title: #1065

type: genomic

city: Hannover

first: Doris

middle: Johanna

last: Steinemann

department: Institute of Human Genetics

country: Germany

institute: Hannover Medical School

hyb_protocol: According to manufacturer's instructions (Agilent), 4x180k

scan_protocol: Microarray slides were scanned immediately after washing using an Agilent microarray scanner G2505B at a resolution of 2 µm

data_processing: Feature extraction and Genomic Workbench (Agilent), algorithm ADM2 .

molecule: genomic DNA

source_name: T-ALL clone #1065 from spleen

label_protocol: According to manufacture's instructions (Agilent) and purifion by Amicon Ultra 30k filters (Millipore, Billerica, MA, USA)

growth_protocol: T-ALL clone developed in mice transplanted with TRK-transduced LSK cells

extract_protocol: DNA was extracted accoding Qiagen GmbH, Hilden, Germany

treatment_protocol: no treatment

value: T-cell acute lymphoblastic leukemia

source_name: reference DNA (spleen)

tag: tissue type

value: spleen


title: BD001-023-231053

status: Public on Jul 15 2014

type: RNA

city: Singapore

first: Sachel

last: Mok

address: 60 Nanyang Drive

country: Singapore

institute: Nanyang Technological University

description:
BD001-023-231053
Reference sample is laboratory strain 3D7.

hyb_protocol: Equal amounts of labelled sample and reference cDNA were hybridized on the microarray chip using the Agilent hybridization system. Hybridizations were performed for 20 hours at 65°C in a rotating hybridization oven at 10rpm.

scan_protocol: Microarray scanning was done using PowerScanner (Tecan, Austria) at 10uM resolution and with autogain PMT adjustments for both channels. Data was acquired using GenePix Pro v6.0 software (Axon Instruments, USA) as described in Mok, S., M. Imwong et al (2011) Artemisinin resistance in Plasmodium falciparum is associated with an altered temporal pattern of transcription. BMC Genomics 12: 391.

data_processing: Features with flag>0 and with median foreground intensity greater than 1.5 fold median background intensity for either channel passed quality control and were accepted. Local background correction using normexp, followed by lowess normalization across all features were carried out to generate the normalized Log2 gene expression ratios.

molecule: total RNA

organism: Plasmodium falciparum

source_name: P. falciparum field isolate, Ramu Bangladesh, BD001-023

label_protocol: Synthesis of aminoallyl-coupled cDNA by reverse transcription and labeling of samples with Cy fluorophore were carried out as described in Bozdech, Z., S. Mok & A. P. Gupta, (2013) DNA microarray-based genome-wide analyses of Plasmodium parasites. Methods in molecular biology 923: 189-211.

extract_protocol: Total RNA was extracted using Trizol following manufacturer's instructions and as described in Bozdech, Z., S. Mok & A. P. Gupta, (2013) DNA microarray-based genome-wide analyses of Plasmodium parasites. Methods in molecular biology 923: 189-211.

tag: culture

value: in vivo

tag: Stage

value: blood

tag: patient sample id

tag: geographic origin

value: Ramu, Bangladesh

tag: barcode

tag: timepoint

value: prior to artemisinin combination therapy (ACT)

tag: parasite clearance halflife upon artemisinin treatment (h)

source_name: P. falciparum 3D7 RNA reference pool

tag: strain/background

value: In vitro

value: asexual blood

tag: composition

value: mixture of equal amounts of RNA harvested every 6 hours over the 48-hour parasite's intraerythrocytic life cycle

tag: sample type

value: reference


title: BD001-018-189577

description:
BD001-018-189577
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Ramu Bangladesh, BD001-018


title: BD001-019-219820

description:
BD001-019-219820
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Ramu Bangladesh, BD001-019


title: Muscle_diabetes_7 days after treatment with STZ_biol. rep. 2

city: Padova

first: Gerolamo

last: Lanfranchi

address: Via U. Bassi, 58/B

department: CRIBI - Biotechnology Center and Biology Department

country: Italy

institute: University of Padova

description: Gene expression profiling of the gastrocnemius muscle from CD1 diabetic-mice (7 days after treatment with STZ, G4.1)

hyb_protocol: Labeled targets (atrophic and control muscle) were mixed and ethanol precipitated. After dissolving the pellet in 120 µl of hybridization buffer (5X SSC, 0.1% SDS, 25% formamide), samples were denatured at 90°C for 2 min and added to the microarrays. Prehybridization was performed overnight at 48°C in the presence of 5X SSC, 5X Denhardt, 0.1% SDS, 100 ng/µl ss-DNA. Competitive hybridizations were carried on for 48 hours at 46°C in an ArrayBooster microarray incubator (Advalytix), followed by a series of post-hybridization washings (Chemello et al., 2011).

scan_protocol: Array scanning was carried out using a GSI Lumonics LITE dual confocal laser scanner with a ScanArray Microarray Analysis System (Perkin Elmer), and raw images were analyzed with QuantArray Analysis Software (GSI Lumonics, Ottawa, Canada).

data_processing: Normalization of the expression levels was performed with MIDAW tool (Romualdi et al., 2005 - Nucleic Acids Res. 33: W644-9). Principal component analysis, cluster analysis and profile similarity searching were performed with tMev that is part of the TM4 Microarray Software Suite (Saeed AI, Bhagabati NK, Braisted JC, Liang W, Sharov V, Howe EA, et al. Methods in Enzymology, 2006;411:134-93). Identification of differentially expressed genes was performed with one and two class Significance Analysis of Microarray (SAM) program (Tusher VG, Tibshirani R, Chu G. Proc Natl Acad Sci USA 2001;98:5116-121) with default settings. SAM uses a permutation-based multiple testing algorithm and identifies significant genes with variable false-discovery rates (FDR). This can be manually adjusted to include a reasonable number of candidate genes with acceptable and well defined error probabilities

organism: Mus musculus

source_name: Gastrocnemius muscle, control

label_protocol: Total RNA (> 200 nt) samples were labeled using the Amino Allyl MessageAmp™ II aRNA Amplification Kit (Ambion), in accordance with the manufacturer's instructions. First strand synthesis with an engineered reverse transcriptase should produce virtually full-length cDNA, which is the best way to ensure reproducible microarray results. The use of a modified oligo(dT) primer bearing a T7 promoter (Van Gelder et al., 1990) allows the next amplification steps: after second strand synthesis and clean-up the cDNA becomes a template for in vitro transcription with T7 RNA polymerase. About 5 µg aminoallyl-labeled aRNA were coupled with Cy5 or Cy3 dyes (GE Healthcare) and purified on column (Ambion).

growth_protocol: Wild-type CD1 mice (Charles River) were housed in a normal environment provided with food and water. All aspects of animal care and experimentation were performed in accordance with the Guide for the Care and Use of Laboratory Animals published by the National Institutes of Health (NIH Publication No. 85-23, Revised 1996) and Italian regulations (DL 116/92) concerning the care and use of laboratory animals. Experimental procedures were approved by the local Ethical Committee of the University of Padova.

extract_protocol: Total RNA was isolated from muscle biopsies by using Trizol® Reagent (Life Technologies, CA) according to the manufacturer’s protocol. Total RNA, enriched for long RNA molecules (> 200 nt) by using PureLink™ miRNA Isolation Kit (Life Technologies), was quantified using the ND-1000 spectrophotometer (Nanodrop, Wilmington, DE), while RNA integrity in each samples were assessed by capillary electrophoresis using the RNA 6000 Nano LabChip using the Agilent Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA). Only total RNA samples with R.I.N. (RNA Integrity Number) values of 6 were used for microarray analysis.

treatment_protocol: CD1 wild-type (wt) mice have been placed under the following muscle wasting conditions: 1) starvation, 2) diabetes and 3) denervation. To confirm the induction of the atrophic process in each condition, we measured in EDL the expression level of Atrogin-1, a muscle specific E3-ubiquitin ligase highly induced during atrophy. 1) To induce muscle wasting by starvation, mice were food deprived for 24 and 48 hours, with free access to water. This procedure reduced body weight by 10%, gastrocnemius muscle mass by 15% and it was accompanied by more than 20 fold increase of Atrogin-1 mRNA. 2) Insulin deficiency or insulin resistance at the level of skeletal muscle tissue also leads to the activation of the atrophic program. In order to recapitulate diabetes-associated muscle atrophy, CD1 wt mice were injected intra-peritoneally with streptozotocin. This drug is recognized and approved by the “Animal Models of Diabetic Complications Consortium” and causes β-cell toxicity, resulting in primary insulin deficiency. After 7 days of an acute injection of 180 mg/Kg of Streptozotocin muscle, atrophy is already established as stated by a 4-5 fold up-regulation of atrogin-1 mRNA. 3) The absence of electrical stimulation and functional load in muscle leads to progressive atrophy. CD1 wt mice underwent sciatic denervation surgery under anaesthesia. The controlateral leg was left intact. Three different time points were analysed: 3, 7 and 14 days after surgery. Three days after surgery expression of Atrogin-1 mRNA was induce by 8–fold when compared to non-denervated muscles.

tag: tissue

value: gastrocnemius muscle

tag: treatment

value: control

tag: strain

source_name: Gastrocnemius muscle, diabetes, 7 days after treatment with STZ

value: diabetic

tag: time

value: 7 days after treatment with STZ


title: HfQ2-cy3_WT2-cy5

city: Paris

first: Monot

last: Marc

address: 25, rue du docteur roux

department: Genomes and Genetics

country: France

institute: Institut Pasteur

description: Biological replicate 2 of 4.

hyb_protocol: Samples were applied to microarrays enclosed in Agilent hybridization chambers for 17h at 65°C. After hybridization, slides were washed with Agilent washing buffers.

scan_protocol: Scanned on a GenePix Pro 6 dual-channel laser scanner.

data_processing: R limma package - Function used - Background correction : backgroundCorrect normexp ; Normalization : normalizeWithinArrays loess - Correlation of spot duplicate : duplicateCorrelation - Adjust to linear method : lmFit - Statistical analysis : eBayes, decideTests global BH.

organism: Clostridioides difficile

source_name: hfQ mutant grown 7.5h Tyt

label_protocol: 10 µg of total RNA and pdN6 primer were heated at 70°C for 5 min, then reversed transcribed at 42°C for 3 h in the presence of 800 U SuperScript III Reverse Transcriptase (Invitrogen), each dATP, dTTP, dGTP, dCTP. cDNA were then incubated with Cy5 or Cy3 dyes 1h at room temperature in the dark.

growth_protocol: C. difficile strain C630E and hfQ mutant were grown in Tyt.

extract_protocol: Total RNA was extracted using QIAgen RNeasy kit.

value: C630E Mullany hfQ::erm

tag: genotype/variation

value: hfQ mutation

source_name: 630E strain grown 7.5h in Tyt (reference)

value: C630E Mullany

value: wild-type


title: #483

source_name: T-ALL clone #483 from thymus

tag: cell type

value: T-cell acute lymphoblastic leukemia

value: spleen


title: #958

source_name: T-ALL clone #958 from thymus

tag: tissue type


title: Muscle_starvation_24 h_biol. rep. 2

description: Gene expression profiling of the gastrocnemius muscle from CD1 starved-mice (24 h, 1969)

source_name: Gastrocnemius muscle, starvation, 24 h

value: starved


title: BD001-017-189534

description:
BD001-017-189534
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Ramu Bangladesh, BD001-017

tag: culture

value: in vivo

value: blood

value: Ramu, Bangladesh


title: Muscle_starvation_48 h_biol. rep. 3

description: Gene expression profiling of the gastrocnemius muscle from CD1 starved-mice (24 h, 832)

source_name: Gastrocnemius muscle, starvation, 48 h


title: Muscle_starvation_24 h_biol. rep. 1

description: Gene expression profiling of the gastrocnemius muscle from CD1 starved-mice (24 h, 1967)


title: #007

source_name: T-ALL clone #007 from thymus


title: Muscle_denervation_14 days_biol. rep. 3

description: Gene expression profiling of the gastrocnemius muscle from CD1 denervated-mice (14 days, 699)

source_name: Gastrocnemius muscle, denervation, 14 days

value: denervated

value: 14 days


title: Muscle_starvation_24 h_biol. rep. 3

description: Gene expression profiling of the gastrocnemius muscle from CD1 starved-mice (24 h, 3097)


title: BD001-016-189526

description:
BD001-016-189526
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Ramu Bangladesh, BD001-016

tag: Stage

value: prior to artemisinin combination therapy (ACT)

value: In vitro

value: asexual blood

value: mixture of equal amounts of RNA harvested every 6 hours over the 48-hour parasite's intraerythrocytic life cycle

value: reference


title: #003

source_name: T-ALL clone #003 from thymus

source_name: reference DNA (spleen)


title: BD001-007-189420

description:
BD001-007-189420
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Ramu Bangladesh, BD001-007

tag: patient sample id

source_name: P. falciparum 3D7 RNA reference pool


title: Muscle_denervation_14 days_biol. rep. 1

description: Gene expression profiling of the gastrocnemius muscle from CD1 denervated-mice (14 days, 696)

value: gastrocnemius muscle

value: control


title: Muscle_denervation_14 days_biol. rep. 2

description: Gene expression profiling of the gastrocnemius muscle from CD1 denervated-mice (14 days, 698)


title: #1003

source_name: T-ALL clone #1003 from spleen


title: Muscle_diabetes_7 days after treatment with STZ_biol. rep. 1

description: Gene expression profiling of the gastrocnemius muscle from CD1 diabetic-mice (7 days after treatment with STZ, G2.1)

source_name: Gastrocnemius muscle, control

value: diabetic

value: 7 days after treatment with STZ


title: BD001-021-219971

description:
BD001-021-219971
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Ramu Bangladesh, BD001-021

tag: geographic origin


title: Muscle_denervation_7 days_biol. rep. 3

description: Gene expression profiling of the gastrocnemius muscle from CD1 denervated-mice (7 days, 1116)

source_name: Gastrocnemius muscle, denervation, 7 days

value: 7 days


title: Muscle_denervation_7 days_biol. rep. 1

description: Gene expression profiling of the gastrocnemius muscle from CD1 denervated-mice (7 days, 1110)


title: Muscle_denervation_3 days_biol. rep. 4

description: Gene expression profiling of the gastrocnemius muscle from CD1 denervated-mice (3 days, G5)

source_name: Gastrocnemius muscle, denervation, 3 days

value: 3 days


title: Muscle_denervation_7 days_biol. rep. 4

description: Gene expression profiling of the gastrocnemius muscle from CD1 denervated-mice (7 days, 1118)


title: BD001-006-219616

description:
BD001-006-219616
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Ramu Bangladesh, BD001-006

tag: barcode


title: BD001-005-219618

description:
BD001-005-219618
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Ramu Bangladesh, BD001-005

tag: timepoint


title: Muscle_starvation_48 h_biol. rep. 2

description: Gene expression profiling of the gastrocnemius muscle from CD1 starved-mice (24 h, 831)

value: starved


title: Muscle_starvation_48 h_biol. rep. 1

description: Gene expression profiling of the gastrocnemius muscle from CD1 starved-mice (24 h, 830)


title: BD001-014-219784

description:
BD001-014-219784
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Ramu Bangladesh, BD001-014

value: in vivo

tag: parasite clearance halflife upon artemisinin treatment (h)


title: BD001-012-189491

description:
BD001-012-189491
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Ramu Bangladesh, BD001-012

value: blood

tag: strain/background


title: BD001-002-219908

description:
BD001-002-219908
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Ramu Bangladesh, BD001-002

value: Ramu, Bangladesh

tag: composition


title: BD001-015-219800

description:
BD001-015-219800
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Ramu Bangladesh, BD001-015

tag: sample type


title: BD001-004-219590

description:
BD001-004-219590
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Ramu Bangladesh, BD001-004


title: BD001-009-189449

description:
BD001-009-189449
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Ramu Bangladesh, BD001-009


title: BD001-008-189436

description:
BD001-008-189436
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Ramu Bangladesh, BD001-008


title: Muscle_denervation_3 days_biol. rep. 2

description: Gene expression profiling of the gastrocnemius muscle from CD1 denervated-mice (3 days, 1101-II)

tag: tissue

value: denervated


title: BD001-010-189463

description:
BD001-010-189463
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Ramu Bangladesh, BD001-010


title: Control Knockdown biological rep 3of3

city: New York

first: Jeffrey

last: Zhao

state: NY

address: 1275 York Avenue

department: Genomics Core

country: USA

institute: Memorial Sloan Kettering Cancer Center

description: Gene expression data from day 3 after knockdown

hyb_protocol: Following fragmentation, cRNA were hybridized for Illumina GX HT12 Array. Slides were washed and stained in the Illumina instrument.

scan_protocol: Slides were scanned using Illumina iScanner

data_processing: The data were analyzed with GenomeStudio using Illumina default analysis settings. No normalization and background correction are performed first, then quantile normalization and background correction are done.

label: biotin

organism: Homo sapiens

label_protocol: Biotinylated cRNA were prepared according to the standard Illumina protocol from total RNA.

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

value: Control Knockdown


title: BD001-003-219688

description:
BD001-003-219688
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Ramu Bangladesh, BD001-003

value: prior to artemisinin combination therapy (ACT)


title: Control Knockdown biological rep 2of3


title: Muscle_denervation_3 days_biol. rep. 3

description: Gene expression profiling of the gastrocnemius muscle from CD1 denervated-mice (3 days, G4)

tag: treatment


title: BD001-001-219888

description:
BD001-001-219888
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Ramu Bangladesh, BD001-001

source_name: P. falciparum 3D7 RNA reference pool

value: In vitro


title: YAP and TAZ Knockdown biological rep 3of3

value: YAP and TAZ Knockdown


title: Control Knockdown biological rep 1of3


title: YAP and TAZ Knockdown biological rep 2of3


title: TAZ Knockdown biological rep 2of3

value: TAZ Knockdown


title: YAP Knockdown biological rep 2of3

value: YAP Knockdown


title: YAP Knockdown biological rep 3of3


title: DCAF1 Knockdown biological rep 2of3

value: DCAF1 Knockdown


title: TAZ Knockdown biological rep 3of3


title: Muscle_cancer cachexia_two weeks_biological rep. 2

description: miRNA expression profiling of the gastrocnemius muscle from CD1 cancer cachectic-mice (Left-B)

hyb_protocol: Microarray hybridization was carried out in a dual slide chamber (HybChamber, Gene Machines, San Carlos, CA, USA) humidified with 100 μL of 3×SSC. Labeled RNA was dissolved in 6 μL of 3X miRNA Hybridization Buffer (Ambion), denatured at 95°C for 3 min and applied directly to the slides. Microarrays were covered with a 24×24 mm cover slip and hybridized for 21 hours at 42°C by immersion in a high precision water bath (W28, Grant, Cambridge, UK). Hybridized slides were successively washed in: Low and High Stringency Buffer (Ambion) for 30 sec. and dried by centrifugation (500 x g).

data_processing: Inter-array normalization of expression levels was performed with loessM+GPA (Risso et al., 2009 - Bioinformatics, 25:2685-91). Principal component analysis, cluster analysis and profile similarity searching were performed with tMev that is part of the TM4 Microarray Software Suite (Saeed et al., 2006 - Methods in Enzymology, 411:134-93). In particular, hierarchical cluster analysis was performed with Pearson correlation or Euclidean distance coefficient as distance measure with complete linkage. Identification of differentially expressed miRNAs was performed with ANOVA one class analysis (p-value <0.05) (Pan et al., 2002 - Bioinformatics, 18: 546-5).

source_name: Gastrocnemius muscle, control

label_protocol: Small RNA molecules (< 200 nt) were labelled with the mirVana Labeling Kit and amine-reactive dyes as recommended by the manufacturer (Ambion). Poly(A) polymerase and a mixture of unmodified and amine-modified nucleotides were used first to append a poly-nucleotide tail to the 3’ end of each miRNA. The amine-modified miRNAs were then cleaned up and coupled to NHS-ester modified Cy5 or Cy3 dyes (GE Healthcare). Unincorpored dyes were removed with a second glass fiber-based cleanup procedure as described by Shingara et al. (2005).

extract_protocol: Total RNA was isolated from muscle biopsies by using Trizol® Reagent (Life Technologies, CA) according to the manufacturer’s protocol. The commercially available PureLink™ miRNA Isolation Kit (Life Technologies) was used to enrich total RNA preparation for small RNA molecules (< 200 bp). Total RNA was quantified using the ND-1000 spectrophotometer (Nanodrop, Wilmington, DE), while RNA integrity and content of microRNAs (%) in each samples were assessed by capillary electrophoresis using the RNA 6000 Nano LabChip and the Small RNA Nano LabChip respectively using the Agilent Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA). Only total RNA samples with R.I.N. (RNA Integrity Number) values of 6, or higher, and the percentage of miRNA < 20% were used for microarray analysis.

value: gastrocnemius muscle

tag: reference

value: wild type

tag: strain

source_name: Gastrocnemius muscle, cancer cachexia, two weeks

tag: disease state

value: cancer cachexia


title: YAP Knockdown biological rep 1of3

tag: genotype/variation


title: Muscle_cancer cachexia_two weeks_biological rep. 4

description: miRNA expression profiling of the gastrocnemius muscle from CD1 cancer cachectic-mice (Right-B)


title: Muscle_cancer cachexia_two weeks_biological rep. 3

description: miRNA expression profiling of the gastrocnemius muscle from CD1 cancer cachectic-mice (Right-A)


title: Muscle_diabetes_7 days after treatment with STZ_biol. rep. 6

description: miRNA expression profiling of the gastrocnemius muscle from CD1 diabetic-mice (7 days after treatment with STZ, G6.1-B)

value: wild-type (control)

source_name: Gastrocnemius muscle, diabetes, 7 days after treatment with STZ

tag: atrophic model

value: diabetic-mice (7 days after treatment with STZ)


title: Muscle_diabetes_7 days after treatment with STZ_biol. rep. 5

description: miRNA expression profiling of the gastrocnemius muscle from CD1 diabetic-mice (7 days after treatment with STZ, G6.1-A)


title: Muscle_diabetes_7 days after treatment with STZ_biol. rep. 4

description: miRNA expression profiling of the gastrocnemius muscle from CD1 diabetic-mice (7 days after treatment with STZ, G4.1-B)


title: DCAF1 Knockdown biological rep 3of3


title: YAP and TAZ Knockdown biological rep 1of3


title: Muscle_cancer cachexia_two weeks_rep. 1

description: miRNA expression profiling of the gastrocnemius muscle from CD1 cancer cachectic-mice (Left-A)


description: miRNA expression profiling of the gastrocnemius muscle from CD1 diabetic-mice (7 days after treatment with STZ, G2.1-B)


description: miRNA expression profiling of the gastrocnemius muscle from CD1 diabetic-mice (7 days after treatment with STZ, G2.1-A)


title: DCAF1 Knockdown biological rep 1of3


title: Muscle_starvation_48 h_biol. rep. 2

description: miRNA expression profiling of the gastrocnemius muscle from CD1 starved-mice (24 h, 831-A)

source_name: Gastrocnemius muscle, starvation, 48 h

value: starved-mice (48 h)


title: Muscle_starvation_48 h_biol. rep. 1

description: miRNA expression profiling of the gastrocnemius muscle from CD1 starved-mice (24 h, 830-A)


title: Muscle_starvation_48 h_biol. rep. 3

description: miRNA expression profiling of the gastrocnemius muscle from CD1 starved-mice (24 h, 831-B)


title: Muscle_starvation_48 h_biol. rep. 5

description: miRNA expression profiling of the gastrocnemius muscle from CD1 starved-mice (24 h, 832-B)


title: TAZ Knockdown biological rep 1of3

description: Gene expression data from day 3 after knockdown


title: Muscle_starvation_48 h_biol. rep. 4

description: miRNA expression profiling of the gastrocnemius muscle from CD1 starved-mice (24 h, 832-A)


title: Muscle_diabetes_7 days after treatment with STZ_biol. rep. 3

description: miRNA expression profiling of the gastrocnemius muscle from CD1 diabetic-mice (7 days after treatment with STZ, G4.1-A)


title: Muscle_starvation_24 h_biol. rep. 6

description: miRNA expression profiling of the gastrocnemius muscle from CD1 starved-mice (24 h, 3097-B)

value: starved-mice (24 h)


title: Muscle_starvation_24 h_biol. rep. 4

description: miRNA expression profiling of the gastrocnemius muscle from CD1 starved-mice (24 h, 1969-B)

source_name: Gastrocnemius muscle, starvation, 24 h


title: U2OS_E773R-2hr-replicate1

city: San Francisco

first: Benjamin

middle: J

last: Schiller

state: CA

institute: University of California, San Francisco

description:
5262624090_G
replicate 1

hyb_protocol: Hybridization was done by the University of Southern California Epigenome Center.

scan_protocol: Scanning and image acquisition was done by the University of Southern California Epigenome Center.

data_processing:
Bead-level data outputted from Illumina’s BeadScan software were read using the beadarray package from Bioconductor. BASH was used to correct for compact and diffuse spatial artifacts on the arrays. Bead-level data were summarized using
beadarray, filtering out beads that were > 3 MADs from the median (this is the raw data). Probe annotations were retrieved using the illuminaHumanv3.db package from Bioconductor; bad quality probes and probes not corresponding to known
HUGO gene symbols were removed from the data before further processing. Bead summary data were log2 transformed and quantile normalized. We then used the non-parametric empirical Bayes method described by Johnson and Rabinovic to
correct for chip-to-chip batch effects. Detection pvalues were not available after batch correction.

source_name: U2OS_2 hours_100 nM dexamethasone_E773R

label_protocol: Labeling was done by the University of Southern California Epigenome Center.

growth_protocol: Cells were plated in 6-well plates using DMEM supplemented with 5% v/v fetal bovine serum.

extract_protocol:
Cells were lysed and total RNA was isolated using QIAshredder and RNeasy mini columns (Qiagen). The quality of RNA samples was evaluated by A260/A280 ratio which was at least 1.9 and the integrity was analyzed using the Bioanalyzer 2100
(Agilent) with the Experion RNA Stdsens analysis kit (Biorad). For each experimental condition 2 μg of high quality total RNA was submitted to the University of Southern California Epigenome Center.

treatment_protocol: Dexamethasone (Sigma) at a final concentration of 100 nM was added to the medium for 2, 4, or 24 hours (hr); for the “0 hr” time point, cells were treated with vehicle (ethanol) only for 4 hr.

tag: cell line

tag: time

value: 2 hours

value: 100 nM dexamethasone

tag: expressed allele


title: U2OS_GRalpha-2hr-replicate4

description:
5262624090_H
replicate 4

source_name: U2OS_2 hours_100 nM dexamethasone_GRalpha

value: GRalpha


title: U2OS_GRgamma-2hr-replicate2

description:
5262624090_F
replicate 2

source_name: U2OS_2 hours_100 nM dexamethasone_GRgamma

value: GRgamma


title: Muscle_starvation_24 h_biol. rep. 2

description: miRNA expression profiling of the gastrocnemius muscle from CD1 starved-mice (24 h, 1967-B)


title: Muscle_starvation_24 h_biol. rep. 3

description: miRNA expression profiling of the gastrocnemius muscle from CD1 starved-mice (24 h, 1969-A)


title: Muscle_starvation_24 h_biol. rep. 1

description: miRNA expression profiling of the gastrocnemius muscle from CD1 starved-mice (24 h, 1967-A)


title: U2OS_30iiB-2hr-replicate4

description:
5262624090_D
replicate 4

source_name: U2OS_2 hours_100 nM dexamethasone_30iiB


title: Muscle_starvation_24 h_biol. rep. 5

description: miRNA expression profiling of the gastrocnemius muscle from CD1 starved-mice (24 h, 3097-A)


title: Muscle_denervation_14 days_biol. rep. 6

description: miRNA expression profiling of the gastrocnemius muscle from CD1 denervated-mice (14 days, 699-B)

source_name: Gastrocnemius muscle, denervation, 14 days

value: denervated-mice (14 days)


title: Muscle_denervation_14 days_biol. rep. 4

description: miRNA expression profiling of the gastrocnemius muscle from CD1 denervated-mice (14 days, 698-B)


title: U2OS_A477T-4hr-replicate2

description:
5262624090_C
replicate 2

source_name: U2OS_4 hours_100 nM dexamethasone_A477T

value: 4 hours


title: Muscle_denervation_14 days_biol. rep. 5

description: miRNA expression profiling of the gastrocnemius muscle from CD1 denervated-mice (14 days, 699-A)


title: Muscle_denervation_14 days_biol. rep. 3

description: miRNA expression profiling of the gastrocnemius muscle from CD1 denervated-mice (14 days, 698-A)


title: Muscle_denervation_14 days_biol. rep. 2

description: miRNA expression profiling of the gastrocnemius muscle from CD1 denervated-mice (14 days, 696-B)


title: WT 3

first: Ulf

last: Klein

address: 1130 St. Nicholas Avenue

department: Herbert Irving Comprehensive Cancer Center

institute: Columbia University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Mouse Genome 430 2.0 Gene Expression Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

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

source_name: WT_Germinal center B lymphocytes

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug amplified cDNA.

extract_protocol: Total RNA of ~3 x 10^4 cells was isolated using the Nucleospin RNA XS isolation kit (Macherey-Nagel) according to the manufacturer’s protocol. ~10 ng of total RNA was reverse transcribed into cDNA with the Ovation RNA Amplification System (NuGEN) according to the manufacturer’s instructions.

treatment_protocol: B cells from 12-week old relfl/flCg1-Cre and Cg1-Cre littermate mice were isolated by flow cytometric sorting from splenic mononuclear cells.

tag: strain background

value: WT; Cg1-Cre

tag: age

value: 12 weeks

tag: time point

value: 7 days after SRBC immunization

tag: cell type

value: FACS-purified germinal center B cells


title: REL 2

source_name: REL_Germinal center B lymphocytes

value: REL; relfl/flCg1-Cre


title: U2OS_E773R-24hr-replicate2

description:
5262624088_H
replicate 2

source_name: U2OS_24 hours_100 nM dexamethasone_E773R

value: 24 hours


title: ABI 1W treatment postnatal 11 wks / Adult Cy5

city: Tsukuba

first: RANDEEP

last: RAKWAL

state: Ibaraki

address: 1-1-1 Tennodai

department: Institute of Health and Sport Sciences

country: Japan

institute: University of Tsukuba

description:
treatment, adult
A one-color matrix format is being used, although we used 2 chips, 8x60K, labeling all 8 samples with Cy3 in one slide, and the same 8 samples with Cy5 using a second chip. Agilent Support Staff was consulted for this exp. After discussion, Agilent recoommended using teh GE2 color scanning protocol, as we regularly do for dye-swap analysis.

hyb_protocol: hybridization_Kit: in situ hybridization plus

scan_protocol: Scanner: Agilent DNA microarray Scanner G2505C

data_processing: Software: Feature Extraction ver 11.0.1.1

source_name: Pooled Right side neocortex

label_protocol: Manual:  Low Input Quick Amp Labeling Kit, Two-Color  (Agilent)

growth_protocol: C57BL/6J mice were purchased from Japan Charles River (Kanagawa, Japan). The animals were housed at the Animal Institution in Showa University. Mice were maintained in cages in a ventilated animal room with controlled temperature and relative humidity with a 12 h light: 12 h dark schedule (lights were turned on at 8:00 AM) and had access to laboratory chow and tap water ad libitum. In the case of neonatal mice, they were unified at the weaning time in postnatal four-weeks. All animal care and experimental procedures were approved by the Institutional Animal Care and Use Committee of Showa University (approval number, M6031).

extract_protocol: kit: QIAGEN, Rneasy Mini

treatment_protocol: Control (NC),Hemidecortication animal model, young (NBI), Hemidecortication animal model, adult (ABI)

value: postnatal 11 wks

value: Hemidecortication

value: right brain neocortex


title: NC 10W control postnatal 10 wks / Adult Cy5

description:
control, adult
A one-color matrix format is being used, although we used 2 chips, 8x60K, labeling all 8 samples with Cy3 in one slide, and the same 8 samples with Cy5 using a second chip. Agilent Support Staff was consulted for this exp. After discussion, Agilent recoommended using teh GE2 color scanning protocol, as we regularly do for dye-swap analysis.

value: postnatal 10 wks

value: control


title: U2OS_30iiB-4hr-replicate2

description:
5262624090_B
replicate 2

source_name: U2OS_4 hours_100 nM dexamethasone_30iiB


title: ABI 4W treatment postnatal 15 wks / Adult Cy5

value: postnatal 15 wks


title: U2OS_A477T-2hr-replicate1

description:
5262624090_E
replicate 1

source_name: U2OS_2 hours_100 nM dexamethasone_A477T

value: 2 hours

value: 100 nM dexamethasone


title: NBI 1W treatment postnatal 14 days / Young Cy5

description:
treatment, young
A one-color matrix format is being used, although we used 2 chips, 8x60K, labeling all 8 samples with Cy3 in one slide, and the same 8 samples with Cy5 using a second chip. Agilent Support Staff was consulted for this exp. After discussion, Agilent recoommended using teh GE2 color scanning protocol, as we regularly do for dye-swap analysis.

value: postnatal 14 days


title: WT 1


title: Muscle_denervation_14 days_biol. rep. 1

description: miRNA expression profiling of the gastrocnemius muscle from CD1 denervated-mice (14 days, 696-A)

source_name: Gastrocnemius muscle, control

value: wild-type (control)

value: gastrocnemius muscle

value: denervated-mice (14 days)


title: WT 2

value: WT; Cg1-Cre

value: 12 weeks


title: NC P35 control postnatal 35 days / Young Cy5

description:
control, young
A one-color matrix format is being used, although we used 2 chips, 8x60K, labeling all 8 samples with Cy3 in one slide, and the same 8 samples with Cy5 using a second chip. Agilent Support Staff was consulted for this exp. After discussion, Agilent recoommended using teh GE2 color scanning protocol, as we regularly do for dye-swap analysis.

value: postnatal 35 days


title: REL 1

value: REL; relfl/flCg1-Cre

value: 7 days after SRBC immunization

value: FACS-purified germinal center B cells


title: NBI 4W treatment postnatal 35 days / Young Cy5

value: Hemidecortication


title: U2OS_GRgamma-24hr-replicate2

description:
5262624090_A
replicate 2

source_name: U2OS_24 hours_100 nM dexamethasone_GRgamma

value: 24 hours

value: GRgamma


title: U2OS_30iiB-2hr-replicate2

description:
5262624088_F
replicate 2


title: NC P14 control postnatal14 days / Young Cy5

value: postnatal14 days

value: control

value: right brain neocortex


title: U2OS_GRgamma-24hr-replicate3

description:
5262624088_G
replicate 3

value: 100 nM dexamethasone


title: Muscle_denervation_7 days_biol. rep. 6

description: miRNA expression profiling of the gastrocnemius muscle from CD1 denervated-mice (7 days, 1118-B)

source_name: Gastrocnemius muscle, denervation, 7 days

value: denervated-mice (7 days)


title: Muscle_denervation_7 days_biol. rep. 5

description: miRNA expression profiling of the gastrocnemius muscle from CD1 denervated-mice (7 days, 1118-A)

value: wild-type (control)


title: Muscle_denervation_7 days_biol. rep. 3

description: miRNA expression profiling of the gastrocnemius muscle from CD1 denervated-mice (7 days, 1116-A)

value: gastrocnemius muscle


title: NC P7 control postnatal 7 days / Young Cy5

value: postnatal 7 days


title: Muscle_denervation_7 days_biol. rep. 4

description: miRNA expression profiling of the gastrocnemius muscle from CD1 denervated-mice (7 days, 1116-B)


title: ABI 1W treatment postnatal 11 wks / Adult Cy3

value: postnatal 11 wks


title: ABI 4W treatment postnatal 15 wks / Adult Cy3

value: postnatal 15 wks


title: U2OS_GRalpha-4hr-replicate1

description:
5262624088_E
replicate 1

source_name: U2OS_4 hours_100 nM dexamethasone_GRalpha

value: 4 hours

value: GRalpha


title: U2OS_GRgamma-0hr-replicate4

description:
5262624088_A
replicate 4

source_name: U2OS_0 hours_ethanol only_GRgamma

value: 0 hours

value: ethanol only


title: NBI 4W treatment postnatal 35 days / Young Cy3

value: postnatal 35 days

value: Hemidecortication


title: U2OS_E773R-0hr-replicate3

description:
5262624075_H
replicate 3

source_name: U2OS_0 hours_ethanol only_E773R


title: U2OS_E773R-2hr-replicate3

description:
5262624088_B
replicate 3

source_name: U2OS_2 hours_100 nM dexamethasone_E773R

value: 2 hours


title: Muscle_denervation_3 days_biol. rep. 6

description: miRNA expression profiling of the gastrocnemius muscle from CD1 denervated-mice (3 days, G5-B)

source_name: Gastrocnemius muscle, denervation, 3 days

value: denervated-mice (3 days)


title: U2OS_A477T-2hr-replicate3

description:
5262624088_D
replicate 3


title: NC 10W control postnatal 10 wks / Adult Cy3

value: postnatal 10 wks

value: control


title: Muscle_denervation_3 days_biol. rep. 5

description: miRNA expression profiling of the gastrocnemius muscle from CD1 denervated-mice (3 days, G5-A)


title: U2OS_GRalpha-24hr-replicate1

description:
5262624088_C
replicate 1

source_name: U2OS_24 hours_100 nM dexamethasone_GRalpha

value: 24 hours

value: 100 nM dexamethasone


title: NC P35 control postnatal 35 days / Young Cy3

value: right brain neocortex


title: Muscle_denervation_3 days_biol. rep. 4

description: miRNA expression profiling of the gastrocnemius muscle from CD1 denervated-mice (3 days, G4bis-A)

value: wild-type (control)

value: gastrocnemius muscle


title: U2OS_30iiB-24hr-replicate4

description:
5262624075_G
replicate 4

source_name: U2OS_24 hours_100 nM dexamethasone_30iiB


title: Muscle_denervation_7 days_biol. rep. 1

description: miRNA expression profiling of the gastrocnemius muscle from CD1 denervated-mice (7 days, 1110-A)

value: denervated-mice (7 days)


title: NBI 1W treatment postnatal 14 days / Young Cy3

value: postnatal 14 days


title: Muscle_denervation_7 days_biol. rep. 2

description: miRNA expression profiling of the gastrocnemius muscle from CD1 denervated-mice (7 days, 1110-B)


title: Muscle_denervation_3 days_biol. rep. 3

description: miRNA expression profiling of the gastrocnemius muscle from CD1 denervated-mice (3 days, G4-A)


title: Muscle_denervation_3 days_biol. rep. 2

description: miRNA expression profiling of the gastrocnemius muscle from CD1 denervated-mice (3 days, 1101-B)


title: U2OS_E773R-4hr-replicate3

description:
5262624075_E
replicate 3

source_name: U2OS_4 hours_100 nM dexamethasone_E773R

value: 4 hours


title: NC P7 control postnatal 7 days / Young Cy3

value: postnatal 7 days


title: NC P14 control postnatal 14 days / Young Cy3


title: U2OS_GRgamma-0hr-replicate1

description:
5262624075_F
replicate 1

value: 0 hours

value: GRgamma


title: U2OS_A477T-24hr-replicate2

description:
5262624075_C
replicate 2

source_name: U2OS_24 hours_100 nM dexamethasone_A477T


title: U2OS_30iiB-4hr-replicate4

description:
5262624075_A
replicate 4


title: U2OS_GRalpha-4hr-replicate4

description:
5262624075_D
replicate 4

value: GRalpha


title: U2OS_GRalpha-0hr-replicate3

description:
5262624075_B
replicate 3

source_name: U2OS_0 hours_ethanol only_GRalpha

value: ethanol only


title: Hfq3-cy3_WT3-cy5

description: Biological replicate 3 of 4.

data_processing: R limma package - Function used - Background correction : backgroundCorrect normexp ; Normalization : normalizeWithinArrays loess - Correlation of spot duplicat : duplicateCorrelation - Adjust to linear method : lmFit - Statistical analysis : eBayes, decideTests global BH.

source_name: Hfq antisense grown 7.5h Tyt

growth_protocol: C. difficile strain C630E and Hfq antisense strains were grown in Tyt.

tag: strain/background

value: C630E Mullany Hfq antisense

value: Hfq antisense

source_name: 630E strain grown 7.5h in Tyt (reference)

value: C630E Mullany

value: wild-type


title: Hfq4-cy5_WT4-cy3

description: Biological replicate 4 of 4.


title: Hfq1-cy3_WT1-cy5

description: Biological replicate 1 of 4.


title: Muscle_denervation_3 days_biol. rep. 1

description: miRNA expression profiling of the gastrocnemius muscle from CD1 denervated-mice (3 days, 1101-A)

value: denervated-mice (3 days)


title: U2OS_30iiB-0hr-replicate1

description:
5262624074_F
replicate 1

source_name: U2OS_0 hours_ethanol only_30iiB


title: U2OS_E773R-24hr-replicate3

description:
5262624074_G
replicate 3

source_name: U2OS_24 hours_100 nM dexamethasone_E773R

value: 24 hours

value: 100 nM dexamethasone


title: U2OS_30iiB-4hr-replicate1

description:
5262624074_D
replicate 1

source_name: U2OS_4 hours_100 nM dexamethasone_30iiB


title: U2OS_GRgamma-2hr-replicate1

description:
5262624074_H
replicate 1

source_name: U2OS_2 hours_100 nM dexamethasone_GRgamma

value: 2 hours


title: 5719 TIVE

city: Gainesville

first: Lauren

last: McIntyre

state: FL

address: 2033 Mowry Rd

institute: University of Florida

hyb_protocol: Chips were hybridized according to manufacturer instructions (Affymetrix).

scan_protocol: not provided

data_processing: Raw data were summarized with Affymetrix Expression Console software (v1.1) using MAS 5.0 algorithm. Probe sets were flagged as 'absent' if they were absent according to Affymetrix probe detection alogorithm in more than half of the samples. F tests for each of the miRNA conditions were conducted. An FDR of 0.05 was used to determine statistical significance for the probe set.

source_name: Telomerase-immortalized human umbilical-vein endothelial cells (TIVE)

label_protocol: RNA was synthesized and labeled using GeneChip® 3' IVT Express Kit.

growth_protocol: BJAB cells were grown in culture suspension in complete RPMI medium with 10% fetal bovine serum (FBS). TIVE cells were grown in Medium 199 supplemented with 20% FBS and 60 µg/mL Endothelial Cell Growth Facter (ECGF).

extract_protocol: RNA was extracted using the RNA-Bee reagent according to manufacturer's instructions.

treatment_protocol: TIVE and BJAB cells were retrovirally transduced at two levels of Multiplicity of Infection (MOI): 1 and 10. 72hr post transduction, positive cells were sorted according to their GFP signal. Cells were aliquoted in 1 million cells per tube and frozen down in liquid nitrogen. Empty vectors without miRNA expression cassettes were used for mock transduction to control for the impact of retrovial integration on the cellular transcriptomes. Cells were later removed from the liquid nitrogen and grown for the same number of passages.

value: TIVE

tag: miRNA condition


title: U2OS_E773R-0hr-replicate1

description:
5262624074_E
replicate 1


title: 5717 TIVE

value: Telomerase-immortalized human umbilical-vein endothelial cells


title: U2OS_A477T-2hr-replicate4

description:
5262624074_C
replicate 4

source_name: U2OS_2 hours_100 nM dexamethasone_A477T


title: Primary HCC sample non-tumor site vs Human Blood 2_2

city: Kawasaki

first: Yoshiyuki

last: Watanabe

state: Kanagawa

address: 2-16-1 Sugao Miyamaeku

department: Department of Internal Medicine, Division of Gastroenterology and Hepatology

institute: St.Marianna University School of Medicine

description: liver vs human blood

hyb_protocol: Scanned on an Agilent G2565AA scanner.

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version A.9.5.1.1).

data_processing: Agilent Feature Extraction Software (v 9.5.1.1) was used for background subtraction and LOWESS normalization.

source_name: hepatoma cell

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

growth_protocol: cells were collected from primary liver cancer tissue

extract_protocol: DNA extracted using phenol following manufacturer's instructions

value: liver

tag: sample

value: primary sample

tag: tumor

value: non-tumor

source_name: human blood cell

value: blood


title: Human Blood vs Human Blood

description: human blood vs human blood

treatment_protocol: DNA extracted using phenol following manufacturer's instructions

tag: tissue


title: 5716 TIVE

value: mock


title: Primary HCC sample non-tumor site vs Human Blood 2_1

description: liver vs human blood


title: U2OS_GRalpha-2hr-replicate3

description:
5262624074_B
replicate 3

source_name: U2OS_2 hours_100 nM dexamethasone_GRalpha

tag: treatment

value: GRalpha


title: 5721 TIVE


title: Hfq2-cy5_WT2-cy3

description: Biological replicate 2 of 4.


title: 5718 TIVE


title: U2OS_GRgamma-4hr-replicate1

description:
5262624074_A
replicate 1

source_name: U2OS_4 hours_100 nM dexamethasone_GRgamma

value: 4 hours

value: GRgamma


title: 5720 TIVE


title: PLC/PRF/5 call line vs Human Blood 2_3

description: liver vs human blood

value: cell line

value: tumor


title: Primary HCC sample tumor site vs Human Blood 1_4

description: liver vs human blood


title: 5079 BJAB

source_name: Burkitt's lymphoma human B cell line (BJAB)

value: BJAB

value: Burkitt's lymphoma human B cell


title: 5715 TIVE


title: U2OS_GRgamma-4hr-replicate4

description:
5262237079_G
replicate 4


title: 5078 BJAB


title: U2OS_A477T-4hr-replicate3

description:
5262237079_F
replicate 3

source_name: U2OS_4 hours_100 nM dexamethasone_A477T


title: 5714 TIVE


title: Primary HCC sample non-tumor site vs Human Blood 1_3

description: liver vs human blood


title: U2OS_GRalpha-2hr-replicate2

description:
5262237079_H
replicate 2


title: Primary HCC sample non-tumor site vs Human Blood 1_1

description: liver vs human blood


title: U2OS_30iiB-24hr-replicate2

description:
5262237079_E
replicate 2

source_name: U2OS_24 hours_100 nM dexamethasone_30iiB

value: 24 hours


title: U2OS_GRgamma-24hr-replicate4

description:
5262237079_D
replicate 4

source_name: U2OS_24 hours_100 nM dexamethasone_GRgamma

value: 100 nM dexamethasone


title: Primary HCC sample tumor site vs Human Blood 1_2

description: liver vs human blood


title: U2OS_30iiB-0hr-replicate3

description:
5262237079_C
replicate 3

value: 0 hours

value: ethanol only


title: U2OS_A477T-0hr-replicate2

description:
5262237079_B
replicate 2

source_name: U2OS_0 hours_ethanol only_A477T


title: 5075 BJAB


title: R3-3

city: Saarbrücken

first: Martin

last: Simon

address: Campus A2 4

department: Centre for Human and Molecular Biology

institute: Saarland University

description: third of three biological replicates

hyb_protocol: using NimbleGen Hybridization System

scan_protocol: NimbleScan software

data_processing: RMA normalization

organism: Paramecium tetraurelia

source_name: Paramecium tetraurelia stock 51, fed with dsRNA against RDR3

label_protocol: cDNA was labeled with Cy3 using Klenow fragement

growth_protocol: Paramecia were grown with dsRNA producing bacteria as desribed by Galvani & Sperling 2002.

extract_protocol: total RNA was extracted by Trizol, DNAse digested, and reverse transcribed

treatment_protocol: Cells were fed either with dsRNA complementary to ICL7a gene or RDR3.

tag: strain

value: stock 51

value: fed with dsRNA against RDR3

tag: phenotype

value: Co-expression of subtelomeric surface antigens


title: U2OS_E773R-2hr-replicate2

description:
5262237079_A
replicate 2

source_name: U2OS_2 hours_100 nM dexamethasone_E773R

value: 2 hours


title: 5077 BJAB


title: 5076 BJAB


title: 5074 BJAB


title: U2OS_E773R-2hr-replicate4

description:
5262237068_H
replicate 4


title: 5073 BJAB


title: U2OS_E773R-4hr-replicate4

description:
5262237068_G
replicate 4

source_name: U2OS_4 hours_100 nM dexamethasone_E773R


title: 5072 BJAB


title: ICL-2

description: second of three biological replicates

source_name: Paramecium tetraurelia stock 51, fed with dsRNA against ICL7a

value: fed with dsRNA against ICL7a

value: Serotype pure 51A


title: R3-1

description: first of three biological replicates


title: ICL-1

description: first of three biological replicates


title: 5070 BJAB


title: U2OS_GRalpha-24hr-replicate3

description:
5262237068_F
replicate 3

source_name: U2OS_24 hours_100 nM dexamethasone_GRalpha

value: GRalpha


title: 5071 BJAB


title: Day 60 (Replicate 3)

type: SRA

city: Basel

first: Jitao David

last: Zhang

address: Grenzacherstrasse 124

department: Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel

country: Switzerland

institute: F. Hoffmann-La Roche

description:
library stratagy: Ampli-seq
iPSC induced into cardiomyocytes at day 60

library_source: transcriptomic

data_processing:
Base-calling, filtering, and alignment is handled automatically by IonTorrent Server Suite (version 4.0.2)
Amplicon coverage is reported by IonTorrent Server Suite (version 4.0.2) as a tab-delimited file, which was converted into GCT format by in-house scripts.
Genome_build: hg19
Supplementary_files_format_and_content: txt

source_name: induced pluripotent stem cells (differentiation into cardiomyocytes)

growth_protocol: Briefly, hiPSCs were generated from a human fibroblast cell line via reprogramming through retroviral expression of SOX2, OCT4, NANOG, and LIN28. This hiPSC clone was propagated and maintained in feeder-free culture using mTeSR1® (Stem Cell Technologies, Vancouver, British Columbia, Canada) on a Matrigel™ substrate (Beckton Dickinson, Franklin Lakes, NJ). These hiPSCs were formed into aggregates and cultured in differentiation medium containing 100 ng/mL zebrafish basic fibroblast growth factor and 10% fetal bovine serum prior to the differentiation of cardiac myocytes. On day 14 of differentiation, the cultures were subjected to blasticidin selection (25 μg/mL) to purify the cardiomyocyte population. Following blasticidin selection, cultures were maintained in Dulbecco's modified Eagle's medium containing 10% fetal bovine serum for the duration of the cultures.  The differentiation protocol and sample collection were performed in 3 independent replicates as indicated by Run 1, 2, and 3.

extract_protocol: 10 ng of total RNA from each time point and biological replicate was reverse transcribed to cDNA and amplified by limited PCR according to the protocol supplied with the Ion AmpliSeq™ RNA Library Kit (Life Technologies, Carlsbad, USA, Catalog number 4482335). After primer digestion, adapters and barcodes were ligated to the amplicons followed by magnetic bead purification. The purified library was amplified, purified and stored at -20°C. Amplicon size and DNA concentration was measured using an Agilent High Sensitivity DNA Kit (Agilent Technologies, Waldbronn, Germany) according to the manufacturer's guide.

tag: replicate


title: U2OS_GRgamma-4hr-replicate2

description:
5262237068_E
replicate 2

value: 4 hours


title: U2OS_GRalpha-0hr-replicate2

description:
5262237068_D
replicate 2

source_name: U2OS_0 hours_ethanol only_GRalpha


title: U2OS_A477T-4hr-replicate4

description:
5262237068_A
replicate 4


title: U2OS_A477T-2hr-replicate2

description:
5262237068_C
replicate 2

source_name: U2OS_2 hours_100 nM dexamethasone_A477T


title: 5069 BJAB

value: mock


title: GntR1-FLAG_2nd

city: Shinjuku-ku

first: Norihiko

last: Takemoto

state: Tokyo

institute: Research Institute of National Center for Global Health and Medicine

hyb_protocol: Hybridization was performed using Agilent Oligo aCGH Hybridization kit according to the manufacture’s manual (Agilent). Equal amount (2.5 μg) of each labeled DNA were mixed and hybridized to microarrays in an Agilent Technologies Microarray chamber at 65˚C for 24 h in a rotating Agilent hybridization oven at 20 rpm. After hybridization, microarrays were washed 5 min at room temperature with Oligo aCGH/ChIP-on-chip Wash Buffer 1 (Agilent), 5 min with 31˚C Oligo aCGH/ChIP-on-chip Wash buffer 2 (Agilent Technologies), 10 sec with acetonitrile, and 30 sec with Stabilization and Drying Solution (Agilent) at room temperature.

scan_protocol: Slides were scanned immediately after washing and placement within an Agilent Ozone Barrier Slide cover (Agilent) the Agilent DNA Microarray Scanner (G2505C) using two color scan setting for 4x44k array Scan resolution 5 microns. Scanning was done in both channels and PMT is set to 100% for both Cy3\cy5 channels.

data_processing: Feature extraction software provided by Agilent (version 10.5.1.1, Agilent Technologies, Palo Alto, CA, USA) was used to quantify the intensity of the fluorescent images and to normalize the results by subtracting local background fluorescence, according to the manufacturer’s instructions.

organism: Corynebacterium glutamicum R

source_name: GntR1-FLAG ChIP DNA from the wild-type strain of Corynebacterium glutamicum

label_protocol: DNA samples were blunted with T4 DNA polymerase, ligated to linkers, and amplified by PCR. Amplified DNA from reference DNA and immunoprecipitated DNA were differentially labeled with Cy3 and Cy5, respectively, by using CGH labeling kit (Invitrogen) according to the manufacture’s instruction.

growth_protocol: C. glutamicum R wild-type and gntR1 deleted cells were grown aerobically in nutrient-rich A medium supplemented with 2% (w/v) glucose.

extract_protocol: Exponentially growing C. glutamicum cultures (35 ml) in A medium with 2% glucose were treated with formaldehyde (at a final concentration of 1%) and incubated for 15 min at room temperature. The cross-linking was quenched by addition of glycine (at a final concentration of 125 mM) and incubated for 5 min at room temperature. Cells were then collected by centrifugation, washed twice with Tris-buffered saline (20 mM Tris-HCl [pH 7.5], 150 mM NaCl), and stored at -80 oC. Pellets were resuspended in 0.5 ml FLAG buffer (20mM Tris-HCl [pH 8.0], 200mM KCl, 5mM MgCl2, 10 % Glycerol, 0.1 % SDS) containing protease inhibitor cocktail (Roche Antiprotease mini). Cell suspension was transfered to 15 mL tube containing ~300 mg of 0.1 mm Zirconia/Silika beads (BIO SPEC). Cell disruption and genomic DNA shearing were conducted using Bioruptor UCD-250 (Cosmo Bio) with conditions as below: 10 cycles of 5 sec on-5 sec at high power at 4 ℃. Average size of sheared DNA was 200 to 500 bp. Cell lysate was collected and centrifuged (20000 x g for 30 min at 4 oC) to prepare cell free extract. Amount of total protein was measured by Bio-Rad Protein Assay (Bio-Rad) using BSA as standards. Cell free extract was diluted with FLAG buffer containing protease inhibitor cocktail to be 0.5 mg/ml total protein. A 150 ul fraction of the cell free extract was saved for later analysis (reference DNA). The remainder was subjected to immunoprecipitation with 80 ul of anti-FLAG M2 agarose (Sigma). The mixture was incubated 90 min on rotating platform at 4 oC. The beads were washed five times with FLAG buffer. Immunoprecipitated complex were eluted from beads by treatment with 240 ul of IP buffer with 100 ng/ul of 3X FLAG-peptide (Sigma). Cross-links of immunoprecipitated samples and of total DNA samples were reversed by incubation overnight at 65 oC. Samples were then treated with RNaseA and Protease K for 2 h at 55 oC. DNA was extracted with phenol-chloroform and purified with a QIAquick PCR purification minElute kit (Qiagen).

tag: genotype

tag: antibody

value: anti-FLAG M2 agarose (Sigma)

source_name: Reference genomic DNA, no IP treatment control


title: GntR1-FLAG_1st


title: wt_3rd

hyb_protocol: Hybridization was performed using Gene Expression Hybridization Kit according to the manufacture’s manual (Agilent). The labeled cDNA was hybridized to microarrays in an Agilent Technologies Microarray chamber at 65˚C for 17 h 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: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) at a resolution of 5 µm using single color scan setting for 4x44k array slides. PMT is set to 100% for Cy3 channels.

data_processing: The scanned images were analyzed quantified with Feature Extraction Software 10.5.5.1 (Agilent) using default parameters (protocol GE1_105_Dec08). Feature extracted data were analyzed using GeneSpring GX v 12.0 software from Agilent. Normalization of the data was done in GeneSpring GX using the recommended Percentile shift normalization (50th percentile).

source_name: wild-type strain

label_protocol: The cDNAs were synthesized from RNA by using reverse transcriptase from 10 μg of total RNAs and labeled with cyanine 3 (Cy3) using the SuperScript Indirect cDNA Labeling system (Life Technologies).

extract_protocol: Total RNA was isolated from exponentially-growing cells (OD610 of 2.0) using the Nucleo Spin RNA (MACHEREY-NAGEL).

tag: background strain

value: R

value: wild type


title: 5067 BJAB

tag: cell line

value: BJAB

value: Burkitt's lymphoma human B cell


title: 5068 BJAB


title: 5066 BJAB


title: U2OS_E773R-24hr-replicate1

description:
5262237036_H
replicate 1

source_name: U2OS_24 hours_100 nM dexamethasone_E773R

tag: time

value: 24 hours

value: 100 nM dexamethasone

tag: expressed allele


title: 5065 BJAB

source_name: Burkitt's lymphoma human B cell line (BJAB)


title: U2OS_GRgamma-0hr-replicate3

description:
5262237068_B
replicate 3

source_name: U2OS_0 hours_ethanol only_GRgamma

value: 0 hours

value: ethanol only

value: GRgamma


title: gntR1 deletion mutant_3rd

source_name: gntR1 deletion mutant strain


title: gntR1 deletion mutant_2nd


title: 5064 BJAB


title: U2OS_GRalpha-4hr-replicate3

description:
5262237036_G
replicate 3

source_name: U2OS_4 hours_100 nM dexamethasone_GRalpha


title: Day 60 (Replicate 1)


title: Day 60 (Replicate 2)


title: 5063 BJAB


title: Day 20 (Replicate 3)

description:
library stratagy: Ampli-seq
iPSC induced into cardiomyocytes at day 20


title: gntR1 deletion mutant_1st


title: wt_1st


title: 5062 BJAB


title: wt_2nd


title: Day 20 (Replicate 2)


title: 5061 BJAB


title: Day 20 (Replicate 1)


title: U2OS_GRgamma-24hr-replicate1

description:
5262237036_E
replicate 1

source_name: U2OS_24 hours_100 nM dexamethasone_GRgamma


title: Day 10 (Replicate 3)

description:
library stratagy: Ampli-seq
iPSC induced into cardiomyocytes at day 10


title: R3-2

description: second of three biological replicates

source_name: Paramecium tetraurelia stock 51, fed with dsRNA against RDR3

value: stock 51

value: fed with dsRNA against RDR3

value: Co-expression of subtelomeric surface antigens


title: Day 10 (Replicate 2)


title: U2OS_30iiB-4hr-replicate3

description:
5262237036_F
replicate 3

source_name: U2OS_4 hours_100 nM dexamethasone_30iiB


title: Day 10 (Replicate 1)


title: U2OS_A477T-0hr-replicate4

description:
5262237036_D
replicate 4

source_name: U2OS_0 hours_ethanol only_A477T


title: Day 0 (Replicate 3)

description:
library stratagy: Ampli-seq
iPSC induced into cardiomyocytes at day 0

source_name: induced pluripotent stem cells


title: U2OS_A477T-24hr-replicate3

description:
5262237036_B
replicate 3

source_name: U2OS_24 hours_100 nM dexamethasone_A477T


title: U2OS_30iiB-2hr-replicate1

description:
5262237036_C
replicate 1

source_name: U2OS_2 hours_100 nM dexamethasone_30iiB

value: 2 hours


title: 5060 BJAB


title: 5059 BJAB


title: U2OS_GRalpha-24hr-replicate2

description:
5098941045_H
replicate 2

source_name: U2OS_24 hours_100 nM dexamethasone_GRalpha

value: GRalpha


title: 5058 BJAB


title: U2OS_E773R-0hr-replicate4

description:
5262237036_A
replicate 4

source_name: U2OS_0 hours_ethanol only_E773R


title: 5056 BJAB


title: DMSO at T24, biological rep 3

city: Los Angeles

first: David

last: Dawson

address: 10833 LeConte Avenue

department: Pathology and Laboratory Medicine

institute: University of California Los Angeles

description: Gene expression data for AsPC1 cells treated with vehicle control (DMSO) for 24 hours

hyb_protocol: Affymetrix standard procol

scan_protocol: Affymetrix standard procol

data_processing: Data analysis was performed in the dChip Analysis software package(31) using invariant set normalization and signal intensities summarized using the MBEI (model-based expression index) algorithm with mismatch probe option for background subtraction.  Initial gene filtering criteria was set at >10% present call and variance across samples of 0.4<standard deviation/mean<1000.

label: Biotin

source_name: AsPC-1 treated with vehicle control (DMSO) for 24 hours

label_protocol: Affymetrix standard procol

growth_protocol: AsPC-1 cells were grown to 70% confluency in standard growth conditions (RPMI + 10% FCS) and maintained in these conditions for the period (6 or 24 hours) with either 10uM ICG-001 or vehicle (DMSO, V/V).  Separately, AsPC1 cells were also transfected with 20 nM control or CTNNB1 siRNA using lipofectamine 2000 with RNA extracted at 48 hours.

extract_protocol: Total RNA was extracted using Qiagen Rneasy mini kit per manufacturer's instructions.

treatment_protocol: See growth protocol

value: DMSO, 24h


title: Day 0 (Replicate 2)


title: Control siRNA at T48, biological rep 1

description: Gene expression data for AsPC1 cells transfected with control siRNA for 48 hours

source_name: AsPC-1 transfected with 20nM control siRNA at 48 hours

value: transfected with 20nM Ctrl siRNA, 48h


title: Control siRNA at T48, biological rep 2


title: U2OS_A477T-0hr-replicate1

description:
5098941045_F
replicate 1


title: CTNNB1 siRNA at T48, biological rep 2

description: Gene expression data for AsPC1 cells transfected with CTNNB1 siRNA for 48 hours

source_name: AsPC-1 transfected with 20nM CTNNB1 siRNA at 48 hours

value: transfected with 20nM CTNNB1 siRNA, 48h


title: CTNNB1 siRNA at T48, biological rep 1


title: U2OS_GRgamma-0hr-replicate2

description:
5098941045_G
replicate 2


title: U2OS_E773R-4hr-replicate2

description:
5098941045_E
replicate 2

source_name: U2OS_4 hours_100 nM dexamethasone_E773R

value: 4 hours


title: U2OS_GRgamma-4hr-replicate3

description:
5098941045_D
replicate 3

source_name: U2OS_4 hours_100 nM dexamethasone_GRgamma


title: DMSO at T24, biological rep 1


title: DMSO at T24, biological rep 2


title: DMSO at T6, biological rep 3

description: Gene expression data for AsPC1 cells treated with vehicle control (DMSO) for 6 hours

source_name: AsPC-1 treated with vehicle control (DMSO) for 6 hours

value: DMSO, 6h


title: ICL-3

description: third of three biological replicates

source_name: Paramecium tetraurelia stock 51, fed with dsRNA against ICL7a

value: fed with dsRNA against ICL7a

value: Serotype pure 51A


title: DMSO at T6, biological rep 2


title: U2OS_30iiB-2hr-replicate3

description:
5098941045_C
replicate 3


title: ICG-001 at T24, biological rep 2

description: Gene expression data for AsPC1 cells treated with ICG-001 for 24 hours

source_name: AsPC-1 treated with 10uM ICG-001 for 24 hours


title: DMSO at T6, biological rep 1


title: U2OS_E773R-4hr-replicate1

description:
5098941038_H
replicate 1


title: U2OS_GRalpha-0hr-replicate4

description:
5098941045_A
replicate 4

source_name: U2OS_0 hours_ethanol only_GRalpha


title: ICG-001 at T24, biological rep 3


title: U2OS_A477T-4hr-replicate1

description:
5098941045_B
replicate 1

source_name: U2OS_4 hours_100 nM dexamethasone_A477T


title: U2OS_GRalpha-0hr-replicate1

description:
5098941038_G
replicate 1


title: U2OS_30iiB-24hr-replicate3

description:
5098941038_E
replicate 3

source_name: U2OS_24 hours_100 nM dexamethasone_30iiB

value: 24 hours


title: U2OS_GRgamma-2hr-replicate4

description:
5098941038_F
replicate 4

source_name: U2OS_2 hours_100 nM dexamethasone_GRgamma

value: 100 nM dexamethasone


title: ICG-001 at T6, biological rep 2

description: Gene expression data for AsPC1 cells treated with ICG-001 for 6 hours

source_name: AsPC-1 treated with 10uM ICG-001 for 6 hours


title: ICG-001 at T24, biological rep 1


title: ICG-001 at T6, biological rep 3


title: U2OS_30iiB-0hr-replicate4

description:
5098941038_D
replicate 4

source_name: U2OS_0 hours_ethanol only_30iiB

value: 0 hours


title: U2OS_E773R-0hr-replicate2

description:
5098941038_C
replicate 2

value: ethanol only


title: U2OS_A477T-24hr-replicate1

description:
5098941038_A
replicate 1

source_name: U2OS_24 hours_100 nM dexamethasone_A477T


title: Oral immortalized dysplasia cell line_CGH_1

city: Vancouver

first: Christopher

middle: Trevor Daniel

last: Dickman

state: BC

address: 675 West 10th Ave

country: Canada

institute: BC Cancer Research Center

hyb_protocol: Mix the two reactions (reference and sample) and add 100ul Cot-1 DNA (1ug/ul), and purified using a microcon YM-30 column. Resuspend the probe in 45 uL hybridization solution (36 uL DIGeasy+ 4.5 uL (20mg/mL) sheared Herring Sperm DNA + 4.5 uL (10mg/mL) yeast tRNA). Denature the samples at 85°C for 5min, and incubate at 45°C for 1 hour to allow Cot-1 to anneal to DNA probe. Add 45uL of the probe solution onto the array slide. Gently lower coverslip (22x60mm, Fisher Scientific) onto slide over probe solution. Place the slide into a pre-warmed (45°C) hybridization cassette (Telechem) and add 10uL of H20 in the lower groove (to control humidity). Incubate for 36 - 40hrs at 45°C. Wash the slide with 0.1X SSC + 0.1% SDS (pH 7.0, pre-warmed to 45°C) for 5 minutes in the dark with agitation, and with 0.1X SCC 5 times. Dry the slides by centrifuging at 500rcf for 1 minute.

scan_protocol: Scaning was completed using the Axon GenePix 4000B scanner. Array images are analyzed with GenePix Pro 6.1.

data_processing: A three-step normalization procedure, including LOWESS fitting, spatial, and median normalization was used.

source_name: Oral immortalized dysplasia cell line

label_protocol: Random-primer labelling reaction 1. For each slide combine: (1 reaction tube for reference & 1 reaction tube for sample) a) DNA (200ng) b) 5uL of 5X (PB) random primers buffer (Final concentration: 5X Promega Klenow buffer and 7ug/ul random octomers) c) Dilute to 16.5uL total volume with ddH2O 2. Boil for 10 min at 100°C in PCR machine. Transfer immediately to ice for 2 min 3. Add 4ul of 10X dNTP mix (2mM each dATP, dGTP, dTTP, 1.2mM dCTP) - Vortex very well 4. Add CyeDyes: Vortex and spin prior to adding • Add 2uL (2nmoles) of Cy3 labelled dCTP to Reference DNA (Novagen Male Genomic) • Add 2uL (2nmoles) of Cy5 labelled dCTP to sample DNA 5. Add 2.5uL of Klenow (9U/uL) and mix by pipetting 6. Incubate 37oC overnight (~18hours).

growth_protocol: Cells were grown in KSFM media suplemented with EGF and bovine pituitary extract

extract_protocol: Total DNA was extracted using a phenol/chloroform extraction

value: Oral keratinocyte

source_name: Male Somatic Tissue Genomic DNA

tag: tissue type

value: Blood


title: U2OS_30iiB-24hr-replicate1

description:
4858944020_H
replicate 1


title: U2OS_E773R-24hr-replicate4

description:
4858944020_F
replicate 4

source_name: U2OS_24 hours_100 nM dexamethasone_E773R


title: U2OS_GRalpha-24hr-replicate4

description:
5098941038_B
replicate 4

source_name: U2OS_24 hours_100 nM dexamethasone_GRalpha


title: U2OS_GRgamma-2hr-replicate3

description:
4858944020_G
replicate 3

value: GRgamma


title: U2OS_GRalpha-2hr-replicate1

description:
4858944020_C
replicate 1

source_name: U2OS_2 hours_100 nM dexamethasone_GRalpha


title: U2OS_A477T-24hr-replicate4

description:
4858944020_D
replicate 4


title: ICG-001 at T6, biological rep 1


title: Oral immortalized normal cell line_CGH_6

source_name: Oral immortalized normal cell line

tag: cell type


title: Oral dysplasia cell line_CGH_1

source_name: Oral dysplasia cell line

growth_protocol: Cells were grown in DMEM media suplemented with 10% FBS and 5ug/ml hydrocortisone


title: Oral immortalized normal cell line_CGH_3


title: Oral immortalized normal cell line_CGH_1


title: Oral immortalized normal cell line_CGH_5


title: U2OS_30iiB-0hr-replicate2

description:
4858944020_A
replicate 2


title: Oral immortalized normal cell line_CGH_2


title: U2OS_A477T-0hr-replicate3

description:
4858944020_E
replicate 3

source_name: U2OS_0 hours_ethanol only_A477T


title: U2OS_GRalpha-4hr-replicate2

description:
4858944020_B
replicate 2

source_name: U2OS_4 hours_100 nM dexamethasone_GRalpha


title: 4-OHT + ICI-treated MCF-7:PF Replicate 2

status: Public on Jul 14 2014

city: Dunedin

first: Heather

middle: E.

last: Cunliffe

state: Otago

address: P O Box 913

department: Department of Pathology

country: New Zealand

institute: University of Otago, Dunedin School of Medicine

hyb_protocol: 1237.5ng of each Cy3-labeled probe was co-hybridized with 825 ng of Cy5-labeled reference probe to Agilent 4x44K (V1) expression microarrays following Agilent protocols.

scan_protocol: Slides were washed with Agilent's Gene Expression Wash Buffers (Part Number 5188-5327) following Agilent's protocol and scanned at 5 μm using an Agilent Microarray Scanner (model G2505B) in an ozone-controlled environment. Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1). Build hg18.

data_processing: Array control features and control targets were removed. Data transformed from Log10 to Log2.

label_protocol: 250 ng of total RNA from all treatment samples was used to generate Cy3-labeled cRNA probes using Agilent's Low Input Quick Amp Labeling Kit (Agilent Technologies; Palo Alto, CA, Catalog# 5190-2306) following manufacturer's instructions. In parallel, 500 ng of total RNA form vehicle-treated MCF-7:PF cells (replicate-matched) was used to generate a Cy5-labeled cRNA probe to serve as the common reference for each of the 5 treatment combinations (replicate-matched).  Cy dye incorporation efficiency was calculated with a Nanodrop ND-1000 Spectrophotometer (Nanodrop; Wilmington, DE) following Agilent-recommended protocols. Details for Cy3 and Cy5 incorporation efficiency (pmoL cy dye/μg cRNA) for all probes are provided with this submission.

growth_protocol: MCF-7:5:PF cells were maintained in phenol-red free RPMI-1640 medium supplemented with 10% dextran-coated charcoal-stripped fetal bovine serum, 1nM 17beta estradiol (E2) and 5μM PP2 (c-Src inhibitor). Medium was changed every 2-3 days, adding fresh compounds.

extract_protocol: Each replicate series of control and treated samples were harvested in Trizol (Invitrogen; Carlsbad, CA).  Total RNA was purified from 200 μl TRIzol lysate using the RNeasy micro kit (Qiagen; Valencia, CA) following manufacturer's instructions including the optional DNAse treatment step. RNA concentration and purity was measured using a Nanodrop ND-1000 Spectrophotometer (Nanodrop; Wilmington, DE). RNA integrity was evaluated using a 2100 Bioanalyzer (Agilent Technologies; Palo Alto, CA). All samples had an RNA integrity # (RIN#) between 9.4 and 10.0

treatment_protocol: For each biological replicate, MCF-7:PF cells were parsed into six 60 mm culture dishes and allowed to adhere overnight. Dishes were treated with vehicle control (0.1% EtOH), E2 (1nM), 4-OHT(1μM), ICI 182,780 (1μM), E2 plus ICI 182,780, and 4-OHT plus ICI 182,780 for 7 days.

value: 1uM 4-hydroxytamoxifen + 1uM ICI 182,780

tag: treatment duration

value: 7 days

tag: series replicate

tag: biomaterial provider

value: Dr. Ping Fan, Laboratory of Dr. V. Craig Jordan

tag: cy3 probe labeling efficiency (pmol cy3/μg crna)

tag: ng cy3 probe hybridized

source_name: Vehicle-treated MCF-7:PF Replicate 2

value: Vehicle

tag: cy5 probe labeling efficiency (pmol cy3/μg crna)

tag: ng cy5 probe hybridized


title: 4-OHT + ICI-treated MCF-7:PF Replicate 1

tag: treatment

source_name: Vehicle-treated MCF-7:PF Replicate 1


title: 4-OHT + ICI-treated MCF-7:PF Replicate 3

source_name: Vehicle-treated MCF-7:PF Replicate 3


title: E2 + ICI-treated MCF-7:PF Replicate 3

source_name: E2 + ICI-treated MCF-7:PF Replicate 3

value: 1nM 17beta-estradiol + 1uM ICI 182,780


title: ICI-treated MCF-7:PF Replicate 2

source_name: ICI-treated MCF-7:PF Replicate 2


title: E2 + ICI-treated MCF-7:PF Replicate 1

source_name: E2 + ICI-treated MCF-7:PF Replicate 1


title: E2 + ICI-treated MCF-7:PF Replicate 2

source_name: E2 + ICI-treated MCF-7:PF Replicate 2


title: ICI-treated MCF-7:PF Replicate 3

source_name: ICI-treated MCF-7:PF Replicate 3


title: ICI-treated MCF-7:PF Replicate 1

source_name: ICI-treated MCF-7:PF Replicate 1


title: 4-OHT-treated MCF-7:PF Replicate 2

source_name: 4-OHT-treated MCF-7:PF Replicate 2

value: 1uM 4-hydroxytamoxifen


title: Oral immortalized normal cell line_CGH_4

source_name: Male Somatic Tissue Genomic DNA


title: E2-treated MCF-7:PF Replicate 1

source_name: E2-treated MCF-7:PF Replicate 1

value: 1nM 17beta-estradiol


title: 4-OHT-treated MCF-7:PF Replicate 1

source_name: 4-OHT-treated MCF-7:PF Replicate 1


title: 4-OHT-treated MCF-7:PF Replicate 3

source_name: 4-OHT-treated MCF-7:PF Replicate 3


title: Day 0 (Replicate 1)

source_name: induced pluripotent stem cells

tag: replicate


title: Superficial temporal artery, sample 10

city: Mishima

first: Hirofumi

last: Nakaoka

state: Shizuoka

address: Yata 1111

department: Department of Human Genetics

institute: National Institute of Genetics

description: Gene expression in superficial temporal artery

hyb_protocol: 1.65 ug of cyanine 3-CTP (Cy3)-labeled cRNA sample was used for 17-hour hybridization at 65 C.

scan_protocol: The Agilent DNA microarray scanner (model G2505A) was used. Signal intensity was quantified from the scanned image by using Feature Extraction Software version 9.1 (Agilent technologies)

data_processing: The signal intensities were corrected for the background intensities with the normexp method, followed by the quantile normalization across arrays with the limma software.

source_name: Superficial temporal artery, sample 10

label_protocol: 500 ng of total RNA was amplified and labeled with the Agilent Quick Amp Labeling Kit according to the manufacturers instructions.

growth_protocol: In case of ruptured intracranial aneurysms, all resections were done within 24 hours after initial subarachnoid hemorrhage.

extract_protocol: Total RNA was extracted with the TRIzol reagent (Invitrogen, Carlsbad, CA, USA).

treatment_protocol: All the specimens were snap-frozen in liquid nitrogen, and stored at -80 °C.

tag: tissue

value: Superficial temporal artery

tag: status

tag: Sex

value: Female

tag: age


title: Superficial temporal artery, sample 6

source_name: Superficial temporal artery, sample 6


title: Superficial temporal artery, sample 8

source_name: Superficial temporal artery, sample 8


title: E2-treated MCF-7:PF Replicate 2

source_name: E2-treated MCF-7:PF Replicate 2

tag: cell line

source_name: Vehicle-treated MCF-7:PF Replicate 2


title: EC-2_rep3

city: Hachioji

first: Atsushi

last: Kouzuma

address: 1432-1 Horinouchi

institute: Tokyo University of Pharmacy and Life Sciences

description: Gene expression in EC-2

hyb_protocol: For each array, 20 μl of the purified Cy3-labeled cDNA (20 ng/μl) was mixed with 5 μL of 10× Blocking Agent and 25 μl of 2× GEx Hybridization Buffer HI-RPM. The resultant mixture (40 μl) was hybridized to an array at 65°C for 17h. After hybridization, each slide was washed in Gene Expression Wash Buffer I (Agilent Technologies) at room temperature for 1 min and in Gene Expression Wash Buffer II (Agilent Technologies) at 37°C for 1 min.

scan_protocol: After the slide was air dried, it was scanned using an Agilent DNA Microarray Scanner at a 5 μm resolution.

data_processing: Data acquisition was performed using the Feature Extraction Software version 8.1 (Agilent Technologies). Gene expression data (n = 3 biological replicates) were normalized and statistically analyzed using GeneSpring GX version 11.5 (Agilent Technologies).

organism: Shewanella oneidensis

source_name: EC-2 replicate 3

label_protocol: Cyanine 3 (Cy3)-labeled cDNA was synthesized from 5 μg of total RNA using the FairPlay III Microarray Labeling KitStratagene and CyDye Cy3 mono-Reactive Dye (GE Healthcare). The labeled cDNA was quantified using NanoDrop ND-1000 Spectrophotometer (Thermo Scientific).

growth_protocol: Shewanella cells were grown anaerobically in LMM (containing 15 mM lactate) supplemented with 20 mM fumarate as the electron acceptor, and cells were harvested at early stationary growth phase (optical density at 600 nm of 0.16-0.18).

extract_protocol: Total RNA was extracted using a Trizol reagent (Invitrogen, Carlsbad, CA) following the manufacturer’s instructions and subsequently purified using an RNeasy Mini Kit and an RNase-Free DNase Set (Qiagen, Valencia, CA). The quality of total RNA was evaluated using an Agilent 2100 Bioanalyzer with RNA 6000 Pico reagents and RNA Pico Chips (Agilent Technologies) according to the manufacture’s instruction.

treatment_protocol: Cells were harvested by centrifugation at 7,000 g for 10 min and stored at -80°C

tag: strain


title: Superficial temporal artery, sample 7

source_name: Superficial temporal artery, sample 7

value: Male


title: Superficial temporal artery, sample 2

source_name: Superficial temporal artery, sample 2


title: Superficial temporal artery, sample 9

source_name: Superficial temporal artery, sample 9

value: Not available


title: Unruptured intracranial aneurysm, sample 5

description: Gene expression in unruptured intracranial aneurysm

value: Intracranial aneurysm

value: Unruptured intracranial aneurysm


title: Unruptured intracranial aneurysm, sample 4


title: Superficial temporal artery, sample 4

source_name: Superficial temporal artery, sample 4


title: Superficial temporal artery, sample 3

source_name: Superficial temporal artery, sample 3


title: delta_SO1860_rep3

description: Gene expression in delta_SO_1860

source_name: delta_SO_1860 replicate 3


title: EC-2_rep1

description: Gene expression in EC-2

source_name: EC-2 replicate 1


title: E2-treated MCF-7:PF Replicate 3

source_name: E2-treated MCF-7:PF Replicate 3

source_name: Vehicle-treated MCF-7:PF Replicate 3


title: Superficial temporal artery, sample 1

source_name: Superficial temporal artery, sample 1


title: Superficial temporal artery, sample 5

source_name: Superficial temporal artery, sample 5


title: 5057 BJAB

source_name: Burkitt's lymphoma human B cell line (BJAB)

value: BJAB

value: Burkitt's lymphoma human B cell

tag: miRNA condition

value: mock


title: Unruptured intracranial aneurysm, sample 3


title: EC-2_rep2

description: Gene expression in EC-2

source_name: EC-2 replicate 2


title: Ruptured intracranial aneurysm, sample 8

description: Gene expression in ruptured intracranial aneurysm

value: Ruptured intracranial aneurysm


title: Ruptured intracranial aneurysm, sample 7


title: delta_SO1860_rep2

description: Gene expression in delta_SO_1860

source_name: delta_SO_1860 replicate 2


title: Unruptured intracranial aneurysm, sample 2


title: delta_SO1860_rep1

description: Gene expression in delta_SO_1860

source_name: delta_SO_1860 replicate 1


title: Ruptured intracranial aneurysm, sample 6


title: SKOV3-OM3-6

city: Houston

first: Sangbae

last: Kim

state: TX

address: 1 Baylor plaza

department: HGSC

institute: Baylor Colleage of Medicine

description: To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software.

hyb_protocol: Labeled, amplified material (750 ng per array) was hybridized to the Illumina HumanHT-12 V3.0 expression beadchip according to the Manufacturer's instructions (Illumina, Inc., San Diego, CA).

scan_protocol: Arrays were scanned with an Illumina Bead array Reader confocal scanner (BeadStation 500GXDW; Illumina, Inc., San Diego, CA) according to the Manufacturer's instructions

data_processing: Array data processing were performed on Illumina BeadStudio software. We normalized gene expression data using Quantile normalization and log2 transformatoin. To export to a data matrix, Sample Gene Profile option of this software was used.

source_name: Ovarian cancer cells

label_protocol: Biotin-labeled cRNA samples for hybridization were prepared according to Illumina's recommended sample labeling procedure: 500 ng of total RNA was used for cDNA synthesis, followed by an amplification/labeling step (in vitro transcription) to synthesize biotin-labeled cRNA using the Illumina. TotalPrep RNA Amplification kit (Ambion Inc., Austin, TX). cRNA concentrations using spectrophotometer (Nanodrop, ND-1000)

extract_protocol: Total RNA was isolated from tissues with mirVana RNA Isolation labeling kit (Ambion Inc) according to the manufacturer protocol. RNA quality and integrity were confirmed by ExperionTM Automated Electrophoresis System (BIO-RAD)

tag: cell type

value: Metastatic cells


title: Ruptured intracranial aneurysm, sample 3


title: Ruptured intracranial aneurysm, sample 4


title: SKOV3_ip1-3

value: Parental cells


title: SKOV3-OM3-4


title: Ruptured intracranial aneurysm, sample 5


title: Unruptured intracranial aneurysm, sample 1


title: SKOV3_ip1-1


title: Ruptured intracranial aneurysm, sample 2


title: SKOV3-OM3-5


title: SKOV3_ip1-2


title: IBC stroma patient 5

city: Malmö

first: Sofie

last: Björner

address: Jan Waldenströms gata 59

country: Sweden

institute: Lund University

data_processing: The normalization and all the data analysis were performed using DataAssist v1.0 (Applied Biosystems) and determined using the comparative threshold cycle (Ct) method with RNU48 and MammU6 as endogenous controls. VALUEs are normalized signal (against housekeeping genes). Fold Change reports test/control (i.e. CCH/TDLU, IBC/TDLU) ratios.

label: FAM

source_name: stroma from breast cancer tissue

label_protocol: 25 ng of total RNA was reverse-transcribed using Megaplex Primer Pools A and B followed by preamplification with Megaplex PreAmp Primers A and B (Applied Biosystems). The arrays were run on the 7900HT Fast Real-Time System according to manufacture’s instructions (Applied Biosystems).

extract_protocol: Total RNA was extracted with Recover All (Ambion) following the manufacture’s instructions.

tag: gender

value: female

value: stroma from breast cancer tissue

tag: disease state

value: cancer


title: CCH stroma patient 5

source_name: premalignant stromal tissue surrounding CCH

value: premalignant


title: 8 week UV irradiated skin (photo array 555)

city: Seoul

first: SP

last: JIN

address: 101 Daehak-ro

country: South Korea

institute: Seoul National University Hospital

description: Gene expression data from UV-induced photoaged mouse skin

hyb_protocol: Affymetrix protocol

scan_protocol: GeneChips were scanned using Affymetrix GeneChip® Scanner 3000 7G

data_processing: The data were analyzed with RMA(Robust Multi-array Average) as normalization method.

source_name: 8 week UV irradiated skin

label_protocol: Affymetrix protocol

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

treatment_protocol: UV irradiation device that included TL20W/12RS UV lamp, with an emission spectrum between 275 and 380 nm (peak, 310-315nm) is used as the UV source.The weekly UV dose is increased weekly by 1 MED (1MED=100 mJ cm-2) up to 4 MED.

value: skin

tag: uv-irradiated

value: UV-irradiated


title: 8 week UV irradiated skin (photo array 551)


title: Fibroblasts control mimic rep 2

description: Gene expression from mammary fibroblasts transfected with control mimic

hyb_protocol: Standard Affymetrix protocol performed by AROS Applied Biotechnology A/S (Aarhus, Denmark). Following fragmentation, cDNA was hybridized for 16 hr at 45C on GeneChip Human Gene 1.0 ST Arrays, followed by washing and staining using buffers from the GeneChip® Hybridization, Wash and Stain Kit.

data_processing: The data were analyzed with R, Bioconductor and Ingenuity Systems (Redwood City, CA). The RMA was used to normalise and summarise the expression values at the probeset level.

source_name: Fibroblasts transfected with control mimic

label_protocol: Standard Affymetrix protocol performed by AROS Applied Biotechnology A/S (Aarhus, Denmark). Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Manual, Version 4, Affymetrix).

growth_protocol: Fibroblasts were grown in DMEM supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin. Human mammary epithelial CCH cells were cultured in DMEM-F12 supplemented with 5% horse serum, cholera toxin (100 ng/ml), hydrocortisone (0.5 μg/ml), insulin (10 μg/ml), EGF (20 ng/ml) and 1% penicillin-streptomycin. All cells were maintained at 37C in a humified incubator (5% CO2).

extract_protocol: Transfection with miRNA mimics and total RNA extraction was perormed according to manufactures instructions.

treatment_protocol: Fibroblasts were transfected with 25nM miRNA mimic (Dharmacon) using Lipofectamine (Invitrogen) in Opti-MEM medium depleted from serum and penicillin-streptomycin. The medium was changed to serum-containing medium 6h after transfection. After 24 hours, cells were either harvested for total RNA extraction (miRNeasy from Qiagen) or put in coculture.

value: Human mammary GFP-tagged immortalized fibroblasts (218TGpp)

value: transfected with control mimic


title: 8 week UV irradiated skin (photo array 552)


title: 6 week UV irradiated skin (photo array 445)

source_name: 6 week UV irradiated skin


title: Epithelial CCH cells co-cultured with control fibroblasts

description: Gene expression from mammary epithelial columnar cell hyperplasia cells cocultured with fibroblasts transfected with control mimic

scan_protocol: Standard Affymetrix protocol performed by AROS Applied Biotechnology A/S (Aarhus, Denmark).

source_name: CCH cells cocultured with control fibroblasts

value: Human mammary epithelial columnar cell hyperplasia cells

value: cocultured with 218TGpp fibroblasts transfected with control mimic


title: T47D_LB_rep3

city: los Angeles

first: Hany

middle: A

last: Abdel-Hafiz

state: California

address: 110 N George Burns RD, DRoom 3057

department: Medicine/ Medical Oncology

institute: Cedars-Sinai Medical Center

description: Gene expression of pLB cells.

hyb_protocol: Hybridization was performed at MOgene LC (www.mogene.com).

scan_protocol: Initial analyses were performed at MOgene LC (www.mogene.com).

data_processing: The data were filtered and any probes with a detection P value less than 0.05 were removed from the normalized dataset. The data was then normalized using log2 transformation and quantile normalization using Partek® Genomics Suite™ 6.6.

source_name: T47D, pure luminobasal cells

label_protocol: Labeling was performed at MOgene LC (www.mogene.com).

growth_protocol: Cells were maintained in Dulbecco's Modified Eagle Medium (DMEM, Life Technologies) containing 5% Charcoal stripped fetal bovine serum (FBS, Japan Serum) in the presence or absence of 1 nM estradiol.

extract_protocol: RNA was extracted (PicoPure; Arcturus) following the manufacturer's recommendations. RNA was quantified using a Nanodrop ND1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: 72 hr 1nM E-treated pLUM and EWD pLB were suspended (Accumax; Millipore), fixed, permeabilized with RNAlater (Ambion Inc.) and incubated with 2 µg anti-CK5 (Novocastra; NCL-L-CK5) labeled with Zenon Alexa Fluor 488 (Invitrogen; Z-25002). Stained cells were centrifuged and resuspended in RNase-free NST buffer containing DAPI, and FACS sorted (Beckman Coulter XDP-100 MoFlo) for CK5+ vs. CK5-. Separated cells were collected, centrifuged, resuspended and RNA was extracted (PicoPure; Arcturus).

tag: parental cell line

value: pure luminobasal cells (pLB)


title: Ruptured intracranial aneurysm, sample 1

value: Intracranial aneurysm

value: Female


title: 6 week UV irradiated skin (photo array 443)


title: T47D_LB_rep2

description: Gene expression of pLB cells.


title: 6 week UV irradiated skin (photo array 441)


title: CCH stroma patient 2

value: premalignant stromal tissue surrounding CCH


title: 4 week UV irradiated skin (photo array 334)

source_name: 4 week UV irradiated skin


title: Fibroblasts miR-132 mimic rep 1

description: Gene expression from mammary fibroblasts transfected with miR-132 mimic

source_name: Fibroblasts transfected with miR-132 mimic

value: transfected with miR-132 mimic


title: Epithelial CCH cells co-cultured with miR-132 overexpressing fibroblasts

description: Gene expression from mammary epithelial columnar cell hyperplasia cells cocultured with fibroblasts transfected with miR-132 mimic

source_name: CCH cells cocultured with miR-132 overexpressing fibroblasts


title: 4 week UV irradiated skin (photo array 333)


title: TDLU stroma patient 5

source_name: normal stromal tissue surrounding TDLUs

value: normal stromal tissue surrounding TDLUs

value: normal


title: TDLU stroma patient 2

value: female


title: CCH stroma patient 1


title: T47D_LB_rep1

description: Gene expression of pLB cells.


title: Fibroblasts miR-132 mimic rep 2


title: Fibroblasts control mimic rep 1


title: TDLU stroma patient 1


title: IBC epithelia patient 5

source_name: epithelial breast cancer tissue

value: epithelial breast cancer tissue


title: 4 week UV irradiated skin (photo array 331)


title: CCH epithelia patient 1

source_name: premalignant epithelial breast tissue

value: premalignant epithelial breast tissue


title: TDLU epithelia patient 5

source_name: normal epithelial breast tissue

value: normal epithelial breast tissue


title: CCH epithelia patient 5

value: premalignant


title: T47D_Lum_rep3

description: Gene expression of pLUM cells.

source_name: T47D, pure luminal cells

value: pure luminal cells (pLUM)


title: CCH epithelia patient 4


title: CCH epithelia patient 3


title: TDLU epithelia patient 3


title: CCH epithelia patient 2


title: TDLU epithelia patient 2


title: TDLU epithelia patient 1


title: T47D_Lum_rep2

description: Gene expression of pLUM cells.


title: 1 week UV irradiated skin (photo array 116)

source_name: 1 week UV irradiated skin

value: skin

value: UV-irradiated


title: T47D_Lum_rep1

description: Gene expression of pLUM cells.


title: 2 week UV irradiated skin (photo array 225)

source_name: 2 week UV irradiated skin


title: TDLU epithelia patient 4


title: 2 week UV irradiated skin (photo array 222)


title: 1 week UV irradiated skin (photo array 112)


title: 2 week UV irradiated skin (photo array 224)


title: 1 week non UV irradiated control (photo array 13)

description: Gene expression data from non UV-induced photoaged mouse skin

source_name: 1 week non UV irradiated control

value: non UV-irradiated


title: 8 week non UV irradiated control (photo array 53)

source_name: 8 week non UV irradiated control


title: Isogenic H3122 (EML4-ALK E13;A20) cells - RESISTANT to the ALK TKI, PF1066 (aka crizotinib). Replicate #3.

city: Nashville

first: Pengcheng

last: Lu

state: TN

address: 2200 Pierce Avenue

institute: Vanderbilt University

description:
Isogenic H3122 (EML4-ALK E13;A20) cells - experimentally derived to be RESISTANT to the ALK TKI, PF1066 (aka crizotinib). Replicate #3.
PF1066R_3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Bioconductor's beadarray package was used for quantile normalization and log2-transformation. All analyses were performed using R software(Version 2.15).

source_name: Isogenic  H3122 (EML4-ALK E13;A20) cells, resistant to PF1066  - replicate 3

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

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


title: Isogenic H3122 (EML4-ALK E13;A20) cells - RESISTANT to the ALK TKI, PF1066 (aka crizotinib). Replicate #1.

description:
Isogenic H3122 (EML4-ALK E13;A20) cells - experimentally derived to be RESISTANT to the ALK TKI, PF1066 (aka crizotinib). Replicate #1.
PF1066R_1

source_name: Isogenic  H3122 (EML4-ALK E13;A20) cells, resistant to PF1066  - replicate 1


title: 1 week UV irradiated skin (photo array 114)


title: Isogenic H3122 (EML4-ALK E13;A20) cells - RESISTANT to the ALK TKI, X-376. Replicate #1.

description:
Isogenic H3122 (EML4-ALK E13;A20) cells - experimentally derived to be RESISTANT to the ALK TKI, X-376. Replicate #1.
X376R_1

source_name: Isogenic  H3122 (EML4-ALK E13;A20) cells, resistant to X376  - replicate 1


title: 8 week non UV irradiated control (photo array 51)


title: 8 week non UV irradiated control (photo array 55)


title: Isogenic H3122 (EML4-ALK E13;A20) cells - RESISTANT to the ALK TKI, X-376. Replicate #3.

description:
Isogenic H3122 (EML4-ALK E13;A20) cells - experimentally derived to be RESISTANT to the ALK TKI, X-376. Replicate #3.
X376R_3

source_name: Isogenic  H3122 (EML4-ALK E13;A20) cells, resistant to X376  - replicate 3


title: Isogenic H3122 (EML4-ALK E13;A20) cells - RESISTANT to the ALK TKI, PF1066 (aka crizotinib). Replicate #2.

description:
Isogenic H3122 (EML4-ALK E13;A20) cells - experimentally derived to be RESISTANT to the ALK TKI, PF1066 (aka crizotinib). Replicate #2.
PF1066R_2

source_name: Isogenic  H3122 (EML4-ALK E13;A20) cells, resistant to PF1066  - replicate 2


title: Isogenic H3122 (EML4-ALK E13;A20) cells - RESISTANT to the ALK TKI, X-376. Replicate #2.

description:
Isogenic H3122 (EML4-ALK E13;A20) cells - experimentally derived to be RESISTANT to the ALK TKI, X-376. Replicate #2.
X376R_2

source_name: Isogenic  H3122 (EML4-ALK E13;A20) cells, resistant to X376  - replicate 2


description:
H3122 (EML4-ALK E13;A20) cells - sensitive to the ALK TKIs, PF1066 (aka crizotinib) and X-376. Replicate #1.
Parental_1

source_name: H3122 (EML4-ALK E13;A20) cells, sensitive to PF1066 and X-376 - replicate 1

value: H3122 Parental


description:
H3122 (EML4-ALK E13;A20) cells - sensitive to the ALK TKIs, PF1066 (aka crizotinib) and X-376. Replicate #3.
Parental_3

source_name: H3122 (EML4-ALK E13;A20) cells, sensitive to PF1066 and X-376 - replicate 3


title: 1 week non UV irradiated control (photo array 12)


title: Control animal 129S2SvPAS rep3

city: PARIS

first: Laurent

last: MESNARD

state: idf

address: 4 rue de la chine, Hôpital Tenon

institute: INSERM

description:
Charles River laboratory
Female, 8-10 weeks old, Day4, antiglomerulonephritis,

hyb_protocol: standard Affymetrix protocol

scan_protocol: GCOS 1.4

data_processing: Normalisation using MAS5 for quality control, GC-RMA for normalisation for analysis.

source_name: Isolated glomeruli

label_protocol: standard Affymetrix protocol

extract_protocol: RNA-easy kit, Qiagen, following the standard protocol

treatment_protocol: Nephrotoxic serum was injected at day 0, day1, day 2, mice were sacrificied at day 4, glomeruli were extracted using different nylon sieves (BD bioscience, 100 µm and 45 µm)

value: glomeruli

value: 8-10 week

tag: time

value: day 4

value: control


description:
H3122 (EML4-ALK E13;A20) cells - sensitive to the ALK TKIs, PF1066 (aka crizotinib) and X-376. Replicate #2.
Parental_2

source_name: H3122 (EML4-ALK E13;A20) cells, sensitive to PF1066 and X-376 - replicate 2


title: Day_4_anti_GBM_GN_129S2SvPAs rep3

value: antiglomerulonephritis


title: Control animal 129S2SvPAS rep2


title: Day_4_anti_GBM_GN_129S2SvPAs rep2


title: Day_4_anti_GBM_GN_C57BL6J rep2


title: Control animal C57BL6J rep1


title: Day_4_anti_GBM_GN_129S2SvPAs rep1


title: Day_4_anti_GBM_GN_C57BL6J rep3


title: Control animal 129S2SvPAS rep1


title: 1 week non UV irradiated control (photo array 16)


title: Control animal C57BL6J rep3


title: Control animal C57BL6J rep2


city: San Diego

first: John

last: Welsh

address: 3030 Bunker Hill Street

institute: Vaccine Research Institute of San Diego

description:
H2B-GFP
Gene expression data from N202 cells adapted to brain, biological replicate, passage 1

hyb_protocol: Arrays were hybridized using the an Affymetrix Genechip hybridization station, and manufacturer's recommended solutions and protocols.

scan_protocol: Chips were scanned using an Affymetrix Genechip Scanner 3000

data_processing: Robust Multiarray Averaging was used according to Laurent Gautier, Leslie Cope, Benjamin M. Bolstad and Rafael A. Irizarry in  affy—analysis of Affymetrix GeneChip data at the probe level (2004) Bioinformatics vol. 20(3), 307-315.

source_name: N202 cells adapted to brain tissue for 21 days, sorted, and expanded in cell culture.

label_protocol: Target was labeled using the Ambion WT expression kit and the Affymetrix WT Terminal and Labeling Control kit according to manufacturer's instructions.

growth_protocol: N202 cells were grown on revascularized, minced brain, bone marrow, or lung tissue in a dorsal skinfold chamber for 21 days for each passage, for up to 4 passages, with intervening growth in cell culture.

extract_protocol: RNA was purified using the Rneasy kit from Qiagen.

treatment_protocol: Between passages, cells were subjected to G418 selection, and before RNA extraction cells containing GFP fluorescence were purified by flow cytometry and placed back into cell culture to increase material for array analysis.

value: Mouse breast tumor-derived N202

tag: passage

tag: co-implanted tissue

value: brain, biological replicate


title: Day_4_anti_GBM_GN_C57BL6J rep1

value: female

tag: treatment