin-labeled cDNA was hybridized to Affymetrix GeneChip Human Gene U133 Plus 2.0 Arrays for 16 hours at 45 °C using the GeneChip Hybridization Oven 640 (Affymetrix).

scan_protocol: Images were acquired using the Affymetrix Scanner 3000 (Affymetrix).

data_processing: Fluorescence intensities captured by the Affymetrix GeneChip Scanner were converted to numerical values and were standardized using quantile normalization with the Robust Multiarray Analysis (RMA) algorithm (Affymetrix GeneChip Operating Software).

source_name: human hepatocytes with both HCV infection and IFN treatment

label_protocol: 300 ng of total RNA underwent first-strand and second-strand cDNA synthesis. Complementary RNA was generated and used to produce sense-strand cDNA, which was fragmented and end-labeled with biotin.

growth_protocol: HCV genotype 1b-containing human serum was injected into human hepatocyte chimeric mice, and human hepatocytes in the mice livers were collected 8 weeks after inoculation.

extract_protocol: Total RNA was extracted using the Qiagen RNeasy Mini Kit according to the manufacturer's protocol (Qiagen).

treatment_protocol: A total of 15 human hepatocyte chimeric mice were prepared and divided into four experimental groups. Mice in group A were neither infected with hepatitis C virus (HCV) nor treated with interferon-alpha (IFN-α). Mice in group B were administered 7000 IU/g body of IFN-α 6 h before sacrifice but were not infected with HCV. The mice in groups C and D were both inoculated via the mouse tail vein with human serum containing HCV genotype 1b particles. At 8 weeks after inoculation, the mice in group D were administered IFN-α 6 h before sacrifice, but the mice in group C were not treated with IFN-α. The human hepatocytes in the mouse livers were collected after sacrifice and subjected to microarray analysis.

value: human hepatocytes from human hepatocyte chimeric mouse liver

value: hepatitis C virus (HCV) and interferon-alpha (IFN-α)

tag: group

value: D


title: With IFN treatment_Mouse#3

description:
GroupB#3
Gene expression data from human hepatocytes.

source_name: human hepatocytes with IFN treatment only

value: interferon-alpha (IFN-α)

value: B


title: With IFN treatment_Mouse#1

description:
GroupB#1
Gene expression data from human hepatocytes.


title: Without HCV infection or IFN treatment_Mouse#3

description:
GroupA#3
Gene expression data from human hepatocytes.

source_name: human hepatocytes without HCV infection or IFN treatment

value: A


title: With IFN treatment_Mouse#4

description:
GroupB#4
Gene expression data from human hepatocytes.

value: hepatitis C virus (HCV)


title: With both HCV infection and IFN treatment_Mouse#3

description:
GroupD#3
Gene expression data from human hepatocytes.


title: With both HCV infection and IFN treatment_Mouse#2

description:
GroupD#2
Gene expression data from human hepatocytes.


title: With HCV infection_Mouse#3

description:
GroupC#3
Gene expression data from human hepatocytes.

source_name: human hepatocytes with HCV infection only

value: C


title: With HCV infection_Mouse#1

description:
GroupC#1
Gene expression data from human hepatocytes.


title: Without HCV infection or IFN treatment_Mouse#4

description:
GroupA#4
Gene expression data from human hepatocytes.


title: With HCV infection_Mouse#2

description:
GroupC#2
Gene expression data from human hepatocytes.


title: With both HCV infection and IFN treatment_Mouse#4

description:
GroupD#4
Gene expression data from human hepatocytes.


title: Without HCV infection or IFN treatment_Mouse#2

description:
GroupA#2
Gene expression data from human hepatocytes.


title: Without HCV infection or IFN treatment_Mouse#1

description:
GroupA#1
Gene expression data from human hepatocytes.


title: Panc198 xenograft GSI_198B Non-sensitive to MRK-003

city: Rahway

first: Oscar

last: Puig

state: NJ

address: 126 East Lincoln Ave

department: Molecular Profiling Research Informatics

institute: Merck Research Laboratories

description: We used pancreatic ductal adenocarcinoma cell lines to determine whether pharmacological targeting of the Notch pathway could inhibit pancreatic tumor growth and potentiate gemcitabine sensitivity.

hyb_protocol: GeneChip microarrays are loaded with the fragmented target sample/hybridization buffer mix using standard manual techniques.  Arrays are hybridized for 18 hours at 45?C with vigorous mixing.   Unbound sample is removed and staining is accomplished through the binding of streptavidin conjugated phycoerythrin to the hybridized target. Excess label is removed.  Washing and staining steps are performed by the Affymetrix FS450 fluidics station using standard protocols.

scan_protocol: Arrays are scanned using a GeneChip Scanner 3000 7G with a 48 array autoloader. The scanner maintains the optimal temperature for the arrays prior to and during scanning.

data_processing: Data were loaded into the Rosetta Resolver? system (Rosetta Biosoftware, Seattle, WA) and processed using the RMA algorithm (http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=PubMed&list_uids=12582260).  Intensities were calculated based on RMA, a Rosetta-developed error, and a MAS-5 p-value.  The Rosetta-developed error is used in the calculation of xdev for the ratio p-values as described in section 2.2 (http://bioinformatics.oxfordjournals.org/cgi/content/full/22/9/1111).

label: Biotin ining process that provides the measurable signal.

label_protocol: The final in vitro transcription incorporates biotin moieties that are later labeled with phycoerythrin.  After amplification, samples are put through a controlled fragmentation to improve hybridization sensitivity and consistency.  The labeled molecules are biotinylated-cRNA.

extract_protocol: Samples are processed in parallel in 96-well plates to minimize potential variation.  Reaction purification is achieved using magnetic binding beads for cDNA and Qiagen RNeasy kits for cRNA purification.

tag: sample

tag: donor cell line

tag: host

value: immunocompromised Athymic Nude-Foxn1nu mouse

tag: phenotype

value: Non-sensitive to MRK-003

tag: tissue

value: Pancreatic ductal adenocarcinoma tumor xenograft


title: Panc219 xenograft GSI_219A Sensitive to MRK-003

source_name: pancreatic ductal adenocarcinoma cell lines

value: Sensitive to MRK-003


title: Panc219 xenograft GSI_219B Sensitive to MRK-003


title: With IFN treatment_Mouse#2

description:
GroupB#2
Gene expression data from human hepatocytes.


title: Panc420 xenograft GSI_420B Sensitive to MRK-003


title: Panc215 xenograft GSI_215B Non-sensitive to MRK-003


title: Panc291 xenograft GSI_291A Non-sensitive to MRK-003


title: Panc420 xenograft GSI_420A Sensitive to MRK-003


title: JH033 xenograft GSI_JH033B Sensitive to MRK-003


title: Panc374 xenograft GSI_374B Sensitive to MRK-003


title: JH033 xenograft GSI_JH033A Sensitive to MRK-003


title: Panc253 xenograft GSI_253A Non-sensitive to MRK-003


title: Panc215 xenograft GSI_215A Non-sensitive to MRK-003


title: Panc265 xenograft GSI_265A Sensitive to MRK-003


title: Panc198 xenograft GSI_198A Non-sensitive to MRK-003


title: Panc374 xenograft GSI_374A Sensitive to MRK-003


title: Panc265 xenograft GSI_265B Sensitive to MRK-003


title: Acute heart failure 9

city: Toulouse

first: Philippe

middle: V

last: Rouet

address: 1 Ave Jean Poulhes

department: Cardiology

country: France

institute: INSERM U1048

hyb_protocol: The hybridization was done on Discovery machine from Ventana. The slides were prehybridized 30min at 42°C, the target probes were hybridized 8h at 42°C with agitation and were washed manually. All the buffers and solutions came from Ventana Society (Roche)

scan_protocol: The slides were scanned on an Axon 4000B scanner and quantified by Genepix Pro 6.0

data_processing: Background subtracted mean data was normalized using the loess method (within arrays) and then Rquantile method (between arrays) using the limma package from bioconductor.

source_name: Acute heart failure

label_protocol: The RNA were labeled with QuickAmp kit following Agilent instructions

extract_protocol: Total RNA were extracted using RNAeasy columns and a Qiacube robotized machine. Integrity was verified by capillary electrophoresis. RNA were quantified using Ribogreen.

treatment_protocol: Blood samples collected in BD CPT tubes and processed as recommended by the manufacturer

value: white blood cells

tag: source

value: total RNA from individual

source_name: white blood cells (pooled common reference)

value: pooled total RNA equimolar amount for each experimental sample


title: Acute heart failure 4


title: Panc253 xenograft GSI_253B Non-sensitive to MRK-003


title: Acute heart failure 7


title: Panc291 xenograft GSI_291B Non-sensitive to MRK-003


title: Acute heart failure 1


title: Acute heart failure 6


title: Chronic heart failure  8

source_name: Chronic heart failure


title: Acute heart failure 3


title: Acute heart failure 8


title: Chronic heart failure  9


title: Chronic heart failure  7


title: Chronic heart failure  2


title: Chronic heart failure  3


title: Chronic heart failure  4


title: Chronic heart failure  1


title: Chronic heart failure  5


title: Chronic heart failure  6


title: left ventricular dysfunction 9

source_name: left ventricular dysfunction


title: left ventricular dysfunction 8


title: left ventricular dysfunction 5


title: left ventricular dysfunction 7


title: left ventricular dysfunction 1


title: left ventricular dysfunction 6


title: left ventricular dysfunction 2


title: left ventricular dysfunction 4


title: left ventricular dysfunction 3


title: heart failure risk patients 6

source_name: heart failure risk patients


title: heart failure risk patients 8


title: heart failure risk patients 7


title: heart failure risk patients 2


title: heart failure risk patients 1


title: heart failure risk patients 9


title: heart failure risk patients 3


title: heart failure risk patients 5


title: heart failure risk patients 4


title: healthy control 8

source_name: healthy control


title: healthy control 9


title: Acute heart failure 2


title: healthy control 6


title: healthy control 2


title: healthy control 7


title: healthy control 1


title: X96R.p5B.M87ACTX_Pre-stasis HMEC Biological replicate #2

city: Montreal

first: Francois

last: Pepin

state: Quebec

address: 1160 Pine Av W

country: Canada

institute: McGill University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HT_HG-U133A Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: Robust multi-array analysis (RMA, from affy package version 1.26.1) was performed to normalize data collected from different samples through R bioconductor (R version 2.11.1). Default parameter values were used.

source_name: pre-stasis HMEC at stasis

label_protocol: For each sample, the RNA target is prepared by annealing 2.0µg of total RNA in 5µl water with 5µl of 10µM T7 (Oligo dt) primer. First and second strand cDNA synthesis is performed and the cDNA products purified using magnetic beads. Labeled cRNA is synthesized from the cDNA using T7 RNA polymerase followed by clean-up with magnetic beads. Purified cRNA is quantitated and fragmented.

growth_protocol: Finite life span HMEC were obtained from reduction mammoplasty tissue of women of the indicated ages. HMEC were grown starting from organoids in the serum-containing M85+CT±X or M87A+CT+X medium.

extract_protocol: Cell were lysed with trizol reagent (Invitrogen) according manufacturer's protocol. RNA was resuspended in 100 µl nuclease free water and subject to a second step purification on ion exchange column (Qiagen).

treatment_protocol: Cell cultures were harvested and different points in their growth from early passage good growing to near stasis.

tag: age

tag: tissue source

value: human mammary gland (reduction mammoplasty tissue)

value: pre-stasis HMEC at stasis

tag: passage number

tag: ±oxytocin

value: +oxytocin


title: healthy control 5


title: healthy control 3


title: Acute heart failure 5


title: healthy control 4


title: X96R.p5A.M87ACTX._Pre-stasis HMEC Biological replicate #1


title: X48RT8X_Pre-stasis HMEC

source_name: intermediate proliferating pre-stasis HMEC


title: X48RT4pM85_Pre-stasis HMEC

source_name: actively proliferating pre-stasis HMEC

value: actively proliferating pre-stasis HMEC


title: X48RT3X_Pre-stasis HMEC


title: X48RT2pM85_Pre-stasis HMEC


title: X96R.p2.M87ACTX_Pre-stasis HMEC


title: X48RT5X_Pre-stasis HMEC


title: X240LB_CD10.5.2_Pre-stasis myoepithelial HMEC Biological replicate #1

source_name: actively proliferating pre-stasis myoepithelial HMEC


title: X240L10X_Pre-stasis HMEC


title: X240L8X_Pre-stasis HMEC

value: intermediate proliferating pre-stasis HMEC


title: X48RT10X_Pre-stasis HMEC


title: X250MK4pM85X.1_Pre-stasis HMEC


title: X48RT12pM85.1_Pre-stasis HMEC Biological replicate #1


title: X240LB_CD10.5.1_Pre-stasis myoepithelial HMEC Biological replicate #1


title: X48RT16X_Pre-stasis HMEC


title: X240L11X_Pre-stasis HMEC


title: X184D9pM85.2_Pre-stasis HMEC Biological replicate #2


title: X48RT15X_Pre-stasis HMEC


title: X250MK3pM85X.1_Pre-stasis HMEC


title: X48RT12pM85.2_Pre-stasis HMEC Biological replicate #2


title: X184D9pM85.1_Pre-stasis HMEC Biological replicate #1


title: X240L5X_Pre-stasis HMEC


title: X240L2X_Pre-stasis HMEC


title: X48RT12X_Pre-stasis HMEC


title: X240LB_EpCam.5.2_Pre-stasis luminal HMEC Biological replicate #1

source_name: actively proliferating pre-stasis luminal HMEC


title: X184D6X_Pre-stasis HMEC


title: X184D6p.1_Pre-stasis HMEC


title: X184D14pM85X.2_Pre-stasis HMEC Biological replicate #2


title: X184D14pM85X.1_Pre-stasis HMEC Biological replicate #1


title: X184D2p_Pre-stasis HMEC


title: X184D4p_Pre-stasis HMEC


title: X184D2pM85X_Pre-stasis HMEC


title: X184D4pM85X_Pre-stasis HMEC


title: X184D11pM85X_Pre-stasis HMEC


title: Cultured chicken embryonic hepatocytes: 10 uM PFUdA replicate 3

city: Ottawa

first: Jason

middle: M.

last: O'Brien

state: ON

address: 1125 Colonel By Drive, Raven Road

institute: Environment Canada

description: 10 uM PFUdA replicate 3

hyb_protocol: Labelled sample and reference cRNA (825 ng each) was fragmented and then hybridized to arrays for 17 hours using Agilent Hybridization kits as per manufacturer’s direction

scan_protocol: Arrays scanned on an Agilent G2505B scanner at 5 um resolution. Data were acquired using Agilent Feature Extraction software version 9.5.3.1.

data_processing: A reference design was used to analyse gene expression data. The design was blocked on the slide as Agilent slides contain four arrays per slide. Background fluorescence was measured using the (-)3xSLv1 probes. Probes with median signal intensities less than the trimmed mean (trim = 5%) plus three trimmed standard deviations of the (-)3xSLv1 probe were flagged as absent. Data were pre-processed using R (http://www.R-project.org).  The median signal intensities were normalized by the global LOWESS method using the transform.madata function in the microarray analysis of variance (MAANOVA) library. Ratio intensity plots, using complete and single linkages, were generated to identify arrays with poor quality. Differentially expressed genes were identified using the MAANOVA library.  The analysis of variance (ANOVA) model included the main effect of treatment and block effect of the microarray.  The Fs statistic, a shrinkage estimator, was used for the gene-specific variance components and the associated p-values for all the statistical tests were estimated using the permutation method (30,000 permutations with residual shuffling). These p-values were then adjusted for multiple comparisons using the false discovery rate approach (FDR). The least-squares means was used to estimate the fold changes for each pairwise comparison.

organism: Gallus gallus

source_name: Cultured chicken embryonic heaptocytes: 10 uM PFUdA treated

label_protocol: Complementary RNA (cRNA) for each microarray hybridization was prepared from 150 ng of total RNA. cRNA from experimental samples was labelled with Cy5 and reference cRNA with Cy3 using Agilent Quick Amp labelling kits as per manufacturer’s instructions

extract_protocol: Total RNA was isolated from CEH using RNeasy 96 kits (Qiagen), including the on-column DNase treatment according to the manufacturer’s instructions

tag: age of embryo

value: day 19

value: hepatocytes

tag: exposure time

value: 24 hrs

source_name: Cultured chicken embryonic hepatocytes: reference pool


title: Cultured chicken embryonic hepatocytes: 10 uM PFUdA replicate 5

description: 10 uM PFUdA replicate 5


title: Cultured chicken embryonic hepatocytes: 10 uM PFUdA replicate 4

description: 10 uM PFUdA replicate 4


title: X153L.p5AM87ACTX_Pre-stasis HMEC Biological replicate #1


title: Arabidopsis xrn4-6-2F

city: Yokohama

first: Yukio

last: Kurihara

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: CSRS

institute: Riken

description: Gene expression data from untreated xrn4-6 plants

hyb_protocol: Following fragmentation, about 10 mg of cRNA was hybridized with the GeneChip Arabidopsis tiling array using the Hybridization Control Kit (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned at 0.7 mm resolution using the GeneChip Scanner 3000 7G (Affymetrix).

data_processing:
For the analysis of transcriptional activities in whole genome, intensities of a total of 3.2 millions 25-nt oligonucleotide probes for each strand genomic sequence, that is, 1.6 millions PM and 1.6 millions MM probes, of individual replicates for all samples were normalized via quantile normalization.
The intensities of (PM-MM) were used in all subsequent data analyses.

organism: Arabidopsis thaliana

source_name: Untreated Arabidopsis xrn4-6 plants

label_protocol:
Eight to fifteen mg of total RNA per one sample was used for synthesis of double-stranded cDNA by the GeneChip One-Cycle cDNA Synthesis Kit (Affymetrix) using an oligo(dT) primer containing the T7 RNA polymerase promoter.
Biotin-labeled cRNA was generated from the cDNA by in vivo transcription using the GeneChIP IVT Labeling Kit (Affymetrix).

growth_protocol: Plants (Arabidopsis thaliana ecotype Columbia) were grown in the plastic dishes (30 plants per plastic dish) containing GM agar (0.85%) medium supplemented with 1% sucrose for 15 days under 16-h-light/8-h-dark (40-80 mmol photons m-2 sec-1) essentially as described previously (Oono et al. 2003, Plant J. 34: 868-887).

extract_protocol: ISOGEN (Nippon Gene Co., Toyama, Japan) extraction of total RNA from untreated seedling samples was performed according to the manufacturer's instructions.

tag: ecotype

value: Columbia

tag: genotype/variation

tag: biological rep

value: 15-day-old plants


title: X153L.p3BM87ACTX_Pre-stasis HMEC Biological replicate #2

tag: cell type


title: X153L.p5BM87ACTX_Pre-stasis HMEC Biological replicate #2


title: X153L.p3AM87ACTX_Pre-stasis HMEC Biological replicate #1


title: X153L.p11AM87ACTX_Pre-stasis HMEC Biological replicate #1


title: Cultured chicken embryonic hepatocytes: 10 uM PFUdA replicate 2

description: 10 uM PFUdA replicate 2


title: X153L.p8AM87ACTX_Pre-stasis HMEC Biological replicate #1


title: Arabidopsis xrn3-3-3F

description: Gene expression data from  untreated xrn3-3 plants

source_name: Untreated Arabidopsis xrn3-3 plants


title: Arabidopsis xrn4-6-1F


title: Cultured chicken embryonic hepatocytes: 1 uM PFUdA replicate 3

description: 1 uM PFUdA replicate 3

source_name: Cultured chicken embryonic heaptocytes: 1 uM PFUdA treated


title: X153L.p8BM87ACTX_Pre-stasis HMEC Biological replicate #2


title: Cultured chicken embryonic hepatocytes: 1 uM PFUdA replicate 2

description: 1 uM PFUdA replicate 2


title: X122L.p6BM87ACTX_Pre-stasis HMEC Biological replicate #2


title: Cultured chicken embryonic hepatocytes: 1 uM PFUdA replicate 4

description: 1 uM PFUdA replicate 4


title: Cultured chicken embryonic hepatocytes: 1 uM PFUdA replicate 1

description: 1 uM PFUdA replicate 1


title: X153L.p2M87ACTX_Pre-stasis HMEC


title: X122L.p9BM87ACTX_Pre-stasis HMEC Biological replicate #2


title: Arabidopsis xrn3-3-2F


title: X153L.p11BM87ACTX_Pre-stasis HMEC Biological replicate #2


title: X122L.p6AM87ACTX_Pre-stasis HMEC Biological replicate #1


title: X122L.p4M87ACTX_Pre-stasis HMEC


title: Cultured chicken embryonic hepatocytes: 10 uM PFUdA replicate 1

description: 10 uM PFUdA replicate 1


title: Arabidopsis xrn2-4-3F

description: Gene expression data from  untreated xrn2-4 plants

source_name: Untreated Arabidopsis xrn2-4 plants


title: X122L.p9AM87ACTX_Pre-stasis HMEC Biological replicate #1


title: X240LB_EpCam.5.1_Pre-stasis luminal HMEC Biological replicate #1


title: del s-u/4.8

city: Houston

first: Linyan

last: Meng

state: TX

address: One Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

description: data under the column of rMedianSignal

hyb_protocol: 1ug of Cy5-labelled cDNA was mixed with Agilent 10X blocking agent,  2X Hi-RPM buffer and Cot-1 DNA following the manufacturers instructions. The samples were incubated at 95°C for 3min and 37°C for 30min and hybridized to Agilent custom microarray overnight at 65°C in a rotating hybridization oven.  After hybridization, microarrays were washed 5 minute at room temperature with GE Wash Buffer 1 (Agilent), 5 minute at 37°C with GE Wash buffer 2 (Agilent) and 1min at room tempature with acetonitrile. The slides were carefully removed from the liquid and processed to scanning immediately.

scan_protocol: The slide was scanned into image files using the Agilent G2505C Microarray Scanner using specific setting for 8X60k array slides (Scan resolution 3um. Dye channel is set to Green and Red channels. Red PMT is set to 10% and Green PMT is set to 1%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.9 (Agilent) using default parameters (protocol GE2-NonAT_107_Sep09). Following probes were further eliminated during processing. 1. Systemic positive and negative control probes generated by Agilent. 2. Probes named CUST. These are genomic tilling probes across the analyzed region, which were demonstrated to generate a lot of background noise during the analysis and thus eliminated. 3. Probes located outside the designing region. Those are backbone probes generated by Agilent CGH array. Average signal intensity was calculated from Tfrc (+ strand), Pgk1 (+ strand), Gapdh (- strand), and Actb (- strand). This average signal intensity for the four control genes of sample 2_WT was set as 1 and other samples were normalized to it to calculate its own normalization factor. Probes from PWS/AS region were then normalized to this normalization factor.

organism: Mus musculus

source_name: Mutant mice with S-U maternal deletion and Snrpn promoter paternal deleiton

label_protocol: 15ug of mouse cortical total RNA or 750ng mRNA supplemented with E. coli rRNA (Roche) was converted to Cy5 labeled first-strand cDNA using random hexamers by ChipShot labeling system according to manufacturer’s instructions (Promega). Labeled cDNA was purified using the BioPrime Array CGH Genomic Labeling System (Invitrogen). Dye incorporation and cDNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: total RNA was extracted from cerebral cortex of P0 mice using Trizol (Invitrogen) followed by miRNeasy kit (Qiagen). On-column DNase digestion was performed as manufacter's instruction. RNA was quantified using a NanoDrop-1000 spectrophotometer and qualified by electrophoriesis and the visualization of 18S and 26S bands. polyA RNA was purified from 30ug total RNA using sera-mag magnetic oligo(dT) beads (part of the Illumina mRNA-seq preparation kit).

tag: background strain

value: cerebral cortex

tag: developmental stage

tag: genotype

value: del s-u/0.9


title: Arabidopsis xrn3-3-1F


title: del s-u/0.9

description: data under the column of rMedianSignal

value: del s-u/4.8


title: Arabidopsis xrn2-4-1F


title: WT2 polyA

description: data under the column of rMedianSignal

molecule: polyA RNA

source_name: WT polyA RNA

value: WT


title: Arabidopsis fry1-6-3F

description: Gene expression data from untreated fry1-6 plants

source_name: Untreated Arabidopsis fry1-6 plants


title: WT2

description: data under the column of rMedianSignal

source_name: WT


title: WT1 polyA

description: data under the column of rMedianSignal


title: X122L.p2BM87ACTX_Pre-stasis HMEC Biological replicate #2


title: Arabidopsis fry1-6-2F


title: X122L.p2AM87ACTX_Pre-stasis HMEC Biological replicate #1


title: 7d_retinoic acid_treated NT2 cells

type: genomic

city: heidelberg

first: michael

middle: thomas

last: bocker

address: Im Neuenheimer Feld

institute: DKFZ Heidelberg

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylation450 Beadchip using standard Illumina protocol

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

data_processing: GenomeStudio V2010.3 [(Unmethylated and methylated) signal_intensities.txt is provided as a Series supplementary file]

label: Cy5 and Cy3

molecule: genomic DNA

source_name: 7d_retinoic acid_treated NT2 cells

label_protocol: Standard Illumina Protocol

growth_protocol: NT2 cells were maintained in Dulbecco's Modified Eagle Medium (D-MEM, with l-glutamine, 4500 mg/l d-glucose, without sodium pyruvat; Gibco) supplemented with 10% fetal bovine serum and 200 U/ml penicillin and 200 µg/ml streptomycin (all from Gibco) in a humidified atmosphere of 5% CO2 in air.

extract_protocol: Genomic DNA from RA-induced and untreated NT2 tissue culture cells was prepared using the DNeasy Blood & Tissue Kit (Invitrogen) according the manufacturer's specifications.  Genomic DNA (500 ng) from each sample was bisulfite converted using the EZ-96 DNA Methylation Kit (Zymo Research Corporation, Irvine, CA, USA) according to the manufacturer's recommendations.

treatment_protocol: NT2 cells were induced to differentiate with 10 µM all-trans retinoic acid (Sigma). Medium containing RA was changed every 2 days.

tag: gender

value: Male

tag: cell line

value: embryocarcinoma


title: untreated_NT2 cells_control2

source_name: untreated_NT2 cells


title: Arabidopsis xrn2-4-2F


title: untreated_NT2 cells_control1


title: 14d_retinoic acid_treated NT2 cells

source_name: 14d_retinoic acid_treated NT2 cells


title: del +/s-u

description: data under the column of rMedianSignal

source_name: Snrpn-Ube3a paternal deletion mutant (del +/s-u)

tag: tissue

value: del +/s-u


title: del s-u/+

description: data under the column of rMedianSignal

source_name: Snrpn-Ube3a maternal deletion mutant (del s-u/+)

value: del s-u/+


title: Arabidopsis fry1-6-1F


title: Arabidopsis WT (XRN)-3F

description: Gene expression data from untreated Arabidopsis WT (XRN) plants

source_name: Untreated Arabidopsis WT (XRN) plants

value: wild type


title: WT1

description: data under the column of rMedianSignal


title: Arabidopsis seedlings_intact seedlings_22-26hr_rep 3_technical replicate 2

city: Lanzhou

first: Hao

last: Yin

address: Tianshuinanlu 222

department: Life Science School

country: China

institute: Lanzhou university

description: Gene expression of intact seedlings at 22-26hr after grafting

hyb_protocol: Each Slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US), Stabilization and Drying Solution (Cat#5185-5979, Agilent technologies, Santa Clara, CA, US)followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565BA, Agilent technologies, Santa Clara, CA, US) and Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US) with default settings，Scan resolution=5μm, PMT 100%，10%. Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

data_processing: Data pre-processing and differential expression analysis of the gene expression data were done in R (version 2.10.0. Bioconductor, http://bioconductor.org/). Data were normalized between arrays using the quantile method. Normalized expression data was subjected to log2 transformation. For differential expression analysis, Student’s t test assumed that the variance of the two classes were not the same was applied. Firstly, data were analysed between A and C with the p-value ≤0.01, q-value≤0.05, and foldchange≥2. Differential probes were subsequently compared between A and B with p-value≤0.01, q-value≤0.05

source_name: Arabidopsis seedlings, intact seedlings, 22-26 hours

label_protocol: Total RNA was amplified and labeled by Low RNA Input Linear Amplification kit (Cat#5184-3523, Agilent technologies, Santa Clara, CA, US), 5-(3-aminoallyl)-UTP (Cat#AM8436, Ambion, Austin, TX,US), Cy3 NHS ester (Cat#PA13105,GE healthcare Biosciences, Pittsburgh, PA,US) followed the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

growth_protocol: Arabidopsis thaliana ecotype Col-0 seeds were sown on the medium. The plates were incubated in the dark at 4°C for 2–3 days, then placed vertically in growth room (temperature: 22–25°C; light intensity: 6000 lux; photoperiod: 16h light, 8h dark) with the thin side pointing downward and the thick side upward. Grafting was performed using a dissecting microscope at 4 days post germination.

extract_protocol: Total RNA from frozen sample A, B and C were extracted by the Trizol reagent (Invitrogen) and purified with QIAGEN RNeasy® Mini Kit (QIAGEN) according to the manufacturer’s instructions. Total RNA concentration was assessed by spectrophotometry (OD 260 nm), and purity and integrity of the RNA were determined by the absorbance ratio at 260/280 nm and visualization after electrophoresis.

treatment_protocol: 4 days old seedlings were cut with razor blade to produce scion and stock. For making sample A, lift the scion up, bring it to the stock, and then pick up the stock carefully to approach the scion and connect them together. For sample B, the scions and stocks were not grafted and reserved until sampling at 22-26 hours after grafting. For sample C, intact seedlings were also reserved during grafting. Sample A, B and C were collected next day at 22-26 hours after grafting for RNA extraction.

value: whole intact seedlings

value: 22-26 hours after grafting


title: Arabidopsis seedlings_intact seedlings_22-26hr_rep 3_technical replicate 1


title: Arabidopsis seedlings_intact seedlings_22-26hr_rep 1


title: Arabidopsis seedlings_intact seedlings_22-26hr_rep 2


title: Arabidopsis seedlings_ungrafted scions and stocks_22-26hr_rep3

description: Gene expression of ungrafted scions and stocks at 22-26hr after cut

source_name: Arabidopsis seedlings, ungrafted scions and stocks, 22-26 hours

value: mixture of ungrafted scions and stocks

value: 22-26 hours after cut


title: Arabidopsis upf3-1-3F

description: Gene expression data from  untreated upf3-1 plants

source_name: Untreated Arabidopsis upf3-1 plants


title: Arabidopsis upf3-1-2F


title: Arabidopsis WT (XRN)-2F


title: Arabidopsis WT (XRN)-1F


title: Arabidopsis seedlings_ungrafted scions and stocks_22-26hr_rep2


title: Arabidopsis seedlings_ungrafted scions and stocks_22-26hr_rep1


title: Arabidopsis upf3-1-1F


title: ATM_103.r

city: Cambridge

first: Ana Teresa

last: Maia

state: Cambridgeshire

address: Robinson Way

country: United Kingdom

institute: University of Cambridge

description: Human female breast tissue hybridised onto Illumina HumanExon510-Sv1 DNA Analysis BeadChip

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Within-array strip-level quantile normalization was used to correct for dye-biases between the two channels (in general X = Cy5 = allele A and Y = Cy3 = allele B) from each array, as previously recommended for Illumina Infinium BeadChip data Ritchie et al. (2009; R/Bioconductor software for Illumina's Infinium whole-genome genotyping BeadChips, Bioinformatics, 25, 2621-3) to obtain normalized intensities for each SNP (X and Y).

label: C-Bio and A-DNP

source_name: Mammoplastic reduction

label_protocol: 250ng of genomic and ds-CDNA (prepared from 1ug of total RNA) were labelled according to Illumina standard protocol.

extract_protocol: DNA from normal breast samples was extracted using a conventional SDS/proteinase K/phenol method. Total RNA was extracted from all samples using Qiazol (Invitrogen, Carlsbad, CA, USA) following manufacturer's instructions. The RNA was subsequently treated with DNaseI and repurified using acidic phenol-chlorophorm, and ethanol precipitation. DNA and RNA integrity were checked using the Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).

value: Normal Breast Sample

value: Female


title: Arabidopsis upf1-1-3F

description: Gene expression data from  untreated upf1-1 plants

source_name: Untreated Arabidopsis upf1-1 plants

value: Columbia


title: Arabidopsis seedlings_grafts_22-26hr_rep 3

description: Gene expression of grafts at 22-26hr after grafting

source_name: Arabidopsis seedlings, grafts, 22-26 hours

value: whole grafts


title: ATM_101.r


title: Arabidopsis upf1-1-2F

value: 15-day-old plants


title: ATM_100.g


title: ATM_95.g


title: ATM_102.g


title: ATM_102.r


title: ATM_98.r


title: ATM_99.r


title: ATM_97.r


title: ATM_103.g


title: Arabidopsis seedlings_grafts_22-26hr_rep 1


title: ATM_99.g


title: ATM_98.g


title: ATM_100.r


title: Arabidopsis WT (UPF)-2F

description: Gene expression data from untreated Arabidopsis WT (UPF) plants

source_name: Untreated Arabidopsis WT (UPF) plants


title: ATM_92.r


title: ATM_101.g


title: Arabidopsis WT (UPF)-1F


title: Arabidopsis upf1-1-1F


title: ATM_94.r


title: Arabidopsis WT (UPF)-3F


title: ATM_96.r


title: Arabidopsis seedlings_grafts_22-26hr_rep 2


title: ATM_93.r


title: ATM_96.g


title: Arabidopsis xrn4-6-3F

source_name: Untreated Arabidopsis xrn4-6 plants


title: ATM_93.g


title: FcR II KO stimulated replicate 3

city: Leiden

first: Peter

last: 't Hoen

address: PO Box 9600

department: Center for Human and Clinical Genetics

country: Netherlands

institute: Leiden University Medical Center

hyb_protocol: Samples were hybridised on Illumina mouse WG-6 V1.1 expression BeadChips.

scan_protocol: BeadChips were scanned on the Illumina BeadArray 500GX Scanner.

data_processing:
Raw data was exported by Illumina BeadStudio V3.0 software and imported and stored in Rosetta Resolver software.
Not Normalized data sheet contains intensities corrected for background by Rosetta's default error model; Normalized data sheet contains intensities normalized with Rosetta's default error model for Illumina arrays on a back-transformed linear scale and where different probes for the same gene are averaged and thus get the same value

label: Biotin

source_name: FcR II KO 3 IC

label_protocol: Illumina RNA amplfication kit includes incorporation of biotin.

growth_protocol: Bone marrow was harvested from the femurs and tibia derived from two female and two male mice of each mouse strain. The cells of all 12 mice were cultured separately in IMDM supplemented with GM-CSF containing supernatant in petri dishes. Non-adherent and semi-adherent cells were transferred to new dishes and fresh medium on days 4 and 7. On day 10, the cells were harvested and the % of immature CD11c+ DCs was determined by flow cytometry, which was typically above 85%.

extract_protocol: Total RNA was isolated from cells by Qiagen RNA Easy kit. RNA was amplified by using the Illumina RNA Amplification kit.

treatment_protocol: Bone marrow-derived dendritic cells (BM-DCs) were transferred to new culture dishes at a density of 1 million BM-DC per 2 ml medium. The BM-DCs were incubated with either medium (unstimulated) or preformed Ag-Ab complexes (IC) containing 1 µg/ml OVA (Worthington) and 50 µg/ml rabbit anti-OVA IgG (ICN biomedicals) at 37 degrees for 4 hours.

tag: treatment

value: OVA-anti OVA immune complexes

value: bone-marrow derived dendritic cells

tag: genetic background

value: Fcγ receptor IIb KO


title: ATM_94.g


title: FcR II KO stimulated replicate 4

source_name: FcR II KO 4 IC


title: ATM_92.g


title: FcR II KO stimulated replicate 2

source_name: FcR II KO 2 IC


title: ATM_91.r


title: ATM_97.g


title: FcR II KO stimulated replicate 1

source_name: FcR II KO 1 IC


title: ATM_89.r


title: wild type stimulated replicate 2

source_name: WT 2 IC

value: Wild type


title: wild type stimulated replicate 1

source_name: WT 1 IC


title: ATM_90.r


title: ATM_95.r


title: ATM_90.g


title: ATM_91.g


title: FcR II KO unstimulated replicate 4

source_name: FcR II KO 4 medium

value: unstimulated


title: ATM_89.g


title: FcR II KO unstimulated replicate 2

source_name: FcR II KO 2 medium


title: FcR II KO unstimulated replicate 3

source_name: FcR II KO 3 medium


title: ATM_86.r


title: ATM_87.g


title: ATM_87.r


title: ATM_85.r


title: FcR II KO unstimulated replicate 1

source_name: FcR II KO 1 medium


title: ATM_86.g


title: ATM_81.g


title: ATM_83.g


title: ATM_85.g


title: ATM_82.r


title: wild type unstimulated replicate 2

source_name: WT 2 medium


title: ATM_83.r


title: ATM_84.r


title: ATM_81.r


title: ATM_84.g


title: γ chain KO stimulated replicate 4

source_name: γ chain KO 4 IC

value: Fc receptor γ chain KO


title: wild type unstimulated replicate 1

source_name: WT 1 medium


title: ATM_79.r

source_name: Mammoplastic reduction


title: ATM_80.g


title: ATM_82.g


title: ATM_78.r


title: ATM_88.r


title: γ chain KO stimulated replicate 3

source_name: γ chain KO 3 IC


title: γ chain KO stimulated replicate 2

source_name: γ chain KO 2 IC


title: wild type stimulated replicate 4

source_name: WT 4 IC


title: ATM_77.r


title: γ chain KO stimulated replicate 1

source_name: γ chain KO 1 IC


title: ATM_75.r


title: set3_mpk11_3h_flg

city: Wuhan

first: Kenichi

last: Tsuda

address: No.1 Shizishan Road

institute: Huazhong Agricultural University

description: All spots on the microrray include DNA fragments which binds to Cy5 labeled oligo DNA so that spots with bad quality can be identified and removed from further analysis.

hyb_protocol: Hybridization was performed as described in Sato et al., The Plant Journal (2007) 49: 565-577

scan_protocol: Scanning was performed as described in Sato et al., The Plant Journal (2007) 49: 565-577

data_processing: The scanned data were subjected to quantile normalization as described in Sato et al., The Plant Journal (2007) 49: 565-577

label_protocol: Labeling was performed as described in Sato et al., The Plant Journal (2007) 49: 565-577

growth_protocol: Ten-day-old Arabidopsis seedlings were grown in MS medium under a 12h dark/12h light regime at 22°C and transferred to multi-well plates containing fresh liquid MS media 48 h before flg22 (1uM) or mock (water) treatment.

extract_protocol: Total RNA from leaves was isolated using the Trizol Reagent method according to the manufacturer’s recommendations (Invitrogen)

treatment_protocol: Arabidopsis seedlings were treated with 1uM flg22 or water

value: Col

tag: time


title: wild type stimulated replicate 3

source_name: WT 3 IC


title: ATM_76.r


title: ATM_80.r


title: ATM_76.g


title: ATM_79.g


title: set3_mpk11_30min_mock

value: mock


title: ATM_75.g


title: ATM_78.g


title: set3_mpk11_30min_flg


title: γ chain KO unstimulated replicate 4

source_name: γ chain KO 4 medium


title: γ chain KO unstimulated replicate 3

source_name: γ chain KO 3 medium


title: ATM_88.g


title: set3_mpk11_3h_mock


title: ATM_77.g


title: ATM_74.g


title: set3_Col_3h_mock

value: wildtype


title: γ chain KO unstimulated replicate 1

source_name: γ chain KO 1 medium


title: wild type unstimulated replicate 4

source_name: WT 4 medium


title: γ chain KO unstimulated replicate 2

source_name: γ chain KO 2 medium


title: ATM_71.g


title: ATM_71.r


title: ATM_74.r


title: ATM_72.r


title: set3_Col_30min_mock


title: ATM_70.r


title: ATM_69.g


title: ATM_73.r


title: Arabidopsis upf3-1-3R

source_name: Untreated Arabidopsis upf3-1 plants

tag: age


title: set3_Col_30min_flg


title: wild type unstimulated replicate 3

source_name: WT 3 medium


title: set3_Col_3h_flg


title: set2_mpk11_3h_mock


title: ATM_73.g


title: ATM_70.g


title: ATM_72.g


title: Arabidopsis upf3-1-2R


title: ATM_68.r


title: set2_mpk11_3h_flg


title: Arabidopsis upf3-1-1R


title: ATM_69.r


title: ATM_67.r


title: ATM_68.g


title: Arabidopsis upf1-1-3R

source_name: Untreated Arabidopsis upf1-1 plants


title: set2_Col_3h_mock


title: ATM_66.g


title: ATM_67.g


title: set2_mpk11_30min_flg


title: set2_mpk11_30min_mock


title: Arabidopsis upf1-1-1R


title: ATM_64.g


title: set2_Col_3h_flg


title: Arabidopsis WT (UPF)-3R

source_name: Untreated Arabidopsis WT (UPF) plants

value: wild type


title: ATM_66.r


title: S288C ΔGCN5, biological rep2

city: AUSTIN

first: Amanda

middle: Morgan

last: Lanza

address: 1 University Station C0400

department: Chemical Engineering

institute: University of Texas at Austin

hyb_protocol: Conducted by Asuragen in Austin, TX

scan_protocol: Conducted by Asuragen in Austin, TX

data_processing: Preliminary data processing was done using R/Bioconductor and the RMA algorithm.

organism: Saccharomyces cerevisiae

source_name: whole cell RNA, GCN5 null strain

label_protocol: Standard Affymetrix protocol

growth_protocol: A 5mL culture of 20g/L glucose, 6.7 g/L nitrogen base and 200 μg/mL G418 was inoculated at an OD of 0.0045.  Extractions proceeded at OD of 0.4 to 0.5

extract_protocol: Extractions were performed using the Ambion Ribo-Pure kit for yeast

tag: strain

value: S288C ΔGCN5

tag: promoter strength


title: Arabidopsis upf1-1-2R


title: set2_Col_30min_mock


title: ATM_65.r


title: Arabidopsis WT (UPF)-2R


title: ATM_63.r


title: ATM_64.r


title: set2_Col_30min_flg


title: Arabidopsis WT (UPF)-1R


title: ATM_62.g


title: Arabidopsis xrn4-6-3R

source_name: Untreated Arabidopsis xrn4-6 plants


title: set1_mpk11_3h_mock


title: TEF11-GCN5 F221A, biological rep3

source_name: whole cell RNA, 68% TEF expression GCN5 F221A

value: TEF11-GCN5 F221A


title: ATM_60.r

source_name: Mammoplastic reduction

value: Normal Breast Sample


title: TEF11-GCN5 F221A, biological rep2


title: ATM_65.g

value: Female


title: ATM_61.r


title: TEF11-GCN5 F221A, biological rep1


title: ATM_62.r


title: S288C ΔGCN5, biological rep1


title: Arabidopsis xrn4-6-2R

value: Columbia


title: S288C ΔGCN5, biological rep3


title: Arabidopsis xrn4-6-1R


title: TEF5-GCN5 F221A, biological rep2

source_name: whole cell RNA, 95% TEF expression GCN5 F221A

value: TEF5-GCN5 F221A


title: TEF5-GCN5 F221A, biological rep3


title: Arabidopsis xrn3-3-2R

source_name: Untreated Arabidopsis xrn3-3 plants

value: 15-day-old plants


title: set1_Col_3h_mock


title: Arabidopsis xrn3-3-3R


title: TEF5-GCN5 F221A, biological rep1


title: set1_mpk11_3h_flg


title: set1_mpk11_30min_flg


title: set1_Col_3h_flg


title: ATM_59.g


title: Arabidopsis xrn3-3-1R


title: TEF3-GCN5 F221A, biological rep3

source_name: whole cell RNA, 32% TEF expression GCN5 F221A

value: TEF3-GCN5 F221A


title: ATM_59.r


title: set1_Col_30min_mock


title: ATM_58.r


title: Arabidopsis xrn2-4-3R

source_name: Untreated Arabidopsis xrn2-4 plants


title: set1_mpk11_30min_mock


title: ATM_57.r


title: ATM_56.r


title: Arabidopsis xrn2-4-2R


title: TEF3-GCN5 F221A, biological rep1


title: ATM_58.g


title: ATM_56.g


title: set1_Col_30min_flg


title: Arabidopsis xrn2-4-1R


title: wild-type S288C, biological rep3

source_name: whole cell RNA, no GCN5 F221A expression


title: Arabidopsis fry1-6-3R

source_name: Untreated Arabidopsis fry1-6 plants


title: ATM_57.g


title: wild-type S288C, biological rep2


title: oxyR mut_anaerobic_nitrate_rep1

city: Cleveland

first: Divya

last: Seth

state: OH

address: 2106 Cornel Road

institute: Case Western Reserve University

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing:
The .chp file contains the MAS 5.0 normalized values for the signal
intensities of the probes on the array.

label: Biotin label

organism: Escherichia coli str. K-12 substr. MG1655

source_name: E. coli oxyR null grown in MOPS minimal medium containing 10 mM nitrate

label_protocol:
Labeling done using Nugen Ovation Pico labeling system according to
manufacturer's instructions

extract_protocol:
The bacterial cultures were treated with RNAprotect bacteria reagent
(Qiagen) to stabilize the RNA. RNA was extracted from harvested cells
with the RNEasy kit (Qiagen).

treatment_protocol:
MG1655 oxyR null were grown anaerobically on MOPS minimal medium
containing 10 mM nitrate as electron acceptor. The cells were
harvested at A600 0.4-0.45.

tag: substrain

value: oxyR null

tag: growth media

tag: condition

value: Anaerobic


title: wild-type S288C, biological rep1

tag: genotype/variation


title: ATM_63.g


title: ATM_55.g


title: Arabidopsis fry1-6-2R

tag: ecotype

tag: biological rep


title: ATM_55.r


title: oxyR mut_anaerobic_nitrate_rep2

value: MOPS minimal medium containing 10 mM nitrate


title: Arabidopsis fry1-6-1R


title: oxyR mut_anaerobic_fumarate_rep1

source_name: E. coli oxyR null grown in MOPS minimal medium containing 10 mM fumarate

treatment_protocol:
MG1655 oxyR null were grown anaerobically on MOPS minimal medium
containing 10 mM fumarate as electron acceptor. The cells were
harvested at A600 0.4-0.45.


title: Arabidopsis WT (XRN)-3R

source_name: Untreated Arabidopsis WT (XRN) plants


title: oxyR mut_anaerobic_fumarate_rep2

value: MOPS minimal medium containing 10 mM fumarate


title: WT_anaerobic_nitrate_rep2

source_name: E. coli MG1655 grown in MOPS minimal medium containing 10 mM nitrate

treatment_protocol:
MG1655 were grown anaerobically on MOPS minimal medium
containing 10 mM nitrate as electron acceptor. The cells were
harvested at A600 0.4-0.45.

value: wild-type


title: TEF3-GCN5 F221A, biological rep2


title: Arabidopsis WT (XRN)-2R


title: genomic DNA from YCC-11 rep2

city: Singapore

first: Tatiana

last: Ivanova

address: 2 Jalan Bukit Merah Singapore 169547

department: Cancer & Stem Cell Biology Program

country: Singapore

institute: Duke-NUS Graduate Medical School

description: gastric cancer

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Goldengate methylation Beadchip using standard Illumina protocol

data_processing: BeadStudio software v3.2

source_name: gastric cancer cell line

extract_protocol: genomic DNA was extracted from gastric cancer cell lines using Qiagen DNeasy Kit according to standard instructions

tag: cell type

value: gastric cancer cell line

tag: disease state

value: cancer


title: ATM_54.g

tag: gender


title: genomic DNA from YCC-11 rep1

description: gastric cancer

tag: cell line


title: Arabidopsis WT (XRN)-1R


title: ATM_53.g

tag: tissue


title: WT_anaerobic_fumarate_rep2

source_name: E. coli MG1655 grown in MOPS minimal medium containing 10 mM fumarate

treatment_protocol:
MG1655 were grown anaerobically on MOPS minimal medium
containing 10 mM fumarate as electron acceptor. The cells were
harvested at A600 0.4-0.45.


title: genomic DNA from YCC-10 rep2

description: gastric cancer


title: ATM_52.r


title: genomic DNA from YCC-16 rep2

description: gastric cancer

label: Cy5 and Cy4


title: WT_anaerobic_fumarate_rep1


title: genomic DNA from YCC-16 rep1

description: gastric cancer


title: Jejunum_Control/MR8

city: Boston

first: Jonathan

middle: M

last: Dreyfuss

state: MA

address: 1 Joslin Pl

department: Bioinformatics & Biostatistics Core

institute: Joslin Diabetes Center

hyb_protocol: Samples were profiled on in situ hybridization arrays (Exiqon, Woburn, MA) against a reference sample consisting of RNA pooled from transected rats.

scan_protocol: Scanning was done using a GenePix 4000B scanner and quantified with GenePix Pro 6.0.1.25.

data_processing: Data was background corrected and loess normalized using the R / Bioconductor package limma. Each spot is printed in quadruplicate on the arrays, and the median log-ratio of each of these 4 spots is given here, where probes given negative flags were excluded.

organism: Rattus norvegicus

source_name: Resections

label_protocol: Samples were labeled as Hy5 or Hy3 using the Exiqon miRCURY LNA microRNA Array labeling kit according to manufacturer's protocols.

extract_protocol: Total RNA from rat jejunum was extracted using the mirVana kit (Ambion; Austin, TX).

treatment_protocol: Rats underwent either 80% massive small bowel resection or transection and were harvested after 48-hours.

value: Sprague-Dawley

source_name: Pooled transected control


title: ATM_53.r


title: PDGF-DD_treated_SMCs

city: Charlottesville

first: Gary

last: Owens

state: VA

address: 415 Lane Road

department: Molecular Physiology and Biological Physics

institute: University of Virginia

description: Gene expression data from PDGF-DD-treated rat aortic smooth muscle cells

hyb_protocol: 10 ug of cRNA was hybridized for 16 hours on Affymetrix rat 230 2.0 GeneChips and stained using Affymetrix Fluidics Station 450 according to Affymetrix protocols.

scan_protocol: GeneChips were scanned using the Affymetrix Scanner 3000.

data_processing: Array normalization and processing was performed using the ExpressionFileCreator module of GenePattern (Broad Institute).  MAS5 was used for processing, and normalization was performed with median scaling.  Significant differences were defined as fold changes greater or less than or equal to 2 and signal differences in signal intensity greater than or equal to 100.

source_name: Rat aortic smooth muscle cells treated with PDGF-DD (30 ng/mL)

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

growth_protocol: Rat aortic SMCs were grown to confluency in serum-containing DMEM/F12 media for 3 days, then serum starved in serum-free media for 3 days, and then were treated.

extract_protocol: Total RNA was extracted using Trizol reagent according to the manufacturer's instructions.

treatment_protocol: Cells were treated with IL-1b (2.5 ng/mL; R&D Systems) or vehicle (0.1% bovine serum albumin [BSA] and 10 mM acetic acid), or PDGF-DD (30 ng/mL; Zymogenetics) or vehicle (0.01% BSA) for 24 hours.


title: Jejunum_MR10/Control


title: PDGF-DD_vehicle_treated_SMCs

description: Gene expression data from PDGF-DD vehicle-treated rat aortic smooth muscle cells

source_name: Rat aortic smooth muscle cells treated with PDGF-DD vehicle (0.01% BSA)


title: IL-1b_treated_SMCs

description: Gene expression data from IL-1b-treated rat aortic smooth muscle cells

source_name: Rat aortic smooth muscle cells treated with IL-1b (2.5 ng/mL)


title: WT_anaerobic_nitrate_rep1


title: ATM_54.r

source_name: Mammoplastic reduction


title: ATM_51.r


title: Jejunum_Control/MR10


title: genomic DNA from YCC-7  rep2

description: gastric cancer


title: ATM_51.g


title: ATM_61.g


title: genomic DNA from YCC-3 rep2

description: gastric cancer


title: Jejunum_MR8/Control


title: genomic DNA from YCC-7  rep1

description: gastric cancer


title: genomic DNA from YCC-10 rep1

description: gastric cancer


title: ATM_52.g


title: genomic DNA from YCC-3 rep1

description: gastric cancer


title: Jejunum_Control/MR9


title: genomic DNA from YCC-1 rep2

description: gastric cancer


title: IL-1b_veh_treated_SMCs

description: Gene expression data from IL-1 vehicle-treated rat aortic smooth muscle cells

source_name: Rat aortic smooth muscle cells treated with IL-1b vehicle (.1% BSA and 10 mM acetic acid)


title: ATM_50.r


title: ATM_60.g


title: Insulin_8_rep_c

city: Padova

first: Barbara

last: Di Camillo

address: via Gradenigo 6B

department: Information Engineering Department

country: Italy

institute: University of Padova

hyb_protocol: Hybridization was performed using protocols described in the Affymetrix GeneChip expression analysis technical manual.

scan_protocol: Image quantification was performed using GeneChip (Affymetrix, SantaClara, CA) scanner and software.

data_processing: Preprocessing steps such as background subtraction, probe cell normalization and expression level calculations were performed using quantile normalization and Robust Microarray Analysis (RMA) software. Genes were pre-filtered using Affymetrix Detection calls (genes that were not present in at least one chip were filtered out). Sample 'Insulin_3_rep_a' (pool of 140', 160', 180') was excluded from the analysis since it had quite poor MvA plots compared to the median microarray signal. All of the methods were implemented using R (http://www.r-project.org/) and packages from BioConductor (http://www.bioconductor.org/) for genomic and microarrays data handling.

source_name: L6 skeletal muscle myoblasts - 20nM insulin treated - pooling of 440', 460', 480'

label_protocol: Sample labeling was performed using protocols described in the Affymetrix GeneChip expression analysis tecnical manual.

growth_protocol: L6 skeletal muscle myoblasts were grown and kept in low glucose (5 mM) DMEM growth media supplemented with fetal bovine serum (FBS) and an antibiotic-antimycotic mixture (10% FBS, 4mM L-Glutamine, 1.0mM sodium pyruvate, 100ug/ml penicillin 100ug/ml streptomycin).  Four plates were prepared for each pre-defined time sample at a density of 6:8 10^5cells per 100 mm dish and incubated overnight in DMEM growth media.  On the second day, the DMEM growth media was changed to DMEM differentiation media with 1% FBS to initiate myotube differentiation.  The differentiation media was changed every 2 days. On the sixth day, differentiation was completed and medium was changed to serum-free DMEM for an 8 hour pre-incubation.

extract_protocol: Total RNAs were purified using an RNeasy Protect Mini Kit from Qiagen.  The quality and quantity of total RNA was measured using the Agilent test on a Bioanalyzer (Agilent Technologies, Palo Alto, CA).

treatment_protocol:
The culture was split into 2 different groups: insulin treated and control.  Just after the collection of the first biological sample at time 0’, for each time point the medium on one plate was changed to serum-free DMEM with 20nM insulin, and the other plate was used as control (DMEM with 0nM insulin). Cells were harvested at the designated time points by decanting off overlying medium, scraping the cells into cryovials and freezing immediately in liquid nitrogen. Samples were collected at times 0, 20, 40, 60, . . . , 480 minutes (every 20 minutes, for 8 hours) from both insulin-treated and control cultures, for a total of 50 biological samples.
Samples (20, 40, 60), (80, 100, 120), (140, 160, 180), (200, 220, 240), (260, 280, 300), (320, 340, 360), (380, 400, 420) and (440, 460, 480) from insulin-treated and control culture were pooled together, obtaining eight joint samples. Consistently, sample 0’ was harvested and collected in triplicates and pooled together (0a-0b-0c) for each culture and two targets for the hybridization were prepared separately. All of the culturing and sampling procedures described above were repeated two additional times on different days, using the same identical cell line, to obtain a complete triplicate of the experiment.

value: skeletal muscle myoblasts

tag: treatment

value: insulin

tag: treatment duration

value: pool of 400 min, 460 min, 480 min


title: Insulin_8_rep_a


title: genomic DNA from YCC-1 rep1

description: gastric cancer


title: genomic DNA from SCH  rep2

description: gastric cancer

value: SCH


title: ATM_49.r

value: Normal Breast Sample

value: Female


title: ATM_49.g


title: Insulin_7_rep_c

source_name: L6 skeletal muscle myoblasts - 20nM insulin treated - pooling of 380', 400', 420'

value: pool of 380 min, 400 min, 420 min


title: ATM_48.g


title: genomic DNA from SCH  rep1

description: gastric cancer


title: genomic DNA from AZ-521 rep2

description: gastric cancer


title: Insulin_7_rep_a


title: Insulin_7_rep_b


title: genomic DNA from AZ-521 rep1

description: gastric cancer


title: ATM_50.g


title: Insulin_8_rep_b


title: Insulin_6_rep_b

source_name: L6 skeletal muscle myoblasts - 20nM insulin treated - pooling of 320', 340', 360'

value: pool of 320 min, 340 min, 360 min


title: genomic DNA from TMK1  rep1

description: gastric cancer


title: Insulin_6_rep_c


title: genomic DNA from IM95  rep2

description: gastric cancer


title: Esophageal squamous cell carcinoma 123

city: Lund

first: Anna

middle: Isinger

last: Ekstrand

address: Barngatan 2b

department: Oncology

institute: Clinical Sciences

description: Esophageal cancer

hyb_protocol: Hybridizations were performed in 4 x SSC, 0.1% SDS, 0,5 NOTE human 0,8-1,0 µg/µl Cot-1 DNA at 42degC overnight. Arrays were washed three times 4xSSC RT, twice 2xSSC / 0.1% SDS at 42degC, one time 0.2xSSC, and  one time 0.1xSSC RT.

scan_protocol: Arrays were scanned in Agilent scanner (Agilent Technologies)

data_processing:
Image analysis was performed using Genepix v4.0. Result files were uploaded into BASE where they were filtered and normalized.
Correction of background intensities of Cy3 and Cy5 were calculated by means of a median-feature and median-local background intensities of the uploaded files. The intensity ratios for the individual probes were calculated as intensity of the background-corrected tumor channel (Cy3) divided with the intensity of the background-corrected reference channel (Cy5). Low-quality spots flagged during image analysis, and spots with a signal-to-noise ratio (SNR) of <1.5 and >10% saturation were excluded from further analysis.    To compensate for dye bias and local background effects, data were normalized by a lowess algorithm in BASE

source_name: Esophageal squamous cell carcinoma, fresh frozen tissue

label_protocol: Direct labeled by random priming (Promega, Pronto)

extract_protocol: Total RNA extracted using Trizol (Invitrogen) according to the manufacures recommendations. RNA integrity was checked on a Bioanalyzer (Agilent).

value: Esophageal squamous cell carcinoma tumor

tag: biomaterial

value: Fresh frozen tissue

value: Male

tag: tumor stage

value: IV

source_name: Human Reference RNA (Stratagene), pool of ten cell lines

value: Pool of 10 different cell lines


title: ATM_46.r


title: Insulin_6_rep_a


title: Insulin_5_rep_c

source_name: L6 skeletal muscle myoblasts - 20nM insulin treated - pooling of 260', 280', 300'

value: pool of 260 min, 280 min, 300 min


title: Esophageal squamous cell carcinoma 120

description: Esophageal cancer

value: III


title: Insulin_5_rep_b


title: genomic DNA from IM95  rep1

description: gastric cancer

value: gastric cancer cell line

value: cancer


title: genomic DNA from TMK1  rep2

description: gastric cancer


title: genomic DNA from MKN74 rep2

description: gastric cancer


title: Esophageal squamous cell carcinoma 116

description: Esophageal cancer


title: Insulin_5_rep_a

value: skeletal muscle myoblasts


title: genomic DNA from MKN74 rep1

description: gastric cancer


title: ATM_48.r


title: Esophageal squamous cell carcinoma 94

description: Esophageal cancer

value: II


title: genomic DNA from MKN45 rep2

description: gastric cancer


title: Esophageal squamous cell carcinoma 50

description: Esophageal cancer


title: ATM_46.g


title: genomic DNA from MKN45 rep1

description: gastric cancer


title: ATM_47.r


title: Insulin_4_rep_a

source_name: L6 skeletal muscle myoblasts - 20nM insulin treated - pooling of 200', 220', 240'

value: insulin

value: pool of 200 min, 220 min, 240 min


title: Insulin_3_rep_c

source_name: L6 skeletal muscle myoblasts - 20nM insulin treated - pooling of 140', 160', 180'

value: pool of 140 min, 160 min, 180 min


title: ATM_45.g

value: Normal Breast Sample

value: Female


title: Insulin_4_rep_b


title: Esophageal squamous cell carcinoma 33

description: Esophageal cancer

value: I


title: genomic DNA from MKN28  rep2

description: gastric cancer

source_name: gastric cancer cell line


title: ATM_47.g


title: ATM_45.r


title: Insulin_4_rep_c


title: genomic DNA from MKN28  rep1

description: gastric cancer


title: Insulin_3_rep_b


title: Esophageal squamous cell carcinoma 24

description: Esophageal cancer

value: Esophageal squamous cell carcinoma tumor


title: Esophageal squamous cell carcinoma 27

description: Esophageal cancer

value: Fresh frozen tissue


title: genomic DNA from MKN7 rep1

description: gastric cancer


title: Insulin_2_rep_c

source_name: L6 skeletal muscle myoblasts - 20nM insulin treated - pooling of 80', 100', 120'

value: pool of 80 min, 100 min, 120 min


title: genomic DNA from MKN7 rep2

description: gastric cancer


title: Esophageal squamous cell carcinoma 10

description: Esophageal cancer

value: Male


title: genomic DNA from MKN1-NCC rep2

description: gastric cancer


title: genomic DNA from MKN1-NCC rep1

description: gastric cancer


title: parietal lobe tissue human male age 2 years 7 months rep1

city: Eugene

first: Kirstin

last: Sterner

state: OR

address: 1218 University of Oregon

department: Anthropology

institute: University of Oregon

hyb_protocol: Illumina Human HT-12v3 chips using the Illumina BeadChip platform.

scan_protocol: Illumina BeadStudio (V.3) was used to process the arrays and obtain background corrected intensity values for all 48,803 probes in 40 arrays (corresponding to 37 unique brain samples) as well as the probe detection p-values.

data_processing:
The preprocessing protocol used to get from the raw to the normalized data for Analysis I (sterner_geo_norm_analysisI.csv) included the following 7 steps: 1) The raw data was background corrected in BeadStudio (Gene Expression module V. 3.4.0); 2) The 6 arrays form patients with AGE>18 years were discarded from further analysis; 3) The detection p values for each probe was averaged over replicate arrays of the same samples; 4) Probes with a average detection p-value of <0.1 in 16 or more samples were retained for further analysis; 5) Let B be the intensity matrix of the probes obtained at step 4. A constant k=abs(min(B))+1 was added to B, to obtain B'. This was needed to allow log transformation of the data; 6) Values in the matrix B' were then log2 transfomed and quantile normalized using the normalize.quantiles from the preprocessCore package (v 1.8.0) of Bioconductor; and 7) Normalized values (on the log scale) were averaged over the replicate arrays of the same samples. The analysis protocol used to get from the raw to the normalized data for Analysis II (sterner_geo_norm_analysisII.csv) was identical with the one above except that the step 2 was skipped since all samples were allowed into this latter analysis.
Values are log2 transfomed and quantile normalized using the normalize.quantiles from the preprocessCore package (v 1.8.0) of Bioconductor.

source_name: surgically resected control tissue taken from the parietal lobe of the cerebral cortex

label_protocol: TotalPrep-96 RNA Amplification Kit (manual number 4397949 revision A) for labeling and the Whole-Genome Gene Expression Direct Hybridization Assay for the hybridization, wash, and stain were used.

extract_protocol: RNA extraction was completed using the TRIzol protocol or the MagMax-96 for Microarray kit following the manufacturers’ instructions. The TURBO DNase treatment or RNeasy kit in conjunction with the RNase-Free DNase Set was used to further purify the initial RNA isolation according to the manufacturer’s recommendations. The DNA-free RNA isolations with ABS 260/280 ratios above 1.7 and two distinct peaks representing the 18S and 28S ribosomal RNA and minimal background banding, were selected for analysis.

tag: Sex

value: male

tag: race/ethnicity

value: White

tag: age

value: 2 years and 7 months

tag: age (in years)

value: parietal lobe

tag: number of replicates


title: Insulin_1_rep_c

source_name: L6 skeletal muscle myoblasts - 20nM insulin treated - pooling of 20', 40', 60'

value: pool of 20 min, 40 min, 60 min


title: genomic DNA from Ist-1 rep2

description: gastric cancer

value: gastric cancer cell line

value: cancer


title: Insulin_2_rep_a

value: skeletal muscle myoblasts

value: insulin


title: temporal lobe tissue human male age 7 years 4 months rep1

source_name: surgically resected control tissue taken from the temporal lobe of the cerebral cortex

value: 7 years and 4 months

value: temporal lobe


title: Insulin_1_rep_b


title: temporal lobe tissue human female age 11 months rep1

value: female

value: 11 months


title: genomic DNA from Ist-1 rep1

description: gastric cancer


title: Insulin_2_rep_b


title: temporal lobe tissue human female age 24 years 4 months rep1

value: 24 years and 4 months


title: Insulin_1_rep_a


title: Esophageal squamous cell carcinoma 51

description: Esophageal cancer

value: Esophageal squamous cell carcinoma tumor

value: Fresh frozen tissue

value: IV

value: Pool of 10 different cell lines


title: genomic DNA from FU97  rep2

description: gastric cancer


title: genomic DNA from FU97  rep1

description: gastric cancer


title: pre-treatment_0_rep_c

source_name: L6 skeletal muscle myoblasts - pre-treatment - pooling of 0',0',0'

value: 0 min


title: temporal lobe tissue human male age 7 years 5 months rep1

value: male

value: White

value: 7 years and 5 months


title: pre-treatment_0_rep_b


title: temporal lobe tissue human female age 13 years 8 months rep1

value: 13 years and 8 months


title: genomic DNA from Hs 746T rep1

description: gastric cancer

value: Hs 746T

value: gastric cancer cell line

value: cancer


title: genomic DNA from Hs 746T rep2

description: gastric cancer


title: Control_8_rep_c

source_name: L6 skeletal muscle myoblasts - control - pooling of 440', 460', 480'

value: skeletal muscle myoblasts

value: DMEM control

value: pool of 400 min, 460 min, 480 min


title: pre-treatment_0_rep_a


title: ATM_44.g

source_name: Mammoplastic reduction

value: Normal Breast Sample

value: Female


title: ATM_42.r


title: genomic DNA from KATOIII  rep2

description: gastric cancer

value: KATOIII


title: ATM_42.g


title: Control_8_rep_b


title: temporal lobe tissue human female age 3 years 4 months rep1

value: female

value: 3 years and 4 months

value: temporal lobe


title: temporal lobe tissue human male age 15 years 11 months rep1

value: 15 years and 11 months


title: genomic DNA from KATOIII  rep1

description: gastric cancer


title: temporal lobe tissue human female age 43 years 6 months rep1

value: 43 years and 6 months


title: temporal lobe tissue human male age 36 years 11 months rep1

value: male

value: White

value: 36 years and 11 months


title: Control_8_rep_a


title: ATM_44.r


title: ATM_41.r


title: Control_7_rep_c

source_name: L6 skeletal muscle myoblasts - control - pooling of 380', 400', 420'

value: pool of 380 min, 400 min, 420 min


title: genomic DNA from AGS rep1

description: gastric cancer

value: AGS

value: gastric cancer cell line


title: temporal lobe tissue human male age 3 years 6 months rep1

description: normalized data is based on two replicates represented as SAMPLE 30 and SAMPLE 40 in the non-normalized.txt raw data file

value: Hispanic

value: 3 years and 6 months


title: ATM_43.r


title: ATM_40.r


title: temporal lobe tissue human female age 10 years 6 months rep1

value: 10 years and 6 months


title: ATM_40.g

value: Normal Breast Sample


title: Control_6_rep_b

source_name: L6 skeletal muscle myoblasts - control - pooling of 320', 340', 360'

value: skeletal muscle myoblasts

value: DMEM control

value: pool of 320 min, 340 min, 360 min


title: temporal lobe tissue human female age 8 years and 2 months rep1

value: female

value: 8 years and 2 months


title: Control_7_rep_a


title: ATM_41.g

value: Female


title: temporal lobe tissue human female age 42 years 6 months rep1

value: 42 years and 6 months

value: temporal lobe


title: temporal lobe tissue human female age 8 years 1 months rep1

value: White

value: 8 years and 1 months


title: genomic DNA from AGS rep2

description: gastric cancer

value: cancer


title: Control_5_rep_b

source_name: L6 skeletal muscle myoblasts - control - pooling of 260', 280', 300'

value: pool of 260 min, 280 min, 300 min


title: temporal lobe tissue human male age 2 years 7 months rep1

value: male

value: 2 years and 7 months


title: temporal lobe tissue human male age 47 years and 10 months rep1

description: normalized data is based on two replicates represented as SAMPLE 24 and SAMPLE 39 in the non-normalized.txt raw data file

value: 47 years  and 10 months


title: ATM_43.g


title: frontal lobe tissue human male age 6 years 3 months rep1

source_name: surgically resected control tissue taken from the frontal lobe of the cerebral cortex

value: 6 years and 3 months

value: frontal lobe


title: ATM_39.g

value: Normal Breast Sample


title: Control_5_rep_c

value: skeletal muscle myoblasts

value: DMEM control


title: ATM_39.r


title: temporal lobe tissue human male age 17 years 8 months rep1

value: 17 years and 8 months


title: temporal lobe tissue human male age 8 years rep1

value: 8 years


title: Control_4_rep_b

source_name: L6 skeletal muscle myoblasts - control - pooling of 200', 220', 240'

value: pool of 200 min, 220 min, 240 min


title: temporal lobe tissue human male age 11 years 10 months rep1

value: 11 years and 10 months


title: Control_3_rep_c

source_name: L6 skeletal muscle myoblasts - control - pooling of 140', 160', 180'

value: pool of 140 min, 160 min, 180 min


title: Control_4_rep_a


title: temporal lobe tissue human male age 8 years 7 months rep1

value: White

value: 8 years and 7 months

value: temporal lobe


title: temporal lobe tissue human female age 3 years 5 months rep1

value: female

value: 3 years and 5 months


title: Control_3_rep_b


title: Control_5_rep_a

value: pool of 260 min, 280 min, 300 min


title: temporal lobe tissue human male age 10 years 2 months rep1

value: male

value: 10 years and 2 months


title: temporal lobe tissue human male age 10 years 4 months rep1

value: 10 years and 4 months


title: Control_3_rep_a


title: Control_6_rep_a

value: pool of 320 min, 340 min, 360 min


title: occipital lobe tissue human male age 7 years 2 months rep1

description: normalized data is based on two replicates represented as SAMPLE 11 and SAMPLE 38 in the non-normalized.txt raw data file

source_name: surgically resected control tissue taken from the occipital lobe of the cerebral cortex

value: 7 years and 2 months

value: occipital lobe


title: frontal lobe tissue human female age 11 years rep1

value: Black

value: 11 years

value: frontal lobe


title: Control_2_rep_c

source_name: L6 skeletal muscle myoblasts - control - pooling of 80', 100', 120'

value: skeletal muscle myoblasts

value: DMEM control

value: pool of 80 min, 100 min, 120 min


title: Control_7_rep_b

value: pool of 380 min, 400 min, 420 min


title: temporal lobe tissue human male age 3 years rep1

value: White

value: 3 years

value: temporal lobe


title: Control_1_rep_b

source_name: L6 skeletal muscle myoblasts - control - pooling of 20', 40', 60'

value: pool of 20 min, 40 min, 60 min


title: Control_1_rep_c


title: Control_2_rep_b


title: temporal lobe tissue human female age 15 years 7 months  rep1

value: female

value: 15 years and 7 months


title: B cell_follicular lymphoma_16

city: Bethesda

first: Weixin

last: Wang

state: MD

address: 9000 Rockville Pike

department: DLM/CC

institute: NIH

description: miRNA profiling

hyb_protocol: Hybridization was done at 56ºC and 20 rpm for 20 h.

scan_protocol: Array images were scanned on Agilent’s G2505C scanner using settings for high-density miRNA arrays.

data_processing: The scanned images were processed with Agilent’s Feature Extraction software (v.10.7.3.1). We normalized the data with "all control probes" option using GeneSpring GX software.

source_name: B cell_follicular lymphoma_16

label_protocol: Total RNA (100 ng) was reverse transcribed and Cyanine3-pCp labeled using the Agilent microRNA labeling kit according to the manufacturer’s protocol.  Labeled cRNA was purified with Micro Bio-Spin 6 columns.

extract_protocol: Total RNA was isolated from enriched follicular lymphoma B cells and follicular hyperplasia B cells using miRNeasy Mini Kit (Qiagen, Germantown, MD). RNA concentration and quality was determined using an Agilent Bioanalyzer 2100 (Agilent, Wilmington, DE) and NanoDrop 2000 instrument (Thermo Scientific, Wilmington, DE).

value: follicular lymphoma B cells


title: B cell_follicular lymphoma_17

description: miRNA profiling

source_name: B cell_follicular lymphoma_17


title: Control_4_rep_c

value: pool of 200 min, 220 min, 240 min


title: cerebral cortex tissue human female age 11 months rep1

source_name: surgically resected control tissue taken from the  cerebral cortex (region unknown)

value: Asian

value: 11 months

value: cerebral cortex (region unknown)


title: temporal lobe tissue human male age 10 years 11 months rep1

value: male

value: 10 years and 11 months


title: temporal lobe tissue human female age 6 years rep1

value: 6 years


title: Control_1_rep_a

value: skeletal muscle myoblasts

value: DMEM control


title: B cell_follicular lymphoma_19

description: miRNA profiling

source_name: B cell_follicular lymphoma_19


title: B cell_follicular lymphoma_15

description: miRNA profiling

source_name: B cell_follicular lymphoma_15


title: Control_2_rep_a

value: pool of 80 min, 100 min, 120 min


title: Control_0_rep_b

source_name: L6 skeletal muscle myoblasts - control - pooling of 0',0',0'

value: 0 min


title: Control_0_rep_c


title: temporal lobe tissue human male age 10 months rep1

source_name: surgically resected control tissue taken from the temporal lobe of the cerebral cortex

value: White

value: 10 months


title: temporal lobe tissue human male age 6 years 2 months rep1

value: 6 years and 2 months

value: temporal lobe


title: Control_6_rep_c

value: pool of 320 min, 340 min, 360 min


title: frontal lobe tissue human male age 14 years 3 months rep1

value: 14 years and 3 months

value: frontal lobe


title: Control_0_rep_a


title: B cell_follicular lymphoma_14

description: miRNA profiling

source_name: B cell_follicular lymphoma_14

value: follicular lymphoma B cells


title: p53 ChIP [1of2]

city: Jackson

first: Luis

middle: A

last: Martinez

state: MS

address: 1500 North State St

department: Biochemistry

institute: University of Mississippi Medical Center

hyb_protocol: Performed by Nimblegen using standard protocol  http://www.nimblegen.com/products/chip/index.html

data_processing: Performed by Nimblegen using standard protocol  http://www.nimblegen.com/products/chip/dataguide/index.html

source_name: MDAH087 fibroblast cell line, ChIP

growth_protocol: Cells were maintained in DMEM + GlutaMax (Invitrogen)

extract_protocol: ChIP DNA was extracted, purified, amplified according to Farnham lab protocol.  The amplicons were sent to Nimblegen where they performed the entire process including the analysis

treatment_protocol: No treatment, harvested at 80% confluency

value: Fibroblast cells from Li Fraumeni patient

tag: antibody

source_name: MDAH087 fibroblast cell line, 1.0% Input


title: B cell_follicular lymphoma_12

description: miRNA profiling

source_name: B cell_follicular lymphoma_12


title: B cell_follicular lymphoma_11

description: miRNA profiling

source_name: B cell_follicular lymphoma_11


title: EGF treated at 100% confluent cell density, rep2

city: Memphis

first: Thomas

middle: R

last: Sutter

state: TN

address: 3774 Walker Ave.

department: Biology

institute: University of Memphis

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
The 16 microarrays were preprocessed using the 5th percentile of region method in dChip.
probe group file: HuGene-1_0-st-v1.r4.pgf
meta-probeset file: HuGene-1_0-st-v1.r4.mps

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: Neonatal foreskin normal human epidermal keratinocyteNeonatal foreskin NHEKs were grown in basal keratinocyte-SFM (KSFM) supplemented with 5 ng/ml EGF and 50 µg/ml bovine pituitary extract (BPE).

extract_protocol: Total RNA was isolated using RNA Stat-60

treatment_protocol: Fifth-passage NHEKs were grown to either 50% or 100% confluent cell density before treatment with basal medium, or medium containing EGF (10 ng/ml) for 48 h, with the treatment medium being replaced once at 24 hr.

tag: passage

value: primary keratinocyte

value: neonatal foreskin


title: B cell_follicular lymphoma_10

description: miRNA profiling

source_name: B cell_follicular lymphoma_10


title: EGF treated at 100% confluent cell density, rep1


title: B cell_follicular lymphoma_8

description: miRNA profiling

source_name: B cell_follicular lymphoma_8


title: Vehicle at 100% confluent cell density, rep4

source_name: Vehicle at 100% confluent cell density


title: B cell_follicular lymphoma_9

description: miRNA profiling

source_name: B cell_follicular lymphoma_9


title: B cell_follicular lymphoma_13

description: miRNA profiling

source_name: B cell_follicular lymphoma_13


title: temporal lobe tissue human male age 8 years 9 months rep1

value: male

value: 8 years and 9 months


title: EGF treated at 100% confluent cell density, rep3


title: B cell_follicular lymphoma_6

description: miRNA profiling

source_name: B cell_follicular lymphoma_6


title: B cell_follicular lymphoma_5

description: miRNA profiling

source_name: B cell_follicular lymphoma_5


title: EGF treated at 100% confluent cell density, rep4


title: occipital lobe tissue human male age 11 years 7 months rep1

source_name: surgically resected control tissue taken from the occipital lobe of the cerebral cortex

value: Asian

value: 11 years and 7 months

value: occipital lobe


title: Trastuzumab and Pertuzumab treated after 4 days (TP1_2)

city: Carrington Crescent

first: Andrew

middle: H

last: Sims

state: Edinburgh

address: Systems Medicine Building

department: Institute of Genetics and Molecular Medicine

institute: University of Edinburgh

description:
replicate 2
TP1_2

data_processing: The data were normalised using quantile normalisation with the BioConductor package, Lumi in R

source_name: Ovarian Cancer xenograft

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

growth_protocol: Adult female nu/nu mice were implanted subcutaneously with SKOV3 tumor fragments (previously established from the cell line) or primary ovarian tumor fragments in the flanks and allowed to grow to 4–6 mm in diameter (over a period of approximately 1 month).

extract_protocol: Total RNA was prepared from 10-50 mg of frozen tissue after 4 days of treatment, preincubated with RNAlater-ICE (Ambion, Austin, TX) using the miRNeasy Mini kit (Qiagen) and TissueRuptor (Qiagen) following the manufacturers’ instructions

treatment_protocol: The mice were treated with trastuzumab (20 mg/kg), pertuzumab (20 mg/kg) and trastuzumab + pertuzumab (20 mg/kg each)


title: Vehicle at 100% confluent cell density, rep3


title: Vehicle at 100% confluent cell density, rep2


title: Trastuzumab and Pertuzumab treated after 4 days (TP2_2)

description:
replicate 2
TP2_2


title: Pertuzumab treated after 4 days (P2_2)

description:
replicate 2
P2_2


title: B cell_follicular lymphoma_4

description: miRNA profiling

source_name: B cell_follicular lymphoma_4


title: Pertuzumab treated after 4 days (P1_2)

description:
replicate 2
P1_2


title: Pertuzumab treated after 4 days (P3_2)

description:
replicate 2
P3_2


title: Trastuzumab treated after 4 days (T3_2)

description:
replicate 2
T3_2


title: cord blood CD34+ from control donors_T18

city: Modena

first: Fabienne

last: Cocchiarella

address: Via G. Gottardi

department: Scienze Biomediche

institute: università di Modena e Reggio Emilia

description: Gene expression data from cord blood-derived mononuclear cells from healty control donor

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

scan_protocol: GeneChips were scanned using the Affymetrix scanner 3000

data_processing:
All data analyses were performed in R using Bioconductor libraries and R statistical packages.
Probe signals were converted to expression values using the robust multi-array average procedure (RMA)

source_name: cord blood cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 150 ng total RNA  ( GeneChip 3'IVT Express Technical Manual, 2008, Affymetrix).

extract_protocol: Cord blood was collected during the third stage of labor with the placenta in utero.Mononuclear cells were separated out, and the CD34+ cell fraction was magnetically sorted.

tag: treatment protocol

value: control

value: cord blood

value: CD34+ hematopoietic progenitors


title: EGF treated at 50% confluent cell density, rep3

tag: cell type


title: IgG ChIP [1of2]

scan_protocol: Performed by Nimblegen using standard protocol  http://www.nimblegen.com/products/chip/index.html

value: IgG (N-20; Santa Cruz; sc-651)


title: Trastuzumab treated after 4 days (T2_2)

description:
replicate 2
T2_2


title: Vehicle at 100% confluent cell density, rep1


title: EGF treated at 50% confluent cell density, rep4


title: EGF treated at 50% confluent cell density, rep2


title: B cell_follicular lymphoma_3

description: miRNA profiling

source_name: B cell_follicular lymphoma_3


title: B cell_follicular lymphoma_1

description: miRNA profiling

source_name: B cell_follicular lymphoma_1


title: B cell_follicular lymphoma_2

description: miRNA profiling

source_name: B cell_follicular lymphoma_2


title: B cell_follicular hyperplasia_9

description: miRNA profiling

source_name: B cell_follicular hyperplasia_9

value: follicular hyperplasia B cells


title: cord blood CD34+ from control donors_T13


title: B cell_follicular hyperplasia_8

description: miRNA profiling

source_name: B cell_follicular hyperplasia_8


title: Vehicle at 50% confluent cell density, rep4

source_name: Vehicle at 50% confluent cell density


title: B cell_follicular hyperplasia_6

description: miRNA profiling

source_name: B cell_follicular hyperplasia_6


title: Trastuzumab treated after 4 days (T1_2)

description:
replicate 2
T1_2


title: B cell_follicular hyperplasia_5

description: miRNA profiling

source_name: B cell_follicular hyperplasia_5


title: Trastuzumab and Pertuzumab treated after 4 days (TP3_1)

description:
replicate 1
TP3_1


title: cord blood CD34+ from control donors_T12


title: Untreated after 4 days (C3_2)

description:
replicate 2
C3_2


title: cord blood CD34+ from control donors_T4


title: Untreated after 4 days (C2_2)

description:
replicate 2
C2_2


title: EGF treated at 50% confluent cell density, rep1


title: Vehicle at 50% confluent cell density, rep3


title: Vehicle at 50% confluent cell density, rep2


title: Vehicle at 50% confluent cell density, rep1


title: B cell_follicular hyperplasia_4

description: miRNA profiling

source_name: B cell_follicular hyperplasia_4


title: Untreated after 4 days (C1_2)

description:
replicate 2
C1_2


title: Trastuzumab and Pertuzumab treated after 4 days (TP2_1)

description:
replicate 1
TP2_1


title: cord blood CD34+ from control donors_T8


title: cord blood CD34+ from  ARV-exposed newborns_A23

description: Gene expression data from cord blood-derived mononuclear cells from HIV-1 uninfected newborn exposed in utero to a zidovudine-based ARV

value: ARV-exposed newborns


title: cord blood CD34+ from control donors_T6


title: Trastuzumab and Pertuzumab treated after 4 days (TP1_1)

description:
replicate 1
TP1_1


title: cord blood CD34+ from  ARV-exposed newborns_A20


title: cord blood CD34+ from  ARV-exposed newborns_A14


title: Pertuzumab treated after 4 days (P3_1)

description:
replicate 1
P3_1


title: TG3

city: Houston

first: Yangjin

last: Bae

address: One Baylor Plaza

department: Molecular Human Genetics

institute: Baylor College of Medicine

description:
SAMPLE 6
Biological Replicate TG 3

hyb_protocol: according to Illumina protocols

scan_protocol: according to Illumina protocols

data_processing: Data was quantile normalized and VST transformed with lumi package in R

label_protocol: according to Illumina protocols

extract_protocol: Calvarial tissue was homogenized with 1 ml of Trizol to isolate total RNA. After total RNA was isolated, Dnase I treatment was done to avoid genomic DNA contamination.

tag: strain

value: FVB/N

tag: genotype/variation

value: miR34c overexpression

value: primary calvaria


title: TG2

description:
SAMPLE 5
Biological Replicate TG 2


title: Pertuzumab treated after 4 days (P2_1)

description:
replicate 1
P2_1

tag: cell line


title: B cell_follicular hyperplasia_1

description: miRNA profiling

source_name: B cell_follicular hyperplasia_1


title: cord blood CD34+ from  ARV-exposed newborns_A9

tag: tissue


title: B cell_follicular lymphoma_18

description: miRNA profiling

source_name: B cell_follicular lymphoma_18

value: follicular lymphoma B cells


title: cord blood CD34+ from  ARV-exposed newborns_A21


title: B cell_follicular hyperplasia_3

description: miRNA profiling

source_name: B cell_follicular hyperplasia_3


title: cord blood CD34+ from  ARV-exposed newborns_A5


title: TG1

description:
SAMPLE 4
Biological Replicate TG 1


title: C2C12 BMP2 1

description:
1_Exiqon*.txt' and '0_Exiqon*.txt' represent the raw data for Hy3 and Hy5, respectively.
Hy3: 1_Exiqon_13776984_S01_Cropped.txt
Hy5: 0_Exiqon_13776984_S01_Cropped.txt

hyb_protocol: The hybridization was performed by Exiqon according to the miRCURY™ LNA array manual using a Tecan HS4800 hybridization station.

scan_protocol: Scanned by Exiqon in an ozone free environment and using the Agilent G2565BA Microarray Scanner System

data_processing: Normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm using ImaGene 7.0 software

source_name: C2C12 BMP2 1

label_protocol: Processed by Exiqon using miRCURY™ LNA Array Power labeling kit

extract_protocol: Total RNA was isolated with mirvana total RNA isolation kit.

treatment_protocol: Treated with BMP2 for 72 hours

value: premyoblast

tag: treated with

value: BMP2 (300 ng/mL) supplemented alpha-MEM media for 72 hr

source_name: Common reference pool

tag: sample type

value: pooled RNA


title: C2C12 Vehicle 1

description:
1_Exiqon*.txt' and '0_Exiqon*.txt' represent the raw data for Hy3 and Hy5, respectively.
Hy3: 1_Exiqon_13776982_S01_Cropped.txt
Hy5: 0_Exiqon_13776982_S01_Cropped.txt

source_name: C2C12 Vehicle 1

value: vehicle (control) supplemented alpha-MEM media for 72hr


title: Pertuzumab treated after 4 days (P1_1)

description:
replicate 1
P1_1

hyb_protocol: Standard Illumina hybridization protocol

source_name: Ovarian Cancer xenograft


title: WT3

description:
SAMPLE 3
Biological Replicate WT 3

value: wild type


title: C2C12 BMP2 2

description:
1_Exiqon*.txt' and '0_Exiqon*.txt' represent the raw data for Hy3 and Hy5, respectively.
Hy3: 1_Exiqon_13776985_S01_Cropped.txt
Hy5: 0_Exiqon_13776985_S01_Cropped.txt

source_name: C2C12 BMP2 2


title: WT2

description:
SAMPLE 2
Biological Replicate WT 2


title: C2C12 Vehicle dye-swap

description:
1_Exiqon*.txt' and '0_Exiqon*.txt' represent the raw data for Hy3 and Hy5, respectively.
Hy3: 1_Exiqon_13776986_S01_Cropped.txt
Hy5: 0_Exiqon_13776986_S01_Cropped.txt


title: Trastuzumab treated after 4 days (T2_1)

description:
replicate 1
T2_1


title: cord blood CD34+ from  ARV-exposed newborns_A1

source_name: cord blood cells


title: Trastuzumab treated after 4 days (T3_1)

description:
replicate 1
T3_1


title: Trastuzumab treated after 4 days (T1_1)

description:
replicate 1
T1_1


title: Untreated after 4 days (C3_1)

description:
replicate 1
C3_1


title: Untreated after 4 days (C2_1)

description:
replicate 1
C2_1


title: Untreated after 4 days (C1_1)

description:
replicate 1
C1_1


title: C2C12 Vehicle 2

description:
1_Exiqon*.txt' and '0_Exiqon*.txt' represent the raw data for Hy3 and Hy5, respectively.
Hy3: 1_Exiqon_13776983_S01_Cropped.txt
Hy5: 0_Exiqon_13776983_S01_Cropped.txt

source_name: C2C12 Vehicle 2


title: 0.1%_DMSO_4_expE

status: Public on May 02 2012

city: Berlin

first: Christopher

last: Weidner

address: Ihnestraße 63

department: Otto Warburg Laboratory

institute: Max Planck-Institute for Molecular Genetics

description: replicate 4, experiment E

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were normalized using cubic spline normalization implemented in Illumina BeadStudio 3.3.

source_name: DMSO

label_protocol: Biotinylated cRNA were prepared with the Ambion Illumina TotalPrep RNA Amplification Kit

growth_protocol: According Zen-Bio's Human Subcutaneous Adipocyte/Preadipocyte Care Manual

extract_protocol: Total RNA was isolated using the RNeasy Mini Kit (QIAGEN) according to their manual. Genomic DNA was digested on column using the DNase-Set (QIAGEN). Quality control was performed with Agilent Bioanalyser

treatment_protocol: Compounds diluted in DMSO (0.1% final DMSO concentration), 24 hours at 37°C, 5% CO2

tag: agent

value: DMSO

tag: gender

value: female

tag: developmental stage

value: differentiated

value: Subcutaneous adipose tissue


title: WT1

description:
SAMPLE 1
Biological Replicate WT 1


title: IgG ChIP [2of2]

source_name: MDAH087 fibroblast cell line, ChIP

label_protocol: Performed by Nimblegen using standard protocol  http://www.nimblegen.com/products/chip/index.html

value: Fibroblast cells from Li Fraumeni patient

source_name: MDAH087 fibroblast cell line, 1.0% Input


title: 0.1%_DMSO_1_expE

description: replicate 1, experiment E


title: 0.1%_DMSO_3_expE

description: replicate 3, experiment E


title: 0.1%_DMSO_2_expE

description: replicate 2, experiment E


title: 0.1%_DMSO_3_expD

description: replicate 3, experiment D