title: Pool x stress trans2 3

city: Greifswald

first: Florian

last: Bonn

address: Jahnstraße 15

department: Institute for Microbiology

institute: University of Greifswald

hyb_protocol: 300 ng of Cy5-labeled cDNA and 300 ng of Cy3-labeled cDNA were hybridized together to the microarray following Agilent's hybridization, washing, and scanning protocol (Two-Color Microarray-Based Gene Expression Analysis, version 5.5)

scan_protocol: Intensity values were extracted and processed (background subtraction and LOWESS normalization) by means of the Feature Extraction software (version 10.5, Agilent Technologies, Santa Clara, CA, USA).

data_processing: Data were extracted using the Agilent Feature Extraction software (version 10.5, Agilent Technologies).

organism: Staphylococcus aureus

source_name: S. aureus reference pool

label_protocol: Total RNA was prepared from three independent experiments. Synthesis and purification of fluorescently labeled cDNA were carried out according to Charbonnier et al. (2005) with minor modifications. In detail, 10 µg of total RNA were mixed with random primers (Promega, Madison, WI, USA) and spike-ins (Two-Color RNA Spike-In Kit, Agilent Technologies, Santa Clara, CA, USA). The RNA/primer mixture was incubated at 70°C for 10 min followed by 5 min incubation on ice. Then, the following reagents were added: 10 µl of 5x First Strand Buffer (Invitrogen, Karlsruhe, Germany), 5 µl of 0.1 M DTT (Invitrogen, Karlsruhe, Germany), 0.5 µl of a dNTP mix (10 mM dATP, dGTP, and dTTP, 2.5 mM dCTP), 1.25 µl of Cy3-dCTP or Cy5-dCTP (GE Healthcare, Little Chalfont, UK) and 2 µl of SuperScript II reverse transcriptase (Invitrogen, Karlsruhe, Germany). The reaction mixture was incubated at 42°C for 60 min and then heated to 70°C for 10 min. After 5 min on ice, the RNA was degraded by incubation with 2 units of RNaseH (Invitrogen, Karlsruhe, Germany) at room temperature for 30 min. Labeled cDNA was then purified using the CyScribe GFX Purification Kit (GE Healthcare, Little Chalfont, UK). The individual samples were labeled with Cy5, whereas the reference pool was labeled with Cy3.

growth_protocol: S. aureus was cultured in LB at 37° and 120 rpm.

extract_protocol: Total RNA was prepared by acid-phenol extraction after mechanical cell disruption as described previously (Otto et al., 2010, Nat Commun).

treatment_protocol: An overnight culture was used to inoculate 100 ml medium to an OD540 of 0.02. Control samples were taken during logarithmic growth phase (OD500=0.9) and transient growth phase (OD540=3.5). Logarithmic growing cells (OD540=0.5) were stressed with 5 mg Linezolid per ml. Stress samples were taken one hour after stress (OD540=0.9), at the onset of the temprorary growth arrest (OD540=1.8) and after the cells reentered the growth cycle (OD540=2.2)

tag: strains

tag: growth phase

value: control logarithmic growth and transient  phase; linezolid stress transient and stanionary phase

source_name: stress second transient growth phase

tag: strain

value: stress second transient growth phase


title: GO-treated equine satellite cells_Cy5 vs. Equine satellite cells without GO treatment_Cy3_rep2

status: Public on Feb 22 2016

type: RNA

city: Warsaw

first: Tomasz

last: Sadkowski

address: Nowoursynowska 159

department: Department of Physiological Sciences

country: Poland

institute: Warsaw University of Life Sciences - SGGW

description: Biological replicate 2 of 4. GO-treated equine satellite cells_Cy5 vs. Equine satellite cells without GO treatment_Cy3_rep1

hyb_protocol: On each two-colour microarray 825 ng of cRNA from GO exposed cells (Cy5) and 825 ng of cRNA from control cells (Cy3) were hybridized using Gene Expression Hybridization Kit (Agilent Technologies, USA) according to the manufacturers protocol. RNA Spike In Kit (Agilent Technologies, USA) was used as an internal control.

scan_protocol: Acquisition and analysis of hybridization intensities were performed using the Agilent DNA microarray scanner and Agilent Feature Extraction software 10.7.3.1. according to the standard manufacturer’s procedures and LOWESS normalization.

data_processing: The statistical analysis was performed using Gene Spring 13 software default protocol (Agilent Technologies, USA). The statistical significance of the differences was evaluated using student test (p<0.05) and fold change FC>1.3. A multiple testing correction was performed using Benjamini and Hochberg False Discovery Rate (FDR) ≤0.05.

molecule: total RNA

organism: Equus caballus

source_name: GO-treated equine satellite cells_Cy5

label_protocol: Low Input Quick Amp Labeling Kit (Agilent Technologies, USA) was used to amplify and label target RNA to generate complementary RNA (cRNA).

growth_protocol: Equine satellite cells were cultured in Primaria culture flask (BD, USA). The growth medium (10%FBS/10%HS/DMEM/AB) was changed every two days. On the 10th day of proliferation cells were transferred to Collagen I Cellware 6-well plate. After obtaining 80% of confluence proliferation medium was replaced by differentiation medium (2%HS/DMEM/AB). FBS - fetal bovine serum, HS - horse serum, DMEM - Dulbecco's Modified Eagle Medium, AB - antibiotics: 1% Penicillin-Streptomycin, 0.5% Amphotericin B.

extract_protocol: Total RNA was isolated according to the protocol supplied with the miRNeasy Mini Kit (Qiagen, USA). RNA quantity was measured spectrophotometrically using NanoDrop (NanoDrop Technologies, USA). The analysis of final RNA quality and integrity was performed with BioAnalyzer 2100 (Agilent Technologies, USA). To ensure optimal data quality only RNA samples with RIN number ≥ 9,2 were included into the analysis.

treatment_protocol: After the 2nd day of differentiation 0,125 µM GO was added and cells were incubated for 24h. Because GO is insoluble in water DMSO (0,04µl/ml) was used as a vehicle. Control medium contained DMSO in the same dose as in GO treated cells. DMSO - Dimethyl sulfoxide.

tag: age

value: 3rd day of differentiation

tag: satellite cell origin

value: m. semitendinosus muscle


title: K562 shControl_2

city: Washington

first: Alexandros

last: Tzatsos

state: DC

address: 800 22nd St NW SEH 8850

department: GW Cancer Center

country: USA

institute: George Washington University

hyb_protocol: Hybridization was performed using a GeneChip Hybridization Oven 640 overnight at 45°C. Microarray washing and staining was done using a GeneChip Fluidics Station 450

scan_protocol: GeneChip Scanner 3000 7G (Affymetrix)

data_processing: Probe level analysis including background subtraction and quantile normalization took placed with the Robust Multi Array Average Algorithm (RMA) using the Affymetrix Expression Console Software 1.3

label: biotin

organism: Homo sapiens

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

growth_protocol: Human leukemia cell lines were maintained in IMDM supplemented with 10% FBS

extract_protocol: Qiagen RNeasy kit

treatment_protocol: Cells were infected with shKDM2B and RNA harvested after 6 days

tag: cell line


title: TA1620_WT_2

description: wild-type

organism: Mus musculus

label_protocol: Labeling took place following Affymetrix protocol

growth_protocol: Lineage negative cells were isolated from bone marrow and cultured  for 24 hours before isolation of total RNA

extract_protocol: Qiagen Rneasy kit

tag: tissue

value: bone marrow

tag: genotype/variation

value: WT


title: DND41 shKDM2B_2


title: PA2685_KO_1

description: knockout

value: KO


title: PA2681_WT_1

description: wild-type


title: Pool x stress trans2 2

country: Germany


title: DND41 shKDM2B_1


title: K562 shKDM2B_1


title: GO-treated equine satellite cells_Cy5 vs. Equine satellite cells without GO treatment_Cy3_rep3

description: Biological replicate 3 of 4. GO-treated equine satellite cells_Cy5 vs. Equine satellite cells without GO treatment_Cy3_rep1


title: H-2Kb-tsA58 stomach muscular wall_biological rep 1

city: Rochester

first: Tamas

last: Ordog

state: MN

address: 200 1st St SW

institute: Mayo Clinic

hyb_protocol: Target cDNA generated from each sample were then processed as per manufacturer's recommendation using an Affymetrix GeneChip 3000 System  Spike controls were added to 15 µg fragmented cRNA before overnight hybridization. Arrays were then washed and stained with streptavidin-phycoerythrin.

scan_protocol: The sample was scanned on an Affymetrix GeneChip 3000 system.

data_processing: Analysis was performed using publicly available software Bioconductor. Simpleaffy was used to preprocess individual probe intensities from CEL files into expression values.  Robust MultiArray Analysis (RMA), which uses quantile normalization for cross-chip normalization, was used to preprocess the data.

source_name: H-2Kb-tsA58 gastric tunica muscularis

label_protocol: Total RNA from each sample was used to prepare biotinylated target RNA, according to the manufacturers' instructions.  Briefly, about 50 ng of total RNA was used to generate first strand cDNA by using a T7-linked oligo(dT) primer. After second-strand synthesis, in vitro transcription was performed with unlabelled ribonucleotides (Ambion, PN AM1333).  A second round of cDNA synthesis was then performed with random primers, followed by in vitro transcription with biotinylated UTP and CTP resulting in a final yield of more than 40ug cRNA.

growth_protocol: Not applicable

extract_protocol: Total RNA was isolated and purified using Trizol (Invitrogen, Carlsbad, CA) and  the RNeasy Mini kit (Qiagen, Valencia, CA), respectively. RNA was  quantified and its quality tested using the RNA 6000 Nano assay  (Agilent Technologies, Palo Alto, CA).

value: gastric tunica muscularis


title: K562 shControl_1


title: TA1620_WT_1

description: wild-type


title: DND41 shControl_1


title: Conditionally immortalized ICC stem cells_biological rep 2

source_name: Cells derived from H-2Kb-tsA58 gastric tunica muscularis

growth_protocol: Cell line was cultured in NeuroCult® Neural Stem Cell Proliferation Medium (NSCPM; STEMCELL Technologies) at 39.5°C and without interferon-gamma

value: ICC


title: H-2Kb-tsA58 stomach muscular wall_biological rep 3


title: PA2681_WT_2

description: wild-type


title: C57BL/6J stomach muscular wall_biological rep 2

source_name: C57BL/6J gastric tunica muscularis


title: Conditionally immortalized ICC stem cells_biological rep 3


title: H-2Kb-tsA58 stomach muscular wall_biological rep 2


title: Conditionally immortalized ICC stem cells_biological rep 1


title: DND41 shControl_2


title: Pool x stress stat 3

source_name: stress stationary growth phase

value: stress stationary growth phase


title: Pool x stress trans2 1


title: Wild-type ICC stem cells_biological rep 3

source_name: Cells derived from C57BL/6J gastric tunica muscularis

growth_protocol: Cell line was cultured in NeuroCult® Neural Stem Cell Proliferation Medium (NSCPM; STEMCELL Technologies) plus 5% cell-free chick embryo extract (CEE; Accurate Chemical) at 37°C


title: Pool x stress stat 2


title: Pool x stress trans1 3

source_name: stress first transient growth phase

value: stress first transient growth phase


title: Pool x stress stat 1


title: Pool x stress trans1 2


title: Pool x stress trans1 1


title: C57BL/6J stomach muscular wall_biological rep 1


title: Pool x control log 3

source_name: control logarithmic growth

value: control logarithmic growth


title: Pool x control log 2


title: ALLSIL shControl_2

value: ALLSIL


title: Pool x control trans 3

source_name: control transient growth

value: control transient growth


title: JURKAT shKDM2B_2

value: JURKAT


title: Pool x control trans 1


title: Pool x control log 1


title: FEX52_NIM

city: Legnaro

first: Massimo

last: Milan

state: PD

address: Viale dell'Università 16

department: Dept. of Department of Public Health, Comparative Pathology,and Veterinary Hygiene

country: Italy

institute: University of Padova

description: Digestive gland  RNA of Mytilus galloprovincialis

hyb_protocol: Hybridized according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol

scan_protocol: Array was scanned according to standard Agilent protocol at a resolution of 2 microns modifying default setting to scan the slide twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%)

data_processing: Quantile normalization always outperformed cyclic loess and quantile-normalized data were further adjusted for the known between-experiments batch effects by implementing the parametric Combat in R (Johnson et al., 2007).

label: Cyanine 3

organism: Mytilus galloprovincialis

source_name: Digestive gland of Mytilus galloprovincialis exposed to Nimesulide (NIM)

label_protocol: Amplified and labeled according to Agilent Low input One-Color Microarray-Based Gene Expression Analysis protocol

extract_protocol: Total RNA was isolated using Extract-all (Eurobio) procedure.

treatment_protocol: Mytilus galloprovincialis (5 ± 1 cm shell length) were obtained from a local farm (Numana, Ancona) and acclimatized for 10 days to laboratory conditions with aerated seawater and 18± 1 °C, salinity at 28–30 ‰.  Mussels were distributed into 17L- glass-beakers for  days. and exposed to nimesulide for 14 days

tag: stress

value: Nimesulide (NIM)

value: Digestive gland


title: FEX53_NIM


title: ALLSIL shKDM2B_1


title: Wild-type ICC stem cells_biological rep 2


title: FEX54_NIM


title: JURKAT shControl_1


title: Pool x control trans 2

value: control logarithmic growth and transient  phase; linezolid stress transient and stanionary phase


title: FEX44_KET

source_name: Digestive gland of Mytilus galloprovincialis exposed to Ketoprofen (KET)

treatment_protocol: Mytilus galloprovincialis (5 ± 1 cm shell length) were obtained from a local farm (Numana, Ancona) and acclimatized for 10 days to laboratory conditions with aerated seawater and 18± 1 °C, salinity at 28–30 ‰.  Mussels were distributed into 17L- glass-beakers for  days. and exposed to  ketoprofen for 14 days

value: Ketoprofen (KET)


title: FEX45_KET


title: ALLSIL shKDM2B_2


title: JURKAT shKDM2B_1


title: FEX43_KET


title: ALLSIL shControl_1


title: FEX51_NIM


title: FEX7_CTRL

source_name: Digestive gland of Mytilus galloprovincialis of control group

treatment_protocol: Mytilus galloprovincialis (5 ± 1 cm shell length) were obtained from a local farm (Numana, Ancona) and acclimatized for 10 days to laboratory conditions with aerated seawater and 18± 1 °C, salinity at 28–30 ‰.  Mussels were distributed into 17L- glass-beakers for  days.

value: control


title: FEX42_KET


title: Wild-type ICC stem cells_biological rep 1


title: FEX6_CTRL


title: Mtb_in_Rapamycin_treated_macrophage_rep1

status: Public on Feb 21 2016

city: Ithaca

first: Yancheng

last: Liu

state: NY

institute: Cornell University

description: Biological replicate 1 of 3

hyb_protocol: An equal amount (400 ng) of labeled aRNA from paired samples was mixed and used for hybridization.  Microarray hybridization and wash were performed by Cornell Core Facility using the protocols described in the Agilent Two-Color Microarray-Based Gene Expression Analysis manual.

scan_protocol: Slides were scanned by an Agilent DNA Microarray Scanner (G2505B) and array data were extracted from raw image files using Feature Extraction software (Version 10.7, Agilent).

data_processing: Data were then imported into Genespring 7.3 (Agilent) using the default Enhanced Agilent FE settings for subsequent normalization (LOWESS), statistical analysis and visualization.  One-way ANOVA test was performed to identify genes with significant differences in expression between different treatment conditions.  Pearson correlation was used for gene or condition clustering analysis.  Genes were identified as drug regulated if they were induced or repressed more than 1.5-fold with a t-test p-value less than 0.05 from an average of at least three biological replicates.

label: Alexa 647

organism: Mycobacterium tuberculosis CDC1551

source_name: Mtb in Rapamycin-treated macrophage

label_protocol: The MessageAmpII-Bacteria kit (Ambion) was used to generate amplified RNA (aRNA) from 100 ng of total RNA input.  Amino-allyl UTP was incorporated into aRNA during in vitro transcription to allow fluorophore labeling.  10 µg of modified aRNA from each sample was then labeled with Alexa Fluors (Invitrogen).  aRNA from drug-treated samples was labeled with Alexa 647 and aRNA from DMSO-treated samples was labeled with Alexa 555.  After excess dyes were quenched by hydroxylamine, the labeled aRNA was purified using a MegaClear Kit (Ambion).

growth_protocol: The clinical isolate strain CDC1551 of M. tuberculosis was grown in Middlebrook 7H9 broth supplemented with OADC, glycerol and 0.05% Tween 80 in standing, vented tissue culture flasks. For macrophage growth and infection, J774A.1 macrophages were seeded in T75 vented tissue culture flasks at a density of ~ 2 x 10^7 per flask.  Next day, mid-log phase (A600 = 0.4~0.5) Mtb strains were harvested by centrifugation, resuspended in basal uptake buffer (PBS with 4.5 mg/ml glucose, 5 mg/ml BSA, 0.1 mg/ml CaCl2, 0.1 mg/ml MgCl2, and 1 mg/ml gelatin), declumped by 10 passages through a 21 gauge needle, and then used to infect macrophages at an MOI of ~4.

extract_protocol: Total Mtb RNA from extracellular and intracellular samples was isolated following established protocols: guanidine thiocyanate (GTC) buffer was added to samples after drug treatment to preserve RNA transcripts. Mtb in GTC were pelleted, washed once with PBS supplemented with 0.1% Tween-80, and treated with lysozyme.   Then bacilli were lysed in 65°C Trizol (Invitrogen) using silicon beads in a BeadBeater.  Bacterial lysate was extracted once with chloroform and total RNA was purified from the aqueous phase using a Qiagen RNeasy kit.  Eluted RNA samples were treated with DNase I (Ambion) for 45 min at 37°C before stored at -70°C.

treatment_protocol: Bacterial cultures were grown from an A600 of 0.05 to ~ 0.4 before treated by either 0.2 µg/ml  INH, 0.4 µg/ml  RIF, 200 µg/ml  PZA, or 12 µg/ml  EMB for 24 h.  As control, a parallel culture was treated with equal amount of vehicle solvent (DMSO) for the same period of time.  For treatment of intracellular Mtb, different antimycobacterial drugs or an equivalent amount of DMSO were added to the infected macrophages at 5 days post infection.  The same concentrations of drugs and treatment duration were used as in broth treatment.

tag: condition

value: autophagic macrophage

tag: drug treatment

value: Rapamycin

label: Alexa 555

source_name: Mtb in resting macrophage treated by DMSO

value: macrophage

value: DMSO


title: Mtb_in_Rapamycin_treated_macrophage_rep3

description: Biological replicate 3 of 3


title: Mtb_in_IFNg_LPS_treated_macrophage_rep1

description: Biological replicate 1 of 2

source_name: Mtb in IFNg+LPS treated macrophage

value: activated macrophage

value: IFNgamma + LPS

source_name: Mtb in resting macrophage


title: Mtb_in_IFNg_LPS_treated_macrophage_rep2

description: Biological replicate 2 of 2


title: FEX5_CTRL


title: Mtb_in_EBSS_treated_macrophage_rep3

description: Biological replicate 3 of 3

source_name: Mtb in EBSS-treated macrophage

value: EBSS


title: Mtb_in_EBSS_treated_macrophage_rep2

description: Biological replicate 2 of 3


title: FEX4_CTRL


title: Mtb_in_macrophage_RIF_rep3

description: Biological replicate 3 of 3

source_name: Mtb in macrophage treated by RIF

value: RIF

source_name: Mtb in macrophage treated by DMSO


title: Mtb_in_7H9_RIF_rep2

description: Biological replicate 2 of 3

source_name: Mtb in 7H9 broth treated by RIF

value: broth

source_name: Mtb in 7H9 broth treated by DMSO


title: Mtb_in_Rapamycin_treated_macrophage_rep2

description: Biological replicate 2 of 3


title: Mtb_in_7H9_RIF_rep1

description: Biological replicate 1 of 3


title: Mtb_in_7H9_RIF_rep3

description: Biological replicate 3 of 3


title: Mtb_in_EBSS_treated_macrophage_rep1

description: Biological replicate 1 of 3


title: Mtb_in_macrophage_RIF_rep1

description: Biological replicate 1 of 3


title: Mtb_in_macrophage_RIF_rep2

description: Biological replicate 2 of 3


title: Mtb_in_7H9_PZA_rep3

description: Biological replicate 3 of 3

source_name: Mtb in 7H9 broth treated by PZA

value: PZA


title: Mtb_in_macrophage_PZA_rep2

description: Biological replicate 2 of 3

source_name: Mtb in macrophage treated by PZA


title: Mtb_in_7H9_PZA_rep2

description: Biological replicate 2 of 3


title: Mtb_in_macrophage_PZA_rep3

description: Biological replicate 3 of 3


title: Mtb_in_7H9_PZA_rep1

description: Biological replicate 1 of 3


title: A997_39b_RAV181_DMSO_GF_3

city: Regensburg

first: Sylvia

last: Moeckel

address: Franz-Josef-Strauss-Allee 11

department: Neurology

institute: University Clinic Regensburg

hyb_protocol: 3 μg of labelled products were hybridized, washed and stained in an Affymetrix GeneTitan system.

scan_protocol: Arrays were scanned in an Affymetrix GeneTitan system.

data_processing: Raw intensities were quantile normalized and summarized with the RMA (Robust Multichip Average) expression measure described in Irizarry et al, Biostatistics (2003). Probesets without EntrezID excluded.

source_name: brain tumor initiating cells

label_protocol: cRNA and ssDNA were prepared from 0,3 µg totalRNA according to the Ambion WT Expression Kit manual. Fragmentation and terminal biotinylation were performed using the Affymetrix Terminal Labeling Kit.

growth_protocol: BTICs were cultured in stem-cell permissive RHB-A media (Stem Cell, Cambridge, UK) supplemented with 20 ng/ml of each human recombinant epidermal growth factor (EGF; R&D Systems, Minneapolis, USA) and human recombinant basic fibroblast growth factor (FGF; Peprotech, Hamburg, Germany).

extract_protocol: Cells were washed twice with ice-cold PBS and harvested in RLT-lysis buffer (provided in the RNeasy Kit, Qiagen, Hilden, Germany) for subsequent RNA-extraction

treatment_protocol: Cells were cultured in growth factor free medium for 16 hours prior to treatment. After starvation, cells were treated with 1 µM Sunitinib in the treatment groups or 0.00025 % DMSO in the control groups either with or without supplementation of recombinant growth factors PDGF-A/B and VEGFA (25 ng/ml) for 6 hours before harvest.

tag: treatment

tag: btic

tag: cell type

value: brain tumor initiating cells


title: A997_37b_RAV181_DMSO_GF_2


title: Mtb_in_macrophage_PZA_rep1

description: Biological replicate 1 of 3


title: A997_36b_RAV181_Su_GF_1_2

value: Sunitinib

tag: treatment response of glioma in vitro proliferation score

tag: treatment response of glioma in vitro proliferation label

value: moderate inhibition


title: A997_38b_RAV181_Su_GF_2


title: Mtb_in_7H9_EMB_rep2

description: Biological replicate 2 of 3

source_name: Mtb in 7H9 broth treated by EMB

value: EMB


title: Mtb_in_7H9_EMB_rep3

description: Biological replicate 3 of 3


title: Mtb_in_7H9_EMB_rep1

description: Biological replicate 1 of 3


title: Mtb_in_macrophage_EMB_rep3

description: Biological replicate 3 of 3

source_name: Mtb in macrophage treated by EMB


title: A997_35b_RAV181_DMSO_GF_1


title: A997_34_RAV73_Su_GF_2


title: A997_40_RAV181_Su_GF_1


title: Mtb_in_macrophage_EMB_rep2

description: Biological replicate 2 of 3


title: A997_32_RAV127_Su_GF


title: A997_29_RAv133_DMSO_GF


title: A997_30_RAV133_Su_GF_2


title: A997_23_RAV128_DMSO_GF


title: A997_33_RAV73_DMSO_GF_2


title: A997_25_RAV47_DMSO_GF


title: A997_24_RAV128_Su_GF


title: A997_22_RAV63_Su_GF


title: A997_28_RAV137_Su_GF


title: A997_26_RAV47_Su_GF

value: moderate induction


title: A997_27_RAV137_DMSO_GF


title: Mtb_in_7H9_INH_rep6

description: Biological replicate 6 of 6

source_name: Mtb in 7H9 broth treated by INH

value: INH


title: Mtb_in_macrophage_EMB_rep1

description: Biological replicate 1 of 3


title: Mtb_in_7H9_INH_rep5

description: Biological replicate 5 of 6


title: A997_31_RAV127_DMSO_GF


title: A997_21_RAV63_DMSO_GF


title: Mtb_in_7H9_INH_rep4

description: Biological replicate 4 of 6


title: A997_20_RAV13_Su_GF


title: A997_19_RAV13_DMSO_GF


title: A997_18_RAV121_Su_GF


title: Mtb_in_7H9_INH_rep3

description: Biological replicate 3 of 6


title: a997_16_RAV88_Su_GF


title: A997_15_RAV88_DMSO_GF


title: A997_14_RAV108_Su_GF_2


title: Mtb_in_macrophage_INH_rep8

description: Biological replicate 8 of 8

source_name: Mtb in macrophage treated by INH


title: A997_13_RAV108_DMSO_GF


title: Mtb_in_7H9_INH_rep1

description: Biological replicate 1 of 6


title: A997_17_RAV121_DMSO_GF_2


title: A997_08_RAV153_Su_GF


title: Mtb_in_7H9_INH_rep2

description: Biological replicate 2 of 6


title: A997_12_RAV15_Su_GF


title: Mtb_in_macrophage_INH_rep7

description: Biological replicate 7 of 8


title: Mtb_in_macrophage_INH_rep6

description: Biological replicate 6 of 8


title: Mtb_in_macrophage_INH_rep4

description: Biological replicate 4 of 8


title: A997_10_RAV87_Su_GF


title: A997_09_RAV87_DMSO_GF


title: A997_07_RAV153_DMSO_GF


title: A997_11_RAV15_DMSO_GF


title: Mtb_in_macrophage_INH_rep3

description: Biological replicate 3 of 8


title: A997_05_RAV145_DMSO_GF


title: A997_04_RAV54_Su_GF


title: A997_03_RAV54_DMSO_GF


title: A997_02_RAV74_Su_GF


title: JURKAT shControl_2

value: JURKAT


title: A997_06_RAV145_Su_GF


title: A997_01_RAV74_DMSO_GF


title: Mtb_in_macrophage_INH_rep2

description: Biological replicate 2 of 8


title: BF2766 mutant_OFF/OFF

city: Kagawa

first: Imaohji

last: Haruyuki

department: Medicine

country: Japan

institute: Kagawa University

description: The BF2766 mutants series, in which the two promoters were locked in different pattern from others (IVp-I/IVp-II=ON/ON, OFF/OFF, ON/OFF or OFF/ON), were constructed.

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

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

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

organism: Bacteroides fragilis

source_name: Bacteroides fragilis strain YCH46 BF2766 mutant

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

growth_protocol: Bacteroides fragilis strains were grown to mid-log phase (O.D.600nm 0.4-0.6) in GAM medium.

extract_protocol: Total RNAs were extracted using hot-phenol method.

value: YCH46 BF2766 mutant

tag: genotype

value: BF2766 mutant OFF/OFF genotype


title: BF2766 mutant_ON/OFF

value: BF2766 mutant ON/OFF genotype


title: BF2766 mutant_ON/ON

value: BF2766 mutant ON/ON genotype


title: BF2766 mutant_OFF/ON

value: BF2766 mutant OFF/ON genotype


title: Mtb_in_macrophage_INH_rep1

description: Biological replicate 1 of 8

value: macrophage

value: DMSO


title: Liver_ZT12_SPF_1

status: Public on Feb 20 2016

city: Toulouse

first: Alexandra

last: Montagner

address: 180 Chemin de Tournefeuille

country: France

institute: INRA

hyb_protocol: Affymetrix Mouse Gene 2.0 ST arrays were hybridized with labeled and amplified cDNA, then washed, stained and scanned according to the protocol described in Affymetrix GeneChip® Expression Analysis Manual (Fluidics protocol FS450_0007)

scan_protocol: Scanning was done on an Affymetrix GeneChip Scanner 7G.

data_processing: Gene level normalized expression signals were calculated from Affymetrix CEL files using RMA (Irizarry et al., 2003) in Affymetrix's Expression Console software.

source_name: liver, zeitgeber time 12, specific pathogen free mouse

label_protocol: For each sample, 100 ng of total RNA were used for target preparation with the Whole Transcript Sense Target Labeling Assay (Affymetrix, High Wycombe, UK) .

growth_protocol: Mice were housed since birth  in 12h Light:12h Dark under GF or SPF conditions

extract_protocol: Total RNA was extracted with TRIzol reagent according to the manufacturer's instructions. RNA amounts were determined by NanoDrop®ND-1000 and the RNA quality was assessed using RNA 6000 NanoChips with the Agilent 2100 Bioanalyzer.

tag: phenotype

value: specific pathogen free mouse

tag: time point

tag: gender

value: male

value: liver


title: Liver_ZT12_GF_5

source_name: liver, zeitgeber time 12, germ free mouse

value: germ free mouse

tag: strain


title: Liver_ZT18_SPF_3

source_name: liver, zeitgeber time 18, specific pathogen free mouse


title: Liver_ZT12_SPF_5


title: Liver_ZT6_SPF_4

source_name: liver, zeitgeber time 6, specific pathogen free mouse


title: Liver_ZT18_GF_5

source_name: liver, zeitgeber time 18, germ free mouse


title: Liver_ZT18_SPF_5


title: Liver_ZT18_SPF_2


title: Liver_ZT12_GF_1


title: Liver_ZT18_GF_1


title: Liver_ZT12_GF_4


title: Liver_ZT12_SPF_3


title: Liver_ZT18_SPF_1


title: MKN74_siSETDB2_VS_NC siRNA

city: Yushima

first: Nishikawaji

last: Taketo

state: Tokyo

address: 1-5-45 Bunkyo-ku

department: Molecular Oncology

institute: Tokyo Medical and Dental University

description: 48 hours after transfection

hyb_protocol: Agilent two-color gene expression hyb/wash protocol

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

data_processing: Agilent Feature Extraction Software Software version 10.7.3.1. Data are filtered by present (P), absent (A) and marginal (M) flags. The log2 Ratio of Cy5/Cy3 of probe showing “P” flag is calculated.

source_name: Gastric cancer cell line

label_protocol: Agilent two-color Low RNA Input Linear Amplification Kit labeling protocol

growth_protocol: MKN74 was grown in RPMI1640 medium containing 10% FBS.

extract_protocol: Total RNAwas extracted by Trizol reagent and then treated with DNA-free.

treatment_protocol: SETDB2 siRNA (SIGMA) or negative control siRNA was transfected at 50nM (final conc.) into gastric cancer cells by using electroporation.

tag: transfection

value: negative control siRNA (SIGMA)

value: SETDB2 siRNA (SIGMA)


title: Liver_ZT18_GF_4


title: Liver_ZT12_GF_2


title: Liver_ZT6_SPF_3


title: Liver_ZT18_SPF_4


title: Liver_ZT18_GF_3


title: Liver_ZT12_SPF_4


title: Liver_ZT12_GF_3


title: Liver_ZT6_SPF_2


title: Liver_ZT6_SPF_5


title: Liver_ZT18_GF_2


title: Liver_ZT6_SPF_1


title: Liver_ZT12_SPF_2


title: Liver_ZT6_GF_5

source_name: liver, zeitgeber time 6, germ free mouse


title: Liver_ZT6_GF_3


title: Liver_ZT6_GF_2


title: Liver_ZT6_GF_4


title: Liver_ZT0_SPF_5

source_name: liver, zeitgeber time 0, specific pathogen free mouse


title: Liver_ZT6_GF_1


title: Liver_ZT0_SPF_3


title: Liver_ZT0_GF_5

source_name: liver, zeitgeber time 0, germ free mouse


title: Liver_ZT0_GF_4


title: Liver_ZT0_SPF_1


title: Liver_ZT0_SPF_4


title: Liver_ZT0_GF_2


title: Liver_ZT0_GF_1


title: Liver_LWT_Fed_rep3

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 10x Agilent fragmentation buffer and 25x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE microarray (8X60K, Design 028005)  enclosed in Agilent SureHyb-enabled hybridization chambers for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed sequentially in Wash buffer 1 (Agilent Technologies, 1 min) and Wash buffer 2 (Agilent Technologies, 37°C, 1 min).

scan_protocol: Slides were scanned immediately after washing on a Agilent G2505C Microarray Scanner with Agilent Scan Control A.8.5.1 software

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent) using default parameters (protocol GE1_1010_Sep10 and Grid: 028005_D_F_20120201). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot): myfunw<-function(x) {okType<-x$ControlType==0; okFoundGreen<-x$gIsFound==1; okPos=x$gIsPosAndSignif==1; okWellAbove<- x$gIsWellAboveBG==1; as.numeric(okType & okFoundGreen & okPos & okWellAbove);} We selected the spots with a weight of 1 for 42 out of 52 microarrays or with a weight of 1 in all 2 microarrays from at least one experimental group. At this step, 38304 spots out of 62976 were selected. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. Data were stored in an ExpressionSet object, then the whashing bath batch effect was substracted (substraction of individual expression values by the averaged values of corresponding batch; batch=1:27,28:52) and the resulting matrice was normalized by the quantile method using the normalize.quantiles function from the preprocessCore library. The resulting matrix has 35516 rows each corresponding to a unique ProbeName (provided as data Matrix) and 52 columns (individuals).

label_protocol: For each sample, Cyanine-3 (Cy3) labeled cRNA was prepared from 200 µg of total RNA using the One-Color Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by Agencourt RNAClean XP (Agencourt Bioscience Corporation, Beverly, Massachusetts) purification. Dye incorporation and cRNA yield were checked with the Nanodrop ND2000 spectrophotometer (Thermo Scientific).

growth_protocol: Mice were housed since birth in 12h light/12h dark period and fed a Safe 04 chow diet.

value: LWT

value: Fed

tag: replicate


title: Liver_ZT0_GF_3

tag: tissue


title: Liver_LWT_Fasted_rep2

value: Fasted


title: Liver_PPARa-LKO_Fed_rep1

value: PPARa-LKO


title: Liver_PPARa-LKO_Fasted_rep5


title: EA_282_V

city: Chicago

first: Silvia

last: Kariuki

state: IL

department: Human Genetics

institute: University of Chicago

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: quantile normalized and variance transformed using LUMI package in R

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

extract_protocol: RNA was extracted with QIAGEN RNeasy Plus mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyzer.

treatment_protocol: Monocytes were treated with 1,25-dihydroxyvitamin D3, bacterial lipopolysaccharide (LPS), or vehicle control (EtOH), for 24 hours

tag: subject status

value: healthy individual

tag: ancestry

value: European-American

tag: treated with

value: 1,25 dihydroxyvitamin D3

value: Primary monocytes


title: Liver_PPARa-LKO_Refed_rep1

value: Refed


title: Liver_WT_Fasted_rep5

value: WT


title: AA_267_VL

value: African-American

value: 1,25 dihydroxyvitamin D3 + lipopolysaccharide


title: AA_284_V


title: Liver_LWT_Refed_rep1

value: male


title: EA_282_EL

value: lipopolysaccharide


title: Liver_WT_Refed_rep1

value: liver


title: EA_282_VL


title: AA_284_VL


title: Liver_LWT_Refed_rep4


title: AA_284_EL


title: AA_284_E

value: vehicle (EtOH)


title: EA_282_E


title: AA_267_EL


title: Liver_ZT0_SPF_2

value: specific pathogen free mouse


title: Liver_WT_Fed_rep4


title: Mtb_in_macrophage_INH_rep5

description: Biological replicate 5 of 8

tag: condition

value: macrophage

tag: drug treatment

value: INH

source_name: Mtb in macrophage treated by DMSO

value: DMSO


title: AA_267_E


title: AA_267_V


title: Liver_PPARa-KO_Refed_rep5

value: PPARa-KO

tag: treatment


title: Liver_LWT_Fed_rep2

value: LWT

value: Fed


title: Liver_PPARa-LKO_Refed_rep3

value: PPARa-LKO


title: Liver_PPARa-KO_Fed_rep1


title: Liver_WT_Fasted_rep4

value: Fasted


title: Liver_PPARa-KO_Fasted_rep3


title: Liver_PPARa-KO_Refed_rep1

value: Refed


title: Liver_PPARa-KO_Fed_rep3


title: EA_270_VL

value: healthy individual

value: European-American

tag: cell type

value: Primary monocytes


title: Liver_PPARa-LKO_Refed_rep2

value: male


title: EA_212_EL

value: lipopolysaccharide


title: EA_212_VL

value: 1,25 dihydroxyvitamin D3 + lipopolysaccharide


title: AA_207_V

value: African-American

value: 1,25 dihydroxyvitamin D3


title: EA_270_V


title: AA_207_VL


title: EA_270_EL


title: Liver_WT_Refed_rep3

value: liver

value: WT


title: Liver_PPARa-LKO_Fasted_rep3


title: EA_270_E

value: vehicle (EtOH)


title: AA_207_EL


title: AA_207_E


title: Liver_PPARa-LKO_Fed_rep2


title: Liver_LWT_Refed_rep2


title: EA_212_V


title: Liver_LWT_Fed_rep1


title: AA_375_EL


title: Liver_PPARa-KO_Refed_rep3

value: PPARa-KO


title: EA_212_E


title: Liver_LWT_Fasted_rep5

value: LWT


title: EA_378_V


title: EA_378_E


title: Liver_PPARa-LKO_Fasted_rep4


title: Liver_WT_Refed_rep5


title: EA_378_EL


title: EA_378_VL


title: Liver_WT_Fed_rep2

value: Fed


title: Liver_PPARa-KO_Fed_rep5


title: AA_375_E


title: Liver_PPARa-LKO_Fasted_rep1

value: PPARa-LKO


title: AA_375_VL


title: Liver_PPARa-LKO_Fed_rep3


title: Liver_PPARa-LKO_Refed_rep5


title: AA_980_V


title: Liver_LWT_Fasted_rep4

value: Fasted


title: Liver_WT_Fasted_rep2


title: Liver_LWT_Refed_rep5

value: Refed


title: AA_375_V

value: healthy individual


title: AA_980_E


title: EA_265_VL

value: European-American


title: AA_980_VL

value: Primary monocytes


title: EA_265_E


title: AA_980_EL


title: Liver_WT_Refed_rep4

value: male


title: Liver_WT_Fasted_rep3


title: EA_265_EL

value: lipopolysaccharide


title: Liver_PPARa-KO_Refed_rep2


title: Liver_LWT_Fasted_rep1


title: Liver_WT_Fed_rep3


title: Liver_PPARa-KO_Fed_rep4


title: Liver_PPARa-LKO_Fasted_rep2


title: Liver_PPARa-KO_Refed_rep4


title: Liver_WT_Refed_rep2


title: Patient3 normal gastric mucosa

city: Haikou

first: Yousheng

last: Huang

state: Hainan

address: The 3rd Xueyuan Road

department: Department of pathology

country: China

institute: Hainan Medical university

description:
The expression profiles of circRAN were compared between garstic cancer and its adjacent normal tissues
[G3B](normalized)

hyb_protocol: The Cy3TM-labeled samples were hybridizedaccording to the manufacturer’s protocol (Arraystar Inc).

scan_protocol: The slides were scanned usingthe Agilent Scanner G2505C.

data_processing: Quantile normalization of raw data and subsequent data processing were performed using the R software package. After quantile normalization of the raw data, low intensity filtering was performed, and the circRNAs that at least 3 out of 6 samples have flags in “P” or “M” (“All Targets Value”) were retained for further analyses.

source_name: normal gastric mucosa

label_protocol: The Arraystar Super RNA Labeling Kit (Arraystar Inc.) was used according to the manufacturer’s guideline for CircRNA labelling

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) according to manufacturer’s instructions, which efficiently recovered all RNA species, including CircRNAs. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis

tag: subject status/id

value: gastric cancer patient 3

tag: status after 1 years

value: alive

tag: age (yrs)

tag: Sex

tag: Stage

value: IIIA

tag: tissue type

value: normal gastric mucosa


title: AA_836_E

value: African-American


title: Liver_PPARa-KO_Fasted_rep2

tag: strain

tag: gender

value: liver

tag: genotype


title: Liver_PPARa-KO_Fasted_rep1

tag: tissue

value: PPARa-KO

tag: replicate


title: EA_901_EL

tag: subject status

tag: ancestry


title: EA_901_V

tag: treated with

value: 1,25 dihydroxyvitamin D3


title: EA_265_V


title: AA_836_V


title: Liver_PPARa-KO_Fed_rep2

value: Fed


title: Liver_PPARa-LKO_Refed_rep4

value: PPARa-LKO


title: Liver_LWT_Fasted_rep3

value: LWT

value: Fasted


title: AA_365_VL

value: healthy individual

value: 1,25 dihydroxyvitamin D3 + lipopolysaccharide


title: EA_252_V

value: European-American

value: Primary monocytes


title: AA_365_V


title: EA_901_VL


title: EA_901_E

value: vehicle (EtOH)


title: AA_836_EL

value: lipopolysaccharide


title: Liver_WT_Fasted_rep1

value: male

value: WT


title: AA_836_VL


title: AA_365_EL


title: EA_252_VL


title: Liver_WT_Fed_rep1


title: AA_365_E


title: Liver_LPPARa-KO_Fenofibrate_rep4

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent) using default parameters (protocol GE1_1010_Sep10 and Grid: 028005_D_F_20120201). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot): myfunw<-function(x) {okType<-x$ControlType==0; okFoundGreen<-x$gIsFound==1; okPos=x$gIsPosAndSignif==1; okWellAbove<- x$gIsWellAboveBG==1; as.numeric(okType & okFoundGreen & okPos & okWellAbove);} We selected the spots with a weight of 1 for 28 out of 34 microarrays or with a weight of 1 in all 3 microarrays from at least one experimental group. At this step, 35089 spots out of 62976 were selected. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes.  Data were stored in an ExpressionSet object, then the whashing bath batch effect was substracted (substraction of individual expression values by the averaged values of corresponding batch; batch=1:3,4:34) and the resulting matrice was normalized  by the quantile method using the normalize.quantiles function from the preprocessCore library.

growth_protocol: Mice were housed since birth in 12h light/12h dark period and fed a Safe 04 chow diet ad libitum.

treatment_protocol: Mice were treated with Fenofibrate (100 mg/kg/day) or vehicle (aqueous solution of gum Arabic 3%) by daily gavage for 10 days.

value: LKO

value: Fenofibrate


title: Patient2 normal gastric mucosa

description:
The expression profiles of circRAN were compared between garstic cancer and its adjacent normal tissues
[G2B](normalized)

value: gastric cancer patient 2

value: alive

value: IIIA

value: normal gastric mucosa


title: Patient2 cancer tissue

description:
The expression profiles of circRAN were compared between garstic cancer and its adjacent normal tissues
[G2A](normalized)

source_name: primary gastric cancer tissue

value: primary gastric cancer tissue


title: Patient1 normal gastric mucosa

description:
The expression profiles of circRAN were compared between garstic cancer and its adjacent normal tissues
[G1B](normalized)

value: gastric cancer patient 1


title: Patient3 cancer tissue

description:
The expression profiles of circRAN were compared between garstic cancer and its adjacent normal tissues
[G3A](normalized)

value: gastric cancer patient 3


title: Liver_PPARa-KO_Fenofibrate_rep2

value: KO

value: liver


title: AA_185_EL

value: healthy individual

value: African-American

value: 1,25 dihydroxyvitamin D3 + lipopolysaccharide


title: AA_185_VL

value: Primary monocytes


title: Patient1 cancer tissue

description:
The expression profiles of circRAN were compared between garstic cancer and its adjacent normal tissues
[G1A](normalized)

value: male


title: LP-5 [human]

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

description: Sample 18

data_processing:
Ct values were exported using Applied Biosystems's SDS v2.3 and RQ Manager v1.2 software, with automatic baseline and a manual Ct threshold of 0.2. Normalization and statistical analysis used the limma software package. Ct values were transformed to a log2 expression scale by subtracting the Ct values from 40.5. The log2 expression values were then normalized by cyclic loess normalization with house-keeping probes up-weighted 100-fold. The cyclic method was set to “affy”, the loess span was 0.7 and 5 cyclic iterations were used. The MammU6, RNU6B, RNU24, RNU43, RNU44 and RNU48 probes were all treated as house-keeping. After normalization, probes were filtered out as unexpressed if they failed to achieve a normalized value of 2 in at least 3 samples. Differential expression analysis used linear models including a batch correction for donor. Statistical significance was assessed using empirical Bayes t-statistics.
Normalized worksheet reports limma normalized log2 expression signals
Fold change worksheet reports a limma topTable giving differentially expressed miRNAs in the MaSC population vs the average of the LP and ML populations.

label: FAM-MGB

source_name: human breast tissue

label_protocol: Complementary cDNA was prepared using TaqMan microRNA Reverse Transcription Kit (ABI 4366596) and the Megaplex RT primer pools (human v2.0 ABI #4401091) according to the manufacturer’s protocol. For each sample, cDNA was made using appropriate Megaplex primer pools and 3 µl of RNA as template. Each pool was pre-amplified for 12 cycles using TaqMan PreAmp Master Mix (ABI #4391128) and Megaplex preAmp primers (human v2.0 ABI #4401091). Quantitative RT-PCR was carried out on an ABI 7900HT machine using Taqman Human MicroRNA Set v2.0 (ABI #4400238) Taqman Low Density Array plates and Universal PCR Master Mix (ABI 4364341) according to the manufacturer’s protocol. U6 was included as an endogenous control and Arabidopsis thaliana-miR159a was included as a negative control on each plate.

growth_protocol: Cells were freshly isolated from human breast tissue for microRNA extraction.

extract_protocol: microRNA was extracted with Qiagen miRNAeasy kit.

treatment_protocol: No treatment

value: Luminal progenitor (LP)

tag: donor


title: AA_185_V

value: 1,25 dihydroxyvitamin D3


title: EA_252_EL

value: European-American


title: Liver_LWT_Fenofibrate_rep5

value: LWT

tag: treatment

value: Fenofibrate


title: ML-5 [human]

description: Sample 17

tag: cell type

value: Mature luminal (ML)


title: EA_252_E

value: vehicle (EtOH)


title: Str-5 [human]

description: Sample 16

value: Stromal (Str)


title: EA_184_E


title: AA_185_E


title: EA_184_V


title: EA_184_VL


title: Liver_LWT_Fenofibrate_rep2


title: Liver_WT_Fenofibrate_rep2

value: WT


title: Liver_PPARa-KO_Fenofibrate_rep5


title: MaSC-5 [human]

description: Sample 15

value: Mammary stem cell (MaSC)


title: Liver_WT_Fenofibrate_rep3


title: Liver_PPARa-KO_vehicle_rep2

value: KO

value: vehicle


title: Str-4 [human]

description: Sample 13


title: EA_184_EL

value: healthy individual

value: lipopolysaccharide


title: EA_904_EL


title: AA_909_E

value: African-American


title: Liver_WT_vehicle_rep2

value: liver


title: AA_909_EL

value: Primary monocytes


title: AA_909_V


title: AA_909_VL

value: 1,25 dihydroxyvitamin D3 + lipopolysaccharide


title: ML-4 [human]

description: Sample 12


title: Liver_LPPARa-KO_Fenofibrate_rep2

value: LKO

value: male


title: MaSC-4 [human]

description: Sample 11


title: EA_428_EL

value: European-American


title: EA_428_E


title: EA_428_VL


title: EA_904_E


title: EA_428_V

value: 1,25 dihydroxyvitamin D3


title: AA_427_VL


title: LP-3 [human]

description: Sample 10

value: Luminal progenitor (LP)


title: AA_427_EL


title: EA_904_VL


title: AA_427_E

value: vehicle (EtOH)


title: ML-3 [human]

description: Sample 9

value: Mature luminal (ML)


title: Liver_WT_vehicle_rep4

value: WT


title: Str-3 [human]

description: Sample 8

value: Stromal (Str)


title: EA_904_V


title: Liver_LWT_vehicle_rep4

value: LWT


title: MaSC-3 [human]

description: Sample 7

value: Mammary stem cell (MaSC)


title: LP-2 [human]

description: Sample 6


title: ML-2 [human]

description: Sample 5


title: Liver_WT_Fenofibrate_rep4

value: Fenofibrate


title: JeKo-1_Tunicamycin_24hr-1

city: Houston

first: Wencai

last: Ma

address: 7455 Fannin st

institute: MD Anderson Cancer Center

hyb_protocol: As per Illumina instructions, with detection by Streptavidin-Cy3 conjugate.

scan_protocol: As per instructions for Illumina BeadArray Reader

data_processing: The non-normalized data were generated by GenomeStudio with background correction. The normalized data were generated from bead-level data by methods previously described (PMID: 20805315). In brief, bead-level values were quantile-normalized, adjusted by a model-based background correction method (PMID: 18450815), trimmed by the 3-MAD method employed by Illumina, and then averaged to give a single probe-level value.

label_protocol: 300 ng of total RNA was reverse-transcribed, amplified, and biotin-labeled using an Illumina TotalPrep RNA Amplification kit (Ambion)

growth_protocol: Cells were grown in RPMI 1640 medium containing 20% fetal bovine serum, in a humidified 5% CO2/air incubator at 37 C.

extract_protocol: Total RNA was extracted from TriZOL-derived RNA using the RNAqueous kit (Ambion, Austin, TX).

treatment_protocol: For drug treatments, cell lines in log-phase growth were plated at a density of 1.5 x 10e5 per mL. Cells were treated with drugs dissolved in DMSO, by adding a small volume of concentration stock solution to reach the desired final concentration. Untreated cultures received the same amount of DMSO alone.

tag: cell line

value: mantle cell lymphoma (MCL) cell line

value: 1 uM tunicamycin for 24hrs


title: JeKo-1_Rapamycin_24hr-2

value: 10 nM rapamycin for 24hrs


title: JeKo-1_Tunicamycin_12hr-1

value: 1 uM tunicamycin for 12hrs


title: Liver_LWT_vehicle_rep2

value: liver

value: vehicle


title: JeKo-1_Tunicamycin_12hr-2


title: JeKo-1_Tunicamycin_24hr-2


title: JeKo-1_Control-1

value: none for 24hrs (control)


title: Liver_LPPARa-KO_vehicle_rep4

value: LKO

value: male


title: Liver_LPPARa-KO_vehicle_rep2


title: Liver_LWT_Fenofibrate_rep4


title: LP-4 [human]

description: Sample 14

value: Luminal progenitor (LP)


title: Liver_PPARa-KO_Fenofibrate_rep3

value: KO


title: JeKo-1_Control-2


title: Z138_resistant_ONC201-1

value: ONC201-resistant cells

value: 5 uM ONC201 for 24hrs


title: Liver_LPPARa-KO_vehicle_rep3


title: Z138_parental_ONC201-2

value: parental, ONC201-naïve cells


title: Z138_resistant_Control-2


title: Z138_resistant_Control-1


title: LP-1 [human]

description: Sample 3


title: Z138_parental_ONC201-1


title: Liver_LPPARa-KO_Fenofibrate_rep5


title: Liver_LWT_vehicle_rep3

value: LWT


title: MaSC-2 [human]

description: Sample 4

value: Mammary stem cell (MaSC)


title: ML-1 [human]

description: Sample 2

value: Mature luminal (ML)


title: MaSC-1 [human]

description: Sample 1


title: Liver_WT_Fenofibrate_rep1

value: WT

value: Fenofibrate


title: JeKo-1_Rapamycin_24hr-1

value: mantle cell lymphoma (MCL) cell line

value: 10 nM rapamycin for 24hrs


title: Z138_resistant_ONC201-2


title: Liver_PPARa-KO_vehicle_rep3

value: liver


title: JeKo-1_ONC201_36hr-3

value: ONC201 for 36hr


title: Liver_WT_vehicle_rep3

value: vehicle


title: Z138_parental_Control-1

value: none for 24hrs (control)


title: JeKo-1_ONC201_24hr-1

value: ONC201 for 24hr


title: JeKo-1_ONC201_12hr-3

value: ONC201 for 12hr


title: JeKo-1_ONC201_36hr-2


title: JeKo-1_ONC201_24hr-3


title: OIM_48hr_3

city: Bethesda

first: Songjoon

last: Baek

state: MD

address: 41 Library Drive

department: CCR

institute: NCI / NIH

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Affymetrix human Genome U133 2.0 array data in CEL files were preprocessed using Affymetrix Expression Console software with mas5 and its quantile normalization method. Mean expression values from biological duplicates were calculated.

source_name: hFOB

label_protocol: standard Affymetrix protocol

growth_protocol: BM, basal madia: DMEM supplemented 10% calf serum, 2mM L-glutamine, 1mM sodium pyruvate, 1X non-essential amino acids, and 1% penicillin-streptomycin

extract_protocol: none provided by submitter

value: hFOB

value: OIM treated, grow at 39oC


title: JeKo-1_ONC201_24hr-2


title: JeKo-1_ONC201_36hr-1


title: Str-4 [mouse]

description: Sample 14

data_processing:
Ct values were exported using Applied Biosystems's SDS v2.3 and RQ Manager v1.2 software, with automatic baseline and a manual Ct threshold of 0.2. Normalization and statistical analysis used the limma software package. Ct values were transformed to a log2 expression scale by subtracting the Ct values from 40.5. The log2 expression values were then normalized by cyclic loess normalization with the MammU6 house-keeping probe up-weighted 100-fold. The cyclic method was set to “affy”, the loess span was 0.7 and 5 cyclic iterations were used. After normalization, probes were filtered out as unexpressed if they failed to achieve a normalized value of 2 in at least 3 samples. Differential expression analysis used linear models including a batch correction for mouse pool. Statistical significance was asssessed using empirical Bayes t-statistics.
Normalized worksheet reports limma normalized log2 expression signals
Fold change worksheet reports a limma topTable giving differentially expressed miRNAs in the MaSC population vs the average of the LP and ML populations.

source_name: mammary gland

label_protocol: Complementary cDNA was prepared using TaqMan microRNA Reverse Transcription Kit (ABI 4366596) and the Megaplex RT primer pools (mouse v2.0 ABI #4401012) according to the manufacturer’s protocol. For each sample, cDNA was made using appropriate Megaplex primer pools and 3 µl of RNA as template. Each pool was pre-amplified for 12 cycles using TaqMan PreAmp Master Mix (ABI #4391128) and Megaplex preAmp primers (human v2.0 ABI #4401091). Quantitative RT-PCR was carried out on an ABI 7900HT machine using TaqMan Rodent MicroRNA Array Set v2.0 (ABI #4400239) Taqman Low Density Array plates and Universal PCR Master Mix (ABI 4364341) according to the manufacturer’s protocol. U6 was included as an endogenous control and Arabidopsis thaliana-miR159a was included as a negative control on each plate.

growth_protocol: Cells were freshly isolated from adult mouse mammary glands for microRNA extraction.

extract_protocol: microRNA was extracted with the Qiagen miRNAeasy kit

treatment_protocol: no treatment

value: FVB/N

value: Stromal (Str)

tag: mouse pool


title: JeKo-1_ONC201_12hr-1


title: Str-3 [mouse]

description: Sample 13


title: Liver_LPPARa-KO_Fenofibrate_rep3

value: LKO

value: male


title: Z138_parental_Control-2

value: parental, ONC201-naïve cells


title: JeKo-1_ONC201_12hr-2


title: AA_427_V

value: healthy individual

value: African-American

value: 1,25 dihydroxyvitamin D3

value: Primary monocytes


title: Str-2 [mouse]

description: Sample 12


title: OIM_48hr_2

treatment_protocol: BM, basal madia: DMEM supplemented 10% calf serum, 2mM L-glutamine, 1mM sodium pyruvate, 1X non-essential amino acids, and 1% penicillin-streptomycin


title: human colon cancer sw480 cells, YWHAE shRNA rep3

hyb_protocol: After fragmentation labeled aRNA was hybridized to Affymetrix PrimeView Human Gene Expression Microarrays for 16h at 45 °C, stained by strepatavidin/phycoerythrin conjugate and scanned as described in the manufacturer´s protocol

scan_protocol: Gene ChIP Scanner 3000 7G (Affymetrix Inc.); AGCC (Vers. 3.3)

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Partek® Genomics SuiteTM. Expression values were RMA normalized, and fold-change values were then calculated using least-squares mean between samples.

source_name: human colon cancer SW480 cells treated with lentivirus meditated YWHAE-shRNA

label_protocol: Synthesis of cDNA and subsequent biotin labeling of cRNA was performed according to the manufacturer´s protocol (GeneChip 3’IVT Express Kit; Affymetrix, Inc.). Briefly, 200 ng of total RNA were converted to cDNA, followed by in vitro transcription and biotin labeling of aRNA

growth_protocol: The human colon cancer cell lines SW480 cells were cultured in DMEM medium(Gibco BRL Co.Ltd.,USA) supplemented with 100 ml/l FBS (Gibco,USA) with the addition of 100 U/ml penicillin and 100 U/ml streptomycin at 37C in a humidified atmosphere of5 % CO2 in air.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) according to manufacturer’s instructions. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis

treatment_protocol: The lentiviral vector GV248 (hU6-MCS-Ubi-EGFP-IRES-Puro) containing YWHAE shRNA hairpin sequence (LV-shYWHAE) and negative control were constructed by Shanghai GeneChem, Transfections were performed using polybrene and enhanced infection solution (Genechem,Shang Hai) according to the manufacturer’s recommended protocol when these cells reached 30% confluence.

value: human colon cancer cell line

tag: transfected with


title: OIM_48hr_1


title: Str-1 [mouse]

description: Sample 11


title: Liver_LWT_Fenofibrate_rep1

value: LWT

value: liver

value: Fenofibrate


title: OIM_24hr_2


title: Liver_LWT_Fenofibrate_rep3


title: Liver_LPPARa-KO_vehicle_rep1

value: vehicle


title: Liver_PPARa-KO_vehicle_rep1

value: KO


title: MaSC-4 [mouse]

description: Sample 10

value: Mammary stem cell (MaSC)


title: OIM_24hr_1

value: hFOB

value: OIM treated, grow at 39oC


title: LP-3 [mouse]

description: Sample 9

value: FVB/N

value: Luminal progenitor (LP)


title: ML-3 [mouse]

description: Sample 8

value: Mature luminal (ML)


title: JeKo-1_ONC201_0hr-3

value: mantle cell lymphoma (MCL) cell line

value: ONC201 for 0hr


title: OIM_4hr_1


title: human colon cancer sw480 cells, control shRNA rep3 [re-analysis]

source_name: human colon cancer SW480 cells treated with lentivirus meditated control shRNA

value: lentiviral vector GV248 (hU6-MCS-Ubi-EGFP-IRES-Puro) containing negative control


title: human colon cancer sw480 cells, YWHAE shRNA rep1

value: lentiviral vector GV248 (hU6-MCS-Ubi-EGFP-IRES-Puro) containing YWHAE shRNA hairpin sequence (LV-shYWHAE)


title: human colon cancer sw480 cells, YWHAE shRNA rep2


title: MaSC-3 [mouse]

description: Sample 7


title: human colon cancer sw480 cells, control shRNA rep3

source_name: SW480_lentivirus meditated control shRNA

growth_protocol: The human colon cancer cell lines SW480 cells were cultured in DMEM medium(Gibco BRL Co.Ltd.,USA) supplemented with 100 ml/l FBS(Gibco,USA) with the addition of 100 U/ml penicillin and 100 U/ml streptomycin at 37℃ in a humidified atmosphere of5 % CO2 in air.

treatment_protocol: The lentiviral vector GV248 (hU6-MCS-Ubi-EGFP-IRES-Puro) containing RAC1 shRNA hairpin sequence (LV-shRAC1) and negative control were constructed by Shanghai GeneChem, Transfections were performed using polybrene and enhanced infection solution (Genechem,Shang Hai) according to the manufacturer’s recommended protocol when these cells reached 30% confluence.


title: human colon cancer sw480 cells, control shRNA rep2 [re-analysis]


title: human colon cancer sw480 cells, RAC1 shRNA rep3

source_name: SW480_lentivirus meditated RAC1-shRNA

value: lentiviral vector GV248 (hU6-MCS-Ubi-EGFP-IRES-Puro) containing RAC1 shRNA hairpin sequence (LV-shRAC1)


title: Patient3 normal gastric mucosa

hyb_protocol: After stopping the labeling procedure, the Hy3™-labeled samples were hybridized on the miRCURYTM LNA Array (v.18.0) (Exiqon) according to array manual

scan_protocol: Then the slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).

data_processing: Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities>=30 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. After normalization, significant differentially expressed miRNAs between two groups were identified through Fold change and P-value. Differentially expressed miRNAs between two samples were filtered through Fold change.

label_protocol: After quality control, the miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) according to manufacturer’s instructions, which efficiently recovered all RNA species, including microRNAs. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis

tag: subject status/id

value: gastric cancer patient 3

tag: status after 1 years

value: alive

tag: age (yrs)

value: male

value: IIIA

value: normal gastric mucosa


title: human colon cancer sw480 cells, control shRNA rep1

value: human colon cancer cell line


title: Liver_PPARa-KO_Fenofibrate_rep1

tag: strain

value: KO

value: liver

value: Fenofibrate


title: Liver_LPPARa-KO_Fenofibrate_rep1

value: LKO

tag: gender


title: LP-2 [mouse]

description: Sample 6

value: FVB/N

value: Luminal progenitor (LP)


title: OIM_4hr_2

value: hFOB

value: OIM treated, grow at 39oC


title: human colon cancer sw480 cells, RAC1 shRNA rep2


title: ML-2 [mouse]

description: Sample 5

value: Mature luminal (ML)


title: B39_48hr_3

value: untreated, grow at 39oC in BM


title: MaSC-2 [mouse]

description: Sample 4

value: Mammary stem cell (MaSC)


title: Patient2 normal gastric mucosa

value: gastric cancer patient 2

tag: Stage

tag: tissue type


title: OIM_4hr_3


title: LP-1 [mouse]

description: Sample 3


title: JeKo-1_ONC201_0hr-1

value: mantle cell lymphoma (MCL) cell line

value: ONC201 for 0hr


title: B39_24hr_2


title: Patient1 normal gastric mucosa

value: gastric cancer patient 1

value: alive

value: male

value: IIIA


title: ML-1 [mouse]

description: Sample 2


title: human colon cancer sw480 cells, RAC1 shRNA rep1

value: human colon cancer cell line

value: lentiviral vector GV248 (hU6-MCS-Ubi-EGFP-IRES-Puro) containing RAC1 shRNA hairpin sequence (LV-shRAC1)


title: Patient3 cancer tissue

value: gastric cancer patient 3

value: primary gastric cancer tissue


title: MaSC-1 [mouse]

description: Sample 1

value: FVB/N


title: Leukocytes_MMT_patient_rep_stage_SS-501015

status: Public on Feb 19 2016

type: genomic

city: Miaoli County

first: Yu-Li

address: 35 Keyan Road, Zhunan

department: Center for Neuropsychiatric Research

country: Taiwan

institute: National Health Research Institutes

hyb_protocol: As per manufacturer (Affymetrix)

scan_protocol: As per manufacturer (Affymetrix)

data_processing:
The genotype calling was performed using the Genotyping Console 4.0 with default parameters.
Post-QC data (344 samples and 615216 SNPs in discovery stage; 76 samples and 613414 SNPs in replication stage) was provided in the postqc.txt files (linked as supplementary files on the Series record). At discovery stage, 5 samples were removed by sex check; 1 sample was removed by genotyping call rate check; 3 samples were removed by homozygosity check; 5 samples were removed by cryptic relatedness check; and 2 samples were removed by divergent ancestry check. At replication stage, 2 samples were removed by homozygosity check. The details of quality control are provided in the citation in this deposited data. Genotype Call (SNP call): AA, AB, BB, and NoCall

label: Biotin

molecule: genomic DNA

source_name: Leukocytes, MMT patient

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: The genomic DNA was isolated from leukocytes by using a Puregene kit (Gentra Systems, Minneapolis, MN). The DNA concentration was measured and adjusted to 15–20 ng/μL by using a NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies, DE)

tag: individual

value: MMT patient

value: replication

tag: age

value: Male

tag: bmi

value: leukocyte


title: Leukocytes_MMT_patient_rep_stage_SS-501014


title: Leukocytes_MMT_patient_rep_stage_SS-501013


title: Patient1 cancer tissue


title: B39_48hr_1

value: hFOB

value: untreated, grow at 39oC in BM


title: Patient2 cancer tissue

value: gastric cancer patient 2


title: Leukocytes_MMT_patient_rep_stage_SS-501012


title: Leukocytes_MMT_patient_rep_stage_SS-501011


title: Liver_LWT_vehicle_rep1

tag: genotype

value: LWT

tag: tissue

value: liver

value: vehicle

tag: replicate


title: Leukocytes_MMT_patient_rep_stage_SS-501010

tag: cell type


title: Leukocytes_MMT_patient_rep_stage_SS-501008


title: OIM_24hr_3

tag: cell line

tag: treatment

value: OIM treated, grow at 39oC


title: B39_24hr_1


title: Leukocytes_MMT_patient_rep_stage_SS-501006


title: Leukocytes_MMT_patient_rep_stage_SS-501007


title: Leukocytes_MMT_patient_rep_stage_SS-501004

value: Female


title: Leukocytes_MMT_patient_rep_stage_SS-501003


title: human colon cancer sw480 cells, control shRNA rep1 [re-analysis]

value: human colon cancer cell line

tag: transfected with

value: lentiviral vector GV248 (hU6-MCS-Ubi-EGFP-IRES-Puro) containing negative control


title: Leukocytes_MMT_patient_rep_stage_SS-501001


title: B39_24hr_3


title: Leukocytes_MMT_patient_rep_stage_SS-401089


title: B39_4hr_2


title: Liver_WT_vehicle_rep1

value: WT

value: male


title: Leukocytes_MMT_patient_rep_stage_SS-401085


title: B34BM_3

value: untreated, grow at 34oC in BM


title: Leukocytes_MMT_patient_rep_stage_SS-401084

value: MMT patient


title: B39_4hr_1


title: Leukocytes_MMT_patient_rep_stage_SS-401081

value: replication


title: Leukocytes_MMT_patient_rep_stage_SS-401083

value: Male


title: Liver_PPARa-KO_Fenofibrate_rep4

value: KO

value: Fenofibrate


title: Leukocytes_MMT_patient_rep_stage_SS-401080

value: leukocyte


title: B39_4hr_3

value: hFOB

value: untreated, grow at 39oC in BM


title: human colon cancer sw480 cells, control shRNA rep2


title: B34BM_1


title: Leukocytes_MMT_patient_rep_stage_SS-401077


title: B39_48hr_2


title: B34BM_2


title: Leukocytes_MMT_patient_rep_stage_SS-401076


title: Leukocytes_MMT_patient_rep_stage_SS-401069


title: JeKo-1_ONC201_0hr-2

value: mantle cell lymphoma (MCL) cell line

tag: treated with

value: ONC201 for 0hr


title: Leukocytes_MMT_patient_rep_stage_SS-401072


title: Leukocytes_MMT_patient_rep_stage_SS-401068


title: Leukocytes_MMT_patient_rep_stage_SS-401064


title: Leukocytes_MMT_patient_rep_stage_SS-401065


title: Leukocytes_MMT_patient_rep_stage_SS-401059


title: Leukocytes_MMT_patient_rep_stage_SS-401062


title: Leukocytes_MMT_patient_rep_stage_SS-401058


title: Leukocytes_MMT_patient_rep_stage_SS-401053


title: Leukocytes_MMT_patient_rep_stage_SS-401061


title: Leukocytes_MMT_patient_rep_stage_SS-401086


title: Leukocytes_MMT_patient_rep_stage_SS-401074


title: Leukocytes_MMT_patient_rep_stage_SS-401047


title: Leukocytes_MMT_patient_rep_stage_SS-401043


title: Leukocytes_MMT_patient_rep_stage_SS-401040


title: Leukocytes_MMT_patient_rep_stage_SS-401050


title: Leukocytes_MMT_patient_rep_stage_SS-401045


title: Leukocytes_MMT_patient_rep_stage_SS-401046


title: Leukocytes_MMT_patient_rep_stage_SS-401044


title: Leukocytes_MMT_patient_rep_stage_SS-401048


title: Leukocytes_MMT_patient_rep_stage_SS-401039


title: Leukocytes_MMT_patient_rep_stage_SS-401041


title: Leukocytes_MMT_patient_rep_stage_SS-401037


title: Leukocytes_MMT_patient_rep_stage_SS-401055


title: Leukocytes_MMT_patient_rep_stage_SS-401034


title: Leukocytes_MMT_patient_rep_stage_SS-401038


title: Leukocytes_MMT_patient_rep_stage_SS-401033


title: Leukocytes_MMT_patient_rep_stage_SS-401031


title: Leukocytes_MMT_patient_rep_stage_SS-401030


title: Leukocytes_MMT_patient_rep_stage_SS-401027


title: Leukocytes_MMT_patient_rep_stage_SS-401026


title: Leukocytes_MMT_patient_rep_stage_SS-401029


title: Leukocytes_MMT_patient_rep_stage_SS-401028


title: Leukocytes_MMT_patient_rep_stage_SS-401022


title: Leukocytes_MMT_patient_rep_stage_SS-401049


title: Leukocytes_MMT_patient_rep_stage_SS-401021


title: Leukocytes_MMT_patient_rep_stage_SS-401019


title: Leukocytes_MMT_patient_rep_stage_SS-401018


title: Leukocytes_MMT_patient_rep_stage_SS-401017


title: Leukocytes_MMT_patient_rep_stage_SS-401016


title: Leukocytes_MMT_patient_rep_stage_SS-401015


title: Leukocytes_MMT_patient_rep_stage_SS-401011


title: Leukocytes_MMT_patient_rep_stage_SS-401010


title: Leukocytes_MMT_patient_rep_stage_SS-401009


title: Leukocytes_MMT_patient_rep_stage_SS-401012


title: Leukocytes_MMT_patient_rep_stage_SS-401006


title: Leukocytes_MMT_patient_rep_stage_SS-401005


title: Leukocytes_MMT_patient_rep_stage_SS-401004


title: Leukocytes_MMT_patient_rep_stage_SS-401003


title: Leukocytes_MMT_patient_rep_stage_SS-401024


title: Leukocytes_MMT_patient_301-157

value: discovery


title: Leukocytes_MMT_patient_rep_stage_SS-401020


title: Leukocytes_MMT_patient_rep_stage_SS-401023

value: Female


title: Leukocytes_MMT_patient_301-149


title: Leukocytes_MMT_patient_301-148


title: Leukocytes_MMT_patient_301-143


title: Leukocytes_MMT_patient_301-142


title: Leukocytes_MMT_patient_301-138


title: Leukocytes_MMT_patient_301-137


title: Leukocytes_MMT_patient_301-129


title: Leukocytes_MMT_patient_301-136


title: Leukocytes_MMT_patient_rep_stage_SS-401013


title: Leukocytes_MMT_patient_rep_stage_SS-401014


title: Leukocytes_MMT_patient_301-126


title: Leukocytes_MMT_patient_301-124


title: Leukocytes_MMT_patient_rep_stage_SS-401008


title: Leukocytes_MMT_patient_301-123


title: Leukocytes_MMT_patient_rep_stage_SS-401002


title: Leukocytes_MMT_patient_301-122


title: Leukocytes_MMT_patient_301-120


title: Leukocytes_MMT_patient_301-116


title: Leukocytes_MMT_patient_301-114


title: Leukocytes_MMT_patient_301-160


title: Leukocytes_MMT_patient_301-159


title: Leukocytes_MMT_patient_301-119


title: Leukocytes_MMT_patient_301-150


title: Leukocytes_MMT_patient_301-111


title: Leukocytes_MMT_patient_301-110


title: Leukocytes_MMT_patient_301-108


title: Leukocytes_MMT_patient_301-096


title: Leukocytes_MMT_patient_301-092


title: Leukocytes_MMT_patient_301-105


title: Leukocytes_MMT_patient_301-089


title: Leukocytes_MMT_patient_301-094


title: Leukocytes_MMT_patient_301-085


title: Leukocytes_MMT_patient_301-084


title: Leukocytes_MMT_patient_301-091


title: Leukocytes_MMT_patient_301-093


title: Leukocytes_MMT_patient_301-077


title: Leukocytes_MMT_patient_301-081


title: Leukocytes_MMT_patient_301-076


title: Leukocytes_MMT_patient_301-083


title: Leukocytes_MMT_patient_301-075


title: Leukocytes_MMT_patient_301-074


title: Leukocytes_MMT_patient_301-064


title: Leukocytes_MMT_patient_301-055


title: Leukocytes_MMT_patient_301-054


title: Leukocytes_MMT_patient_301-053


title: Leukocytes_MMT_patient_301-049


title: Leukocytes_MMT_patient_301-051


title: Leukocytes_MMT_patient_301-050


title: Leukocytes_MMT_patient_301-044


title: Leukocytes_MMT_patient_301-039


title: Leukocytes_MMT_patient_301-042


title: Leukocytes_MMT_patient_301-038


title: Leukocytes_MMT_patient_301-035


title: Leukocytes_MMT_patient_301-030


title: Leukocytes_MMT_patient_301-017


title: Leukocytes_MMT_patient_301-024


title: Leukocytes_MMT_patient_301-022


title: Leukocytes_MMT_patient_301-021


title: Leukocytes_MMT_patient_301-015


title: Leukocytes_MMT_patient_301-013


title: Leukocytes_MMT_patient_301-006


title: Leukocytes_MMT_patient_301-009


title: Leukocytes_MMT_patient_301-005


title: Leukocytes_MMT_patient_301-008


title: Leukocytes_MMT_patient_301-073


title: Leukocytes_MMT_patient_301-003


title: Leukocytes_MMT_patient_301-056


title: Leukocytes_MMT_patient_301-007


title: Leukocytes_MMT_patient_301-004


title: Leukocytes_MMT_patient_301-002


title: Leukocytes_MMT_patient_206-071


title: Leukocytes_MMT_patient_206-065


title: Leukocytes_MMT_patient_206-067


title: Leukocytes_MMT_patient_206-058


title: Leukocytes_MMT_patient_206-068


title: Leukocytes_MMT_patient_206-053


title: Leukocytes_MMT_patient_401-021


title: Leukocytes_MMT_patient_401-018


title: Leukocytes_MMT_patient_401-022


title: Leukocytes_MMT_patient_206-057


title: Leukocytes_MMT_patient_401-017


title: Leukocytes_MMT_patient_401-016


title: Leukocytes_MMT_patient_401-015


title: Leukocytes_MMT_patient_401-014


title: Leukocytes_MMT_patient_401-013


title: Leukocytes_MMT_patient_401-005


title: Leukocytes_MMT_patient_401-009


title: Leukocytes_MMT_patient_401-011


title: Leukocytes_MMT_patient_401-010


title: Leukocytes_MMT_patient_401-003


title: Leukocytes_MMT_patient_401-002


title: Leukocytes_MMT_patient_401-001


title: Leukocytes_MMT_patient_306-008


title: Leukocytes_MMT_patient_306-004


title: Leukocytes_MMT_patient_306-005


title: Leukocytes_MMT_patient_306-025


title: Leukocytes_MMT_patient_306-022


title: Leukocytes_MMT_patient_217-028


title: Leukocytes_MMT_patient_217-026


title: Leukocytes_MMT_patient_217-023


title: Leukocytes_MMT_patient_217-030


title: Leukocytes_MMT_patient_217-018


title: Leukocytes_MMT_patient_217-013


title: Leukocytes_MMT_patient_217-008


title: Leukocytes_MMT_patient_217-003


title: Leukocytes_MMT_patient_217-002


title: Leukocytes_MMT_patient_212-016


title: Leukocytes_MMT_patient_217-004


title: Leukocytes_MMT_patient_217-010


title: Leukocytes_MMT_patient_212-014


title: Leukocytes_MMT_patient_401-004


title: Leukocytes_MMT_patient_212-010


title: Leukocytes_MMT_patient_212-011


title: Leukocytes_MMT_patient_212-007


title: Leukocytes_MMT_patient_306-009


title: Leukocytes_MMT_patient_212-002


title: Leukocytes_MMT_patient_212-012


title: Leukocytes_MMT_patient_211-036


title: Leukocytes_MMT_patient_212-001


title: Leukocytes_MMT_patient_211-034


title: Leukocytes_MMT_patient_212-013


title: Leukocytes_MMT_patient_211-026


title: Leukocytes_MMT_patient_211-035


title: Leukocytes_MMT_patient_211-030


title: Leukocytes_MMT_patient_211-025


title: Leukocytes_MMT_patient_212-005


title: Leukocytes_MMT_patient_211-020


title: Leukocytes_MMT_patient_217-012


title: Leukocytes_MMT_patient_211-017


title: Leukocytes_MMT_patient_211-021


title: Leukocytes_MMT_patient_211-014


title: Leukocytes_MMT_patient_211-022


title: Leukocytes_MMT_patient_211-007


title: Leukocytes_MMT_patient_211-011


title: Leukocytes_MMT_patient_211-008


title: Leukocytes_MMT_patient_211-002


title: Leukocytes_MMT_patient_211-005


title: Leukocytes_MMT_patient_206-052


title: Leukocytes_MMT_patient_206-051


title: Leukocytes_MMT_patient_206-046


title: Leukocytes_MMT_patient_206-050


title: Leukocytes_MMT_patient_206-042


title: Leukocytes_MMT_patient_206-039


title: Leukocytes_MMT_patient_206-037


title: Leukocytes_MMT_patient_206-031


title: Leukocytes_MMT_patient_206-035


title: Leukocytes_MMT_patient_206-036


title: Leukocytes_MMT_patient_206-026


title: Leukocytes_MMT_patient_206-025


title: Leukocytes_MMT_patient_206-024


title: Leukocytes_MMT_patient_206-020


title: Leukocytes_MMT_patient_206-013


title: Leukocytes_MMT_patient_206-027


title: Leukocytes_MMT_patient_206-022


title: Leukocytes_MMT_patient_206-011


title: Leukocytes_MMT_patient_206-047


title: Leukocytes_MMT_patient_206-017


title: Leukocytes_MMT_patient_206-010


title: Leukocytes_MMT_patient_206-006


title: Leukocytes_MMT_patient_206-012


title: Leukocytes_MMT_patient_301-163


title: Leukocytes_MMT_patient_206-002


title: Leukocytes_MMT_patient_301-162


title: Leukocytes_MMT_patient_301-158


title: Leukocytes_MMT_patient_301-161


title: Leukocytes_MMT_patient_301-154


title: Leukocytes_MMT_patient_301-153


title: Leukocytes_MMT_patient_301-151


title: Leukocytes_MMT_patient_301-152


title: Leukocytes_MMT_patient_301-147


title: Leukocytes_MMT_patient_301-146


title: Leukocytes_MMT_patient_301-145


title: Leukocytes_MMT_patient_301-140


title: Leukocytes_MMT_patient_301-144


title: Leukocytes_MMT_patient_301-139


title: Leukocytes_MMT_patient_206-009


title: Leukocytes_MMT_patient_301-134


title: Leukocytes_MMT_patient_301-135


title: Leukocytes_MMT_patient_206-008


title: Leukocytes_MMT_patient_301-127


title: Leukocytes_MMT_patient_301-121


title: Leukocytes_MMT_patient_301-131


title: Leukocytes_MMT_patient_301-125


title: Leukocytes_MMT_patient_301-132


title: Leukocytes_MMT_patient_301-118


title: Leukocytes_MMT_patient_301-130


title: Leukocytes_MMT_patient_301-128


title: Leukocytes_MMT_patient_301-117


title: Leukocytes_MMT_patient_301-113


title: Leukocytes_MMT_patient_301-155


title: Leukocytes_MMT_patient_301-106


title: Leukocytes_MMT_patient_301-115


title: Leukocytes_MMT_patient_301-104


title: Leukocytes_MMT_patient_301-103


title: Leukocytes_MMT_patient_301-102


title: Leukocytes_MMT_patient_301-141


title: Leukocytes_MMT_patient_301-099


title: Leukocytes_MMT_patient_301-100


title: Leukocytes_MMT_patient_301-133


title: Leukocytes_MMT_patient_301-095


title: Leukocytes_MMT_patient_301-098


title: Leukocytes_MMT_patient_301-087


title: Leukocytes_MMT_patient_301-090


title: Leukocytes_MMT_patient_301-082


title: Leukocytes_MMT_patient_301-088


title: Leukocytes_MMT_patient_301-086


title: Leukocytes_MMT_patient_301-079


title: Leukocytes_MMT_patient_301-078


title: Leukocytes_MMT_patient_301-068


title: Leukocytes_MMT_patient_301-080


title: Leukocytes_MMT_patient_301-109


title: Leukocytes_MMT_patient_301-072


title: Leukocytes_MMT_patient_301-066


title: Leukocytes_MMT_patient_301-069


title: Leukocytes_MMT_patient_301-112


title: Leukocytes_MMT_patient_301-065


title: Leukocytes_MMT_patient_301-071


title: Leukocytes_MMT_patient_301-060


title: Leukocytes_MMT_patient_301-070


title: Leukocytes_MMT_patient_301-059


title: Leukocytes_MMT_patient_301-101


title: Leukocytes_MMT_patient_301-052


title: Leukocytes_MMT_patient_301-057


title: Leukocytes_MMT_patient_301-058


title: Leukocytes_MMT_patient_301-048


title: Leukocytes_MMT_patient_301-047


title: Leukocytes_MMT_patient_301-097


title: Leukocytes_MMT_patient_301-046


title: Leukocytes_MMT_patient_301-045


title: Leukocytes_MMT_patient_301-040


title: Leukocytes_MMT_patient_301-043


title: Leukocytes_MMT_patient_301-036


title: Leukocytes_MMT_patient_301-034


title: Leukocytes_MMT_patient_301-031


title: Leukocytes_MMT_patient_301-033


title: Leukocytes_MMT_patient_301-029


title: Leukocytes_MMT_patient_301-027


title: Leukocytes_MMT_patient_301-026


title: Leukocytes_MMT_patient_301-028


title: Leukocytes_MMT_patient_301-023


title: Leukocytes_MMT_patient_301-025


title: Leukocytes_MMT_patient_301-018


title: Leukocytes_MMT_patient_301-014


title: Leukocytes_MMT_patient_206-070


title: Leukocytes_MMT_patient_301-020


title: Leukocytes_MMT_patient_301-019


title: Leukocytes_MMT_patient_301-016


title: Leukocytes_MMT_patient_206-064


title: Leukocytes_MMT_patient_206-069


title: Leukocytes_MMT_patient_206-063


title: Leukocytes_MMT_patient_206-060


title: Leukocytes_MMT_patient_401-024


title: Leukocytes_MMT_patient_401-012


title: Leukocytes_MMT_patient_206-061


title: Leukocytes_MMT_patient_401-007


title: Leukocytes_MMT_patient_301-037


title: Leukocytes_MMT_patient_401-008


title: Leukocytes_MMT_patient_206-062


title: Leukocytes_MMT_patient_401-019


title: Leukocytes_MMT_patient_306-024


title: Leukocytes_MMT_patient_306-021


title: Leukocytes_MMT_patient_306-020


title: Leukocytes_MMT_patient_306-019


title: Leukocytes_MMT_patient_306-018


title: Leukocytes_MMT_patient_306-017


title: Leukocytes_MMT_patient_306-015


title: Leukocytes_MMT_patient_306-014


title: Leukocytes_MMT_patient_306-011


title: Leukocytes_MMT_patient_306-010


title: Leukocytes_MMT_patient_306-012


title: Leukocytes_MMT_patient_306-006


title: Leukocytes_MMT_patient_306-007


title: Leukocytes_MMT_patient_306-002


title: Leukocytes_MMT_patient_306-003


title: Leukocytes_MMT_patient_306-001


title: Leukocytes_MMT_patient_217-029


title: Leukocytes_MMT_patient_401-006


title: Leukocytes_MMT_patient_401-020


title: Leukocytes_MMT_patient_217-015


title: Leukocytes_MMT_patient_217-009


title: Leukocytes_MMT_patient_217-020


title: Leukocytes_MMT_patient_217-025


title: Leukocytes_MMT_patient_217-007


title: Leukocytes_MMT_patient_217-022


title: Leukocytes_MMT_patient_217-019


title: Leukocytes_MMT_patient_217-021


title: Leukocytes_MMT_patient_217-011


title: Leukocytes_MMT_patient_217-017


title: Leukocytes_MMT_patient_212-018


title: Leukocytes_MMT_patient_217-006


title: Leukocytes_MMT_patient_212-017


title: Leukocytes_MMT_patient_217-001


title: Leukocytes_MMT_patient_217-005


title: Leukocytes_MMT_patient_212-008


title: Leukocytes_MMT_patient_217-016


title: Leukocytes_MMT_patient_212-009


title: Leukocytes_MMT_patient_212-006


title: Leukocytes_MMT_patient_212-004


title: Leukocytes_MMT_patient_212-003


title: Leukocytes_MMT_patient_211-032


title: Leukocytes_MMT_patient_211-031


title: Leukocytes_MMT_patient_306-016


title: Leukocytes_MMT_patient_211-033


title: Leukocytes_MMT_patient_211-029


title: Leukocytes_MMT_patient_217-014


title: Leukocytes_MMT_patient_211-028


title: Leukocytes_MMT_patient_211-023


title: Leukocytes_MMT_patient_211-018


title: Leukocytes_MMT_patient_211-019


title: Leukocytes_MMT_patient_211-016


title: Leukocytes_MMT_patient_211-027


title: Leukocytes_MMT_patient_211-024


title: Leukocytes_MMT_patient_211-012


title: Leukocytes_MMT_patient_212-015


title: Leukocytes_MMT_patient_211-010


title: Leukocytes_MMT_patient_206-056


title: Leukocytes_MMT_patient_211-003


title: Leukocytes_MMT_patient_206-048


title: Leukocytes_MMT_patient_206-045


title: Leukocytes_MMT_patient_206-044


title: Leukocytes_MMT_patient_206-040


title: Leukocytes_MMT_patient_206-033


title: Leukocytes_MMT_patient_206-034


title: Leukocytes_MMT_patient_206-032


title: Leukocytes_MMT_patient_206-030


title: Leukocytes_MMT_patient_211-013


title: Leukocytes_MMT_patient_206-029


title: Leukocytes_MMT_patient_206-028


title: Leukocytes_MMT_patient_211-006


title: Leukocytes_MMT_patient_206-019


title: Leukocytes_MMT_patient_211-015


title: Leukocytes_MMT_patient_206-016


title: Leukocytes_MMT_patient_206-004


title: Leukocytes_MMT_patient_206-018


title: Leukocytes_MMT_patient_206-054


title: Leukocytes_MMT_patient_206-023


title: Leukocytes_MMT_patient_206-049


title: Leukocytes_MMT_patient_206-043


title: Leukocytes_MMT_patient_211-009


title: Leukocytes_MMT_patient_206-038


title: Leukocytes_MMT_patient_206-001


title: Leukocytes_MMT_patient_206-014


title: Leukocytes_MMT_patient_206-015


title: Leukocytes_MMT_patient_206-003


title: Leukocytes_MMT_patient_206-021


title: Leukocytes_MMT_patient_211-001


title: Leukocytes_MMT_patient_206-041


title: GMP_array_bio2

city: Paris

first: samuel

last: Collombet

address: 46 rue d'Ulm

department: Biology

institute: Ecole Normale Superieure

hyb_protocol: 600ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human Gene Expression 8x60K arrays (G4851A-028004) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent)

scan_protocol: Scanned on an Agilent G2539A scanner at 3um resolution and 100%PMT. The intensity data of each individual hybridization were extracted and the quality was assessed with the Feature Extraction software 10.7 (Agilent).

data_processing: Raw data was corrected for background noise using the normexp method. Quantile normalization was applied to assure comparability across samples.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100ng RNA using the LowInputQuick Amp Labeling kit (Agilent 5190-2305) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: ESCs (E14TG2) were cultured on gelatinized plates in N2B27 media (50 %DMEM/F12, 50% Neurobasal medium, N2 (500X), B27 (1000X)) supplemented with small-molecule inhibitors PD (1 μM, PD0325901), CHIR (3 μM, CHIR99021) and LIF. CD19+ pre-B cells were obtained from bone marrow with monoclonal antibody to CD19 (BD Pharmingen) using MACS sorting (Miltenyi Biotech). The purity of the sorted cell fractions was confirmed by FACS using an LSR2 machine (BD). After isolation, B cells were grown in RPMI medium supplemented with 10% FBS and 10ng/ml IL-7 (Peprotech). All medium contain 100 X L-glutamine, 100X penicillin/streptomycin, 100X nonessential amino acids, 1000X β-mercaptoethanol. All reagents are from Life Technologies unless otherwise specified. Lin- c-Kit+ Sca-1- CD16+/CD32+ CD34+ GMP cells were isolated by FACS sorting using a BD INFLUX sorting machine and culture in STEMSPAN medium (Stemcell technologies) supplemented with 100ng/ml SCF, 50ng/ml IL3, 50ng/ml Flt3L and 50ng/ml mTPO (all from Peprotech). The antibodies used from GMPs isolation were from BD Biosciences.

extract_protocol: RNA isolation was performed with the miRNeasy mini kit (Qiagen) following manufacturers instruction. To remove the feeders, cells were pre-plated for 30 minutes before RNA processing. RNA was eluted from the columns using RNase-free water and quantified by Nanodrop. cDNA was produced with the High Capacity RNA-to-cDNA kit (Applied Biosystem).

treatment_protocol: For the reprogramming experiments B cells were exposed for 18h to 100nM of β-Estradiol (E2) in gelatinized plates seeded with a feeder layer of the MEFs in RPMI medium. After E2 washout, the cultures were switched to serum-free N2B27 medium supplemented with 2μg/ml of doxycycline, IL-4 10ng/ml, IL-7 10ng/ml and IL-15 2ng/ml. B cells were seeded at a density of 500 cells/cm2 in 12 well plates.

value: bone marrow

value: GMP


title: GMPslow_array_bio1


title: GMPfast_array_bio2


title: GMPfast_array_bio1


title: ES_array_bio2

source_name: ES

value: ES


title: GMPslow_array_bio2


title: d3_Oct4Positive_array_bio2

value: Bcell


title: GMP_array_bio1


title: miR-146a-/- CTRL-Ear-1

city: Stockholm

first: Ankit

last: Srivastava

state: - Select a State -

address: CMM L8:02

department: Department of Medicine

country: Sweden

institute: Karolinska Institutet

hyb_protocol: cRNA were hybridized  to the standard Affymetrix protocol  (GeneTitan® Instrument User Guide for Expression  Array Plates Affymetrix).

scan_protocol: Array plate was scanned using Affymetrix GeneTitan Scanner.

data_processing: The data were analyzed with Expression Console using  global scaling as normalization method.

source_name: ear challanged with vehicle control

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from  total RNA (GeneTitan® Instrument User Guide for Expression  Array Plates Affymetrix).

growth_protocol: Mice were maintained under specific pathogen free (SPF) environment

extract_protocol: Total RNA was extracted using Fastprep-24 lysing matrix and RNeasy Mini Kit according to the manufacturer's instructions.

treatment_protocol: A daily topical dose of 31.25 mg of Aldara cream (5% IMQ) was applied on the right ear of miR-146a -/- and C57BL/6 mice on three consecutive days to induce psorisis-like skin inflammation. Mice were sacrificed at day 4. Ear flaps were collected for total RNA extraction and hybridization on Affymatrix GeneTitan plate format Gene ST 2.1 (mouse).

tag: background strain

value: Ear

value: B6/Mir-146a-/- knock-out mice

value: 8 to 11 weeks old


title: WT-IMQ-Ear-3

source_name: ear challanged with IMQ

value: wild type


title: miR-146a-/- CTRL-Ear-3


title: d2_Oct4Positive_array_bio1


title: miR-146a-/- CTRL-Ear-4


title: miR-146a-/- IMQ-Ear-1


title: iPS_array_bio2

source_name: iPS

value: iPS


title: miR-146a-/- IMQ-Ear-3


title: pulse_array_bio2


title: miR-146a-/- IMQ-Ear-2


title: d2_Oct4Positive_array_bio2


title: Bcell_array_bio1

source_name: Bcell


title: pulse_array_bio1


title: d1_Oct4Positive_array_bio1


title: d3_Oct4Positive_array_bio1


title: iPS_array_bio1


title: miR-146a-/- IMQ-Ear-4


title: miR-146a-/- CTRL-Ear-2


title: Bcell_array_bio2


title: WT-IMQ-Ear-4


title: d1_Oct4Positive_array_bio2


title: ES_array_bio1


title: NCOA2 R1881 3

city: buffalo

first: Dan

last: Wang

address: Elm & Carlton Streets

institute: RPCI

hyb_protocol: Hybrization to 8x15K Custom gene expression arrays (Agilent) was done according to the manufacturer’s recommendations

scan_protocol: Scanning was performed using the G2565AA Microarray Scanner System (Agilent) according to the manufacturer’s recommendations

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

source_name: LNCaP

label_protocol: One-color gene expression labeling protocol (Agilent) was done according to the manufacturer’s recommendations

growth_protocol: 9% double charcoal-stripped FBS in RPMI1640

extract_protocol: Trizol RNA extraction followed by Qiagen RNAeasy column purification

treatment_protocol: 48 h R1881 5 nM or ethanol vehicle, biological triplicates

value: Synthetic androgen R1881 (5nM)

tag: sirna


title: normalizer 2

value: N


title: NCOA2 vehicle 3

value: Vehicle


title: NCOA2 R1881 2


title: NCOA2 R1881 1


title: WT-CTRL-Ear-3


title: NCOA1 vehicle 1


title: NCOA1 R1881 2


title: WT-IMQ-Ear-1


title: PRKCL1 R1881 3


title: NCOA1 R1881 3


title: NCOA2 vehicle 2


title: NCOA1 vehicle 2


title: PRKCL1 vehicle 1


title: WT-IMQ-Ear-2


title: PRKCL1 R1881 1


title: PRKCL1 vehicle 2


title: NCOA2 vehicle 1


title: PRKCL1 R1881 2


title: PRKCL1 vehicle 3


title: NCOA1 R1881 1


title: WT-CTRL-Ear-1


title: RCHY1 R1881 2


title: NCOA1 vehicle 3


title: WT-CTRL-Ear-2


title: WT-CTRL-Ear-4


title: RCHY1 R1881 3


title: RCHY1 R1881 1


title: RCHY1 vehicle 2


title: RCHY1 vehicle 3


title: Control R1881 3 quad

value: Con


title: RCHY1 vehicle 1


title: Control vehicle 3 quad


title: PARK7 R1881 3


title: CAV1 R1881 1


title: Control vehicle 1 quad


title: PARK7 R1881 1


title: PARK7 R1881 2


title: Control vehicle 2 quad


title: Control R1881 1 quad


title: PARK7 vehicle 2


title: CTNNB1 R1881 3


title: CAV1 vehicle 1


title: CTNNB1 R1881 2


title: PARK7 vehicle 3


title: CAV1 vehicle 3


title: CAV1 vehicle 2


title: CTNNB1 vehicle 3


title: PARK7 vehicle 1


title: CAV1 R1881 2


title: Control R1881 2 quad


title: SMARCA4 R1881 3


title: CTNNB1 vehicle 1


title: CTNNB1 vehicle 2


title: SMARCA4 R1881 2


title: SMARCA4 R1881 1


title: SMARCA4 vehicle 3


title: SMARCA4 vehicle 2


title: SMARCA4 vehicle 1


title: BAG1 R1881 2


title: BAG1 R1881 1


title: BAG1 vehicle 3


title: SMARCC1 R1881 2


title: CAV1 R1881 3


title: SMARCC1 R1881 3


title: BAG1 vehicle 1


title: BAG1 vehicle 2


title: SMARCC1 R1881 1


title: T47D bmp4 repeat 3

city: Zurich

first: Michal

last: Rajski

address: Winterthurerstrasse 190

department: Institute of Physiology

country: Switzerland

institute: University of Zurich

description: Simple annotation: control, Control experiment

hyb_protocol: Following a denaturing step at 100° C, the probe was placed on the microarray for competitive hybridization. After 18 h, the slides with hybridized probe were sequentially washed, immediately dried in an ozone-free environment and scanned using an Axon Scanner 4100A (Axon Instruments, CA, USA). The data analysis and clustering Microarray fluorescent image analysis were performed using the software Genepix Pro version 5.0 3.0.6.89 (Axon Instruments, Union City, CA, USA). Any spots with obvious array artifacts or poor technical quality were manually removed from any further analysis.

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1360, 6360; Software: type: feature extraction; Performer: Martin,,Buess

data_processing: The data were expressed as the log2 ratio of the fluorescence intensity of the sample and fluorescence intensity of the reference for each element on the array.

source_name: stratagene universal reference

label_protocol: not provided

extract_protocol: not provided

tag: reference

value: stratagene universal reference

source_name: T47D bmp4 repeat 3

label_protocol: For the microarray experiments, 8 ug of amplified RNA (aRNA) was mixed with the doping controls. The samples were vacuum dried, resolved in coupling buffer and labeled with Cy5 dye. The labeled samples were pooled with equal amounts of reverse color Cy3-labeled amplified reference RNA from Stratagene (Stratagene, Santa Rosa, CA, USA). The labeled aRNA was purified using an AminoAllyl MasageAmp II aRNA Amplification Kit (Ambion) according to the manufacturer's instructions and fragmented using fragmentation reagents (Ambion). The fragmented probe was added to a hybridization buffer containing Cot/PolyA/tRNA (0.05 ug/uL each), 0.3% SDS and 3.3 × SSC supplemented with HEPES buffer.

growth_protocol: Primary human fibroblasts (CCL-171) and the human breast cancer cell lines MDA-MB-231 and T47D were obtained from the American Type Culture Collection (ATTC, Atlanta, Georgia, USA) on the 15. November 2005. After resuscitation the cells were propagated in Dulbecco's modified Eagle's medium (D-MEM, Invitrogen, Carlsbad, USA) supplemented with 10% heat-inactivated FBS (Invitrogen, Carlsbad, CA, USA), 4.5 g/l glucose, 4 mM L-glutamine, 100 U/ml penicillin and 100 ug/ml streptomycin (Gibco, Carlsbad, CA, USA). The cells were maintained by regular passages when confluence was reached and used for the experiments within 3-4 months. The study was approved by the Ethikkommission beider Basel, Switzerland (approval No. 271/05).

extract_protocol: RNA extraction and amplification: After aspirating the culture medium, the cell monolayer was washed once with phosphate-buffered saline. The cells were lysed in a buffer containing guanidine isothiocyanate (RLT buffer, QIAGEN, CA, USA). The total RNA was extracted with an RNeasy kit (QIAGEN, Valencia, CA, USA) according to the manufacturer?s instructions. The RNA concentration was measured with a NanoDrop system spectrophotometer (ND-1000 Spectrophotometer Technologies, Wilmington, NC, USA). The integrity of extracted RNA was assessed by electrophoresis in a 1% agarose gel in MOPS buffer. For mRNA amplification, an Amino Allyl MasageAmp II aRNA Amplification Kit was used (Ambion, Austin, TX, USA). The amplification of mRNA from 500 ng total RNA, purification of the cDNA, in vitro transcription and purification of aRNA were performed according to the manufacturer's instructions. The integrity and quantity of the amplified RNA were verified as described above.

treatment_protocol: BMP stimulation experiments: For the experiment, 30?000 cells/cm2 were seeded in 3 ml of 5% FBS D-MEM and incubated for 6 h to allow attachment. The cells were washed extensively with phosphate-buffered saline and starved for 48 h in fresh low-serum D-MEM supplemented with 0.2% FBS. The cells were starved to reduce the effects of any stimulation from the regular cell culture medium. The medium was subsequently replaced with fresh low-serum D-MEM with or without 200 ng/ml BMP2 (human recombinant in Escherichia coli; Sigma Aldrich, St. Louis, MO, USA), 24 ng/ml BMP4, 200 ng/ml BMP7, 240 ng/ml Noggin or 1 ug/ml Gremlin. The cells were stimulated for 24 h, and the RNA was harvested to test the effects of BMP and their antagonists on mRNA expression patterns.


title: BAG1 R1881 3


title: SH-SY5Y

city: Philadelphia

first: Pichai

last: Raman

state: PA

address: 3501 Civic Center Blvd

institute: Children's Hospital of Philadelphia

hyb_protocol: Affymetrix GeneChip Hybridization Wash and Stain Kit (PN:  900720) protocol was used for all hybridization, wash and staining steps.  Fragmented and labeled cDNA (130ul at 25ng/uL) were hybridized for 17hrs at 45C to Affymetrix GeneChip Human Gene 1.0ST Arrays (PN:  901086).

scan_protocol: Chips were washed and stained on an Affymetrix Genechip Wash Station 450 using the FS450_0007 protocol and scanned on the Affymetrix GeneChip Scanner 3000.  Cel files were generated for analysis using Affymetrix GeneChip Command Console v3.2.

data_processing: Data were  processed using the RMA normalization algorithm and log2 transformed within the R/Bioconductor framework.

source_name: neuroblastoma cell line

label_protocol: Sense-strand single-stranded cDNA was prepared from 100ng of total RNA using the Ambion WT Expression Kit (PN:  4411974).  Both cRNA and cDNA were assessed using UV absorbance.  5.5ug of single-stranded cDNA was fragmented and labeled using the Affymetrix GeneChip WT Terminal Labeling kit (PN: 900671).

growth_protocol: All neuroblastoma cell  lines were grown in basal media (either RPMI1640 or DMEM) supplemented with 10% FBS and 1% gentamycin. Cells were cultured at 37C and 5% CO2

extract_protocol: All cell lines were collected 48h after plating at approximately 80-90% conflunce. RNA was extracted from 10cm dishes using the Qiagen AllPrep kit. Total RNA was assessed by UV absorbance and all had 260/280 ratios above 1.7.  Additionally, samples were run on the Agilent RNA 6000 Nano chip and all had RINs above 8.6.


title: SMARCC1 vehicle 3


title: SK-N-KAN

value: SK-N-KAN


title: SK-N-SH

value: SK-N-SH


title: RPE-1-MYCN-VEH

description: RPE-1 transfected with the MYCN:ER chimeric construct, with vehicle control (ethanol)

source_name: immortalized retinal pigmented epithelium cell line

tag: transfection

value: MYCN-VEH


title: CTNNB1 R1881 1


title: SMS-SAN

value: SMS-SAN


title: RPE-1-4OHT

description: An RPE-1 cell immortalized with the hTERT telomerase gene, with 4OHT (4-hydroxytamoxifen)

value: RPE-1 immortalized with the hTERT telomerase gene


title: RPE-1-MYCN-4OHT

description: RPE-1 transfected with the MYCN:ER chimeric construct, in which the MYCN transactivation is activated using 4OHT (4-hydroxytamoxifen)


title: SK-N-FI

value: SK-N-FI


title: NGP

value: NGP