title: THIOGUANINE_OCI-Ly7_6_TH001_NG_101118_03_B05

description:
tumor cell line
Therasis_Plate10_TH001_NG_20101118_03_B05

value: THIOGUANINE


title: PCg1_BaselineF

status: Public on Jul 08 2015

type: RNA

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

country: USA

institute: Yerkes National Primate Research Center

hyb_protocol: Arrays were washed, stained and scanned as described in the Affymetrix GeneChip® Expression Analysis Technical Manual

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

data_processing: Background adjustment, normalization, and median polish summarization of .CEL files were performed with the robust multichip average (RMA) algorithm using the affy Bioconductor package.

label: biotin

molecule: total RNA

organism: Macaca nemestrina

source_name: PCg1 Vaginal pinch biopsy follicular phase

label_protocol: Five µg of the amplified cDNA was fragmented, biotinylated, and hybridized to arrays using the NuGEN Ovation Encore Biotin Module, according to kit instructions.

extract_protocol: Total RNA extraction was performed using the RNeasy mini kit (QIAGEN, Hilden, Germany)

tag: animal id

tag: menstrual phase

value: follicular

tag: tissue

value: Vaginal pinch biopsy


title: PBm1_BaselineL

source_name: PBm1 Vaginal pinch biopsy luteal  phase

value: luteal


title: PZm1_BaselineL

source_name: PZm1 Vaginal pinch biopsy luteal  phase


title: TRIFLUPROMAZINE.HYDROCHLORIDE_OCI-Ly7_6_TH001_NG_101118_03_B07

city: New York

first: Andrea

last: Califano

state: NY

address: 1130 St. Nicholas Avenue, Rm. 906

institute: Columbia University

description:
tumor cell line
Therasis_Plate10_TH001_NG_20101118_03_B07

hyb_protocol: Following fragmentation with a buffered zinc solution  (Fragmentation Reagent, Ambion), 7.5 ug of labelled cRNA were hybridized on HG-U219 arrays in 120ul volume/well. The GeneTitan Hybridization, Wash and Stain kit (Affymetrix) was used for preparing hybridization mixes and processing of 96-array plates on the GeneTitan Instrument (Affymetrix).

scan_protocol: Human Genome U219 array plate was processed in GeneTitan according to manufacturer's instructions

data_processing: The data were analyzed with RMA method in R

organism: Homo sapiens

label_protocol: 300ng of each of the samples with RIN value >7 were converted to biotinylated cRNA with the Illumina TotalPrep-96 RNA Amplification Kit (Ambion) using a standard T7-based amplification protocol

growth_protocol: Cell lines were cultured in Iscove’s Modified Dulbecco Medium supplemented with 10% fetal bovine serum at 37°C in a 5% CO2 atmosphere.

extract_protocol: Total RNA was isolated with the RNAqueous-96 Automated Kit (Ambion) on the Janus automated liquid handling system (Perkin Elmer Inc.), quantified by NanoDrop 6000 spectrophotometer and quality checked by Agilent Bioanalyzer.

treatment_protocol: A stock concentration of the IC20 at 24 hour was created by dilution in DMSO. Cells were treated with the 24hr IC20 of each of the compounds for 6, 12, and 24hrs at 37°C, 5% CO2 under humidified conditions. 0.2% DMSO vehicle treated samples were used as controls.

tag: compound treated

tag: cell line

tag: time

value: 6 hrs


type: genomic

city: Beijing

first: Haibo

last: Yang

address: No.1 Beichen West Road, Chaoyang District

country: China

institute: Institute of Microbiology, Chinese Academy of Sciences

description: Haloferax mediterranei DF50 genomic DNA of 12h vs that of stationary phase

hyb_protocol: standard CapitalBio Methods

scan_protocol: Arrays were scanned on an MS200 scanner per manufacturer's protocol

data_processing: Arrays were processed using Nimblegen's standard protocol. The ratios were calculated as exponential phase values (or at time points 12h, 18h, 24h, 36h and 42h) versus stationary phase values for each probe. As the probes were designed according to the former version genome of Haloferax mediterranei (CP001868.1-CP001871.1), the position of the probes was adjusted according to the latest version genome of Haloferax mediterranei (CP001868.2, CP001869.1-CP001871.1) when we plot the replication profile. The difference between the former version CP001868.1 and the latest version CP001868.2 is a 1 Mb fragment inversion between the two rRNA operons in the chromosome, while the nucleotide sequences are the same. Thus, we just invert the position of probes between two rRNA operons (corresponding to probes between 33500CHROMOSOMES001745415 and 33500CHROMOSOMES002842080). Due to the high density of the probes, the ratios of the thirty probes were averaged as one point located at the first probe. The MFA graph was plotted with a 5-point window and 1-point slide.

molecule: genomic DNA

organism: Haloferax mediterranei

source_name: Genomic DNA of Haloferax mediterranei at 12h

label_protocol: 1 µg sonicated genomic DNA  was labeled by Klenow (New England Biolabs) random priming with Cy3 or Cy5 nonamers per manufacturer's protocol

growth_protocol: Cells were cultivated at 37°C for 12h in AS-168 medium supplemented with uracil

extract_protocol: Proteinase K, ethanol precipitation, RNaseA treatment, phenol-chloroform extraction as described previously [PMID: 24271389]

treatment_protocol: no treatment

tag: strain

tag: time point

source_name: Genomic DNA of Haloferax mediterranei DF50 at stationary phase

growth_protocol: Cells were cultivated at 37°C to stationary phase in AS-168 medium supplemented with uracil

tag: phase

value: stationary phase


title: T-PLL pre 3

city: Hershey

first: Penn State

last: COM

state: PA

address: 500 University Drive

department: Genome Sciences Facility

institute: Penn State College of Medicine

description:
Replicate 3
5154922028_I

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalization

source_name: PBMC

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

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

tag: treatment status

value: pre-treatment

tag: treatment

value: alemtuzumab, cladribine

tag: additional treatment


title: FENOFIBRATE_OCI-Ly7_6_TH001_NG_101118_03_B01

description:
tumor cell line
Therasis_Plate10_TH001_NG_20101118_03_B01

value: FENOFIBRATE


title: 96PO47_BaselineF

source_name: 96PO47 Vaginal pinch biopsy follicular phase


title: GE2-14 compared to GE2-14 ΔaguR Replicate 5

city: Villaviciosa

first: Victor

last: Ladero

state: Select if applicable

address: Paseo Rio Linares S/N

department: Technology and Biotechnology of dairy products

country: Spain

institute: IPLA-CSIC

description:
GE2-14 vs. GE2-14 ΔaguR.rep5
Biological replicate 3 of 3. L. lactis subsp. cremoris GE2-14 compared with L. lactis subsp. cremoris GE2-14 ΔaguR

hyb_protocol: Hybridization (17 h at 60°C) was performed with 900 ng of Cy3 and 900 ng of Cy5 labeled cDNA using the In situ Hybridization Kit Plus (Agilent Technologies, CA, USA) following the instructions provided by the supplier

scan_protocol: Slides were scanned in a GenePix 4200A Microarray Scanner (Molecular Devices, CA, USA). Slide images were analyzed using the GenePix Pro 6.0 software to generate the gpr data files.

data_processing: Analysis were performed using standard routines included in the LimmaR package through the GENOME2D software using the pipeline at the http://server.molgenrug.nl/index.php/dna-microarrays webserver for background subtraction and LOWESS normalization.

organism: Lactococcus cremoris subsp. cremoris GE214

label_protocol: cDNA synthesis was performed using the SuperScript® III Reverse Transcriptase kit (Life Technologies, Bleiswijk, Netherlands), following the instructions of the supplier. 20 ug of cDNA were labeled with Cy-3/Cy-5 using the DyLight® Amine-Reactive Dyes kit (Thermo Scientific), using protocols provided by the supplier

growth_protocol: Cells were grown in M17 culture media (Oxoid, UK) supplemented with 1% galactose (w/v) and 20 mM agmatine (Sigma-Aldrich, St. Louis, MO) for 6h at 30°C without aeration

extract_protocol: Cell pellets were resuspended in 500 ul of 10 mM Tris-HCl, 1 mM EDTA pH 8.0, after which 50 ul of 10% SDS, 500  ul of phenol/chloroform, 500 mg of glass beads (75–150 um), and 175  ul of Macaloid suspension (Bentone) were added. RNA isolation was completed with the Roche High Pure RNA isolation kit (Roche Diagnostics GmbH, Mannheim, Germany).

tag: putrescine producer

value: Yes

source_name: Lactococcus lactis subsp. cremoris GE2-14 ΔaguR

value: GE2-14 ΔaguR

value: No


title: Metixene.hydrochloride_OCI-Ly7_6_TH001_NG_101118_03_A11

description:
tumor cell line
Therasis_Plate10_TH001_NG_20101118_03_A11


title: PKI2_BaselineL

source_name: PKI2 Vaginal pinch biopsy luteal  phase


title: PKg2_BaselineF

source_name: PKg2 Vaginal pinch biopsy follicular phase


title: CHLOROXINE_OCI-Ly7_6_TH001_NG_101118_03_A07

description:
tumor cell line
Therasis_Plate10_TH001_NG_20101118_03_A07

value: CHLOROXINE


title: PBm1_BaselineF

source_name: PBm1 Vaginal pinch biopsy follicular phase


title: TUBOCURARINE.CHLORIDE_OCI-Ly7_6_TH001_NG_101118_03_A10

description:
tumor cell line
Therasis_Plate10_TH001_NG_20101118_03_A10


title: GE2-14 compared to GE2-14 ΔaguR Replicate 4

description:
GE2-14 vs. GE2-14 ΔaguR.rep4
Biological replicate 2 of 3. L. lactis subsp. cremoris GE2-14 compared with L. lactis subsp. cremoris GE2-14 ΔaguR

source_name: Lactococcus lactis subsp. cremoris GE2-14


title: PVI2_BaselineL

source_name: PVI2 Vaginal pinch biopsy luteal  phase


title: NISOLDIPINE_OCI-Ly7_6_TH001_NG_101118_03_A09

description:
tumor cell line
Therasis_Plate10_TH001_NG_20101118_03_A09

value: NISOLDIPINE


title: DMSO_OCI-Ly7_6_TH001_NG_101118_03_A12

description:
tumor cell line
Therasis_Plate10_TH001_NG_20101118_03_A12

value: DMSO


title: PPy1_BaselineL

source_name: PPy1 Vaginal pinch biopsy luteal  phase


title: POH2_BaselineF

source_name: POH2 Vaginal pinch biopsy follicular phase


title: GE2-14 compared to GE2-14 ΔaguR Replicate 2

description:
GE2-14 vs. GE2-14 ΔaguR.rep2
Technical replicate 2 of 2. L. lactis subsp. cremoris GE2-14 compared with L. lactis subsp. cremoris GE2-14 ΔaguR


title: MITOXANTHRONE.HYDROCHLORIDE_OCI-Ly7_6_TH001_NG_101118_03_A08

description:
tumor cell line
Therasis_Plate10_TH001_NG_20101118_03_A08


title: GE2-14 compared to GE2-14 ΔaguR Replicate 3

description:
GE2-14 vs. GE2-14 ΔaguR.rep3
Biological replicate 1 of 3. L. lactis subsp. cremoris GE2-14 compared with L. lactis subsp. cremoris GE2-14 ΔaguR


title: CLOMIPHENE.CITRATE_OCI-Ly7_6_TH001_NG_101118_03_A03

description:
tumor cell line
Therasis_Plate10_TH001_NG_20101118_03_A03


title: SULFINPYRAZONE_OCI-Ly7_6_TH001_NG_101118_03_A05

description:
tumor cell line
Therasis_Plate10_TH001_NG_20101118_03_A05

value: SULFINPYRAZONE


title: PPy1_BaselineF

source_name: PPy1 Vaginal pinch biopsy follicular phase


title: POH2_BaselineL

source_name: POH2 Vaginal pinch biopsy luteal  phase


title: HEXACHLOROPHENE_OCI-Ly7_6_TH001_NG_101118_03_A04

description:
tumor cell line
Therasis_Plate10_TH001_NG_20101118_03_A04

value: HEXACHLOROPHENE


title: PVI2_BaselineF

source_name: PVI2 Vaginal pinch biopsy follicular phase


title: PINDOLOL_OCI-Ly7_6_TH001_NG_101118_03_A06

description:
tumor cell line
Therasis_Plate10_TH001_NG_20101118_03_A06

value: PINDOLOL


title: PDT1_BaselineL

source_name: PDT1 Vaginal pinch biopsy luteal  phase


title: Liver_1h_rep3

status: Public on Jul 07 2015

city: Newark

first: Daniel

middle: J

last: Cook

state: DE

address: 104 Academy St.

department: Chemical and Biomolecular Engineering

institute: University of Delaware

description: ChIP-chip Regenerating rat liver, 1h, NFkB

hyb_protocol: The labeled ChIP DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in 45 ul of buffer containing 20% formamide, 1.2 M betaine, 0.1 ug/ul herring sperm DNA and 10 ug of human COT1 DNA (Invitrogen). Arrays were hybridized in Maui hybridization stations for 16-18 h at 42C, and then washed in 42C 0.2% SDS/0.2x SSC, room temperature 0.2x SSC, and 0.05x SSC. Hybridization buffers and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html)

scan_protocol: Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction. Array images were used for data extraction as paired files; genomic feature format files were then produced for analysis of scaled log2-ratio data. The intensity ratio of immunopreciptated to total DNA (not taken through immunoprecipitation steps) was calculated at each genomic position to identify regions where increased signal (i.e. DNA fragment enrichment) was observed relative to the control sample. Peak regions identified as statistically significant binding sites were generated from the scaled log2-ratio data. The possible binding regimes (peaks) that correspond to the binding targets were detected if 4 or more probes showed a signal above the cutoff value ranging from 90% to 15% using a 500bp sliding window. Cut-off values were set as a fraction of the hypothetical maximum signal (mean signal plus six standard deviations). An empirical false discovery rate (FDR) was calculated for each peak using a bootstrapping method, which randomized the probe signals 20 times. The calculated FDR is an approximation of the probability of a false positive. Peaks were annotated with candidate target genes with the assumption that the distance between a center of binding peak and the transcription start site (TSS) of the gene is shorter than a threshold cutoff.  We defined these “gene regions” as spanning from 5kb upstream of the TSS to 1.5 kb downstream of the end of transcription. The peak files were annotated with Ensembl version 5.0 (Rnor_5.0) transcript genes using a 5000 base pair cutoff distance from the TSS using the Chip Peak Anno Bioconductor package in R. The peaks were then annotated with detailed characteristic genomic features: peak region location, gene annotation of nearest transcript (intron, exon, intragenic, etc.), chromosome, start and end of genes, nearest transcripts and transcript boundaries, distance from TSS, RefSeq IDs, Entrez IDs, TSS, trophoblast-specific element (TSE)  and average phastcon scores obtained.

organism: Rattus norvegicus

source_name: NF-kB ChIP DNA from Rattus norvegicus regenerating liver at 1h post PHx, biological replicate 3

label_protocol: 1 µg ChIP DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy5 nonamers (ChIP DNA isolated from normal rabbit IgG-immunoprecipitated cells) per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

extract_protocol: 5x10E6 cells were fixed with 1% formaldehyde in culture medium for 10 min at room temperature followed by quenching with 0.125 M glycine for 5 min. The cells were washed twice with ice-cold PBS and lysed in 1 ml of lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris pH8.0) for at least 30 min on ice. The crosslinked chromatin was sheared to an average size of 500 bp by ten 30-second pulses using a BiorupterTM sonicator (Diagenode). The lysate was then centrifuged to remove cell debris, and the chromatin was quantified in a UV spectrophotometer. The chromatin (400 µg) was diluted 10-fold in dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA 16.7 mM Tris pH8.10, 167 mM NaCl) and pre-cleared with 25 µl protein A sepharose beads (pre-absorbed with salmon sperm DNA and BSA) for 2 h at 4C. The chromatin supernatant was then incubated overnight with 5 µg of purified antibody at 4C. After incubation with protein A sepharose beads (50 µl) for 2h at 4C, the immune complexes were collected by centrifugation and washed with the following buffers each for 10 min at 4C; RIPA buffer (150 mM NaCl, 50 mM Tris pH8.0, 0.1% SDS), high-salt buffer (500 mM NaCl, 50 mM Tris pH8.0, 0.1% SDS, 1% NP40) LiCl buffer (250 mM LiCl, 50 mM Tris pH8.0, 0.5% Na deoxycholate, 1% NP40) and 2x TE (20 mM Tris pH8.0, 2 mM EDTA). The protein-DNA complexes were eluted from the beads in 450 µl elution buffer (1% SDS, 100 mM NaHCO3) at 55C for 2 h followed by the addition of proteinaseK to 500 µg/ml and overnight incubaton at 65C. Genomic DNA was isolated from the precipitated material as well as from the sheared chromatin input (1/100 of the material used for ChIP) by phenol extraction and ethanol precipitation.

tag: genotype

value: Wild-type

tag: gender

value: Male

value: Sprague Dawley

tag: age

value: 8-10 weeks

tag: weight

tag: liver lobe

value: Right median, right lateral, and caudate lobe

tag: chip antibody

value: NF-κB antibody (Cat#ab7970, Rabbit polyclonal NF-κB p65 antibody and negative control IgG antibody from Abcam Inc, Cambridge, MA)

source_name: Input DNA from Rattus norvegicus regenerating liver at 1h post PHx, biological replicate 3

label_protocol: 1 µg Input DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy3 nonamers per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

value: none, input DNA


title: Liver_1h_rep2

source_name: NF-kB ChIP DNA from Rattus norvegicus regenerating liver at 1h post PHx, biological replicate 2

source_name: Input DNA from Rattus norvegicus regenerating liver at 1h post PHx, biological replicate 2


title: GE2-14 compared to GE2-14 ΔaguR Replicate 1

description:
GE2-14 vs. GE2-14 ΔaguR.rep1
Technical replicate 1 of 2. L. lactis subsp. cremoris GE2-14 compared with L. lactis subsp. cremoris GE2-14 ΔaguR


title: Liver_0h_rep3

description: ChIP-chip Regenerating rat liver, 0h, NFkB

source_name: NF-kB ChIP DNA from Rattus norvegicus regenerating liver at 0h post PHx, biological replicate 3

value: Left lateral and median lobe

source_name: Input DNA from Rattus norvegicus regenerating liver at 0h post PHx, biological replicate 3


title: PKI2_BaselineF

source_name: PKI2 Vaginal pinch biopsy follicular phase

tag: animal id

tag: menstrual phase

value: follicular

tag: tissue

value: Vaginal pinch biopsy


title: Liver_0h_rep2

source_name: NF-kB ChIP DNA from Rattus norvegicus regenerating liver at 0h post PHx, biological replicate 2

source_name: Input DNA from Rattus norvegicus regenerating liver at 0h post PHx, biological replicate 2


title: Liver_6h_rep3

description: ChIP-chip Regenerating rat liver, 6h, NFkB

source_name: NF-kB ChIP DNA from Rattus norvegicus regenerating liver at 6h post PHx, biological replicate 3

source_name: Input DNA from Rattus norvegicus regenerating liver at 6h post PHx, biological replicate 3


title: PDT1_BaselineF

source_name: PDT1 Vaginal pinch biopsy follicular phase


title: REF_HeLa_NA_TH001_NG_101118_03_A01

description:
tumor cell line
Therasis_Plate10_TH001_NG_20101118_03_A01

source_name: HeLa

tag: compound treated

value: REF

tag: cell line

value: HeLa

tag: time


title: Liver_6h_rep1

source_name: NF-kB ChIP DNA from Rattus norvegicus regenerating liver at 6h post PHx, biological replicate 1

tag: strain

source_name: Input DNA from Rattus norvegicus regenerating liver at 6h post PHx, biological replicate 1


title: Complicated malaria 6 PFC-21

city: Pilani

first: Ashis

middle: Kumar

last: Das

state: Rajasthan

address: Vidya Vihar

department: Biological Sciences

country: India

institute: Birla Institute of Technology & Science,Pilani (Pilani Campus)

description: Gene expression of parasite isolates

hyb_protocol: The labeled cRNA samples were hybridized on to a custom P. falciparum 8x15k Array (AMADID: 24956) designed by Genotypic Technology Pvt. Ltd., Bangalore, India. 600ng of Cy3 labeled samples were fragmented and hybridized.  Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5188-5242). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327).

scan_protocol: Scanning was performed using the Agilent Microarray Scanner (Agilent, Palo Alto, CA, G Model G2565BA) at 5 micron resolution.

data_processing: Data extraction from Images was done using Feature Extraction software (Agilent Technologies).Feature extracted data was analyzed using GeneSpring GX Version12.5 software from Agilent. Data was filtered by considering all those probes detected in at least in 6 samples out of 12 samples based on flag option. Filtered probes were normalized using quantile based normalization method. For var, rifin and stevor genes, data was filtered by considering all those probes detected in at least 1 sample out of 12 samples based on falg option.

organism: Plasmodium falciparum

source_name: P. falciparum parasites from patient's blood

label_protocol: Thirteen parasite total RNA samples  for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). Five hundred nanograms each of the samples were incubated with reverse trancription mix at 40°C and converted to double stranded cDNA primed by oligodT with a T7 polymerase promoter. The cleaned up double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C.

growth_protocol: P. falciparum isolates collected directly from infected patients with differing clinical symptoms

extract_protocol: Total RNA extracted using TriReagent (Sigma Aldrich, USA) following manufacturer's instructions

treatment_protocol: Blood was immediately (Within 15 minutes of collection) subjected to density gradient based separation (Histopaque 1077, Sigma Aldrich, USA) to separate the Peripheral Blood Mononuclear Cells (PBMCs) from the infected and uninfected erythrocytes following manufacturer’s instructions. Both fractions were washed with Phosphate buffered saline (PBS) twice and lysed using 4 volume of Tri-Reagent (Sigma Aldrich, USA) and stored at -80°C.

value: M

tag: disease state

value: Renal Failure,thrombocytopenia

value: blood


title: Liver_1h_rep1

source_name: NF-kB ChIP DNA from Rattus norvegicus regenerating liver at 1h post PHx, biological replicate 1

source_name: Input DNA from Rattus norvegicus regenerating liver at 1h post PHx, biological replicate 1


title: SULCONAZOLE.NITRATE_OCI-Ly7_6_TH001_NG_101118_03_A02

description:
tumor cell line
Therasis_Plate10_TH001_NG_20101118_03_A02

value: 6 hrs


title: Complicated malaria 4 PFC-18

description: Gene expression of parasite isolates

value: Jaundice, renal failure, thrombocytopenia


title: Complicated malaria 7 PFC-22

description: Gene expression of parasite isolates

value: Jaundice, renal failure, thrombocytopenia, anemia


title: Complicated malaria 3 PFC-10

description: Gene expression of parasite isolates

value: F

value: Jaundice, anemia


title: Liver_0h_rep1

source_name: NF-kB ChIP DNA from Rattus norvegicus regenerating liver at 0h post PHx, biological replicate 1

value: Wild-type

value: Male

value: Sprague Dawley

value: 8-10 weeks

source_name: Input DNA from Rattus norvegicus regenerating liver at 0h post PHx, biological replicate 1


title: Complicated malaria 2 PFC-05

description: Gene expression of parasite isolates


title: Uncomplicated malaria 3 PFU-05

description: Gene expression of parasite isolates

value: uncomplicated malaria


title: Complicated malaria 5 PFC-19

description: Gene expression of parasite isolates

value: Renal Failure,


title: Breast tumor 49

city: Santiago

first: Carolina

last: Alvarez

state: Santiago

address: Portugal 49

department: Cellular and Molecular Biology

country: Chile

institute: Pontificia Universidad Católica de Chile

hyb_protocol: Equal amounts of test and reference labeled DNA (total volume of 50 µl) were mixed with 5 µg of Human Cot-1 DNA and 2X hybridization buffer (dextran sulfate 10%, 3X SSC and Tween 20 1.5%). Samples were hybridized under rotation for 40 h at 65°C using a hybridization oven

scan_protocol: scanned using GenePix 4100A scanner, Axon Images were quantified either using Agilent Feature Extraction Software or GenePix Pro 5.1).

data_processing: Background substracted ratios were normalized in R using CGH Normaliter package and processed in CGH Analytics.

source_name: FFPE tumor

label_protocol: 6-8 micrograms of DNA were labeled with Bioprime CGH labeling kit using Cy3 or Cy5-dUTP.

extract_protocol: DNA was isolated from microdissected tumor cells by Proteinase K diggestion at 37°C for 48 hours and DNA was ethanol precipitated. Later, whole genome amplification was performed with Phi29 polymerase.

treatment_protocol: All tumor tissues were formalin-fixed, paraffin- embedded and tumor cells were microdissected

tag: histology

value: Invasive Ductal Carcinoma

tag: grade

value: II

tag: estrogen receptor

value: positive

value: negative

tag: brca1 expression

tag: brca mutation

source_name: normal lymph nodes

value: female

tag: malignancy

value: normal


title: Uncomplicated malaria 4 PFU-06

description: Gene expression of parasite isolates

tag: age

tag: gender

value: M

value: blood


title: Breast tumor 50

value: III

value: ND


title: Uncomplicated malaria 1 PFU-03

description: Gene expression of parasite isolates


title: Breast tumor 48


title: ROSIGLITAZONE_OCI-Ly7_6_TH001_NG_101118_03_B02

description:
tumor cell line
Therasis_Plate10_TH001_NG_20101118_03_B02

value: ROSIGLITAZONE

value: 6 hrs


title: Uncomplicated malaria 5 PFU-07

description: Gene expression of parasite isolates

value: F


title: Breast tumor 47


title: PHx 72 Hrs_3

city: Carlsbad

first: Sagar

middle: S

last: Damle

state: CA

address: 2855 Gazelle Ct

institute: Ionis Pharmaceuticals

description: Gene expression at 72 hours after 2/3 partial hepatectomy

hyb_protocol: manufacturer instructions

scan_protocol: manufacturer instructions

data_processing: normalized for intensity dependent variance using the vsn package (bioconductor).  The method uses a robust variant of the maximum-likelihood estimator for the stochastic model of  microarray data

organism: Mus musculus

source_name: mouse liver RNA collected at 72 hours after 2/3 partial hepatectomy

label_protocol: manufacturer instructions

growth_protocol: Male Balb/c mice, 8 weeks old

extract_protocol: Mouse livers were homogenized in guanidine isothiocyanate solution (Invitrogen) supplemented with 8% 2-mercaptoethanol (Sigma-Aldrich). Total RNA was prepared using the Qiagen RNeasy columns.

treatment_protocol: 2/3 PHx or sham surgery

value: liver

value: male

tag: treatment

value: 72 hours after 2/3 partial hepatectomy


title: Breast tumor 21

value: Invasive Lobular Carcinoma


title: PHx 72 Hrs_5


title: PHx 72 Hrs_2


title: PHx 72 Hrs_1


title: PHx 72 Hrs_4


title: Breast tumor 26

value: Invasive Ductal Carcinoma


title: PHx 36 Hrs_4

description: Gene expression at 36 hours after 2/3 partial hepatectomy

source_name: mouse liver RNA collected at 36 hours after 2/3 partial hepatectomy

value: 36 hours after 2/3 partial hepatectomy


title: PHx 36 Hrs_3


title: Breast tumor 22

value: II

value: positive


title: PHx 36 Hrs_5


title: PHx 36 Hrs_2


title: Breast tumor 16

value: I

value: negative

value: female


title: Breast tumor 17

value: normal


title: Breast tumor 15


title: PHx 12 Hrs_5

description: Gene expression at 12 hours after 2/3 partial hepatectomy

source_name: mouse liver RNA collected at 12 hours after 2/3 partial hepatectomy

value: 12 hours after 2/3 partial hepatectomy


title: PHx 36 Hrs_1


title: PHx 12 Hrs_2


title: PHx 12 Hrs_1


title: PHx 12 Hrs_3


title: Breast tumor 12


title: Breast tumor 14

value: Ductal Carcinoma In Situ


title: PHx 4 Hrs_3

description: Gene expression at 4 hours after 2/3 partial hepatectomy

source_name: mouse liver RNA collected at 4 hours after 2/3 partial hepatectomy

value: 4 hours after 2/3 partial hepatectomy


title: PHx 4 Hrs_4


title: Breast tumor 11

value: III


title: PHx 4 Hrs_2


title: Sham_5

description: Gene expression at hours after sham surgery

source_name: mouse liver RNA collected at 4 hours after sham surgery

value: sham surgery


title: PHx 12 Hrs_4

value: liver


title: Sham_4

value: male


title: PHx 4 Hrs_5


title: Sham_2


title: sgu421fvsby4743-2

city: FLORENCE

first: DAMARIZ

last: RIVERO

state: FLORENCE

address: VIALE PIERACCINI 6

department: NEUROFARBA

country: Italy

institute: UNIFI

description: Comparative genomic hybridization Sgu421 vs By4743

hyb_protocol: Hybridization took place at 65 °C for 16 h.

scan_protocol: Fluorescent DNA bound to the microarray was detected with a GenePix 4000B microarray scanner (Axon Instruments), using the GenePixPro6.1 software package to quantify microarray fluorescence.

data_processing: Data were normalized using the limma R package and DEGs (Differentially Expressed Genes) were identified with the RankProduct R package

organism: Saccharomyces cerevisiae

source_name: natural strain, Sgu421, diploid, prototrophic

label_protocol: The genomic DNA extracted was concentrated using the filter Microcon YM-30 (Millipore) and fragmented by sonication. The labeling of the DNA was performed, at 37°C for 2 hours, using the BioPrime DNA labeling Sytem (Invitrogen, Life Technologies), but using 100mM dNTP set (Invitrogen, Life Technologies) instead of the biotinilated nucleotides present in the kit, as well as the fluorescent nucleotides Cy3-dCTP and Cy5-dCTP of Amersham, GE Healthcare. Once finished the reaction, the DNA was purified with the Microcon YM-30 and the appropriate pairs of samples labeled with the different fluorochromes were combined in a single eppendorf in 450µL of TE (Tris-EDTA), pH 8.0 (Sigma-Aldrich). We used Human cot-1 DNA (Invitrogen, Life Technologies) to block non-specific hybridization, and Yeast tRNA (Invitrogen, Life Technologies) as coprecipitant.

growth_protocol: Yeast cells were grown in YPD at 28 °C with shaking for 16 hours

extract_protocol: DNA was extracted from 1*108 following the protocol by Hoffman CS and Winston F, 1987. Gene 57:267-272.

treatment_protocol: no special treatment

source_name: laboratory strain, By4743, auxotrophic

value: laboratory strain, By4743, auxotrophic


title: sgu165vsby4743-2

description: Comparative genomic hybridization Sgu165 vs By4743

source_name: natural strain, Sgu165, diploid, prototrophic


title: sgu421fvsby4743-1

value: natural strain, Sgu421, diploid, prototrophic


title: Breast tumor 4

value: Invasive Ductal Carcinoma


title: Breast tumor 6


title: Time1_rep4

hyb_protocol: Arrays were hybridized as described by the manufacturer. Hybridization took place at 63 °C for 14–16 h.

scan_protocol: Fluorescent cDNA bound to the microarray was detected with a GenePix 4000B microarray scanner (Axon Instruments), using the GenePixPro6.1 software package to quantify microarray fluorescence.

source_name: Sgu421, SWM, 144hs

label_protocol: The labeling method used was the indirect method described by DeRisi (see the University of California San Francisco DeRisi laboratory Web site).

growth_protocol: Sgu421 was grown in SWM or Sgu165 spent medium at 28 °C with shaking at 2x104 cells/mL.

extract_protocol: RNA was extracted from about 1 *109 cells using the hot acid phenol/chloroform protocol. RNAs were quantified spectrophotometrically using Nanodrop and by measuring the absorbance at 230, 260, and 280 nm and then calculating the 260/230 and 260/280 ratios and considering good data to be values of 1.8–2.2. RNA integrity was checked by electrophoresis in 1% agarose gel stained with ethidium bromide.

treatment_protocol: Cell-free spent medium were prepared from an overnight pre-culture of the strain Sgu165  in YPD. The cells were centrifugated at 4500g for 10 minutes, washed twice with sterile water and then were resuspended in SWM at1x108 cells/mL and left them to grow for 6 days. After centrifugation, the supernatant was taken and filtered using a 0.2 micron sterile syringe filter (Merck Millipore). For the growth of the strains using the spent medium, it was diluted in a 1:3 ratio with fresh SWM in order to ensure the minimum of nutrients necessary for the growth.

source_name: Sgu421, spent_medium of Sgu165, 144hs


title: Breast tumor 5


title: Time1_rep3


title: Sham_1


title: Time1_rep2


title: Sham_3


title: Breast tumor 1


title: PHx 4 Hrs_1


title: Breast tumor 10


title: Breast tumor 3


title: Time1_rep1


title: Time0_rep4

source_name: Sgu421, SWM, 48hs

source_name: Sgu421, spent_medium of Sgu165, 48hs


title: Breast tumor 2


title: Time0_rep3


title: sgu165vsby4743-1

value: natural strain, Sgu165, diploid, prototrophic


title: SRFdam

city: Westmead

first: Ashley

last: Waardenberg

state: NSW

address: 214 Hawkesbury Road

country: Australia

institute: Children's Medical Research Institute

description: SRF-dam DamID Biological Rep 1-3, promoter

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing:
Probe remapping to NCBI Build 37 (mm9) was performed using the Starr R package. Data was quantile normalized and analyzed with TileMapv2 implemented in cisGenome. TileMapv2 moving average (ma) >3.5 and a minimum of 8 probes were used as thresholds for contrasting inputs versus controls. Statistics are reported in the COD files.
DamID.bed
.cod are generated by CisGenome software and summarises binding regions detected and summary statistics. File DamID.bed contains all binding regions (18,505 peaks) detected for each C/N-terminal fusion as reported in the paper; this file has been prepared for uploading into the UCSC genome browser.

source_name: SRF-dam DamID DNA from HL1 cells (experiment #1)

label_protocol: standard Affymetrix protocol

growth_protocol: HL-1 cells were grown in Claycomb medium, 10% FBS, 0.1mM Norepinephrine and 2mM L-Glutamine at 37°C in an atmosphere of 5% CO2 at a relative humidity of ~95%

extract_protocol: Genomic DNA was extracted using Gentra PureGene (Qiagen) following manufacturers instructions, digested by DpnI, LM-PCR amplified and fragemented with DNaseI

treatment_protocol: HL-1 cells were transduced for 18 hours with Dam fusions and then cultered for another 23 hours before extraction

value: HL-1 cardiomyocyte

value: SRF-dam

source_name: dam-ONLY DamID DNA from HL1 cells (experiment #1)

value: control


title: damNKX2-5YRD^(Y-A)

description: dam-NKX2-5YRD^(Y-A) DamID Biological Rep 1-4, promoter

hyb_protocol: 7.5μg of fragmented, biotin labelled DNA was hybridized to each array. Arrays were hybridized for 16 hours at 45° at 60rpm using an Affymetrix hybridization oven. The arrays were washed according to manufacturers instructions on an Affymetrix FS450 fluidics station.

scan_protocol: Arrays were scanned on an Affymetrix Scanner GC3000 7G

source_name: dam-NKX2-5YRD^(Y-A) DamID DNA from HL1 cells (experiment #3)

label_protocol: Fragmented double-stranded DNA was end labelled with biotin according to manufacturers instructions.

source_name: dam-ONLY DamID DNA from HL1 cells (experiment #2)


title: damNKX2-5(repeat)

description: dam-NKX2-5 DamID Biological Rep 1-4, promoter

source_name: dam-NKX2-5 DamID DNA from HL1 cells (experiment #3)


title: ASMC_VersicanV3_repC_exp1

city: Charleston

first: Jeremy

last: Barth

state: SC

address: 173 Ashley Ave, BSB 627

institute: MUSC

hyb_protocol: GeneChips were hybridized for 16h at 45oC with rotation in an Affymetrix Hybridization Oven 640 and then washed and stained using Fluidics Station 450 instruments and reagents in the Affymetrix Hybridization Wash and Stain kit according to manufacturer recommedations.

scan_protocol: GeneChips were scanned in an Affymetrix 7G scanner.

data_processing: Raw data (CEL files) were normalized by RMA algorithm using Affymetrix Expression Console software.

label_protocol: Total RNA (100ng) was converted to biotin-labeled cRNA using the Affymetrix 3' IVT Express Plus kit.

growth_protocol: Fischer rat ASMCs were obtained and cultured as described by Clowes et al. (1994).

extract_protocol: Total RNA was first isolated by the Single Step Method by solubilizing the cells in solution D and 2.0M sodium acetate (Chomczynski, P., and Sacchi, N., 1987).  The soluble phase from subsequent phenol/chloroform/isoamyl alcohol extraction was precipitated with isopropanol.  Pelleted RNA was further purified using an Agilent Total RNA Isolation Mini Kit (Agilent Technologies, Santa Clara, CA) according to manufacturer specifications.

treatment_protocol: Retroviral vectors containing either the versican V3 gene (LV3SN) or an empty control vector (LXSN) were used to infect Fischer rat ASMCs using PA317 packaging cells as described by Clowes et al. (1994) and Lemire et al. (2002). Retrovirally-transduced cells were maintained in Dulbecco’s high glucose Modified Eagle Medium (DMEM) supplemented with 10% FBS, sodium pyruvate, nonessential amino acids, glutamine and penicillin-streptomycin (Invitrogen, Carlsbad, CA). Cells were used between 4 and 8 passages after the initial transduction.

value: FischerRat

tag: cell type

value: Arterial smooth muscle cells (ASMCs)

tag: transduced with

value: retroviral vector expressing the Versican V3 splice variant (LV3SN)

tag: experiment


title: ASMC_VersicanV3_exp2


title: ASMC_VersicanV3_repD_exp1


title: damNKX2-5ΔHD

description: dam-NKX2-5ΔHD DamID Biological Rep 1-3, promoter (RB_RS12.CEL was removed at QC and not used in the pairwise analysis)

source_name: dam-NKX2-5ΔHD DamID DNA from HL1 cells (experiment #2)


title: damSRF

description: dam-SRF DamID Biological Rep 1-3, promoter

source_name: dam-SRF DamID DNA from HL1 cells (experiment #1)

value: dam-SRF


title: damNKX2-5

description: dam-NKX2-5 DamID Biological Rep 1-3, promoter

source_name: dam-NKX2-5 DamID DNA from HL1 cells (experiment #2)


title: ASMC_VersicanV3_repA_exp1


title: Uncomplicated malaria 2 PFU-04

description: Gene expression of parasite isolates

source_name: P. falciparum parasites from patient's blood

value: F

value: uncomplicated malaria

tag: tissue

value: blood


title: ASMC_VersicanV3_exp3


title: ASMC_Control_exp2

value: empty control vector (LXSN)


title: Time0_rep2


title: ELK4dam

description: dam-ELK4 DamID Biological Rep 1-3, promoter

source_name: dam-ELK4 DamID DNA from HL1 cells (experiment #1)

tag: cell line


title: ASMC_VersicanV3_repB_exp1


title: ASMC_Control_repB_exp1


title: ASMC_Control_repD_exp1


title: ASMC_Control_repC_exp1


title: Time0_rep1


title: ASMC_Control_exp3


title: ELK1dam

description: ELK1-dam DamID Biological Rep 1-3, promoter

source_name: ELK1-dam DamID DNA from HL1 cells (experiment #1)


title: damELK1

description: dam-ELK1 DamID Biological Rep 1-3, promoter

source_name: dam-ELK1 DamID DNA from HL1 cells (experiment #1)


title: ASMC_Control_repA_exp1


title: damELK4

description: ELK4-dam DamID Biological Rep 1-3, promoter

source_name: ELK4-dam DamID DNA from HL1 cells (experiment #1)


title: Liver_6h_rep2

description: ChIP-chip Regenerating rat liver, 6h, NFkB

source_name: NF-kB ChIP DNA from Rattus norvegicus regenerating liver at 6h post PHx, biological replicate 2

tag: genotype

value: Wild-type

value: Male

value: Sprague Dawley

value: 8-10 weeks

tag: weight

tag: liver lobe

value: Right median, right lateral, and caudate lobe

tag: chip antibody

value: NF-κB antibody (Cat#ab7970, Rabbit polyclonal NF-κB p65 antibody and negative control IgG antibody from Abcam Inc, Cambridge, MA)

source_name: Input DNA from Rattus norvegicus regenerating liver at 6h post PHx, biological replicate 2

value: none, input DNA


title: LMP2A/CD19(cy3) vs C76/CD19(cy5) dyeswap

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

hyb_protocol: After washing in GE washing buffer, the slide was scanned with Agilent Microarray Scanner G2505C.

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version.10.7.3.1).

data_processing: Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction and LOWESS normalization.

source_name: GFP/CD19-Cre mouse splenic B220+ B cells

label_protocol: 100 ng of total RNA was labeled using Low Input Quick-Amp Labeling Kit (Agilent Technologies, Pato Alto, CA, USA). Differentially labeled 825 ng of each cRNA samples were hybridized on microarray slides. Samples were then hybridized on Agilent 4X44K ver.2 whole mouse genome arrays (Agilent Design # 026655) at 65 °C for 17 h with rotation in the dark. Hybridization was performed using the Gene Expression Hybridization Kit (Agilent Technologies Inc., Santa Clara, CA, USA) following the manufacturer's instructions.

growth_protocol: B220+ B cells were isolated from splenocytes using B220 MicroBeads (Miltenyi Biotec).

extract_protocol: Total RNA was purified using Trizol (Invitrogen, Carlsbad, CA) following the protocol of the manufacturer.

treatment_protocol: Isolated B cells were immediately used for RNA extraction without treatment.

value: splenic B220+ B cells

source_name: LMP2A/CD19-Cre mouse splenic B220+ B cells


title: 15p-mEpSCs (Cy3) vs. 0p-mEpSCs (Cy5), biological replicate 2 dyeswap

description:
15p-mEpSCs(cy3) vs 0p-mEpSCs(cy5) biological replicate 2 dyeswap
15p-EpSCs-rep4

hyb_protocol: Samples were hybridized on Agilent 4X44K ver.2 whole mouse genome arrays (Agilent Design # 026655) at 65 °C for 17 h with rotation in the dark. Hybridization was performed using the Gene Expression Hybridization Kit (Agilent Technologies Inc., Santa Clara, CA, USA) following the manufacturer's instructions. After washing in GE washing buffer, the slide was scanned.

scan_protocol: Slides were scanned with Agilent Microarray Scanner G2505C. Images were quantified using Agilent Feature Extraction Software (version.10.7.3.1).

source_name: FACS-sorted CD49f+ CD34+ cells

label_protocol: 200 ng of total RNA was labeled using Low Input Quick-Amp Labeling Kit (Agilent Technologies, Palo Alto, CA, USA). Differentially labeled 825 ng of each cRNA samples were hybridized on microarray slides.

growth_protocol: Adult C3H/HeN mouse-derived primary skin epithelial cells (MPSECs) were exposed to anti-α6 integrin (CD49f) or rat IgG2a isotype (control) directly coupled to PE (R&D systems, Inc.) antibodies directly coupled with a fluorochrome for 30 minutes on ice. After FACS analysis, the cells were resuspended in EpilifeTM serum-free culture medium. FACS-collected CD49f+CD34+ cells from MPSECs were suspended in EpilifeTM serum-free culture medium.

treatment_protocol: After assessing their viability by trypan blue staining, they were used for the primary culture, for which they were plated at a density of 5X10^4 cells per dish and cultured for 10 days in the presence of Wnt-3a in 60-mm dishes coated with collagen type I (Nippon Ham, Tsukuba, Japan). The culture medium was changed every 2 days. On day 10, all cells were collected and analyzed for their expression of CD49f and CD34 by FACS. By repeating the procedure of CD49f+CD34+ cell sorting on day 10 and subsequent passage to the next 10-day culture with Wnt-3a, sequential cultures were performed up to the 15th culture.

tag: strain

value: adult

value: mouse primary skin epithelial cells (MPSECs)

tag: cell subtype

value: FACS-sorted CD49f+ CD34+ cells (0p-EpSCs)

value: 15th passaged and sorted CD49f+ CD34+ cells (15p-EpSCs)


title: C76/CD19(cy3) vs LMP2A/CD19(cy5)

description: C76/CD19(cy3) vs LMP2A/CD19(cy5)


title: 0p-mEpSCs (Cy3) vs. 15p-mEpSCs (Cy5), biological replicate 2

description:
0p-mEpSCs(cy3) vs 15p-mEpSCs(cy5) biological replicate 2
15p-EpSCs-rep3

source_name: 15th passaged and sorted CD49f+ CD34+ cells


title: Complicated malaria 1 PFC-03

description: Gene expression of parasite isolates

value: M

tag: disease state

value: Jaundice, renal failure, thrombocytopenia


title: LE-1

city: Los Angeles

first: Muller

last: Fabbri

address: 4650 Sunset Blvd

institute: University of South California - Children's hospital Los Angeles

description: LoVo infected with an empty lentivirus (control of L339)

hyb_protocol: 15 ug of biotin-labeled cRNA was hybridized to Affymetrix Genechip Human Genome U133 Plus 2.0

scan_protocol: The arrays were scanned using the GeneChip Scanner 3000.

data_processing: Affymetrix CEL files were imported to the BRB software tools, normalized using the robust multichip analysis (RMA) procedure and log 2 transform.

source_name: colorectal cancer

label_protocol: RNA was linearly amplified and labeled using the BioArray High Yield RNA Transcript labeling kit (Enzo Life Sciences.

growth_protocol: A549 and LoVo cells were grown in F12K medium (ATCC), supplemented with 10% FBS.

extract_protocol: Total RNA was extracted using the TRIzol reagent (Invitrogen). RNA concentration and quality were assessed with a NanoDrop ND-1000 Spectrophotometer (Thermo Scientific).

treatment_protocol: The uc.339 plasmid and empty plasmid were transfected with the pPACK Lentivector Packaging System (System Biosciences) in the 293TN packaging cell line to generate lentiviral particles carrying uc.339 (or its empty control). A549 and LoVo cells were infected at an MOI of 10 and were selected for green fluorescence by cytofluorimetry with a BD FACSCalibur platform (BD Biosciences). After selection, the expression of uc.339 was validated by qRT-PCR and cells were plated at a confluence of 60%. After 48h cells were harvested and total RNA extracted.

tag: histology

value: adenocarcinoma

value: LoVo


title: 15p-mEpSCs (Cy3) vs. 0p-mEpSCs (Cy5), biological replicate 1 dyeswap

description:
15p-mEpSCs(cy3) vs 0p-mEpSCs(cy5) biological replicate 1 dyeswap
15p-EpSCs-rep2


title: 0p-mEpSCs (Cy3) vs. 15p-mEpSCs (Cy5), biological replicate 1

description:
0p-mEpSCs(cy3) vs 15p-mEpSCs(cy5) biological replicate 1
15p-EpSCs-rep1


title: LE-3


title: L339-3

description: LoVo infected with a lentivirus over-expressing uc.330


title: LE-2


title: ifn_torin1_total_4

city: Stockholm

first: Ola

last: Larsson

department: Department of oncology-pathology

country: Sweden

institute: Karolinska Institutet

description: WISH cells were starved followed by treatment with dmso or with interferon in the presence of dmso, rapamycin or torin-1

hyb_protocol: Samples were hybridized with the Affymetrix Human Gene 1.1 ST Array according the instructions of the manufacturer

scan_protocol: Arrays were scanned using the GeneArray Scanner 3000 according to the instructions from the manufacturer.

data_processing: Data were extracted and normalized using a custom CDF and Robust Multi-array Average (RMA) in R (r-project.org) with default settings.

label: Biotin

source_name: WISH cells

label_protocol: Single round labeling recommended by manufacturer.

growth_protocol: WISH cells were cultured as previously described [Francois-Newton V, Livingstone M, Payelle-Brogard B, Uze G, Pellegrini S (2012) USP18 establishes the transcriptional and anti-proliferative interferon alpha/beta differential. Biochem J 446: 509-516 and Marijanovic Z, Ragimbeau J, van der Heyden J, Uze G, Pellegrini S (2007) Comparable potency of IFNalpha2 and IFNbeta on immediate JAK/STAT activation but differential down-regulation of IFNAR2. Biochem J 407: 141-151]. WISH cells were obtained from G. Uzé (CNRS, Montpellier) and originate from ATCC (CCL-25). Their identity was compared to HeLa S3 cells by short tandem repeat (STR) loci profiling. This analysis, performed by IdentiCell (Department of Molecular Medicine, Aarhus University Hospital), showed that the two cell lines have identical STR profiles.

extract_protocol: RNAeasy (Qiagen)

treatment_protocol: WISH cells were trypsinized and plated in 10cm tissue culture dishes at 4 X 10^6 cells/dish. After 30 hrs, cells were re-fed with fresh medium with or without IFN  (100pM) and/or mTOR inhibitors at saturating concentrations (rapamycin 100nM or Torin1 1M) for 12h.

value: WISH

tag: rna type

value: total

tag: replicate


title: ifn_torin1_total_1


title: ifn_torin1_polysome_2

value: Polysome-associated


title: ifn_torin1_polysome_3


title: ifn_torin1_total_3


title: AE-1

description: A549 infected with an empty lentivirus (control of A339)

source_name: lung cancer


title: AE-3


title: L339-2


title: AE-2


title: A339-2

description: A549 infected with a lentivirus over-expressing uc.339


title: A339-1


title: ifn_rap_total_4


title: ifn_torin1_total_2


title: ifn_torin1_polysome_1


title: L339-1


title: A339-3


title: ifn_torin1_polysome_4


title: ifn_rap_total_2


title: ifn_rap_total_3


title: Breast tumor 46

source_name: FFPE tumor

value: Invasive Ductal Carcinoma

tag: grade

value: III

tag: estrogen receptor

value: negative

value: positive

tag: brca1 expression

source_name: normal lymph nodes

tag: gender

value: female

tag: malignancy

value: normal


title: Breast tumor 44

value: Ductal Carcinoma In Situ

tag: brca mutation


title: PBMC-HD-04

city: Kanazawa

first: Shinji

last: Kitajima

address: 13-1 Takara-machi

institute: Kanazawa University hospital

hyb_protocol: The labelled cRNA was cleaned, quantified and hybridized to Affymetrix HG-U133 Plus2.0 GeneChips after fragmentation.

scan_protocol: The chips were washed and stained with streptavidin phycoerythrin was amplified using a biotinylated antibody solution in an Affymetrix Fluidics Station 450 according to the Affymetrix GeneChip protocol.

data_processing: Data was extracted using the GeneChip scanner 3000 (Affymetrix, Santa Clara, CA) and raw data file formats were generated using the Gene Chip Operating Software (GCOS).

source_name: peripheral blood cells in patients with hemodialysis

label_protocol: After the second cycle cDNA synthesis, biotin-labelled cRNA was generated using the Affymetrix IVT labelling kit

growth_protocol: Blood specimens (2.5 ml) were collected from AM 8 to 10’, before hemodialysis in PAXgene tubes from each patient.

extract_protocol: Total RNA (100 ng) was used for the generation of biotin-labelled cRNA  using the Affymetrix Two-Cycle cDNA Synthesis Kit (Affymetrix, Santa Clara, CA)

treatment_protocol: RNA was extracted from whole blood using the PAXgene Blood RNA System Kit

tag: cell type

value: PBMC

value: male


title: ifn_rap_total_1

tag: cell line

tag: treatment


title: Breast tumor 45

value: II


title: ifn_rap_polysome_4


title: Breast tumor 51

value: ND


title: Breast tumor 42


title: PBMC-HD-01


title: PBMC-HD-02


title: ifn_rap_polysome_3


title: Breast tumor 39


title: ifn_rap_polysome_2


title: Breast tumor 36

value: I


title: Breast tumor 35


title: Breast tumor 37


title: PBMC-CKD-07

source_name: peripheral blood cells in patients with chronic kidney disease


title: Breast tumor 34


title: PBMC-CKD-06


title: Breast tumor 38

value: Lobular Carcinoma In Situ


title: ifn_rap_polysome_1


title: Breast tumor 43


title: PBMC-CKD-05

value: fimale


title: Breast tumor 41


title: PBMC-CKD-03


title: ifn_total_4

value: WISH

value: ifn


title: PBMC-CKD-04


title: Breast tumor 32


title: Breast tumor 30

value: Invasive Lobular Carcinoma


title: Breast tumor 33

value: Invasive Ductal Carcinoma


title: PBMC-HD-03


title: PBMC-CKD-02


title: ifn_total_2

value: total


title: ifn_total_1


title: Breast tumor 31

value: negative


title: Breast tumor 28

value: positive


title: PBMC-CKD-01


title: Breast tumor 29

value: female


title: ifn_polysome_3

value: Polysome-associated


title: ifn_polysome_2


title: Breast tumor 25

value: III

value: normal


title: PBMC-HT-06

source_name: peripheral blood cells in patients with hypertension

value: PBMC

value: male


title: Breast tumor 24

value: II


title: PBMC-HT-07


title: ifn_total_3


title: Breast tumor 13

value: Ductal Carcinoma In Situ


title: Breast tumor 20

value: Lobular Carcinoma In Situ


title: PBMC-HT-08


title: PBMC-HT-05


title: Breast tumor 8


title: Breast tumor 19


title: Breast tumor 9


title: ifn_polysome_1


title: Breast tumor 23


title: L-02_plNCX2_MEN1

city: Xiamen

first: Shubin

last: Gao

address: Chengzhi building 110,Xiang'an South Road

department: Basic Medical Sciences

institute: Medical College,Xiamen University

description: Gene expression in L-02 cells with constructs expressing MEN1

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid:014850_D_F_20090416 ) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.  Further analysis was performed in Agilent GeneSpring GX software (version11.0). Data were normalized in GeneSpring GX using the Agilent FE one-color scenario (mainly median normalization).

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

extract_protocol: RNA was extracted from HepG2 cells or L-02 cells transfected with empty vector or a construct expressing MEN1 using TRIzol (Invitrogen). The RNA samples were hybridized to the microarray according to the manufacturer’s protocol.

treatment_protocol: The HepG2 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM, Gibco)  supplemented with 10% fetal bovine serum (FBS, Hyclone) and 1% penicillin–streptomycin.


title: ifn_polysome_4


title: dmso_total_4

value: dmso


title: PBMC-HT-04


title: dmso_total_3

value: WISH


title: dmso_polysome_4


title: dmso_total_2


title: 7A3_dye_swap

city: London

first: Paolo

last: Cremaschi

state: Non-US

address: 72 Huntley Street

department: Oncology

country: United Kingdom

institute: UCL Cancer Institute

hyb_protocol: Equal amounts of labeled specimens from 46BR.1G1 and 7A3 cell lines were put together, fragmented and hybridized to oligonucleotide glass arrays representing 19,596 Entrez Gene RNAs (Whole Human Genome Microarray, 4x44K, Agilent Technologies). All steps were performed using the In Situ Hybridization kit-plus (Agilent Technologies) and following the 60-mer oligo microarray processing protocol (Agilent Technologies). Then, slides were washed with the Agilent wash procedure. For each sample, a dye-swap replicate was performed.

scan_protocol: Slides were scanned with the dual-laser microarray scanner Agilent G2505B.

data_processing: Images were analysed using Feature Extraction software (Agilent Technologies) version 5.95. Raw data elaboration was carried out with Bioconductor (Gentleman et al., 2004), using R statistical language. Background correction was performed with the normexp method with an offset of 50, loess was used for the within array normalization and Aquantile for between-array normalization. The limma package was used to identify differentially expressed genes. The empirical Bayes method was used to compute a moderated t-statistics.

label_protocol: mRNA was amplified by means of the Amino Allyl MessageAmp II aRNA Kit (Life Technologies) to obtain amino allyl antisense RNA (aaRNA) following the method developed by Eberwine and coworkers. Briefly: mRNA was reverse transcribed in cDNA single strand; after the second strand synthesis, cDNA was in vitro transcribed in aaRNA including amino allyl modified nucleotides (aaUTP). Both dsDNA and aaRNA underwent a purification step using columns provided with the kit.Labeling was performed using NHS ester Cy3 or Cy5 dyes (Amersham, GE Healthcare) able to react with the modified RNA. mRNA quality and quantity were checked by means of RNA 6000 nano chip assays (Agilent Technologies) and NanoDrop 1000 Spectrophotometer (Thermo Scientific), respectively.

growth_protocol: 46BR.1G1 fibroblasts (European Collection of Cell Cultures # CB2577) were maintained in monolayer culture in DMEM supplemented with 10% FBS, 4 mM glutamine, and 50 µg/ml gentamicin (complete DMEM). 46BR.1G1 derivatives 7A3 were grown in complete DMEM supplemented with 300 µg/ml geneticin (Sigma).

extract_protocol: total RNA quality and quantity were checked by means of RNA 6000 nano chip assays (Agilent Technologies) and NanoDrop 1000 Spectrophotometer (Thermo Scientific), respectively

treatment_protocol: For total RNA extraction  4x10^6 cells were trypsinized and lyzed according to the RNA extraction kit Promega.

value: human fibroblasts

tag: genotype/variation

value: wild type (reference cell line)

tag: cell info

value: 7A3 (46BR.1G1 derivative)

value: expressing wild type LigI


title: PBMC-HT-03


title: HepG2_plNCX2_MEN1

description: Gene expression in HepG2 cells with constructs expressing MEN1


title: DsR-7F4 600 MeV/u (56)Fe 0 Gy rep 2

city: Atlanta

first: Zhentian

last: Li

address: 1510 Cliton Rd, RRC 4172

institute: Emory University

hyb_protocol: Samples were processed using Affymextrix Standard Operating Procedure.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner 2000, and data files were generated using AGCC

data_processing: Raw data (.cel files) were imported into the Partek Genomics Suite (Partek, Inc., St. Louis, MO) and the data were normalized using Robust Multichip Averaging (RMA), with adjustment for GC content.

source_name: DsR-7F4 600 MeV/u (56)Fe 0 Gy rep 2

extract_protocol: Total RNA was isolated using an RNeasy Mini Kit from treated cells according to manufacture's instruction.

tag: dose group

value: 0 Gy


title: dmso_total_1

value: total


title: DsR-7F4 600 MeV/u (56)Fe 0 Gy rep 3

source_name: DsR-7F4 600 MeV/u (56)Fe 0 Gy rep 3

label_protocol: Samples were processed using Affymextrix Standard Operating Procedure.


title: DsR-7F4 600 MeV/u (56)Fe 0 Gy rep 1

source_name: DsR-7F4 600 MeV/u (56)Fe 0 Gy rep 1


title: L-02_plNCX2

description: Gene expression in L-02 cells with plNCX2 vector


title: DsR-7F4 600 MeV/u (56)Fe 0.3 Gy rep 3

source_name: DsR-7F4 600 MeV/u (56)Fe 0.3 Gy rep 3


title: HepG2_plNCX2

description: Gene expression in HepG2 cells with plNCX2 vector


title: PBMC-HT-02


title: 7A3_marc_norm

value: 46BR.1G1 fibroblasts (European Collection of Cell Cultures # CB2577)

tag: cell line info


title: DsR-7F4 600 MeV/u (56)Fe 1.0 Gy rep 3

source_name: DsR-7F4 600 MeV/u (56)Fe 1.0 Gy rep 3


title: dmso_polysome_3

value: Polysome-associated


city: Beijing

first: Haibo

last: Yang

institute: Institute of Microbiology, Chinese Academy of Sciences

description: Haloferax mediterranei DF50ΔoriC1ΔoriC2ΔoriC3 genomic DNA of exponential phase vs that of stationary phase

hyb_protocol: standard CapitalBio Methods

scan_protocol: Arrays were scanned on an MS200 scanner per manufacturer's protocol

data_processing: Arrays were processed using Nimblegen's standard protocol. The ratios were calculated as exponential phase values (or at time points 12h, 18h, 24h, 36h and 42h) versus stationary phase values for each probe. As the probes were designed according to the former version genome of Haloferax mediterranei (CP001868.1-CP001871.1), the position of the probes was adjusted according to the latest version genome of Haloferax mediterranei (CP001868.2, CP001869.1-CP001871.1) when we plot the replication profile. The difference between the former version CP001868.1 and the latest version CP001868.2 is a 1 Mb fragment inversion between the two rRNA operons in the chromosome, while the nucleotide sequences are the same. Thus, we just invert the position of probes between two rRNA operons (corresponding to probes between 33500CHROMOSOMES001745415 and 33500CHROMOSOMES002842080). Due to the high density of the probes, the ratios of the thirty probes were averaged as one point located at the first probe. The MFA graph was plotted with a 5-point window and 1-point slide.

source_name: Genomic DNA of Haloferax mediterranei DF50ΔoriC1ΔoriC2ΔoriC3 at exponential phase

label_protocol: 1 µg sonicated genomic DNA  was labeled by Klenow (New England Biolabs) random priming with Cy3 or Cy5 nonamers per manufacturer's protocol

growth_protocol: Cells  were grown at 37°C until OD600 reached 0.5 in AS-168 medium supplemented with uracil

extract_protocol: Proteinase K, ethanol precipitation, RNaseA treatment, phenol-chloroform extraction as described previously [PMID: 24271389]

tag: strain

tag: phase

value: exponential phase

source_name: Genomic DNA of Haloferax mediterranei DF50ΔoriC1ΔoriC2ΔoriC3 at stationary phase

value: stationary phase


title: DsR-7F4 600 MeV/u (56)Fe 0.3 Gy rep 1

source_name: DsR-7F4 600 MeV/u (56)Fe 0.3 Gy rep 1


title: Replicate 3: BDF1 Wt vs F33-Tat

status: Public on Jul 06 2015

city: Catanzaro

first: Giuseppe

last: Fiume

address: Viale Europa - Germaneto

department: Department of Experimental and Clinical Medicine

institute: University of Catanzaro "Magna Graecia"

hyb_protocol: Standard LC Sciences protocol

scan_protocol: Standard LC Sciences protocol

data_processing: Standard LC Sciences protocol, Global Normalization

source_name: Sample A - BDF-1 Wild type

label_protocol: Standard LC Sciences protocol

extract_protocol: Total RNA was Extracted by thymus of 8 weeks old BDF1 wild type mice and F33 (HIV-1 Tat-Tg- mice)

value: wild type

tag: tissue

value: Thymus

source_name: Sample B - F33 Tat

value: Tat-Transgenic


title: dmso_polysome_2

source_name: WISH cells

tag: rna type

tag: replicate


title: Replicate 1: BDF1 Wt vs F33-Tat


title: Replicate 2: F33-Tat vs BDF1 Wt

source_name: Sample A - F33 Tat

source_name: Sample B - BDF-1 Wild type


title: DsR-7F4 600 MeV/u (56)Fe 0.3 Gy rep 2

source_name: DsR-7F4 600 MeV/u (56)Fe 0.3 Gy rep 2


title: PBMC-HT-01

value: PBMC

value: female


title: DsR-7F4 600 MeV/u (56)Fe 1.0 Gy rep 2

source_name: DsR-7F4 600 MeV/u (56)Fe 1.0 Gy rep 2


title: Ms5Yah mouse hippocampus 8

city: Durham

first: arbogast

last: thomas

state: NC

address: 300N Duke Street

department: neurosciences

institute: Duke University

hyb_protocol: Samples were hynridized with Mouse Exon 1.0 ST Arrays (Affymetrix), washed and scaned using the GeneChip® Scanner 3000

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Raw data were processed with the Robust Multiarray Average (RMA) algorithm and values log transformed using Partek and GeneSptring softwares.

source_name: Mutant Ms5Yah  mouse

label_protocol: In conjunction with the Affymetrix GeneChip WT Terminal Labeling Kit, the Ambion WT Expression Kits was designed to generate amplified and biotylated sense-strand DNA targets from the entire expressed genome

growth_protocol: Hippocampi cere isolated from 4-month mice and flash frozen.Total RNA was prepared using Trizol (Invitrogen) according to the manufacturer's instructions.

extract_protocol: RNA was prepared using Trizol (Invitrogen) and purified with the Rneasy Mini Kit (Quiagen) according to the manufacturer's instructions.

value: mixed C57BL/B6N:C3B

value: hippocampus


title: dmso_polysome_1

value: WISH

value: dmso


title: Ms5Yah mouse hippocampus 9


title: Ms5Yah mouse hippocampus 7


title: Ms5Yah mouse hippocampus 4


title: Ms5Yah mouse hippocampus 6


title: Ms5Yah mouse hippocampus 3


title: wild-type mouse hippocampus 8

source_name: Wild-type mouse


title: wild-type mouse hippocampus 5


title: wild-type mouse hippocampus 3


title: Ms5Yah mouse hippocampus 1


title: wild-type mouse hippocampus 7


title: Ms5Yah mouse hippocampus 2


title: wild-type mouse hippocampus 4


title: wild-type mouse hippocampus 6


title: wild-type mouse hippocampus 1


title: wild-type mouse hippocampus 2


title: 5ml/kg NTS WKY kidney at D14, biological rep4

city: Wuppertal

first: Heidrun

middle: Christine

last: Ellinger-Ziegelbauer

address: Aprather Weg 18a

country: Germany

institute: Bayer Pharma AG

description: Gene expression of kidney homogenate from WKI rats with glomerulonephritis 14 days after injection of 5 ml/kg NTS

hyb_protocol: Following fragmentation, 12.5 µg of aRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome Array. GeneChips were washed and stained in the GeneChip® Fluidics Station 450 running th Prime_450 protocol.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using GeneData Expressionist® Pro Refiner. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: whole kidney homogenate from WKI rats with glomerulonephritis 14 days after injection of 5 ml/kg NTS

label_protocol: Biotinylated aRNA were prepared according to the standard Affymetrix protocol from 500 ng high quality total kidney RNA (GeneChip® 3 IVT Express Kit).

growth_protocol: All animal experiments were performed according to the German guidelines for care and use of laboratory animals. Male Wistar Kyoto (WKY) and Sprague Dawley (SD) rats, 8 weeks old, were purchased from Charles River laboratories (Sulzbach, Germany). Animals were individually housed in type III makrolon cages, with a 12h light-dark cycle. Standard rodent chow pellets and water were provided ad libitum.

extract_protocol: On day 14 rats were euthanized and the kidneys were removed for histopathological examination and RNA isolation. Kidney tissue for RNA isolation was shock frozen with liquid nitrogen and stored at -80°C. Total kidney RNA was isolated with the RNeasy Mini Kit (Qiagen; Hilden, Germany) from 70 mg kidney tissue,  according to the manufacturer’s instructions. The quality of isolated RNA was assessed using Bioanalyzer Small RNA Kits (Agilent; Santa Clara, CA) and the quantity was determined with a spectrophotometer.

treatment_protocol: Rats were randomly grouped (WKY: control group n=3, treatment groups n=5; SD: all groups n=6) and dosed once iv with 0, 1 (WKY), 1.5 (SD), 2.5 (WKY) or 5 ml/kg nephrotoxic serum (NTS; Sheep Anti-Rat Glomerular Basement Membrane (GBM) Serum (PTX-001S); Probetex, San Antonio, TX). Control groups received appropriate volumes of saline.

value: Wistar Kyoto (WKY/NCr)

value: male

value: kidney


title: 5ml/kg NTS WKY kidney at D14, biological rep5


title: 2.5ml/kg NTS WKY kidney at D14, biological rep3

description: Gene expression of kidney homogenate from WKI rats with glomerulonephritis 14 days after injection of 2.5 ml/kg NTS

source_name: whole kidney homogenate from WKI rats with glomerulonephritis 14 days after injection of 2.5 ml/kg NTS


title: 5ml/kg NTS WKY kidney at D14, biological rep2


title: 2.5ml/kg NTS WKY kidney at D14, biological rep1


title: 5ml/kg NTS WKY kidney at D14, biological rep3


title: 2.5ml/kg NTS WKY kidney at D14, biological rep5


title: 2.5ml/kg NTS WKY kidney at D14, biological rep4


title: 5ml/kg NTS WKY kidney at D14, biological rep1


title: 1ml/kg NTS WKY kidney at D14, biological rep3

description: Gene expression of kidney homogenate from WKI rats with glomerulonephritis 14 days after injection of 1 ml/kg NTS

source_name: whole kidney homogenate from WKI rats with glomerulonephritis 14 days after injection of 1 ml/kg NTS


title: DsR-7F4 600 MeV/u (56)Fe 1.0 Gy rep 1

source_name: DsR-7F4 600 MeV/u (56)Fe 1.0 Gy rep 1


title: Ms5Yah mouse hippocampus 5


title: Control WKY kidney at D14, biological rep3

description: Gene expression of kidney homogenate from control WKY rats

source_name: whole kidney homogenate from control WKY rats


title: Control WKY kidney at D14, biological rep1


title: Control WKY kidney at D14, biological rep2


title: 5ml/kg NTS SD kidney at D14, biological rep3

description: Gene expression of kidney homogenate from SD rats with glomerulonephritis 14 days after injection of 5 ml/kg NTS

source_name: whole kidney homogenate from SD rats with glomerulonephritis 14 days after injection of 5 ml/kg NTS

value: Sprague Dawley (Crl:SD)


title: 1ml/kg NTS WKY kidney at D14, biological rep4


title: 1ml/kg NTS WKY kidney at D14, biological rep1


title: 2.5ml/kg NTS WKY kidney at D14, biological rep2


title: 5ml/kg NTS SD kidney at D14, biological rep1


title: 1ml/kg NTS WKY kidney at D14, biological rep5


title: 5ml/kg NTS SD kidney at D14, biological rep4


title: 1.5ml/kg NTS SD kidney at D14, biological rep5

description: Gene expression of kidney homogenate from SD rats with glomerulonephritis 14 days after injection of 1.5 ml/kg NTS

source_name: whole kidney homogenate from SD rats with glomerulonephritis 14 days after injection of 1.5 ml/kg NTS


title: 5ml/kg NTS SD kidney at D14, biological rep5


title: 5ml/kg NTS SD kidney at D14, biological rep6


title: 1.5ml/kg NTS SD kidney at D14, biological rep6


title: 1.5ml/kg NTS SD kidney at D14, biological rep4


title: 1.5ml/kg NTS SD kidney at D14, biological rep1


title: Control SD kidney at D14, biological rep5

description: Gene expression of kidney homogenate from control SD rats

source_name: whole kidney homogenate from control SD rats


title: 84A

city: Gainesville

first: M Cecilia

last: Lopez

state: FL

address: 1376 Mowry Road

department: Molecular Genetics and Microbiology

institute: University of Florida

hyb_protocol: 10ug cDNA were hybridized on a Human GGh3 following the protocol described in the GeneChip Expression Analysis Technical manual (Affymetrix, Santa Clara, CA).

scan_protocol: The GeneChip arrays were stained and scanned in an Affymetrix GCS 3000 7G Scanner.

data_processing: The data was normalized  using RMA. Analyzed using BRB array tools

source_name: EARLY_uninfected_whole blood

label_protocol: Biotinylated cDNA were prepared using Nugen Ovation Pico WTA V2 kit and labeled and fragmented with the Encore® Biotin Module from total RNA.

extract_protocol:
Human patients' peripheral blood immediately stabilized after phlebotomy
Whole blood RNA was stabilized immediately after blood draw using PaxGene™ reagent and stored at -80°C until batch processing.
Total RNA was isolated from human neonatal whole blood using the PaxGene™ Blood RNA System

tag: age group

value: EARLY

tag: age in days

value: <3 days

tag: infection

value: uninfected

value: EARLY-uninfected

value: whole blood


title: 1.5ml/kg NTS SD kidney at D14, biological rep3

tag: gender


title: 1ml/kg NTS WKY kidney at D14, biological rep2


title: Control SD kidney at D14, biological rep6


title: 57C

source_name: LATE_uninfected_whole blood

value: LATE

value: >3 days

value: LATE-uninfected


title: 53B


title: 84B


title: 57A


title: 5ml/kg NTS SD kidney at D14, biological rep2


title: Control SD kidney at D14, biological rep4


title: 57B


title: 1.5ml/kg NTS SD kidney at D14, biological rep2


title: Control SD kidney at D14, biological rep3


title: 135C

source_name: EARLY_Sepsis_whole blood

value: Sepsis

value: EARLY Sepsis


title: 83A


title: Control SD kidney at D14, biological rep2


title: 135B


title: 311B

source_name: LATE_clinical sepsis_whole blood

value: clinical sepsis

value: LATE-clinical sepsis


title: 133B


title: 133A


title: 92A

source_name: EARLY_clinical sepsis_whole blood

value: EARLY-clinical sepsis


title: 306B


title: 110Cr2

source_name: EARLY_uninfected chorio_whole blood

value: uninfected chorio

value: EARLY-uninfected chorio


title: 306C


title: 137C


title: 306A


title: Control SD kidney at D14, biological rep1

value: male

value: kidney


title: 302C

source_name: LATE_Sepsis_whole blood

value: LATE Sepsis


title: 113C

value: EARLY

value: <3 days


title: 302B


title: 71A


title: 69A


title: 64A

value: uninfected

value: EARLY-uninfected


title: 61B

value: whole blood


title: 67B


title: 65A


title: 302A

value: LATE

value: >3 days


title: 64B


title: 70A

value: LATE-uninfected


title: 68A


title: 59A


title: 58C


title: 60A


title: 301B


title: 125A

value: Sepsis


title: 116C


title: 111C


title: 118C

value: EARLY Sepsis


title: 301C


title: 301A


title: 125C


title: 110C


title: 60B


title: 116B


title: 115C


title: 104A

value: clinical sepsis


title: 68B

value: EARLY-clinical sepsis


title: 105A


title: 109B

value: LATE-clinical sepsis


title: 103B


title: 112C


title: 100A

value: uninfected chorio

value: EARLY-uninfected chorio


title: 99C


title: 100B


title: 121C


title: 104B


title: 103A


title: 112A


title: 119B


title: 105B


title: 111B


title: 96B


title: 94C


title: 94A


title: 99B


title: 79A


title: 82C


title: 82B


title: 54B


title: 79C


title: 51C


title: 54C


title: 56C


title: 51B


title: 52C


title: 55C


title: 51A


title: 50C


title: 48B


title: 48A


title: 45C


title: 44B


title: 43A


title: caudal parts of the corpus callosum-12 weeks-Knockout(TREM2-/-)-5

city: Trieste

first: Danilo

last: Licastro

department: Genomica Funzionale

institute: CBM

description: Gene expression data from Twelve week-old KO TREM2 mice fed a standard diet containing 0.2% CPZ

hyb_protocol: Following fragmentation with NuGen Encore Biotin Module, 2.5 ug of cDNA were hybridized into the GeneChip Hybridization Oven 640 for 18 h at 45 °C on Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: Affymetrix GeneChip 7G 3000 Scanner

data_processing: Command Console (Affymetrix, Inc),Robust Multichip Analysis package ‘oligo’ version 1.30.0 target Level of summarization=core

source_name: caudal parts of the corpus callosum

label_protocol: NuGen WT- Ovation Pico RNA Amplification

extract_protocol: RNeasy mini kit (Qiagen) according to the manufacturer’s protocol

treatment_protocol: Six to tweelve-week-old TREM2-/- and WT mice were fed a standard diet (Harlan) containing 0.2% CPZ [finely powdered oxalic bis(cyclohexylidenehydrazide); Sigma-Aldrich] for 4, 6 or 12 weeks.

tag: diet

value: mice standard diet containing 0.2% powdered CPZ (oxalic bis(cyclohexylidenehydrazide))

tag: Stage

value: 12 weeks

value: Knockout TREM2-/-


title: caudal parts of the corpus callosum-12 weeks-Knockout(TREM2-/-)-6


title: 49B

value: LATE Sepsis


title: 43C

value: EARLY

value: <3 days


title: 44C

value: uninfected

value: whole blood


title: 41C


title: caudal parts of the corpus callosum-12 weeks-Knockout(TREM2-/-)-2


title: 41B


title: caudal parts of the corpus callosum-12 weeks-Wild_Type-3

description: Gene expression data from Twelve week-old  WT mice fed a standard diet containing 0.2% CPZ


title: 46C

value: LATE

value: >3 days


title: caudal parts of the corpus callosum-12 weeks-Wild_Type-4


title: caudal parts of the corpus callosum-6 weeks-Knockout(TREM2-/-)-3

description: Gene expression data from Six week-old  KO TREM2 mice fed a standard diet containing 0.2% CPZ

value: 6 weeks


title: caudal parts of the corpus callosum-12 weeks-Knockout(TREM2-/-)-1


title: caudal parts of the corpus callosum-12 weeks-Wild_Type-5


title: caudal parts of the corpus callosum-12 weeks-Wild_Type-1


title: caudal parts of the corpus callosum-12 weeks-Knockout(TREM2-/-)-4


title: 40C


title: 39C


title: 39B


title: 40B


title: caudal parts of the corpus callosum-12 weeks-Wild_Type-2


title: caudal parts of the corpus callosum-6 weeks-Knockout(TREM2-/-)-2


title: caudal parts of the corpus callosum-12 weeks-Knockout(TREM2-/-)-3


title: 38A


title: 38B


title: 36C

value: EARLY-uninfected


title: 37C


title: 59B


title: 38C


title: 35C


title: caudal parts of the corpus callosum-6 weeks-Knockout(TREM2-/-)-1


title: caudal parts of the corpus callosum-6 weeks-Wild_Type-4

description: Gene expression data from Six week-old  WT mice fed a standard diet containing 0.2% CPZ


title: 34C


title: caudal parts of the corpus callosum-6 weeks-Wild_Type-2


title: 32C


title: 35B


title: 33C


title: 43B


title: caudal parts of the corpus callosum-6 weeks-Wild_Type-1


title: caudal parts of the corpus callosum-6 weeks-Wild_Type-3


title: 32B


title: 8C


title: Breast.Tumour.3mLet.patient373R

city: Carrington Crescent

first: Andrew

middle: H

last: Sims

state: Edinburgh

address: Systems Medicine Building

department: Institute of Genetics and Molecular Medicine

institute: University of Edinburgh

hyb_protocol: Labelled cDNA was hybridised to Human HT-12v4 whole-genome expression beadarrays (Illumina) according to the standard protocol for NuGEN amplified samples.

scan_protocol: Scanning was performed on a Illumina scanner using the manufacturers protocol

data_processing: Illumina probe profiles were quantile normalised using the lumi package

label_protocol: RNA was reverse transcribed and amplified using the WT-Ovation FFPE System Version 2 (NuGEN), purified using the Qiaquick PCR Purification Kit (Qiagen), biotinylated using the IL Encore Biotin Module (NuGEN), purified using minElute Reaction Cleanup Kit (Qiagen) and quantified once again using the Nanodrop 2000c (Thermo Scientific).

growth_protocol: Tumour biopsies were taken with a 14-guage needle before and approximately 2 weeks and 3 months following commencement of continuous letrozole treatment. Samples were snap-frozen in liquid nitrogen and frozen sections taken, stained with haematoxylin and eosin (H&E) and the cellularity and percentage presence of cancerous tissue within each specimen was assessed by a pathologist.

extract_protocol: Biopsies were homogenised and RNA was extracted using the RNeasy Mini Kit with RNAse-free DNAse treatment (Qiagen). RNA quantity and quality was verified on a Bioanalyser 2100 with RNA 6000 Nano Kit (Agilent) and Nanodrop 2000c (Thermo Scientific).

treatment_protocol: Patients were treated within a neoadjuvant protocol in which letrozole (Femara, 2.5mg; Novartis Pharma AG, Basel, Switzerland) was given daily

tag: patient id

value: Female

tag: clinical response

value: Responder

tag: time point

value: 3 months of letrozole treatment

value: tumour biopsies


title: 7C

tag: treatment


title: 7A


title: 8A


title: Breast.Tumour.PreLet.patient373R

source_name: PreLet

value: pre-treatment


title: 4C

value: clinical sepsis

value: EARLY-clinical sepsis


title: Breast.Tumour.3mLet.patient369


title: Breast.TumourwLet.patient373R

value: 2 wks of letrozole treatment


title: 4B


title: 8B


title: 4A


title: 7B


title: Breast.Tumour.PreLet.patient369


title: 29B


title: 29C


title: 82A


title: 26C


title: Breast.Tumour.PreLet.patient367

value: Non-responder


title: Breast.Tumour.3mLet.patient367


title: Breast.TumourwLet.patient367


title: 29A

value: EARLY


title: 28C

value: <3 days


title: 30A

value: uninfected

value: LATE-uninfected


title: Breast.TumourwLet.patient364


title: 24B

value: whole blood


title: 23C

value: uninfected chorio

value: EARLY-uninfected chorio


title: 23B


title: 26A

value: EARLY-uninfected


title: 24A


title: 26B


title: Breast.Tumour.3mLet.patient364

value: Female


title: 20C


title: 21C


title: 18C


title: 19C


title: 20C 2

description: 6233_20C 2_(hGlue_3_0_v1).CEL.pimg


title: 19B


title: Breast.TumourwLet.patient363


title: Breast.Tumour.PreLet.patient364


title: 18B


title: 22C

source_name: EARLY _ Sepsis_whole blood

value: Sepsis

value: EARLY Sepsis


title: Breast.Tumour.PreLet.patient355

value: Responder

value: tumour biopsies


title: Breast.Tumour.3mLet.patient346

value: 3 months of letrozole treatment


title: Breast.TumourwLet.patient355


title: Breast.Tumour.PreLet.patient363

value: pre-treatment


title: Breast.Tumour.PreLet.patient357


title: Breast.TumourwLet.patient357

value: 2 wks of letrozole treatment


title: Breast.Tumour.3mLet.patient357


title: Breast.TumourwLet.patient346


title: 16B


title: Breast.Tumour.3mLet.patient355


title: MCF10A cells treated with 23 IR doses delivered by IOERT-replicate7

city: Cefalù

first: Valentina

last: Bravatà

address: Contrada Pietrapollastra Pisciotto

institute: IBSBC CNR

description:
Biological replicate 7 of 7
MCF10A_23Gy_rep7

hyb_protocol: The microarrays (Agilent Whole Human Genome, 4x44k) were hybridazed according to an established protocol by Agilent Technologies (Santa Clara, CA, USA). Two-channel arrays were hybridized using Cy3 and Cy5 and quantified using Feature Extraction v9.5 software. The Agilent Whole Human Genome Array (4x44K) was used for competitive hybridization and the slides were washed, dried, and scanned in an Agilent microarray scanner (Agilent Technologies, Palo Alto, CA, USA).

scan_protocol: Images were scanned using Agilent scanner, G2505B (Agilent Technologies, Palo Alto, CA, USA).

data_processing: Agilent Data Processing Protocol Calculation Method: Images were auto gridded, analyzed and data extracted using Agilent Feature Extraction Software. FeatureExtractor_Version: 9.5.3.1. Protocol_Name: GE2-v5_95_Feb07.

source_name: MCF10A cells treated with 23 IR doses

label_protocol: 500 ng of total RNA was amplified according to the manufacturer’s instructions by double strand cDNA synthesis, followed by T7-based in vitro transcription. Untreated MCF10A epithelial breast cell line was used as a control for all samples. Amplified complementary RNA (cRNA) was labeled with cyanine 5 (Cy5)-conjugated dUTP, whereas cRNA from untreated MCF10A cells was labeled with cyanine 3 (Cy3)-conjugated dUTP.

growth_protocol: MCF10A epithelial breast cell line were collected after 24 hours post treatments

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

tag: cell line

tag: cell type

value: human non-tumorigenic breast epithelial cell line

tag: treated with

value: 23 IR doses delivered by IOERT

tag: harvest time post treatment

value: 24 hours

tag: sample type

value: non-exposed to IR tratments (control)


title: Breast.Tumour.3mLet.patient363

value: Non-responder

tag: tissue


title: 16A

value: EARLY

value: <3 days

value: uninfected

value: whole blood


title: Breast.TumourwLet.patient369

value: Female


title: 12B

value: LATE

value: >3 days

value: LATE-uninfected


title: MCF10A cells treated with 23 IR doses delivered by IOERT-replicate6

description:
Biological replicate 6 of 7
MCF10A_23Gy_rep6


title: 11C

value: clinical sepsis

value: EARLY-clinical sepsis


title: 12A


title: 11B


title: MCF10A cells treated with 23 IR doses delivered by IOERT-replicate5

description:
Biological replicate 5 of 7
MCF10A_23Gy_rep5


title: Breast.TumourwLet.patient341

value: Responder

value: tumour biopsies


title: Breast.Tumour.3mLet.patient341

value: 3 months of letrozole treatment


title: MCF10A cells treated with 23 IR doses delivered by IOERT-replicate4

description:
Biological replicate 4 of 7
MCF10A_23Gy_rep4

value: human non-tumorigenic breast epithelial cell line

value: 23 IR doses delivered by IOERT


title: Breast.Tumour.3mLet.patient340


title: 10B

value: EARLY-uninfected


title: Breast.Tumour.PreLet.patient340

value: pre-treatment


title: Breast.TumourwLet.patient340

value: 2 wks of letrozole treatment


title: 9B

value: EARLY

value: <3 days


title: 10A

value: uninfected

value: whole blood


title: Breast.Tumour.3mLet.patient332

value: Female


title: MCF10A cells treated with 9 IR doses delivered by IOERT-replicate7

description:
Biological replicate 7 of 7
MCF10A_9Gy_rep7

source_name: MCF10A cells treated with 9 IR doses

value: 9 IR doses delivered by IOERT

value: 24 hours

value: non-exposed to IR tratments (control)


title: MCF10A cells treated with 23 IR doses delivered by IOERT-replicate3

description:
Biological replicate 3 of 7
MCF10A_23Gy_rep3


title: Breast.Tumour.PreLet.patient341


title: MCF10A cells treated with 9 IR doses delivered by IOERT-replicate6

description:
Biological replicate 6 of 7
MCF10A_9Gy_rep6


title: 9A

value: clinical sepsis

value: EARLY-clinical sepsis


title: MCF10A cells treated with 23 IR doses delivered by IOERT-replicate1

description:
Biological replicate 1 of 7
MCF10A_23Gy_rep1


title: 9C


title: 18hr3 (cAMP)

city: Piscataway

first: Ronald

middle: P.

last: Hart

state: NJ

address: 604 Allison Rd Rm B430

department: Cell Biology & Neuroscience

institute: Rutgers University

hyb_protocol: Hybridization was performed using an automated protocol on a Ventana Discovery System.

scan_protocol: Arrays were scanned on an Axon GenePix 4000B scanner using Axon GenePix 4.0 software.

data_processing: Images were aligned with array maps and data extracted.  Raw data was loaded into GeneSpring

source_name: cultured rat DRG cells

label_protocol: RNA samples were labeled with the Genisphere 3DNA dendrimer system.  Control (untreated) cultures were labeled in one fluorescent color and the cAMP (treated) samples in another.

growth_protocol: L4 and L5 dorsal root ganglia (DRG) were removed from juvenile rate and dissociated.  Cells were resuspended in Sato medium and plated in 6-well dishes (1 x 10^6 cells/well) coated with poly-L-lysine or myelin.

extract_protocol: Cells were harvested by trypsinization, centrifuged, and medium aspirated.  The cell pellet was dissociated in Trizol and homogenized with a tissue grinder.  Chloroform was added to extract the aqueous phase, which was adjusted to 35% ethanol and loaded onto a Qiagen RNeasy column.  The column was washed and eluted following the manufacturer's recommendations.  A260/A280 ratios were between 1.9 and 2.1 for all samples.

treatment_protocol: DRG cells were incubated with medium alone or with 1.5 mM dibutyryl cAMP (dbcAMP) for 0, 3, 6, 12, or 18 hours.

value: 1.5 mM dbcAMP vs medium control

tag: time

value: 18 hr

value: cultured rat DRG cells

value: Control


title: Breast.TumourwLet.patient332

value: Responder

value: tumour biopsies


title: Breast.Tumour.3mLet.patient331

value: Non-responder

value: 3 months of letrozole treatment


title: MCF10A cells treated with 23 IR doses delivered by IOERT-replicate2

description:
Biological replicate 2 of 7
MCF10A_23Gy_rep2

value: human non-tumorigenic breast epithelial cell line

value: 23 IR doses delivered by IOERT


title: MCF10A cells treated with 9 IR doses delivered by IOERT-replicate5

description:
Biological replicate 5 of 7
MCF10A_9Gy_rep5


title: 18hr2 (cAMP)


title: MCF10A cells treated with 9 IR doses delivered by IOERT-replicate4

description:
Biological replicate 4 of 7
MCF10A_9Gy_rep4


title: 18hr1 (cAMP)


title: MCF10A cells treated with 9 IR doses delivered by IOERT-replicate2

description:
Biological replicate 2 of 7
MCF10A_9Gy_rep2


title: 12hr3 (cAMP)

value: 12 hr


title: Breast.TumourwLet.patient331

value: Female

value: 2 wks of letrozole treatment


title: 12hr2 (cAMP)


title: Breast.Tumour.PreLet.patient332

value: pre-treatment


title: 12hr1 (cAMP)


title: MCF10A cells treated with 9 IR doses delivered by IOERT-replicate3

description:
Biological replicate 3 of 7
MCF10A_9Gy_rep3

value: 9 IR doses delivered by IOERT

value: 24 hours

value: non-exposed to IR tratments (control)


title: MCF10A cells treated with 9 IR doses delivered by IOERT-replicate1

description:
Biological replicate 1 of 7
MCF10A_9Gy_rep1


title: 6hr3 (cAMP)

value: 1.5 mM dbcAMP vs medium control

value: 6 hr


title: Breast.Tumour.3mLet.patient329


title: Breast.Tumour.PreLet.patient329


title: Breast.Tumour.PreLet.patient331


title: 6hr2 (cAMP)

value: cultured rat DRG cells


title: 32d_XAV939_RPE-D_4K

city: Santa Barbara

first: Monte

middle: J.

last: Radeke

address: Neuroscience Research Institiute

department: Neuroscience Research Institute

institute: University of California, Santa Barbara

description:
XAV939 32days
raw data: Cy3 channel of XAV939_32d.txt

hyb_protocol: Probe fragmentation and hybridization was carried out using the Agilent Gene Expression Hybridization Kit (Part #: 5188-5242) according to the methods of the manufacturer (Quick Amp Labeling Protocol, Version 5.7). Two samples (one labeled with Cy3 and the other with Cy5 were hybidized to each array for 17 hr at 65°C. Arrays were washed for 1 min using Agilent Gene Expression Wash Buffer 1 (Part #: 5188-5325) + 0.005% Triton X-102 at room temperature and for 1 min at 37°C with Agilent Gene Expression Wash Buffer 2 (Part #: 5188-5326) + 0.005% Triton X-102. The washed arrays were then rinsed with acetonitrile for 10 sec and coated with Agilent Stabilization and Drying solution for 30 sec.

scan_protocol: Scanner: Bio-Rad VersArray™ ChipReader 3 micron System.  Median Raw Spot intensities (Threshold = 5 to 6535) were determined using  VersArray™ Analyzer 4.5. LOWESS Net Intensity Spot Intensity was calculated using Global Median Background Subtraction (global background from negative control cells, zero order polynomial approximation) and the uncorrected net intensity values were normalized using local regression cross-channel normalization of net intensity values (span = 10%, sub-sampling = 5, single pass). Raw data files contain the  LOWESS normalized net intensity values, the raw intensity values, and the background values.

data_processing: The LOWESS normalized data were further background corrected by subtraction of the minimum value of the Agilent negative controls (3xSLv1) to obtain the net intensity. Any values less than one standard deviation of the negative control probes were set to a value equal to the standard deviation of the negative controls for that sample. For the 200 unique probes with 10 replicates each, the average of the replicates were determined. The entire data set was then quantile normalized.

source_name: Fetal RPE-Donor D

label_protocol: All probe labeling was carried out using the Agilent Low Input Quick Amp Labeling Kit (Part #: 5190-2306, Version 5.7) according to the methods of the manufacturer using 250 ng of total RNA with the exception that spike-in controls were not used.

growth_protocol: RPE cells were isolated from fetal donor eyes (Advanced Biosciences Resources, Alameda, CA USA) according to the methods of Hu and Bok [Mol. Vis. 2001, 7:14-19; Methods Mol. Biol. 2010, 652:55-73]. Beyond the initial isolation, all cell culture was carried out using a base medium described by Maminiskis [Invest. Ophthalmol. Vis. Sci.2006, 47:3612-3624]. For 2-3 days post-plating the medium included 15% heat inactivated fetal calf serum. Thereafter, it was reduced to 5%. To generate a working cell bank, primary fetal RPE stocks were expanded approximately 10-fold and these working stocks were designated Passage 0. For routine serial passage, cells were harvested using trypsin digestion and plated at 4,000 cells/cm2. At approximately 80% confluence (every 3-5 days depending on passage number) the cells were enzymatically harvested and re-seeded at 4,000 cells/cm2. Cultures were carried out on laminin-coated porous supports (mouse laminin, Life Technologies, Grand Island, NY USA; Millicell-HA Culture Inserts, EMD Millipore Inc., Billerica, MA USA) or laminin-coated tissue culture plastic as indicated. All cultures were fed every 2-4 days by complete exchange of the medium.

extract_protocol: Total RNA was purified using miRNeasy mini-preps (Qiagen Inc., Valencia, CA USA)

tag: donor id

tag: plating density

value: 4,000 cells/cm2

tag: passage number

tag: culture time

value: 32 Days

tag: cultureware

value: 6-well Multiwell Plate

value: 5 mM XAV939


title: 32d_LDN193189&FGF_RPE-D_4K

description:
LDN193189 FGF 32days
raw data: Cy3 channel of LDN193189_32d.txt


title: 32d_Thiazovivin_RPE-D_4K

description:
Thiazovivin 32days
raw data: Cy5 channel of Thiazovivin_32.txt

value: 500 nM Thiazovivin


title: 32d_XAV939&FGF_RPE-D_4K

description:
XAV939 FGF 32days
raw data: Cy5 channel of XAV939_32d.txt

value: 5 mM XAV939 + 2ng FGF


title: Breast.Tumour.3mLet.patient328

tag: gender

value: Responder

value: 3 months of letrozole treatment

value: tumour biopsies


title: 32d_LDN193189_RPE-D_4K

description:
LDN193189 32days
raw data: Cy5 channel of LDN193189_32d.txt


title: 3hr3 (cAMP)

value: 3 hr

value: Control


title: Breast.TumourwLet.patient328

tag: patient id

value: Female

value: 2 wks of letrozole treatment


title: Breast.Tumour.PreLet.patient328

tag: clinical response

value: pre-treatment


title: 32d_Thiazovivin&FGF_RPE-D_4K

description:
Thiazovivin FGF 32days
raw data: Cy3 channel of Thiazovivin_32.txt

value: 500 nM Thiazovivin + 2ng FGF


title: 3hr2 (cAMP)

value: 1.5 mM dbcAMP vs medium control


title: 6hr1 (cAMP)

value: 6 hr

value: cultured rat DRG cells


title: 3hr1 (cAMP)


title: Breast.Tumour.3mLet.patient311

tag: time point


title: 32d_A8301&FGF_RPE-D_4K

description:
A8301 FGF 32days
raw data: Cy5 channel of A8301_32d.txt

value: 4,000 cells/cm2

value: 32 Days

tag: treatment


title: 1hr3 (cAMP)

value: 1 hr


title: 1hr2 (cAMP)


title: 3d_XAV939&FGF_RPE-D_4K

description:
XAV939 FGF 3day
raw data: Cy3 channel of XAV939_3d.txt

value: 3 Days

value: 6-well Multiwell Plate


title: 32d_A8301_RPE-D_4K

description:
A8301 32days
raw data: Cy3 channel of A8301_32d.txt


title: 3d_XAV939_RPE-D_4K

description:
XAV939 No FGF 3day
raw data: Cy5 channel of XAV939_3d.txt

value: 5 mM XAV939


title: 3d_LDN193189_RPE-D_4K

description:
LDN193189 NoFGF3day
raw data: Cy3 channel of LDN193189_3d.txt


title: 3d_LDN193189&FGF_RPE-D_4K

description:
LDN193189 FGF3day
raw data: Cy5 channel of LDN193189_3d.txt


title: Breast.Tumour.PreLet.patient311

value: Responder


title: Breast.TumourwLet.patient311

value: tumour biopsies


title: Breast.Tumour.3mLet.patient300

value: 3 months of letrozole treatment


title: Breast.TumourwLet.patient300


title: 1hr1 (cAMP)

value: Control


title: 296hr2 (conditioning lesion)

extract_protocol: DRS were collected in Trizol and homogenized with a tissue grinder.  Chloroform was added to extract the aqueous phase, which was adjusted to 35% ethanol and loaded onto a Qiagen RNeasy column.  The column was washed and eluted following the manufacturer's recommendations.  A260/A280 ratios were between 1.9 and 2.1 for all samples.

treatment_protocol: Postnatal day 20-24 Long-Evans rats were anesthetized using 2.5% isoflourane.  The sciatic nerve was transected using surgical micro-scissors.  The incision was closed.  Animals were allowed to survive for 4 to 294 hrs after which they were sacrificed by asphyxiation with CO2.  DRGs L4 and L5 were removed.

value: lesioned

value: 294 hrs

value: Intact


title: 296hr1 (conditioning lesion)

value: 296 hrs


title: 3d_Thiazovivin&FGF_RPE-D_4K

description:
Thiazovivin FGF3day
raw data: Cy5 channel of Thiazovivin_3.txt

value: 500 nM Thiazovivin + 2ng FGF


title: 3d_A8301&FGF_RPE-D_4K

description:
A8301 FGF 3 day
raw data: Cy3 channel of A8301_3d.txt


title: 148hr2 (conditioning lesion)

value: 148 hrs


title: 148hr3 (conditioning lesion)

value: cultured rat DRG cells


title: 3d_FGF_RPE-D_4K

description:
DMSO FGF 3 days
raw data: Cy3 channel of FGF_3d&32d.txt

value: 4,000 cells/cm2

value: 2 ng/ml FGF2


title: 3d_Thiazovivin_RPE-D_4K

description:
Thiazovivin NoFGF3day
raw data: Cy3 channel of Thiazovivin_3.txt

value: 500 nM Thiazovivin


title: 148hr1 (conditioning lesion)


title: 48hr3 (conditioning lesion)

value: 48 hrs


title: 3d_A8301_RPE-D_4K

description:
A8301 no FGF 3 day
raw data: Cy5 channel of A8301_3d.txt

value: 3 Days

value: 6-well Multiwell Plate


title: Breast.Tumour.PreLet.patient300

value: Female

value: Responder

value: pre-treatment


title: 32d_FGF_RPE-D_4K

description:
DMSO FGF 32 days
raw data: Cy5 channel of FGF_3d&32d.txt

value: 32 Days


title: Breast.TumourwLet.patient226

value: 2 wks of letrozole treatment

value: tumour biopsies


title: Breast.TumourwLet.patient269


title: 32d_DMSO_RPE-D_4K

description:
DMSO 32 days
raw data: Cy3 channel of DMSO_3d&32d.txt

value: DMSO


title: Breast.Tumour.PreLet.patient269


title: 48hr2 (conditioning lesion)

value: lesioned

value: Intact


title: Breast.Tumour.3mLet.patient215

value: 3 months of letrozole treatment


title: 48hr1 (conditioning lesion)

value: cultured rat DRG cells


title: 3d_DMSO_RPE-D_4K

description:
DMSO 3 days
raw data: Cy5 channel of DMSO_3d&32d.txt

value: 4,000 cells/cm2


title: Breast.Tumour.3mLet.patient226


title: Breast.TumourwLet.patient215


title: 64d_P5_RPE-C_80K

description:
Bok081309 p5day64insert
raw data: Cy5 channel of RPE-C_64d_P0&P5.txt

source_name: Fetal RPE-Donor C

value: 64 Days

value: Micropourous Membrane


title: Breast.Tumour.3mLet.patient269


title: Breast.Tumour.PreLet.patient346


title: 24hr3 (conditioning lesion)

value: 24 hrs


title: 18hr3 (conditioning lesion)

value: 18 hrs


title: 24hr2 (conditioning lesion)


title: 24hr1 (conditioning lesion)


title: 18hr2 (conditioning lesion)


title: 18hr1 (conditioning lesion)


title: 12hr3 (conditioning lesion)

value: 12 hrs


title: 11A

tag: age group

value: EARLY

tag: age in days

value: <3 days

tag: infection

value: clinical sepsis

value: EARLY-clinical sepsis

value: whole blood


title: 32d_P5_RPE-C_80K

description:
Bok081309 p5day32insert
raw data: Cy3 channel of RPE-C_32d_P0&P5.txt

value: 32 Days


title: 64d_P5_RPE-B_80K

description:
Bok071709 p5day64insert
raw data: Cy3 channel of RPE-B_64d_P0&P5.txt

source_name: Fetal RPE-Donor B


title: 64d_P0_RPE-A_80K

description:
Bok020207-2 p0day64insert
raw data: Cy3 channel of RPE-A_64d_P0&P5.txt

source_name: Fetal RPE-Donor A


title: 64d_P5_RPE-A_80K

description:
Bok020207-2 p5 day64insert
raw data: Cy5 channel of RPE-A_64d_P0&P5.txt


title: Breast.Tumour.3mLet.patient203

value: Female

value: Non-responder

value: tumour biopsies


title: Breast.TumourwLet.patient214

value: 2 wks of letrozole treatment


title: Breast.Tumour.PreLet.patient215

value: Responder

value: pre-treatment


title: Breast.Tumour.3mLet.patient214

value: 3 months of letrozole treatment


title: Breast.TumourwLet.patient203


title: Breast.Tumour.PreLet.patient226


title: 32d_P0_RPE-C_80K

description:
Bok081309 p0day32insert
raw data: Cy5 channel of RPE-C_32d_P0&P5.txt

value: Micropourous Membrane