title: siNT E2 r3

city: Cambridge

first: Suraj

last: Menon

address: Li Ka Shing Center, Robinson Way

institute: Cambridge Research Institute, Cancer Research UK

hyb_protocol: An aliquot of cRNA is run in triplicate on a Nanodrop spectrophotometer to determine sample concentration and yield. Samples were normalised to 150ng/µl. An aliquot of normalised cRNA is run on an Agilent Bioanalyser RNA Nano capillary electrophoresis chip to determine quality.   750ng of labelled cRNA was hybridised to Illumina BeadArrays overnight following Illumina WGGX DirectHyb Assay Guide (11286331 RevA)

scan_protocol: BeadArrays were washed and stained with streptavidin Cy3 following Illumina WGGX DirectHyb Assay Guide (11286331 RevA), BeadArrays scanned using the AutoLoader and BeadArray scanner at default settings following BeadArray Reader User Guide (11179510 RevB). Metric files produced automatically save P95 and P05 readings and .xml files save scanner settings.

data_processing: Using the R beadarray package the data was corrected for spatial artefacts, logged (base 2) and quantile normalised

source_name: MCF-7 human cell lines

label_protocol: An aliquot of Total RNA is run in triplicate on a Nanodrop spectrophotometer to determine sample concentration. An aliquot of Total RNA is run on an Agilent Bioanalyser RNA Nano capillary electrophoresis chip to determine quality. Good quality samples were normalised to 22.7ng/µl. 250ng of quality Total RNA processed following the Ambion Illumina® TotalPrep™-96 RNA Amplification Kit standard protocols.

growth_protocol: MCF7 cells were cultured in DMEM and ZR-75-1 cells in RPMI media (Invitrogen) at 10% FCS. For hormonal deprivation, cells were cultured for 3 days in phenol-red free DMEM or RPMI respectively, supplemented with 5% charcoal-treated serum. E2 (Sigma) was added at a final concentration of 100nM for 6 hours.

extract_protocol: RNA was extracted using TRIzol RNA Isolation reagents from Life Technologies as per manufacturer guidelines

treatment_protocol: We used three different siRNAs against GATA3: ON-TARGET plus siRNA J-0033781-09 and two additional custom made targeting the 3'UTR of the RefSeq NM_002051. The sense sequences of the custom made ones are siGATA3-Custom-1: AAACUAGGUCUGAUAUUCAUU and siGATA3-Custom-2: CUUUAUUGCAUCUGGGUAGUU.  AllStars Negative Control siRNA (Cat nr: 1027281, Qiagen) was used as a negative control. All siRNA experiments were at a final concentration of 50nM. Transfections were conducted using Lipofectamine 2000 (Invitrogen).

tag: treatment

tag: knockdown

value: sINT


title: DNA_Physically Healthy_2

status: Public on Nov 27 2012

type: genomic

city: Kodaira

first: Daimei

last: Sasayama

address: 4-1-1 Ogawahigashi-machi

country: Japan

institute: National Center of Neurology and Psychiatry

description: Sample name: S0982

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing:
GenomeStudio software was used for data processing.
Matrix_signal_intensities.txt (linked as supplementary file on Series record): X Raw and Y Raw columns represent raw intensities of A allele and B allele, respectively. X and Y columns represent normalized intensities of A allele and B allele, respectively.
Genotyping was performed by Riken Genesis (Yokohama, Japan) using the Illumina HumanOmni1-Quad BeadChip (Illumina, Inc., San Diego). A total of 713,495 autosomal SNPs were assessed for quality using the PLINK v1.07 software. All SNPs with a call rate below 95%, a deviation from Hardy-Weinberg equilibrium at an error level of P < 0.001, or a minor allele frequency of less than 10% were excluded. The remaining 534,404 SNPs were used for further analysis.

label: C-Bio and A-DNP

molecule: genomic DNA

organism: Homo sapiens

source_name: Peripheral blood

label_protocol: standard Illumina protocol

extract_protocol: The buffy coat was collected from venous blood collected in tubes containing EDTA. DNA was extracted using Maxwell 16 Tissue DNA Purification Kit (Promega, Madison, WI) according to manufacturer's instructions.

tag: tissue

value: Peripheral blood

tag: gender

value: male

tag: age

tag: physical status

value: healthy


title: DNA_Physically Healthy_8

description: Sample name: S1036


title: siGATA 2 E2 r2

status: Public on Nov 26 2012

type: RNA

country: United Kingdom

molecule: total RNA

tag: sigata variant

tag: cell line


title: siGATA 2 E2 r1


title: siNT Veh r2

value: vehicle


title: siGATA 0 Veh r2


title: siGATA 0 E2 r1


title: siGATA 1 Veh r1


title: siGATA 1 E2 r2


title: DNA_Physically Healthy_5

description: Sample name: M0093


title: siNT Veh r4


title: siNT E2 r4


title: DNA_Physically Healthy_10

description: Sample name: M0160


title: siNT E2 r1


title: siGATA 0 Veh r1


title: DNA_Physically Healthy_6

description: Sample name: S0785


title: siGATA 0 E2 r2


title: siGATA 2 Veh r1


title: siGATA 2 Veh r2


title: siNT Veh r5


title: siNT Veh r3


title: siNT E2 r5


title: siGATA 1 E2 r1


title: C17 (gene expression data)

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

country: Italy

institute: IRCSS Istituto Nazionale Tumori

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were extracted  with BeadStudio software v3.8

label: biotin

source_name: tumor

label_protocol: Total RNA from each sample was labeled according to the manufacturers recommendations.

extract_protocol: Tissues were mechanically disrupted and simultaneously homogenized in the presence of QIAzol Lysis reagent (Qiagen, Valencia, CA, USA), using a Mikrodismembrator (Braun Biotech International, Melsungen, Germany). RNA was extracted using the miRNeasy Mini kit (Qiagen) according to manufacturer’s instructions, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit. RNA concentrations were measured with the NanoDrop ND-100 Spectrophotometer (NanoDrop Technologies, Wilmington, DE) while RNA quality was assessed with the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA) using the RNA 6000 Nano kit (Agilent Technologies). Samples, included in the present analysis, had a RIN score greater than 5 and a 28S:18S rRNA ratio near to 2:1.

value: Colon

tag: patient

tag: t=tumor; n=normal

value: T


title: DNA_Physically Healthy_4

description: Sample name: M0153


title: C18 (gene expression data)

source_name: normal

value: N


title: DNA_Physically Healthy_3

description: Sample name: S0978

value: female


title: MDA-MB-231-GATA3

city: San Francisco

first: Jonathan

last: Chou

address: 513 Parnassus Ave, Box 0452, HSW1301

department: Anatomy

country: USA

institute: Univ of California, San Francisco

description: Test

data_processing:
SABioscience normalization software was used.
Data are normalized to the following house-keeping RNAs: SNORD48, SNORD47, SNORD44, RNU6-2
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target - Ct_HKG)]
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.

label: Sybr Green

label_protocol: PCR assays were performed using the Human Cancer miRNA PCR assay panel (SA Biosciences, Frederick, MD) following the Manufacturer’s instructions. Reverse transcription was performed from 1 microgram total RNA using the RT2 First Strand Kit (SA Biosciences). Quantitative real-time PCR were performed (ABI) with 45 cycles at 94 degrees C for 15 seconds and 60 degrees C for 60 seconds.

growth_protocol: DMEM-H21 high glucose + 10% FBS + Pen/Strep in normal 2D tissue culture plates

extract_protocol: Qiagen miRNeasy Kit for Total RNA

tag: disease state

value: breast cancer

tag: overexpression


title: DNA_Physically Healthy_1

description: Sample name: S0945


title: C16 (gene expression data)


title: C11 (gene expression data)


title: C13 (gene expression data)


title: C15 (gene expression data)


title: C15 (Exiqon data)

hyb_protocol: Labeled RNA was hybridized using the GeneTaq Hybridization Station and slides were manually washed

scan_protocol: Fluorescent signals were detected using a GenePix4100 scanner

data_processing: Raw data were extracted  with GenePix 6.0

label_protocol: Total RNA from each sample was labeled using miRCURY labelling Exiqon kit (Exiqon, Vedbaek, Denmark)

extract_protocol: Tissues were mechanically disrupted and simultaneously homogenized in the presence of QIAzol Lysis reagent (Qiagen, Valencia, CA, USA), using a Mikrodismembrator (Braun Biotech International, Melsungen, Germany). RNA was extracted using the miRNeasy Mini kit (Qiagen) according to manufacturer’s instructions. RNA concentrations were measured with the NanoDrop ND-100 Spectrophotometer (NanoDrop Technologies, Wilmington, DE) while RNA quality was assessed with the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA) using the RNA 6000 Nano kit (Agilent Technologies). Samples, included in the present analysis, had a RIN score greater than 5 and a 28S:18S rRNA ratio near to 2:1.


title: C17 (Exiqon data)


title: C16 (Exiqon data)


title: C9 (gene expression data)


title: C8 (gene expression data)


title: C5 (gene expression data)


title: C14 (Exiqon data)


title: C13 (Exiqon data)


title: C3 (gene expression data)


title: C4 (gene expression data)


title: C2 (gene expression data)


title: C7 (gene expression data)


title: C6 (gene expression data)


title: C12 (Exiqon data)


title: C14 (gene expression data)


title: C18 (Exiqon data)


title: C11 (Exiqon data)


title: C10 (Exiqon data)


title: J-GFP PMA/iono 4h

city: Braunschweig

first: Andreas

last: Jeron

state: Nierdersachsen

address: Inhoffenstraße 7

department: Viral Immunology

country: Germany

institute: Helmholtz Center for Infection Research

hyb_protocol: Following fragmentation, 10 µg of cRNA were hybridized for 16 h at conditions recommended by the manufacturer. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GCS 3000

data_processing: Data were analyszed using GeneSpring GX10.0 software applying RMA probe summarization algorithm.

source_name: PMA/iono stimulated Jurkat T cells containing GFP-expressing control retrovirus

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

growth_protocol: Jurkat T cells were cultivated in IMDM medium supplemented with 10% FCS (PAA Laboratories) and 100 U/ml penicillin/streptomycin.

extract_protocol: RNeasy Kit according to manufacturer's recommendations

treatment_protocol: Prior usage dead cells were removed from Jurkat cell cultures by ficoll gradient centrifugation. If stated, cells were stimulated with PMA (10 ng/ml, Sigma-Aldrich) and ionomycin (1 µg/ml, Sigma-Aldrich) for 4 h.

value: Jurkat T cells

tag: foxp3 expression

value: no

tag: activation status

value: stimulated


title: C9 (Exiqon data)


title: C10 (gene expression data)


title: C6 (Exiqon data)


title: C7 (Exiqon data)


title: C5 (Exiqon data)


title: C2 (Exiqon data)


title: C8 (Exiqon data)


title: C3 (Exiqon data)


title: C1 (gene expression data)


title: J-FOXP3 resting

source_name: resting Jurkat T cells containing FOXP3Δ2/GFP-expressing retrovirus

value: yes

value: resting


title: C4 (Exiqon data)


title: C17 (Mitenyi data)

hyb_protocol: Labeled RNA was hybridized using the a-Hyb Hybridization Station and following standard Miltenyi protocols


title: C18 (Mitenyi data)


title: J-FOXP3 PMA/iono 4h

source_name: PMA/iono stimulated Jurkat T cells containing FOXP3Δ2/GFP-expressing retrovirus


title: E24377A_NonAdh_60m_1

city: Baltimore

first: David

middle: A

last: Rasko

state: MD

address: 801 W. Baltimore Street, Room 619

department: Istitute for Genome Sciences/Microbiology and Immunology

institute: University of Maryland School of Medicine

hyb_protocol: All protocols were done according to manufacturer's specifications: http://www.affymetrix.com/support/technical/manual/expression_manual.affx

data_processing: Data has not been processed other than those protocols within GCOSv1.4

organism: Escherichia coli O139:H28 str. E24377A

source_name: total RNA from non-adherent E. coli, 60 min

extract_protocol: RNeasy Mini Kit (Qiagen Cat # 74104) and was treated with DNAse (Ambion Cat #AM1907).

tag: cell type

value: non-adherent bacteria


title: J-GFP resting

source_name: resting Jurkat T cells containing GFP-expressing control retrovirus


title: siGATA 1 Veh r2


title: siNT Veh r1


title: C1 (Exiqon data)


title: E24377A_NonAdh_120m_2

scan_protocol: All protocols were done according to manufacturer's specifications: http://www.affymetrix.com/support/technical/manual/expression_manual.affx

source_name: total RNA from non-adherent E. coli, 120 min


title: E24377A_broth_120m_2

source_name: total RNA from planktonic grown bacteria, 120 min after dilution

label_protocol: All protocols were done according to manufacturer's specifications: http://www.affymetrix.com/support/technical/manual/expression_manual.affx

value: planktonic bacteria


title: C12 (gene expression data)


title: E24377A_NonAdh_60m_2


title: C16 (Mitenyi data)


title: E24377A_broth_120m_3


title: E24377A_NonAdh_30m_2

source_name: total RNA from non-adherent E. coli, 30 min


title: E24377A_NonAdh_120m_1


title: E24377A_NonAdh_30m_1


title: E24377A_broth_60m_2

source_name: total RNA from planktonic grown bacteria, 60 min after dilution


title: E24377A_broth_60m_3


title: E24377A_broth_120m_1


title: C13 (Mitenyi data)


title: E24377A_broth_30m_2

source_name: total RNA from planktonic grown bacteria, 30 min after dilution


title: E24377A_broth_30m_1


title: C15 (Mitenyi data)


title: C9 (Mitenyi data)


title: C14 (Mitenyi data)


title: C11 (Mitenyi data)


title: C8 (Mitenyi data)


title: E24377A_Adh_120m_2

source_name: total RNA adherent bacteria, 120 minutes

value: adherent bacteria


title: C7 (Mitenyi data)


title: C10 (Mitenyi data)


title: C16 (Agilent data)

hyb_protocol: Standard Agilent hybridization protocol

scan_protocol: Standard Agilent scanning protocol

data_processing: The data were extracted  with Agilent Feature Extraction software


title: E24377A_Adh_60m_1

source_name: total RNA adherent bacteria, 60 minutes


title: C15 (Agilent data)


title: C6 (Mitenyi data)


title: C17 (Agilent data)


title: E24377A_broth_60m_1


title: E24377A_broth_30m_3


title: siNT E2 r2

value: sINT


title: E24377A_Adh_30m_2

source_name: total RNA adherent bacteria, 30 minutes


title: E24377A_Adh_60m_2


title: E24377A_Adh_120m_1


title: C5 (Mitenyi data)


title: E24377A_Adh_30m_1


title: C18 (Agilent data)


title: C14 (Agilent data)


title: C3 (Mitenyi data)


title: C13 (Agilent data)


title: C4 (Mitenyi data)


title: C1 (Mitenyi data)


title: C12 (Agilent data)


title: C10 (Agilent data)


title: C9 (Agilent data)


title: C11 (Agilent data)


title: C2 (Mitenyi data)


title: C7 (Agilent data)


title: control sample at 60 min, biological rep2

city: ljubljana

first: simona

last: kamensek

address: večna pot 111

department: department of biology

country: Slovenia

institute: university of ljubljana, biotechnical faculty

description: Gene expression data from control culture following 60 min incubation after reaching OD600 0.6

hyb_protocol: Following fragmentation, cDNA were hybridized for 16 hr at 45C in an Affymetrix hybridization oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Data were normalized using RMA algorithm from R/Bioconductor/XPS package.

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

source_name: Escherichia coli MG1655 after 60 min incubation

label_protocol: Biotinylated cDNA were prepared as proposed by the Affymetrix protocol from 10 ug total RNA (GeneChip® Expression Analysis Technical Manual, 2005, Affymetrix).

growth_protocol: Overnight cultures of E. coli MG1655  grown at 37°C with shaking at 200 rpm were diluted 1:625 into 50 ml of LB broth (Roth), and incubated at 37°C with shaking at 200 rpm.

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

treatment_protocol: When the cultures reached an OD600 0.6 they were split into two flasks, each containing 20 ml of the culture. One was treated with a subinhibitory concentration of purified colicin M, while the untreated served as a control. 2-ml culture aliquotes were harvested from each flask after 30 min and 60 min incubation at 37°C  and were mixed with 4 ml RNAProtect Bacteria Reagent (Qiagen).

value: untreated culture


title: C8 (Agilent data)


title: treated sample at 60 min, biological rep2

description: Gene expression data from treated culture following 60 min incubation after reaching OD600 0.6, when exposed to colicin M.

source_name: Escherichia coli MG1655 after 60 min incubation following colicin M treatment

value: treated culture


title: treated sample at 30 min, biological rep2

description: Gene expression data from treated culture following 30 min incubation after reaching OD600 0.6, when exposed to colicin M.

source_name: Escherichia coli MG1655 after 30 min incubation following colicin M treatment


title: C6 (Agilent data)

source_name: normal


title: treated sample at 60 min, biological rep1


title: control sample at 30 min, biological rep2

description: Gene expression data from control culture following 30 min incubation after reaching OD600 0.6

source_name: Escherichia coli MG1655 after 30 min incubation


title: C5 (Agilent data)

source_name: tumor


title: C4 (Agilent data)


title: Trunk-muscle_progenitor_E9.5_rep2

city: Rehovot

first: Eldad

last: Tzahor

address: Herzel 234

country: Israel

institute: The Weizmann Institute of Science

description: RNA from mouse embryo’s trunk or head at E9.5, 10.5 and 11.5. The myogenic lineage was labeled with Myf5Cre;RosaYFP. Trunk and head tissues were isolated, dispersed into a single cell suspension and FACs sorted for YFP+ population. Thereafter RNA was purified with the QIAzol Lysis Reagent (Qiagen) according to the manufacturer instructions and amplified using message-amp kit (Ambion).

hyb_protocol: According to the manufacturer’s instructions

scan_protocol: Each hybridized Affymetrix GeneChip array was scanned with GeneChip Scanner 3000

data_processing: MAS5 using Affymetrix Expression Console Software and then corrected by a Lowess multi array procedure. Normalized data were log2 transformed.

organism: Mus musculus

source_name: Trunk muscle progenitors, mouse embryos at E9.5

label_protocol: The doublestranded DNA was transcribed in vitro into biotinylated cRNA

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

tag: strain

value: ICR

tag: genotype/variation

value: Trunk muscle progenitors

tag: developmental stage


title: Trunk-muscle_progenitor_E11.5_rep2

source_name: Trunk muscle progenitors, mouse embryos at E11.5


title: Trunk-muscle_progenitor_E11.5_rep1


title: C2 (Agilent data)

value: Colon


title: control sample at 60 min, biological rep1

tag: treatment


title: treated sample at 30 min, biological rep1


title: C3 (Agilent data)

tag: tissue

value: T


title: control sample at 30 min, biological rep1


title: Trunk-muscle_progenitor_E9.5_rep1


title: Trunk-muscle_progenitor_E10.5_rep1

source_name: Trunk muscle progenitors, mouse embryos at E10.5


title: C1 (Agilent data)


title: Head-muscle_progenitor_E11.5_rep2

source_name: Head muscle progenitors, mouse embryos at E11.5

value: Head muscle progenitors


title: ChIP/chip of H3K9me2 in WT under low glucose

city: Bethesda

first: Shiv

last: Grewal

address: NCI bldg 37 Rm 6068 9000 Rockville Pike

department: LBMB

institute: NCI

hyb_protocol: Hybridyzation mix [37.5ul(containing 500ng of cy5-labeled DNA and 500ng of cy3-labeled DNA), 12.5ul of Human Cot1 DNA(1mg/ml:Invitrogen), 12.5ul of 10x Agilent blocking Agent, 62.5ul of 2x Agilent hybridization buffer(high rpm)] is hybridized to array at 65C for 24 hours.

scan_protocol: Scanned on an Agilent G2600D scanner

data_processing: Agilent Feature Extraction Software (version 11.0.1.1) was used for quantifying the image, background subtraction, and normalization.

organism: Schizosaccharomyces pombe

source_name: WT cultured under low glucose condition

label_protocol: 1ug of DNA(ChIPed/WCE) are suspended in 5ul of 2Xcoupling buffer (Invitrogen) and mixed with 5ul of cy5(Amersham:PA15101) or cy3(Amersham:PA13101). Coupling reaction lasts 2 hours at room temperature.

growth_protocol: Yeast cells are cultured under YEA medium. For low glucose condition, yeast cells are cultured under EMM medium containing 0.5% glucose.

extract_protocol: Sonicated DNA are immunoprecipitated by using H3K9me2 anti-bory(abcam:ab1220)

treatment_protocol: Cells are fixed with para-formaldehyde for 30min at room temperature.

tag: chip antibody

value: H3K9me2 anti-bory

tag: chip antibody manufacturer

value: Abcam

tag: chip antibody catalog #

value: low glucose

tag: genotype

value: Wild type yeast

tag: sample type

value: ChIPed DNA

value: DNA from whole cell extract


title: Trunk-muscle_progenitor_E10.5_rep2


title: Head-muscle_progenitor_E10.5_rep2

source_name: Head muscle progenitors, mouse embryos at E10.5


title: ChIP/chip of H3K9me2 in ago1∆ under low glucose

source_name: ago1∆ cultured under low glucose condition


title: C12 (Mitenyi data)

tag: patient

value: N


title: ChIP/chip of H3K9me2 in rrp6∆ pab2∆

source_name: rrp6∆ pab2∆

value: rrp6∆ pab2∆


title: slide 342609

city: Jena

first: Akos

middle: T

last: Kovacs

address: Neugasse 23

department: Institute of Microbiology

institute: Friedrich Schiller University of Jena

description: comparison of wild type and cshA mutant at exponential phase

hyb_protocol: The protocol was performed as described in Lulko, et. al. J. Mol. Microbiol. Biotechnol. 12:82-95 PMID: 17183215

scan_protocol: Scanning was done using the Genepix 4200AL laser scanner

data_processing:
Dual-channel array images were analyzed with ArrayPro 4.5 software (Media Cybernetics Inc.). Spots were screened visually to identify those of low quality. Slide data were processed with MicroPreP as previously described (den Hengst et al J. Biol. Chem. 280:34332-34342; PMID: 16040604). Prior to analysis, automatically and manually flagged spots and spots with very low background subtracted signal intensity (5% of the weakest spots [sum of Cy3 and Cy5 net signals]) were filtered out of all data sets. Net signal intensities were calculated by grid-based background subtraction. A grid-based Lowess transformation was performed for slide normalization, negative and empty values were removed, and outliers were removed by the deviation test. Expression ratios of mutant strain over the wild-type strain were calculated. Further analysis was performed with a Cyber-T Student t test for paired data.
Net{A} is the raw signal of channel A minus the local corner background signal of channel A
Net{B} is the raw signal of channel B minus the local corner background signal of channel B

organism: Bacillus subtilis

source_name: B subtilis cshA exponential {A}

label_protocol: Total RNA was incubated for 16 h at 42°C in the presence of 400 U Superscript III RNase H reverse transcriptase (Invitrogen), 0.2 mM aminoallyl dUTP (Amersham), 0.5 mM dATP, 0.5 mM dCTP, 0.5 mM dGTP, 0.3 mM dTTP, and 3.2 g random nonamers. The synthesized cDNA was then labeled by coupling either Cy3 or Cy5 to the dUTP aminoallyl reactive group (CyScribe postlabeling kit; Amersham Biosciences) and was purified using NucleoSpin Extract II columns

growth_protocol: B subtilis wild type (168) and its cshA derivative strain were grown in CSE-Glu medium and cells were harvested at mid exponential (OD600 ~0.8) and early stationary phase (OD600 ~2.2-2.4).  For both time points, 4 biological replicates were used (2-2 mixed after cDNA labeling, resulting 2 slides for exponential and staioner phase).  RNA purification was performed on the samples.

extract_protocol: RNA was isolated and purified using the High Pure RNA isolation kit (Roche diagnostics) as described (Lulko, et. al. J. Mol. Microbiol. Biotechnol. 12:82-95 PMID: 17183215). Contaminating genomic DNA was removed by treatment with RNase-free DNase I (Roche diagnostics). RNA was isolated from three replicate cultures.

treatment_protocol: no treatment

tag: background strain

value: cshA mutant

source_name: B subtilis 168 exponential {B}

value: wild type


title: Head-muscle_progenitor_E11.5_rep1


title: slide 342613

description: comparison of wild type and cshA mutant at stationary phase

source_name: B subtilis 168 stationary {A}

source_name: B subtilis cshA stationary {B}


title: ChIP/chip of H3K9me2 in rrp6∆ pla1-37

source_name: rrp6∆ pla1-37

value: rrp6∆ pla1-37


title: Head-muscle_progenitor_E9.5_rep1

source_name: Head muscle progenitors, mouse embryos at E9.5


title: slide 342617

source_name: B subtilis cshA stationary {A}

source_name: B subtilis 168 stationary {B}


title: Head-muscle_progenitor_E10.5_rep1


title: ChIP/chip of H3K9me2 in rrp6∆ red1∆

source_name: rrp6∆ red1∆

value: rrp6∆ red1∆


title: mo17.zmet2.m1

city: St. Paul

first: Steve

middle: R

last: Eichten

state: MN

address: 1445 Gortner Ave

department: Plant Biology

institute: University of Minnesota

hyb_protocol: Samples were hybridized to the custom 3x1.4M probe array for 16–20 hrs at 42C.

scan_protocol: Slides were washed and scanned according to NimbleGen’s protocol using the MS200 microarray scanner. Images were aligned and quantified using NimbleScan software (Roche NimbleGen) producing raw data reports for each probe on the array.

data_processing: The resulting microarray data were imported into the Bioconductor statistical environment (http://bioconductor.org/).  Non-maize probes and vendor-supplied process control probes were configured to have analytical weights of zero. Variance-stabilizing normalization was used to account for array-specific effects. Factor-specific hybridization coefficients were estimated by fitting fixed linear model accounting for dye and sample effects to the data using the limma package [55].

organism: Zea mays

source_name: mo17.zmet2 input

label_protocol: For each amplified IP and input sample, 3 ug of amplified DNA were labeled using the Dual-Color Labeling Kit (Roche NimbleGen, Cat # 05223547001) according to the array manufacturer’s protocol (Roche NimbleGen Methylation User- Guide v7.0).  Each IP sample was labeled with Cy5 and each input/control sonicated DNA was labeled with Cy3.

extract_protocol: DNA was isolated using the CTAB method (Doyle 1987). 5-10ug of gDNA in 650-700uL nuclease-free water was sonicated for five, ten- second pulses as per the methods of Haun et al., 2008. Samples were quantified and run on 1.5% agarose gels to verify that DNAs were fragmented to 100-500bp. Methylated DNA was immunoprecipitated with an anti-5-methylcytosine monoclonal antibody from 400ng sonicated DNA using the Methylated DNA IP Kit (Zymo Research, Orange, CA; Cat # D5101).

treatment_protocol: sonicated, amplified gDNA control

tag: replication

value: 14 day whole seedling

tag: dna

value: input

source_name: mo17.zmet2 IP

treatment_protocol: sonicated, amplified, meDIP DNA

value: 5mc enriched DNA


title: Enucleated oocyte

first: Joseph

middle: G.

last: Gall

address: 3520 San Martin Drive

department: Department of Embryology

institute: Carnegie Institution for Science

description: Total RNA from 20 defolliculated, enucleated oocytes of a mature female Xenopus tropicalis frog

hyb_protocol: The samples were ice quenched and combined with the hybridization cocktail (5 ul oligonucleotide B2 control, 15 ul 20X eukaryotic hybridization controls, 150 ul 2X hybridization buffer, 30 ul 100% DMSO and 70 ul water).  After 10 minutes of pre-hybridizing the Xenopus tropicalis arrays at 45ºC, 60 rpm, 200 ul of cocktail was loaded onto each array and the arrays were hybridized for 16 hours at 45ºC, 60 rpm. The cocktail was removed and the arrays were stained and washed using the Affymetrix GeneChip Fluidics Station 450 and FS450_001 fluidics script.

scan_protocol: Fluorescence was detected using the Affymetrix G3000 GeneArray Scanner and image analysis of each GeneChip was perfomed through the Affymetrix GeneChip Command Console version 3.4 (AGCC v3.4) Affymetrix software.

data_processing: Data were extracted from the  CEL files, RMA normalized across all samples and converted to Log2 notation with Partek Genomics Suite (Partek, Missouri, USA).  These values were labeled as to their source and the groups compared.

organism: Xenopus tropicalis

source_name: Enucleated oocyte

label_protocol: Following the Affymetrix  ribosomal reduction  step, 1 ug total RNA was combined with 2 ul T7 oligo(dT) primer and 2 ul Poly-A controls and brought to a volume of 12 ul. The samples were incubated at 70ºC for 10 minutes to label as per standard Affymetrix protocol.

growth_protocol: Adult female X. tropicalis animals were anesthetized with 0.15% tricaine methane sulfo-  nate, and one or both ovaries were removed surgically.  Pieces of ovary were placed in OR2 medium (Wallace et al. 1973) at room temperature, where the oocytes maintain normal morphology and biochemical properties for several days.

extract_protocol: TRIzol (Ambion) according to the manufacturer’s protocol.

treatment_protocol: Oocytes were treated with collagenase with gentle swirling in plastic culture dishes for 2–3 hours to remove follicle cells.  We developed a manual technique using jewelers’ forceps to remove the nuclear envelope without losing the GV contents.  GVs were isolated in an isotonic saline solution at pH 5.6–5.8 (83 mM KCl, 17 mM NaCl, 6.0 mM Na2HPO4, 4.0 mM KH2PO4, 1 mM MgCl2, 1.0 mM dithiothreitol, adjusted to pH 5.6–5.8 with HCl). At this pH, the nuclear contents begin to gel within seconds after isolation from the oocyte. Simultaneously, the nuclear envelope swells away from the gelled contents and can be removed with jewelers’ forceps because it adheres to the forceps' tips. GV contents were collected in batches of 10–20 and transferred to 10 mM sodium citrate and 5mMEDTA (pH 5.0) for storage. For isolation of cytoplasmic RNA, oocytes were transferred from OR2 medium to the same solution used for GV isolation, except at pH 7.0. The GV was removed with jewelers’ forceps and the enucleated cytoplasm  transferred in minimal liquid to a 2-mL Eppendorf tube on dry ice.

tag: gender

value: female

value: enucleated oocyte


title: ChIP/chip of H3K9me2 in WT

source_name: Wild type yeast

value: H3K9me2 anti-bory


title: GV without envelope RNA

description: Total RNA from 1,008 hand-isolated, demembranated germinal vesicles from oocytes of a mature Xenopus tropicalis frog

source_name: GV without envelope RNA

value: germinal vesicle (GV) without envelope


title: GV with envelope RNA

description: Total RNA from 716 hand-isolated germinal vesicles from oocytes of a mature Xenopus tropicalis frog

source_name: GV with envelope RNA

value: germinal vesicle (GV) with envelope


title: ChIP/chip of H3K9me2 in rrp6∆

value: Abcam


title: Knock Out 2

city: Perth

first: Abdul

last: Baten

state: WA

address: Level 6, Rear 50 Murray Street

department: WAIMR

country: Australia

institute: The University of Western Australia

description: replicate 2

scan_protocol: Scanning setting: 1.6 for Beadarray reader

data_processing: The data was normalised using RSN normalisation with Lumi moduleI in R

source_name: Islets

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep RNA amplification kit from Ambion

extract_protocol: RNA was extracted with Trizol reagent. Quality check performed with Agilent Bioanalyser 2100

value: Pancreas

value: Pdx1-controled bone morphogenetic protein receptor 1a gene knockout


title: slide 342605

source_name: B subtilis 168 exponential {A}

source_name: B subtilis cshA exponential {B}


title: Wild Type 2

description: replicate 2


title: Knock Out 1

description: replicate 1


title: Wile Type 1

description: replicate 1


title: C17 (Illumina data)

source_name: tumor

label_protocol: Total RNA from each sample was labeled according to the manufacturers recommendations (Illumina MicroRNA Expression Profiling Assay Guide).

value: Colon

tag: t=tumor; n=normal

value: T


title: C15 (Illumina data)


title: C16 (Illumina data)

source_name: normal

value: N


title: C14 (Illumina data)


title: C13 (Illumina data)


title: C11 (Illumina data)


title: C12 (Illumina data)


title: b73.zmet2.m1

source_name: b73.zmet2 input

source_name: b73.zmet2 IP


title: C10 (Illumina data)


title: C9 (Illumina data)


title: C7 (Illumina data)


title: C8 (Illumina data)


title: C18 (Illumina data)


title: C6 (Illumina data)


title: mop1

source_name: mop1 input

source_name: mop1 IP


title: C4 (Illumina data)


title: C5 (Illumina data)


title: C3 (Illumina data)


title: H378

city: Aalborg

first: Julie

middle: Støve

last: Bødker

address: Sdr. Skovvej 15

department: Department of Heamatology

country: Denmark

institute: Aalborg University Hospital

description: Hybridized to SNP6.0

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

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

data_processing:
The SNP6.0 CEL files were imported in Genotyping Console version 4.1 (Affymetrix) and copy number/LOH analysis performed using regional GC correction and the CN baseline file generated from 270 HapMap samples; GenomeWideSNP_6.hapmap270.na32.r1.a5.ref (downloaded from Affymetrix webpage). Individual SNPs were not assessed. The resulting CNCHP-files were viewed using the software; Chromosome Analysis Suite, version 1.1 (Affymetrix). TXT files of normalized data were exported from the Chromosome Analysis Suite software. All genomic positions were annotated to the hg19 version of the human genome (NCBI build 37).
Detection of CNVs larger than 200 kb with size being the only restriction.

label: Biotin

source_name: Sample from patient with diffuse large B-cell lymphoma

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: The tumor sample was after removal snap frozen and stored in OCT at - 80 oC. From each OCT block, 3x20 µm cuts were obtained using a microtome; the slices were washed twice in PBS and homogenized using the TissueLyser II (Qiagen). DNA extraction was performed using the DNeasy Blood & Tissue kit (Qiagen). From one of the patients (H380) a peripheral blood sample was included as a normal control sample (BB39). Mononuclear cells were isolated from the blood sample by Ficoll-Paque Plus (GE Health Care, Uppsala, Sweden) and stored in 10 % DMSO and 20 % serum at – 80 oC. For DNA extraction, the cells were thawed, washed twice in PBS and genomic DNA extracted using the DNeasy Blood & Tissue kit (Qiagen). The DNA was eluted in water and the concentration measured using a Nanodrop (Thermo Scientific)

value: sample of diffuse large B-cell lymphoma


title: C2 (Illumina data)


title: C1 (Illumina data)


title: H321

description: Hybridized to SNP6.0


title: Head-muscle_progenitor_E9.5_rep2

source_name: Head muscle progenitors, mouse embryos at E9.5

value: ICR

tag: cell type

value: Head muscle progenitors


title: H35

description: Hybridized to SNP6.0


title: H285

description: Hybridized to SNP6.0


title: ChIP/chip of H3K9me2 in rrp6∆ ago1∆

source_name: rrp6∆ ago1∆

value: rrp6∆ ago1∆

value: ChIPed DNA

value: DNA from whole cell extract


title: H380

description: Hybridized to SNP6.0


title: H296

description: Hybridized to SNP6.0


title: BB39

description: Hybridized to SNP6.0

source_name: Blood sample of patient H380

value: mononuclear cells


title: B73_k9

description: each Sample represents three replicates.

hyb_protocol: Samples were hybridized to the custom 2.1 M probe array (GEO Platform GPL13499) for 16–20 hrs at 42C.

scan_protocol: Slides were washed and scanned according to NimbleGen’s protocol using the GenePix 4000B. Images were aligned and quantified using NimbleScan software (Roche NimbleGen) producing raw data reports for each probe on the array.

data_processing:
The resulting microarray data were imported into the Bioconductor statistical environment (http://bioconductor.org/). Microarray data channels were assigned the following factors: B73 immunoprecipitation, Mo17 immunoprecipitation, B73 input, or Mo17 input depending on sample derivation. Non-maize probes and vendor-supplied process control probes were configured to have analytical weights of zero. Variance-stabilizing normalization was used to account for array-specific effects. Factor-specific hybridization coefficients were estimated by fitting fixed linear model accounting for dye and sample effects to the data using the limma package [55].
values averaged across reps developing average log2(IP / input) ratios for both genotypes. Mo17 samples are corrected for cgh effects.

source_name: B73 r1 input

extract_protocol: For each replicate, 1 g of plant material was harvested on ice, rinsed with water, and crosslinked with 1% formaldehyde for 10 minutes under vacuum.  Cross-linking was quenched by adding Glycine solution to a final concentration of 0.125M under vacuum infiltration for 5 minutes.  Treated tissue was frozen in liquid nitrogen and stored at -800C until chromatin extraction.  Chromatin extractions were performed using EpiQuik™ Plant ChIP Kit (Epigentek, Brooklyn, USA) according to manufacturer’s recommendations.  Extracted chromatin was sheared in 600 μl of the EpiQuick buffer CP3F with 5 10-second pulses on a sonicator.  To test and optimize sonication conditions, cross-linking was reversed in a sample of sheared chromatin and the resulting products were analyzed on agarose gel.  Sonication conditions were optimized to yield predominantly 200 – 500 bp DNA samples.  Chromatin immunoprecipitations, reverse cross-linking, and DNA cleanup were performed using EpiQuik™ Plant ChIP Kit (Epigentek) according to manufacturer’s recommendations.  For each genotype, antibody, and replicate, 50 – 100 ng of input and immunoprecipitated (IP using spicific H3K9me2 antibody #07-441 from Millipore) DNA was amplified with a whole genome amplification kit (WGA2, Sigma, St. Louis, USA).  The amplification of no antibody control (negative control) was always 5 – 10 fold less efficient confirming specificity of immunoprecipitation.

value: 14 day whole seedling

value: input

source_name: B73 r1 IP

treatment_protocol: sonicated, amplified, h3k9 antibody pulldown IP DNA

value: h3k9 antibody [NRG1583062] pulldown enriched DNA


title: Mo17_k9

source_name: Mo17 r1 IP

source_name: Mo17 r1 input


title: H35

description: Hybridized to cytogenetic 2.7M whole-genome array

data_processing:
CEL files from the Cyto2.7M array were imported and analyzed using ChAS with default analysis parameter settings (file: Cytogenetics_Array.single_sample.def.NA31.chasparam), except for a change to regional GC correction to generate CYCHP-files, which were also viewed in ChAS. TXT files of normalized data were exported from the Chromosome Analysis Suite software. All genomic positions were annotated to the hg19 version of the human genome (NCBI build 37).
Detection of CNVs larger than 200 kb with size being the only restriction.


title: therapy-related  AML T52

status: Public on Nov 24 2012

city: Chicago

first: Megan

middle: E.

last: McNerney

state: Illinois

address: 900 East 57th Street, KCBD 5128

department: Pathology

institute: The University of Chicago

hyb_protocol: Per manufacturer's protocol

scan_protocol: Per manufacturer's protocol

data_processing: Log R ratio and B allele frequencies were generated using GenomeStudio (Illumina)

label: per manufacturer's protocol

source_name: bone marrow white blood cells

label_protocol: Per manufacturer's protocol

growth_protocol: Patient samples were not cultured

extract_protocol: Qiagen AllPrep kit

treatment_protocol: White blood cells were purified by Ficoll density gradient separation

tag: cytogenetic status of chromosome 7

tag: Sex

value: female

tag: primary disease

value: astrocytoma

tag: age at diagnosis

tag: blast %

value: bone marrow white blood cells

tag: disease state

value: therapy-related  AML


title: H285

tag: tissue


title: H296


title: therapy-related  AML T29

value: male

value: heart transplant


title: therapy-related  AML T16

value: Hodgkin lymphoma


title: therapy-related  AML T67

value: pancreatic cancer


title: H378

value: sample of diffuse large B-cell lymphoma


title: therapy-related  AML T75

value: systemic lupus erythematosus


title: H321


title: therapy-related  AML T40

source_name: peripheral blood white blood cells

value: breast cancer

value: peripheral blood white blood cells


title: therapy-related  AML T39


title: therapy-related  AML T20

value: breast and lung cancer


title: H380


title: BB39

value: mononuclear cells


title: therapy-related  AML T12


title: therapy-related  AML T68


title: therapy-related  AML T25

value: osteosarcoma


title: H302


title: therapy-related  AML T55


title: H385


title: DCs stimulated with LPS-1

city: Seoul

first: Taek-Chin

last: Cheong

address: Daehakro 103

country: South Korea

institute: Seoul National University

hyb_protocol: 750 ng of labeled cRNA samples were hybridized to each mouse-8 expression bead array for 16-18 h at 58°C, according to the manufacturer's instructions (Illumina, Inc., San Diego, USA). Detection of array signal was carried out using Amersham fluorolink streptavidin-Cy3 (GE Healthcare Bio-Sciences, Little Chalfont, UK) following the bead array manual.

scan_protocol: Arrays were scanned with an Illumina bead array Reader confocal scanner according to the manufacturer's instructions.

data_processing: Raw data were extracted using the software provided by the manufacturer (Illumina GenomeStudio v2009.2 (Gene Expression Module v1.5.4)). Array data were filtered by detection p-value < 0.05 (similar to signal to noise) in at least 50% samples (we applied a filtering criterion for data analysis; higher signal value was required to obtain a detection p-value < 0.05). Selected probe signal value was transformed by logarithm and normalized by quantile method. The comparative analysis between test group and control group was carried out using LPE test and fold-change. False discovery rate (FDR) was controlled by adjusting p value using Benjamini-Hochberg algorithm.

source_name: Bone marrow-derived DCs_LPS

label_protocol: Total RNA was amplified and purified using the Ambion Illumina RNA amplification kit (Ambion, Austin, USA) to yield biotinylated cRNA according to the manufacturer’s instructions.

growth_protocol: DCs were generated from the bone marrow of six-week-old Rag2 KO mouse. The Bone marrow cells were flushed out of the femurs and tibias with Iscove`s modified eagle medium (IMDM, Gibco Invitrogen, Grand Island, NY, USA) medium. DCs were culture in IMDM supplemented with 10% FBS (Gibco Invitrogen), recombinant mouse GM-CSF (1.5 ng/ml, PeproTech, Rocky Hill, NJ, USA), recombinant mouse IL-4 (1.5 ng/ml, PeproTech), penicillin (100 units/ml, Gibco invitrogen), streptomycin (0.1 mg/ml, Gibco Invitrogen), gentamicin (0.05 mg/ml, Gibco Invitrogen), L-Glutamine (2 mM, Gibco Invitrogen), and 2-mercaptoethanol (50 nM, Gibco Invitrogen). Half of the medium was replaced every other day with an equal volume of complete IMDM medium for 6 d.

extract_protocol: Total RNA was extracted using Trizol (Invitrogen Life Technologies, Carlsbad, USA), purified using RNeasy columns (Qiagen, Valencia, USA) according to the manufacturers’ protocol.

treatment_protocol: DCs were incubated with 1 ug/ml of Hematoporphyrin (HP; 8,13-Bis(1-hydroxyethyl)-3,7,12,17-tetramethyl-21H, 23H-porphine-2,18-dipropionic acid, Sigma Aldrich, Saint Louis, MO, USA) for 1 h, washed twice with complete IMDM medium without phenol red, illuminated by a home built light emitting diode (LED), which has wide excitation wavelength ranging from 450 to 600 with peak wavelength at 515 nm at the intensity of 3.1 mW cm-2, equipped with a UV cutoff filter for 3 min, and then cultured for 18 h to prepare total RNA. DCs were also stimulated with 1 ug/ml Lipopolysaccharide (LPS; Sigma Aldrich) for 18 h.

tag: strain background

tag: genotype/variation

value: C57BL/10NAGCSnAi-(KO) Rag2

tag: age

value: 6 weeks

value: bone marrow

value: dendritic cells (DCs)

tag: stimulated with

value: 1ug/ml Lipopolysaccharide for 18 h


title: therapy-related  AML T19

value: chronic lymphocytic leukemia

value: bone marrow white blood cells

value: therapy-related  AML


title: de novo AML cell line  UCM1

source_name: cell line

value: male

value: AML cell line

value: de novo AML

tag: cell line


title: DCs stimulated with intracellular ROS-2

source_name: Bone marrow-derived DCs_intracellular ROS

value: intracellular ROS


title: DCs stimulated with intracellular ROS-1


title: DCs stimulated with LPS-2


title: CL1-5/ANGPTL1

city: Taipei

first: Tsang-Chih

last: Kuo

address: No. 1, Section 1, Jen-Ai Road

country: Taiwan

institute: National Taiwan University

description: Test

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions: http://genome.med.harvard.edu/documents/qpcr/microRNATaqManAssayProtocol.pdf
For the normalization it uses the small nucleolar RNAs (snoRNAs), RNU48 (SNORD48) as endogenous control
Target miRNAs signals normalized to RNU48 (endogenous control); 2^-deltaCt, where deltaCt = (Ct_Target − Ct_Endogenous Control)]
Fold Change  reports test/control (CL1-5/ANGPTL1/CL1-5/pcDNA3.1) ratios.

label: FAM

source_name: CL1-5 cells expressing ANGPTL1

label_protocol: PCR assays were performed using the TaqMan Low Density Array Human MicroRNA Panel v1.0 (ABI) following the Manufacturer’s instructions. Reverse transcription was performed from 500 ng total RNA using the Taqman Multiplex RT for Taqman MicroRNA Assays and Taqman MicroRNA Reverse Transcription Kit. Quantitative real-time PCR were performed (Applied Biosystems 7900HT Fast Real-Time PCR system) with 40 cycles at 95℃ for 15 seconds and 60℃ for 60 seconds.

growth_protocol: Cells were cultured in 5% CO2 incubator at 37℃.

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

treatment_protocol: Cell were selected with G418 for four weeks.  Stably transduced cells were use for this experiment.

value: CL1-5 cells expressing ANGPTL1

tag: treatment

value: ANGPTL1 overexpression


title: therapy-related  AML T70

value: female

value: Hodgkin lymphoma


title: unstimulated DCs-2

source_name: Bone marrow-derived DCs_unstimulated


title: H2-Db GP33-specific CD8+ T cells from C57BL/6 d15 p i  with LCMV-Clone 13 CD8+ Chronic Day15-3

status: Public on Nov 23 2012

city: Philadelphia

first: E

middle: John

last: Wherry

address: 421 Curie Blvd.

institute: University of Pennsylvania

description: H2-Db GP33-specific CD8+ T cells from C57BL/6 d15 p.i. with LCMV-Clone 13

hyb_protocol: cDNA was amplified with NuGen WT Ovation Pico kit and hybridized to Affymetrix GeneChip Mouse Gene 1.0 ST microarrays at the University of Pennsylvania's Microarray facility

scan_protocol: A confocal scanner was used to collect fluorescence signal at 3um resolution after excitation at 570 nm. The average signal from two sequential scans was calculated for each microarray feature.

data_processing: Affymetrix Power Tools were used to process and quantile normalize fluorescent hybridization signals using Robust Multichip Averaging. Transcript values were log2 normalized.

label_protocol: Microarrays were washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain

growth_protocol: Naive CD44Lo CD8+ T cells were isolated and sorted from uninfected C57BL/6 mice and H2-Db GP33-specific CD8+ T cells were sorted using MHC-I tetramers at d6, 8, 15, and 30 p.i. with either LCMV Arm or LCMV clone 13.

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

value: H2-Db GP33-specific CD8+ T cells

tag: strain

tag: time (dpi)

tag: infection

value: LCMV-Clone 13


title: H2-Db GP33-specific CD8+ T cells from C57BL/6 d15 p i  with LCMV-Clone 13 CD8+ Chronic Day15-2

source_name: H2-Db GP33-specific CD8+ T cells from C57BL/6 d15 p.i. with LCMV-Clone 13

treatment_protocol: Naive CD44Lo CD8+ T cells were isolated and sorted from uninfected C57BL/6 mice and H2-Db GP33-specific CD8+ T cells were sorted using MHC-I tetramers at d6, 8, 15, and 30 p.i. with either LCMV Arm or LCMV clone 13.

tag: cell type


title: H2-Db GP33-specific CD8+ T cells from C57BL/6 d30 p i  with LCMV-Clone 13 CD8+ Chronic Day30

description: H2-Db GP33-specific CD8+ T cells from C57BL/6 d30 p.i. with LCMV-Clone 13


title: H2-Db GP33-specific CD8+ T cells from C57BL/6 d30 p i  with LCMV-Clone 13 CD8+ Chronic Day30-3

source_name: H2-Db GP33-specific CD8+ T cells from C57BL/6 d30 p.i. with LCMV-Clone 13


title: therapy-related  AML T08

tag: cytogenetic status of chromosome 7


title: CL1-5/pcDNA3.1

description: Control

source_name: CL1-5 cells expressing pcDNA3.1

value: CL1-5 cells expressing pcDNA3.1

value: pcDNA3.1 control


title: H2-Db GP33-specific CD8+ T cells from C57BL/6 d30 p i  with LCMV-Clone 13 CD8+ Chronic Day30-1


title: H2-Db GP33-specific CD8+ T cells from C57BL/6 d15 p i  with LCMV-Clone 13 CD8+ Chronic Day15


title: H2-Db GP33-specific CD8+ T cells from C57BL/6 d30 p i  with LCMV-Clone 13 CD8+ Chronic Day30-2


title: unstimulated DCs-1

value: C57BL/10NAGCSnAi-(KO) Rag2

value: 6 weeks

value: bone marrow

value: dendritic cells (DCs)


title: H2-Db GP33-specific CD8+ T cells from C57BL/6 d15 p i  with LCMV-Clone 13 CD8+ Chronic Day15-1


title: therapy-related  AML T72

tag: Sex

value: Crohn's disease

value: bone marrow white blood cells

value: therapy-related  AML


title: therapy-related  AML T03

value: male

tag: primary disease

value: heart transplant


title: therapy-related  AML T04

value: breast cancer

tag: age at diagnosis


title: H2-Db GP33-specific CD8+ T cells from C57BL/6 d30 p i  with LCMV-Arm CD8+ Acute Day30

description: H2-Db GP33-specific CD8+ T cells from C57BL/6 d30 p.i. with LCMV-Arm

value: LCMV-Arm


title: H2-Db GP33-specific CD8+ T cells from C57BL/6 d8 p i  with LCMV-Clone 13 CD8+ Chronic Day8-2

description: H2-Db GP33-specific CD8+ T cells from C57BL/6 d8 p.i. with LCMV-Clone 13


title: H2-Db GP33-specific CD8+ T cells from C57BL/6 d30 p i  with LCMV-Arm CD8+ Acute Day30-1

source_name: H2-Db GP33-specific CD8+ T cells from C57BL/6 d30 p.i. with LCMV-Arm


title: H2-Db GP33-specific CD8+ T cells from C57BL/6 d8 p i  with LCMV-Clone 13 CD8+ Chronic Day8-1

source_name: H2-Db GP33-specific CD8+ T cells from C57BL/6 d8 p.i. with LCMV-Clone 13


title: H2-Db GP33-specific CD8+ T cells from C57BL/6 d15 p i  with LCMV-Arm CD8+ Acute Day15-3

description: H2-Db GP33-specific CD8+ T cells from C57BL/6 d15 p.i. with LCMV-Arm


title: H2-Db GP33-specific CD8+ T cells from C57BL/6 d8 p i  with LCMV-Clone 13 CD8+ Chronic Day8


title: H2-Db GP33-specific CD8+ T cells from C57BL/6 d15 p i  with LCMV-Arm CD8+ Acute Day15-2

source_name: H2-Db GP33-specific CD8+ T cells from C57BL/6 d15 p.i. with LCMV-Arm


title: H2-Db GP33-specific CD8+ T cells from C57BL/6 d30 p i  with LCMV-Arm CD8+ Acute Day30-2


title: H2-Db GP33-specific CD8+ T cells from C57BL/6 d8 p i  with LCMV-Clone 13 CD8+ Chronic Day8-3


title: therapy-related  AML T05

value: melanoma, NHL

tag: blast %


title: H2-Db GP33-specific CD8+ T cells from C57BL/6 d6 p i  with LCMV-Clone 13 CD8+ Chronic Day6

description: H2-Db GP33-specific CD8+ T cells from C57BL/6 d6 p.i. with LCMV-Clone 13


title: H2-Db GP33-specific CD8+ T cells from C57BL/6 d6 p i  with LCMV-Clone 13 CD8+ Chronic Day6-2

source_name: H2-Db GP33-specific CD8+ T cells from C57BL/6 d6 p.i. with LCMV-Clone 13


title: H2-Db GP33-specific CD8+ T cells from C57BL/6 d8 p i  with LCMV-Arm CD8+ Acute Day8-3

description: H2-Db GP33-specific CD8+ T cells from C57BL/6 d8 p.i. with LCMV-Arm


title: H2-Db GP33-specific CD8+ T cells from C57BL/6 d8 p i  with LCMV-Arm CD8+ Acute Day8-2

source_name: H2-Db GP33-specific CD8+ T cells from C57BL/6 d8 p.i. with LCMV-Arm


title: H2-Db GP33-specific CD8+ T cells from C57BL/6 d15 p i  with LCMV-Arm CD8+ Acute Day15


title: H2-Db GP33-specific CD8+ T cells from C57BL/6 d30 p i  with LCMV-Arm CD8+ Acute Day30-3


title: H2-Db GP33-specific CD8+ T cells from C57BL/6 d8 p i  with LCMV-Arm CD8+ Acute Day8


title: H2-Db GP33-specific CD8+ T cells from C57BL/6 d6 p i  with LCMV-Clone 13 CD8+ Chronic Day6-3


title: H2-Db GP33-specific CD8+ T cells from C57BL/6 d8 p i  with LCMV-Arm CD8+ Acute Day8-1


title: H2-Db GP33-specific CD8+ T cells from C57BL/6 d6 p i  with LCMV-Arm CD8+ Acute Day6-3

description: H2-Db GP33-specific CD8+ T cells from C57BL/6 d6 p.i. with LCMV-Arm


title: H2-Db GP33-specific CD8+ T cells from C57BL/6 d6 p i  with LCMV-Arm CD8+ Acute Day6-2

source_name: H2-Db GP33-specific CD8+ T cells from C57BL/6 d6 p.i. with LCMV-Arm


title: de novo  AML A56

tag: disease state

value: de novo  AML


title: H2-Db GP33-specific CD8+ T cells from C57BL/6 d6 p i  with LCMV-Arm CD8+ Acute Day6-1

value: H2-Db GP33-specific CD8+ T cells


title: H2-Db GP33-specific CD8+ T cells from C57BL/6 d6 p i  with LCMV-Arm CD8+ Acute Day6


title: therapy-related  AML T02

value: female

value: breast and ovarian cancer


title: de novo  AML A65


title: de novo  AML A72


title: de novo  AML A36


title: H2-Db GP33-specific CD8+ T cells from C57BL/6 d15 p i  with LCMV-Arm CD8+ Acute Day15-1


title: Naive CD44Lo CD8+ T cells from C57BL/6  CD8+ Naive-1

description: Naive CD44Lo CD8+ T cells from C57BL/6

source_name: Naive CD44Lo CD8+ T cells from C57BL/6

value: Naive CD44Lo CD8+ T cells


title: Naive CD44Lo CD8+ T cells from C57BL/6  CD8+ Naive-3

description: Naive CD44Lo CD8+ T cells from C57BL/6


title: de novo  AML A44

source_name: bone marrow white blood cells


title: de novo  AML A21

source_name: peripheral blood white blood cells

value: peripheral blood white blood cells


title: de novo  AML A35


title: de novo  AML A53


title: TS_cells_arrested_at_G2/M_stage_repC

city: Singapore

first: Rohan

last: Williams

address: Medical Drive

country: Singapore

institute: SCELSE-NUS

description: M.C

hyb_protocol: We employed standard Affymetrix hybridisation protocol (45C for 17 hours at 60 rpm)

scan_protocol: Arrays were scanned using a GCS 3000 7G scanner

data_processing:
CEL files were generated Affymetrix GeneChip Command Console (AGCC) software.
RMA expression summaries from apt-probeset-summarize in Affymetrix Power Tools software referenced to mm9 and imported into R (v. 2.11.1)for further analysis.

source_name: TS cells arrested at G2/M stage

label_protocol: Standard Affymetrix Biotin labelling as per manufacturers protocol

growth_protocol: Mouse Trophoblast Stem (TS) cells  were cultured in TS cell specific media with FGF4 and heparin 3

extract_protocol: Total RNA was extracted from TS cells arrested at G1; S and M stages of cell cycle using TRizol (Invitrogen) extraction protocol and purified further the by RNAeasy Extraction Kit (Qiagen). RNA quality was assesed on Bioanalyzer total RNA  chip

treatment_protocol: To synchronize TS cells at the G2/M boundary, cells were treated with nocodazole (40ng/ml) for 7 hr before harvesting. This concentration was chosen after an extensive analysis to determine the minimum concentration required to synchronize cells without any adverse effects to the cell cycle or subsequent differentiation. In order to synchronize TS cells in S phase, TS cells were washed following treatment with nocodazole (40ng/ml) an allowed to grow for an additional 7 hr in drug free fresh TS medium. To synchronize TS cells at the G1/S boundary following nocodazole treatment, TS cells were washed and grown for 3 hr in fresh medium. Hydroxyurea (5mM) was then added and the cells were grown for an additional 5 hr before they were harvested.

tag: developmental stage

value: blastocysts

value: Trophoblast stem (TS) cell


title: H2-Db GP33-specific CD8+ T cells from C57BL/6 d6 p i  with LCMV-Clone 13 CD8+ Chronic Day6-1

value: LCMV-Clone 13


title: de novo  AML A20


title: de novo  AML A74


title: TS_cells_arrested_at_S_stage_repC

description: S.C

source_name: TS cells arrested at S stage


title: TS_cells_arrested_at_S_stage_repB

description: S.B


title: de novo  AML A34


title: Naive CD44Lo CD8+ T cells from C57BL/6  CD8+ Naive

description: Naive CD44Lo CD8+ T cells from C57BL/6


title: therapy-related  AML T01


title: TS_cells_arrested_at_G1_stage_repC

source_name: TS cells arrested at G1 stage


title: de novo  AML A24


title: TS_cells_arrested_at_G1_stage_repA


title: HCT116p53+/+ cells untreated 2

city: buffalo

first: Dan

last: Wang

state: NY

address: Elm & Carlton Streets

institute: RPCI

hyb_protocol: The labeled probes were then mixed with hybridization reagents and hybridized overnight to the HumanHT-12 v3 BeadChips.

scan_protocol: Following washing and staining, the BeadChips were imaged using the Illumina BeadArray Reader to measure fluorescence intensity at each probe.

data_processing: BeadChip data files are analyzed with Illumina’s GenomeStudio gene expression module (V1.6.0)

source_name: HCT116p53+/+ cells untreated

label_protocol: Initially, we converted 250-500 ng total RNA to cDNA, followed by in vitro transcription to generate biotin-labeled cRNA (Illumina TotalPrep RNA Amplification Kit, Ambion Inc., Austin, TX).

extract_protocol: Total RNA was isolated from frozen tissue samples using TRIZOL reagent (Invitrogen).

value: colon cancer


title: P2-treated HCT116p53+/+ cells 2

source_name: P2-treated HCT116p53+/+ cells


title: TS_cells_arrested_at_G2/M_stage_repA

description: M.A


title: HCT116p53+/+ cells untreated 1


title: P2-treated HCT116 p53-/- cells 2

source_name: P2-treated HCT116 p53-/- cells


title: P2-treated HCT116 p53-/- cells 1


title: P2-treated HCT116p53+/+ cells 1


title: HCT116p53-/- cells untreated 1

source_name: HCT116p53-/- cells untreated


title: Naive CD44Lo CD8+ T cells from C57BL/6  CD8+ Naive-2

description: Naive CD44Lo CD8+ T cells from C57BL/6


title: HCT116p53-/- cells untreated 2


title: tet-off day 3 [L428tetPU.1 cells]

status: Public on Nov 22 2012

city: Kumamoto

first: Yutaka

last: Okuno

state: Kumamoto

address: 1-1-1 Honko, Chuo Ku

department: Department of Hematology

institute: Kumamoto university of Medicine

description: SAMPLE 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The non-normalized data were generated using BeadStudio version 3.3.7. The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: L428tetPU.1 cells

label_protocol: Ambion®‘s Illumina® TotalPrep™ RNA Amplification Kit

growth_protocol: RPMI1640 + 10% fetal bovine serum + 500 ng/ml of tetracycline

extract_protocol: TRIzol® Reagent

treatment_protocol: tetracycline removal

value: Classical Hodgkin Lymphoma L428-derived cell line

tag: protocol

value: PU.1 induction

tag: time

value: day 3


title: tet-off day 1 [L428tetPU.1 cells]

description: SAMPLE 2

value: day 1


title: tet-off day 0 [L428tetPU.1 cells]

description: SAMPLE 1

value: day 0


title: Ex vivo spleen CD4-CD8- DCs rep1

first: Alexander

last: Mildner

address: 234 Herzl street

department: Immunology

institute: Weizmann Institute of Science

description: miRNA expression profile of mouse CD4-CD8- DCs

hyb_protocol: Labeled RNA was hybridized with a 8X15 mouse miRNA array rel 12 v2 (design number 021828) for chip 1 and 8X15 mouse miRNA array rel v15 (design number 029152) for chip 2 at 55°C and 20 rpm for 20 hours, and then washed according to the manufacturer’s instructions.

scan_protocol: Agilent Technologies Scanner G2505B US22502692 using 5uM resolution

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol miRNA_107_Sep09 and Grid: 029152_D_F_20100702) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: spleen

label_protocol: Cyanine-3 (Cy3) labeled miRNA was prepared from 100ng total RNA using Agilent miRNA Complete Labeling and Hyb Kit according to the manufacturer's instructions

extract_protocol: The miRNeasy total RNA extraction kit was used for RNA isolation. DNase treatment was performed on columns according to the instructions of the manufacturer.

treatment_protocol: Cells were isolated ex vivo and cells were directly isolated within a total range of time of 5h.

tag: gender

tag: age

value: 6 weeks

tag: pool of x animals

tag: replicate

value: biological replicate 1

tag: surface markers


title: Ex vivo spleen CD8+ DCs rep1

description: miRNA expression profile of mouse CD8+ DCs

tag: strain


title: Ex vivo spleen CD4+ DCs rep1

description: miRNA expression profile of mouse CD4+ DCs


title: Ex vivo BM Gr1+ monocytes rep1

description: miRNA expression profile of mouse Gr1+ monocytes

source_name: bone marrow (femur and tibia)


title: Ex vivo BM CDPs rep1

description: miRNA expression profile of mouse CDPs


title: Ex vivo BM MDPs rep1

description: miRNA expression profile of mouse MDPs


title: Ex vivo BM MPs rep1

description: miRNA expression profile of mouse MPs


title: Ex vivo BM PDCs rep1

description: miRNA expression profile of mouse PDCs

value: B220+CD11c int, SiglecH+, CD317+


title: Apal_G3-Acer x Apal 4

city: Thuwal

first: Christian

middle: Robert

last: Voolstra

address: Red Sea Research Center

country: Saudi Arabia

institute: King Abdullah University of Science and Technology

hyb_protocol: according to manufacturer's instructions

data_processing: Microarray slides were scanned and spot intensities were extract and background subtracted using TIGR Spotfinder 2.2.3. The data were quality filtered, and normalized using TIGR MIDAS 2.21 printtip-specific LOWESS. For all analyses, we only considered spots that were present in at least 3 out of 4 replicates.

organism: Acropora cervicornis

source_name: Acer Cy3

label_protocol: according to manufacturer

extract_protocol: Between 50-100 mg of frozen coral tissue were scraped off the samples using a metal corer and DNA was extracted using the PowerPlant DNA extraction kit (MoBio Laboratories, Carlsbad, CA, USA) with the following modifications: following tissue homogenization, samples were spun twice to pellet skeletal debris; and during incubation with Buffer PB1, 1mg/mL RNase A was added. Extracted DNA was quantified using a NanoDrop ND-1000 spectrophotometer. Fragmentation of the DNA for whole genome amplification was assessed using the Agilent Bioanalyzer DNA7500 Kit and subsequent fragmentation steps were omitted since the DNA already fulfilled the required fragment size. A total of 25 ng of DNA from each sample was amplified using the GenomePlex Complete Whole Genome Amplification Kit (Sigma Aldrich, Saint Louis, MO, USA) according to the manufacturer's instructions but using 16 cycles of amplification.

tag: species

value: Acropora cervicornis

organism: Acropora palmata

source_name: Apal Cy5

value: Acropora palmata


title: Apal_G3-Acer x Apal 2

scan_protocol: according to manufacturer's instructions

source_name: Apal Cy3

source_name: Acer Cy5


title: Apal_G3-Acer x Apal 1


title: Apal_G3-Acer x Apal 3


title: TS_cells_arrested_at_S_stage_repA

description: S.A

tag: cell line

tag: cell type


title: PLNs AAT Treated 2

city: Boston

first: Manoj

last: Bhasin

state: MA

address: 330 Brookline Avenue  RN 380E

institute: Beth Israel Deaconess Medical Center

description: PLNs of female NOD mouse,AAT treated

hyb_protocol: Fragmented and labelled cDNA was hybridized onto Affymetrix human MG 430 2.0 gene chips, followed by washing and scanning.

scan_protocol: Hybridised Arrays were Scanned using Affymetrix Scanner

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

source_name: PLNs

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1Purified RNA was reverse transcribed and amplified using the WT-Ovation™ Pico RNA Amplification system (NuGEN Technologies) following the manufacturer’s instructions. ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Standard light-dark cycle and standard diet prior to and during experiment

treatment_protocol: Streptozotocin (STZ) induction of diabetes: B-cells were destroyed in formerly spontaneously diabetic NOD mice in whom anti-TNF-α treatment rendered mice euglycemic by administration of streptozotocin (STZ; 275 mg/kg i.p), a beta cell toxin.

value: NOD (NOD/LtJx) mice

tag: Sex

value: female

tag: tissue

value: PLNs

tag: disease/treatment status

value: AAT treated


title: PLNs AAT Treated 3

description: PLNs of female NOD mouse,AAT treated


title: PLNs Normal 4

description: PLNs of female NOD mouse, Normal

value: normal


title: PLNs Diabetic 1

description: PLNs of female NOD mouse, Diabetic

value: diabetic


title: PLNs Diabetic 2

description: PLNs of female NOD mouse, Diabetic


title: PLNs AAT Treated 4

description: PLNs of female NOD mouse,AAT treated


title: PLNs Normal 3

description: PLNs of female NOD mouse, Normal


title: PLNs AAT Treated 1

description: PLNs of female NOD mouse,AAT treated


title: FAT Power Mix Treated 3

description: Fat of female NOD mouse,PW treated

source_name: FAT

value: FAT

value: Power mix treated


title: PLNs Normal 2

description: PLNs of female NOD mouse, Normal


title: PLNs Normal 1

description: PLNs of female NOD mouse, Normal


title: WT replicate 1

city: Essen

first: Cyrus

last: Khandanpour

address: Hufelandstr. 55

department: Hematology

institute: University Hospital Essen

hyb_protocol: hybridization was done following the manufacturers instructions

scan_protocol: scanning was done on a Genechip scanner 3000 using the manufacturers instructions

data_processing: data was processed using the AltAnalyze software (http://altanalyze.org) using standard RMA analysis settings

source_name: bone marrow derived granulocyte monocyte precursors (GMPs) from wt mice

label_protocol: for array hybridization total RNA was amplified and labeled using the following kits from Nugen (San Carlos, California; USA): WT-Ovation Pico Amplification system, WT-Ovation Exon module and FL-Ovation cDNA Biotin Module V2 and the Affymetrix's Hybridization Wash and Stain kit

growth_protocol: All mice were housed under SPF conditions and all animal experiments were approved by the institutional animal ethics committee

extract_protocol: total RNA was purified using the Qiagen (Hilden, Germany) Rneasy Micro Kit according to the manufacturers instructions

tag: genotype/variation

value: wt mice


title: WT replicate 3


title: wtKI1 replicate 1

source_name: bone marrow derived granulocyte monocyte precursors (GMPs) from human Gfi1-wt knock-in mice

value: human Gfi1-wt knock-in mice


title: wtKI1 replicate 3


title: de novo  AML A19

source_name: peripheral blood white blood cells

value: male

tag: primary disease

tag: age at diagnosis

tag: blast %

value: peripheral blood white blood cells

tag: disease state

value: de novo  AML


title: WT replicate 2


title: SNP replicate 2

source_name: bone marrow derived granulocyte monocyte precursors (GMPs) from human Gfi1-SNP knock-in mice

value: human Gfi1-SNP knock-in mice


title: wtKI1 replicate 2


title: FAT Power Mix Treated 2

description: Fat of female NOD mouse,PW treated


title: FAT AAT Treated 2

description: Fat of female NOD mouse,AAT treated


title: tet-off day 3 [KM-H2tetPU.1 cells]_rep4

description: Day 3 SAMPLE 4

source_name: KM-H2tetPU.1 cells

value: Classical Hodgkin Lymphoma KM-H2-derived cell line

tag: protocol

value: PU.1 induction

tag: time

value: day 3


title: SNP replicate 3


title: FAT Diabetic 2

description: Fat of female NOD mouse, Diabetic

value: NOD (NOD/LtJx) mice


title: tet-off day 3 [KM-H2tetPU.1 cells]_rep2

description: Day 3 SAMPLE 2


title: FAT AAT Treated 1

description: Fat of female NOD mouse,AAT treated

value: female


title: TS_cells_arrested_at_G2/M_stage_repB

description: M.B

source_name: TS cells arrested at G2/M stage

tag: developmental stage

value: blastocysts

value: Trophoblast stem (TS) cell


title: FAT Power Mix Treated 1

description: Fat of female NOD mouse,PW treated


title: KO replicate 1

source_name: bone marrow derived granulocyte monocyte precursors (GMPs) from Gfi1 knock-out mice

value: Gfi1 knock-out mice


title: tet-off day 3 [KM-H2tetPU.1 cells]_rep3

description: Day 3 SAMPLE 3


title: KO replicate 3


title: TS_cells_arrested_at_G1_stage_repB

source_name: TS cells arrested at G1 stage


title: S10

city: Amsterdam

first: Elisa

last: Giovannetti

address: De Boelelaan 1117

department: Medical Oncology

country: Netherlands

institute: VUmc

description: SAMPLE 6

hyb_protocol: Hybridized for 16 hr at 32C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc. The labeled samples were individually hybridized onto DNA chip surface, and incubated at 42 ℃ for 16 hours.

scan_protocol: Microarrays were scanned and the obtained images were numerated using 3D-GeneTM scanner 3000 (Toray Industries). Washed and dried DNA chip in an ozone-removed environment was scanned using a ProScanArray™ microarray scanner. The obtained microarray images were analyzed using the Genepix Pro™ 4.0 software.

data_processing:
The signal intensity (SpotMedian 635nm) was subtracted with the background and the mean of the duplicated gene spots were calculated if the original signal is larger than (the background + 2 standard deviation). If one of the duplicated spots shows the signal intensity of less than (BG mean +2SD), the remaining spot represents the gene. The background-subtracted signals were then globally normalized by adjusting the median signal intensity for each DNA chip to be 25.
The median values of the foreground signal minus the local background were represented as feature intensities. All data obtained from microarray experiments were normalized by a quantile normalization method, and filtered.

source_name: short OS_PDAC

label_protocol:
The labeling was performed using Exiqon mercury LNATM microRNA Array Power Labeling kit.
For each patient, 500 ng of total RNA derived from tumor and non-tumor samples were labeled using miRCURY LNA™ microRNA Power Labeling Kits Hy5

extract_protocol:
10um-thick FFPE tissue was treated with xylene to remove paraffin, and washed with ethanol twice to remove xylene.  Tissues were then treated with proteinase K at 37˚C overnight. Following centrifugation, the supernatant was processed with a silica‑based spin column in order to obtain purified total RNA
Tumor and non-tumor tissues were obtained and frozen in liquid nitrogen immediately after hepatic resection, and stored in liquid nitrogen until RNA extraction. Total RNA samples were extracted by a phenol-chloroform RNA extraction method.

value: primary pancreatic cancer

tag: status

value: Dead

tag: histology

value: Ductal Adenocarcinoma

tag: age

tag: gender

value: Male

tag: Stage

tag: overall survival (os)

value: short (<12 months)


title: KFAM 149

city: Bordeaux

first: Michel

last: Longy

address: 229 Cours de l'Argonne

department: Genetics

country: France

institute: Bergonie Cancer Institute

hyb_protocol: Illumina Human 610 Quad protocol

scan_protocol: Illumina Human 610 Quad protocol

data_processing:
Illumina Genome Studio Software 2010.1
Genotyping model v.1.6.3

source_name: Breast cancer

label_protocol: Illumina Human 610 Quad protocol

extract_protocol: Classic Phenol Chloroform extraction and ethanol precipitation

tag: diagnosis

value: breast cancer

value: BRCA2 tumor


title: SNP replicate 1

tag: strain


title: FAT Diabetic 1

description: Fat of female NOD mouse, Diabetic

tag: Sex

tag: tissue

value: FAT

tag: disease/treatment status

value: diabetic


title: KFAM 148


title: S12

description: SAMPLE 5

value: Female


title: S13

description: SAMPLE 4


title: S4

description: SAMPLE 3


title: S6

description: SAMPLE 2


title: tet-off day 1 [KM-H2tetPU.1 cells]_rep2

description: Day 1 SAMPLE 2

tag: cell line

value: Classical Hodgkin Lymphoma KM-H2-derived cell line

value: PU.1 induction

value: day 1


title: cDNA from wild type cells rep2

city: London

first: Rahul

last: Thadani

address: 44 Lincoln's Inn Fields

institute: Cancer Research UK

description:
K699_20062012
3461_K699_WT.CEL

hyb_protocol: Hybridization was performed following the manufacturers instructions (Affymetrix). Samples were hybridized in buffer containing SSPE, TritonX-100, denatured salmon sperm DNA and biotin-labelled control oligonucleotide, oligo B2. Samples were denatured at 95ºC for 10 minutes before being hybridized to the arrays for 16 hours at 42ºC in a GeneChip Hybridization Oven 640.

scan_protocol: The washing and scanning protocol (FlexMini_euk2v3_450), provided by Affymetrix, was performed automatically on a GeneChip Fluidics Station 450. Arrays were scanned using the GeneChip Scanner 3000 7G, and primary analysis of the chip data was performed using the Affymetrix GeneChip Operating Software (GCOS).

data_processing: The data provided was pre-processed and normalised using the standard RMA procedure, as provided by the affy package in Bioconductor 2.11.

organism: Saccharomyces cerevisiae

source_name: wild type cells

label_protocol: 10 mg of dscDNA was digested with DNase I and end-labeled using biotin-N6-ddATP using terminal transferase TdT (Roche, 400 U/µl) and Biotin-N6-ddATP (Enzo Life Sciences).

growth_protocol: Cells were grown in YP + 2% Glucose to an OD600 of 0.3.

extract_protocol: Total RNA was extracted following the manufacturers instructions (QUIAGEN). dscDNA was amplified using IVT (Invitrogen).

treatment_protocol: Exponentially growing cells were harvested.

tag: genotype/variation

value: MATa


title: tet-off day 0 [KM-H2tetPU.1 cells]_rep2

description: Day 0 SAMPLE 2

value: day 0


title: tet-off day 0 [KM-H2tetPU.1 cells]_rep4

description: Day 0 SAMPLE 4


title: tet-off day 0 [KM-H2tetPU.1 cells]_rep3

description: Day 0 SAMPLE 3


title: tet-off day 1 [KM-H2tetPU.1 cells]_rep1

description: Day 1 SAMPLE 1


title: KFAM 144

value: BRCA2 Tumor


title: cDNA from wpl∆ cells rep2

description:
wpl1∆_20062012
3607_WPL-del.CEL

source_name: wpl∆ cells

value: MATa, wpl1∆::KAN


title: ES cells Esrrb&Sox2 shRNA rep1-rep4

city: Shenzhen

first: Andrew

middle: P

last: Hutchins

address: 1088 Xueyuan Rd

department: Bioinformatics

country: China

institute: Southern University of Science and Technology

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing: The data was normalised using GeneSpring 7. Merged 4 biological replicates to give a mean (transformed) expression and stdev value.

source_name: ES cells Esrrb&Sox2 shRNA

label_protocol: Standard Illumina Protocol

growth_protocol: normal ES cell conditions

extract_protocol: RNA was extracted with TRIzol reagent, followed by purification using the QIAGEN RNeasy mini kit according to the manufacturers protocol. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: shRNAs for GFP, Esrrb and Sox2 were transfected into mouse ES cells using lipofecatmine. Transfectants were slected by puromycin for 2 days and RNA harvested for microarray analysis

tag: dev stage

tag: cell type

value: Embryonic Stem Cells


title: tet-off day 1 [KM-H2tetPU.1 cells]_rep3

description: Day 1 SAMPLE 3

tag: protocol

tag: time


title: FAT Normal 2

description: Fat of female NOD mouse, Normal

value: NOD (NOD/LtJx) mice

value: female

value: normal


title: tet-off day 0 [KM-H2tetPU.1 cells]_rep1

description: Day 0 SAMPLE 1


title: cDNA from wpl∆ cells rep1

description:
wpl1∆_29052012
51130800921268011914415882843604.CEL


title: tet-off day 1 [KM-H2tetPU.1 cells]_rep4

description: Day 1 SAMPLE 4


title: L1

description: SAMPLE 19

source_name: Long OS_PDAC

value: primary pancreatic cancer

tag: status

value: Dead

value: Ductal Adenocarcinoma

value: long ( >30 months)


title: KFAM 133

value: breast cancer

value: BRCA2 tumor


title: cDNA from wild type cells rep1

description:
K699_29052012
51130800921268011914415882843535.CEL


title: Input DNA chromatin binding pattern

description:
Supernatant DNA
M57.SupA

hyb_protocol: Hybridization was performed as previously described (Katou et al. 2003). Samples were hybridized in buffer containing SSPE, TritonX-100, denatured salmon sperm DNA and biotin-labelled control oligonucleotide, oligo B2. Samples were denatured at 95ºC for 10 minutes before being hybridized to the arrays for 16 hours at 42ºC in a GeneChip Hybridization Oven 640.

scan_protocol: The washing and scanning protocol (FlexMidi_euk2v3_450), provided by Affymetrix, was performed automatically on a GeneChip Fluidics Station 450. Arrays were scanned using the GeneChip Scanner 3000 7G, and primary analysis of tiling chip data was performed using the Affymetrix GeneChip Operating Software (GCOS).

data_processing:
Signal intensities between the ChIP and supernatant samples were normalized across all probe sets. The data provided was pre-processed and normalised using the standard RMA procedure as detailed in the Affymetrix Statistical Algorithms Reference Guide (http://www.affymetrix.com/support/technical/technotes/statistical_reference_guide.pdf). Probe sets and changes were averaged within adjacent 100 bp windows for graphical depiction.
Seq= Chromosome number; PMX and PMY= coordinates of the probe in the array; SIGNAL Intensity= unprocessed signal intensity; Signal Log Ratio= Log2 binding ratio of protein of interest compared to supernatant fraction.

source_name: input DNA from yeast cells

label_protocol: 10 ng of amplified DNA was digested with DNase I and end-labeled using biotin-N6-ddATP using terminal transferase TdT (Roche, 400 U/µl) and Biotin-N6-ddATP (Enzo Life Sciences).

growth_protocol: Cells were grown in YP + 2% Raffinose to an OD600 of 0,3. Cells were then arrested in G1 by adding a-factor to a final concentration of 0.5mg/ml during 2h. Galactose was added to the culture 30 min before release from G1 to a final concentration of 2% and then cells were grown 2h in YP + 2% Raffinose + 2% Galeactose for the late G1 arrest. For the metaphase arrest, cells were release from a-factor mediated G1 arrest and grown 2h in YP + 2% Raffinose + 5 mg/ml Nocodazole.

extract_protocol: Chromatin Immunoprecipitation followed by hybridization to a high-density oligonucleotide microarray (ChIP on chip) were performed as previously described (Katou et al. 2003; Lengronne et al. 2004; Lengronne et al. 2006). Briefly, cross-linked cells were disrupted using a Multi-Beads Shocker, and whole cell extracts were sonicated to obtain 400-600 bp genomic DNA fragments. Chromatin immunoprecipitation (ChIP) was performed with anti-PK monoclonal antibody (clone SV5-Pk1, Serotec) coupled to protein A Dynabeads. Immunoprecipates were eluted and incubated overnight at 65ºC to reverse the cross-link. An aliquot of the supernatant fraction of the immunoprecipitation was treated in parallel to provide a whole genome DNA sample for comparison.  The ChIP and supernatant samples were then incubated with proteinase K, extracted twice with phenol/chloroform/isoamylalcohol, precipitated, resuspended in TE and incubated with RNaseA. The DNA was purified, concentrated by ethanol precipitation and amplified by PCR after random priming.

treatment_protocol: Late G1 or Metaphase arrested cells were cross-linked with 1% Formaldehide for 30 minutes at room temperature. The reaction was stopped with 0.125 M Glycine for 10 minutes.

value: MATa, Scc1-9Pk::TRP


title: FAT Normal 1

description: Fat of female NOD mouse, Normal

value: FAT


title: KFAM 146


title: S3

description: SAMPLE 1

tag: histology

value: Female

value: short (<12 months)


title: Scc1-9Pk chromatin binding pattern in Nocodazole arrested cells

source_name: ChIP DNA from yeast cells

tag: chip antibody

value: anti-PK clone SV5-Pk1

tag: chip antibody vendor

value: Serotec

tag: chip antibody cat. #

tag: chip antibody lot #


title: L2

description: SAMPLE 18

tag: age

tag: gender

value: Male

tag: Stage

tag: overall survival (os)


title: Scc1-9Pk chromatin binding pattern in late G1 arrested cells

tag: strain


title: HPRT knockdown (Neuron)-3

city: La Jolla

first: Tae Hyuk

last: Kang

state: CA

address: 9500 Gilman Drive # 0634

department: Pediatrics

institute: University of California, San Diego

description: replicate 3

data_processing: The data were normalised by loess normalization method (31. Sásik, R., Woelk, C. H., and Corbeil, J. (2004) J. Mol. Endocrinol. 33, 1-9)

source_name: HPRT knockdown_D3_final neuron stage

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

growth_protocol: The D3 embryonic stem cells were maintained on primary mouse embryo fibroblast feeder cells in ES medium consisting of DMEM/F12 medium, 20% (v/v) KOSR, 1 mM of L-glutamine, 4ng/ml of bFGF, 1,000 U/ml of LIF, 1% (v/v) NEAA, 50 U/ml of penicillin, 50 ug/ml of streptomycin and 0.1 mM of 2-mercaptoethanol. All cell cultrue and neuronal differentiations were carried out in established cell culture conditions (5% CO2, 37 °C). Dopaminergic neuronal differentiation was carried out according to the protocol published Cho et al. (Nature Protocols 2008, 3, 1888 - 1894.

extract_protocol: Total RNAs from HPRT knockdown and control cells were purified by Rneasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer's instruction. The pooled total RNAs of HPRT knockdown and control sample were obtained from the independently replicated cultures.

treatment_protocol: HPRT knockdown cells were infected by retrovirus with shRNA against HPRT and control cells were infected by retrovirus with shRNA against luciferase.

value: D3 embryonic stem cell

tag: cell subtype

value: final neuron stage


title: L6

description: SAMPLE 17

tag: tissue


title: L3

description: SAMPLE 16


title: MCF-7Dox2-12 vs MCF-7cc12 reverse labeling set 3 replicate 4

city: Sudbury

first: Baoqing

last: Guo

state: ON

address: 41 Ramsey Lake Road

department: Tumor Biology

country: Canada

institute: Advanced Medical Research Institute of Canada

description: technical replicate 4 of 4

hyb_protocol: Microarray hybridization process was conducted as per description by Agilent Two-clour Microarray-based gene expression Analysis

scan_protocol: After hybridization, the microarray slides were scanned by using an Agilent G2505C scanner as discribed in Agilent manual.

data_processing:
Images were quantified and background subtraction was performed using Agilent Feature Extraction Software (version A.9_5_3, and version 10_7_3).
Data analysis was done using Partek Genomic Suite after feature extraction.  A 4-way ANOVA model was performed by using Method of Moments (Eisenhart, 1947) as outlined below:                                                              Model: Yijklm = μ + Cell line(i)+Dye(j)+Exp batch(k)+arrays(Exp batch)(kl)+ εijklm  Where Yijklm represents the mth observation on the ith Cell line jth Dye kth Exp batch lth arrays   μ is the common effect for the whole experiment.  εijklm represents the random error present in the mth observation on the ith Cell line jth Dye kth Exp batch lth arrays .The errors εijklm are assumed to be normally and independently distributed with mean 0 and standard deviation δ for all measurements.  arrays is a random effect.Exp batch is a random effect.  The following contrast, MCF-7Dox2-12 vs. MCF-7cc12, (Tamhane and Dunlop, 2000) was performed to compare:     Fold changes of the differentially expressed genes between drug resistant and parental cells were calculated and genes with more than two-fold difference were selected with FDR at either 0.05 or 0.01. (Tamhane, Ajit C., & Dunlop, Dorothy D. 2000)

source_name: human breast adenocacinoma cancer cells

label_protocol: Agilent 4×44k oligonucleotide arrays (Agilent, Product #: G4112F.) were used in our microarray experiments to compare the expression of genes between drug-selected doxorubicin resistant cells and its parental cells. 500 ng of RNA  was used. Labelling was done using the Quick Amp labeling kit (Agilent, #5190-0444) as described in Agilent manual.

growth_protocol: Cells were grown in tissue culture flucks with DMEM H21 medium at 37C with 5% of CO2, and subcultured when cell density reached 80-90% confluence.

extract_protocol: Total RNA was isolated using RNeasy Mini Kit (Qiagen), and quantity and quality were assessed using Agilent BioAnalyizer. 3 separate isolations with RIN at 10 were pooled together for labelling.

treatment_protocol: Cell were cultured and selected for survival in increasing doses of doxorubicin as previously described (Guo B, Villeneuve DJ, Hembruff SLet al. Breast Cancer Res Treat. 2004;85(1):31-5126;27).  MCF-7 cells selected to maximally tolerated dose of doxorubicin at the concentrations of 9.81E-08 M (dose 12, MCF-7Dox2-12). A parallel selection process was conducted to the same selection dose number in the absence of drug for co-cultured control cells MCF-7cc12.

tag: cell line

tag: phenotype

value: dox sensitive

value: dox resistant


title: L4

description: SAMPLE 15

value: primary pancreatic cancer


title: Control (Neuron)-3

description: replicate 3

source_name: Control_D3_final neuron stage

tag: cell type


title: HPRT knockdown (SNM)-3

description: replicate 3

source_name: HPRT knockdown_D3_spherical neural mass (SNM) stage

value: spherical neural mass (SNM) stage


title: L5

description: SAMPLE 14

value: Dead

value: Ductal Adenocarcinoma


title: Ex vivo spleen CD4-CD8- DCs rep2

city: Rehovot

source_name: spleen

value: female

value: 6 weeks

tag: pool of x animals

tag: replicate

value: biological replicate 2

tag: surface markers


title: ES cells Esrrb shRNA rep1-rep4

source_name: ES cells Esrrb shRNA

tag: dev stage

value: Embryonic Stem Cells


title: tet-off day 3 [KM-H2tetPU.1 cells]_rep1

country: Japan

description: Day 3 SAMPLE 1

source_name: KM-H2tetPU.1 cells

value: Classical Hodgkin Lymphoma KM-H2-derived cell line

tag: protocol

value: PU.1 induction

tag: time

value: day 3


title: Ex vivo spleen CD8+ DCs rep2


title: Control (SNM)-3

description: replicate 3

source_name: Control_D3_spherical neural mass (SNM) stage


title: S5

description: SAMPLE 13

tag: status

tag: histology

value: Female

value: short (<12 months)


title: HPRT knockdown (ES)-3

description: replicate 3

source_name: HPRT knockdown_D3_embrionic stage

value: D3 embryonic stem cell

value: embryonic stage


title: S9

description: SAMPLE 12

source_name: short OS_PDAC

tag: age

tag: gender

value: Male


title: Ex vivo spleen CD4+ DCs rep2


title: MCF-7Dox2-12 vs MCF-7cc12 reverse labeling set 3 replicate 3

description: technical replicate 3 of 4

value: dox sensitive

value: dox resistant


title: ES cells GFP shRNA rep1-rep4

source_name: ES cells GFP shRNA


title: MCF-7Dox2-12 vs MCF-7cc12 forward labeling set 3 replicate 1

description: technical replicate 1 of 4


title: MCF-7Dox2-12 vs MCF-7cc12 forward labeling set 3 replicate 2

description: technical replicate 2 of 4


title: Ex vivo BM PDCs rep2

description: miRNA expression profile of mouse PDCs

source_name: bone marrow (femur and tibia)

value: B220+CD11c int, SiglecH+, CD317+


title: MCF-7Dox2-12 vs MCF-7cc12 reverse labeling set 2 replicate 4

description: technical replicate 4 of 4


title: MCF-7Dox2-12 vs MCF-7cc12 reverse labeling set 2 replicate 3

description: technical replicate 3 of 4


title: HPRT knockdown (SNM)-2

description: replicate 3

value: spherical neural mass (SNM) stage


title: KO replicate 2

source_name: bone marrow derived granulocyte monocyte precursors (GMPs) from Gfi1 knock-out mice

tag: genotype/variation

value: Gfi1 knock-out mice


title: HPRT knockdown (Neuron)-2

description: replicate 3

tag: strain

value: final neuron stage


title: Control (ES)-3

description: replicate 3

source_name: Control_D3_embrionic stage

tag: cell subtype


title: MCF-7Dox2-12 vs MCF-7cc12 forward labeling set 2 replicate 2

description: technical replicate 2 of 4


title: Control (Neuron)-2

description: replicate 3


title: S8

description: SAMPLE 11

tag: tissue

value: primary pancreatic cancer

value: Dead

value: Ductal Adenocarcinoma

tag: Stage

tag: overall survival (os)


title: S7

description: SAMPLE 10


title: S2

description: SAMPLE 8


title: S11

description: SAMPLE 9


title: Ex vivo BM Gr1+ monocytes rep2

value: female

value: 6 weeks

value: biological replicate 2


title: Ex vivo BM CDPs rep2

description: miRNA expression profile of mouse CDPs


title: Ex vivo BM MDPs rep2

description: miRNA expression profile of mouse MDPs


title: Ex vivo BM MPs rep2

description: miRNA expression profile of mouse MPs


title: S1

description: SAMPLE 7


title: Control (SNM)-2

description: replicate 3

tag: cell type


title: Apal_G3-Mfav x Apal 4

organism: Orbicella faveolata

source_name: Mfav Cy3

tag: species

value: Montastraea faveolata

source_name: Apal Cy5

value: Acropora palmata


title: MCF-7Dox2-12 vs MCF-7cc12 forward labeling set 2 replicate 1

description: technical replicate 1 of 4

tag: cell line

tag: phenotype


title: HPRT knockdown (Neuron)-1

description: replicate 3

value: D3 embryonic stem cell


title: HPRT knockdown (ES)-2

description: replicate 3

value: embryonic stage


title: Apal_G3-Sra x Apal 4

organism: Siderastrea radians

source_name: Sra Cy3

value: Siderastrea radians


title: Apal_G3-Sra x Apal 3


title: Apal_G3-Mfav x Apal 3


title: MCF-7Dox2-12 vs MCF-7cc12 forward labeling set 1 replicate 7

description: technical replicate 7 of 8

value: dox sensitive


title: MCF-7Dox2-12 vs MCF-7cc12 forward labeling set 1 replicate 8

description: technical replicate 8 of 8

value: dox resistant


title: MCF-7Dox2-12 vs MCF-7cc12 forward labeling set 1 replicate 6

description: technical replicate 6 of 8


title: Control (ES)-2

description: replicate 3


title: Control (Neuron)-1

description: replicate 3


title: MCF-7Dox2-12 vs MCF-7cc12 forward labeling set 1 replicate 5

description: technical replicate 5 of 8


title: MCF-7Dox2-12 vs MCF-7cc12 forward labeling set 1 replicate 4

description: technical replicate 4 of 8


title: Control (SNM)-1

description: replicate 3


title: HPRT knockdown (SNM)-1

description: replicate 3


title: Apal_G3-Sra x Apal 2

source_name: Apal Cy3

source_name: Sra Cy5


title: MCF-7Dox2-12 vs MCF-7cc12 forward labeling set 1 replicate 2

description: technical replicate 2 of 8

source_name: human breast adenocacinoma cancer cells


title: MCF-7Dox2-12 vs MCF-7cc12 forward labeling set 1 replicate 3

description: technical replicate 3 of 8


title: HPRT knockdown (ES)-1

description: replicate 3


title: Apal_G3-Mfav x Apal 2

source_name: Mfav Cy5


title: Apal_G3-Sra x Apal 1


title: Apal_G3-Mfav x Apal 1


title: MCF-7Dox2-12 vs MCF-7cc12 forward labeling set 1 replicate 1

description: technical replicate 1 of 8


title: age 69y 11084

status: Public on Nov 21 2012

city: Seattle

first: Justin

last: Guinney

address: 2606 E Roy St

institute: Sage Bionetworks

description: whole blood

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

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

data_processing: BeadStudio software v3.2

label: Cy5 and Cy3

extract_protocol: genomic DNA was extracted and purified Qiagen FlexiGene DNA kit

tag: age (y)

tag: source

value: UCSD

tag: plate

value: F

tag: ethnicity

value: Caucasian - European

value: whole blood


title: age 71y 11093

description: whole blood

value: M


title: ES cells Sox2 shRNA rep1-rep4

source_name: ES cells Sox2 shRNA

tag: dev stage

value: Embryonic Stem Cells


title: Control (ES)-1

description: replicate 3


title: age 73y 11096

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description: whole blood

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title: age 47y 9085

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title: age 41y 9030

description: whole blood