title: Control_vs_Cold_Nipponbare_02H_R1_A

description: This experiment was performed with two independent biological replicates (R1 and R2). The whole genome microarray consisting of a total of ~45,000 oligonucleotides was printed on two separate slides (Slides A and B).

treatment_protocol: Control samples (seedlings at V3 stage) were incubated at ambient temperature (29C) for 02 hr

source_name: Rice (Oryza sativa, spp. japonica cv. Nipponbare) seedlings at 02 hours at cold stress (10C)

treatment_protocol: Treatment samples (seedlings at V3 stage) were incubated at low temperature (10C) for 02 hrs


title: untreated campylobacter (0.5 hour) cy3 slide 47

status: Public on Dec 28 2009

type: RNA

city: Ames

first: Yang

last: Wang

state: IA

address: 1113 Vet Med

department: VMPM

country: USA

institute: Iowa State University

hyb_protocol: After purification, the fluorescent labeling of the DNA was quantitated, and equal amounts of labeled cDNA of the wild-type and the mutant were mixed and dried in a speed vacuum concentrator. After resuspension with hybridization buffer provided by the slide manufacturer, the mixture was denatured by heating at 95 ◦C for 10 min. The hybridization mixture was loaded onto a microarray slide and hybridized in a shaking incubator at 42 ºC for 24 h. Slides were washed as the manufacture’s recommendations and dried by centrifugation.

scan_protocol: Using a ScanArray Express laser scanner (Applied Biosystem Inc., Foster City, CA) each dye channel of each slide was scanned at a 10 μm resolution using three predetermined laser power and photomultiplier gain settings. Thus for each slide six scans were performed, three separate scans at different settings of each of the two dye channels.

data_processing: ImaGene software (BioDiscovery, El Segundo, CA) was used for spot finding and to measure the spot-specific mean signal strength of each spot. The fluorescentc intensities of all spots were log2 transformed. The median of the three log2-transformed spot signals was determined and this value was used as spot signal for all further calculations. As an additional measure against intensity dependent dye bias the data was then subjected to LOWESS normalization.

molecule: total RNA

organism: Campylobacter jejuni

source_name: C. jejuni NCTC-11168

label_protocol: cDNA was synthesized using aminoallyl-dNTP according to the manufacturer’s instruction. After purification, aminoallyl labeled cDNA was fluorescently labeled with Cy-3/cy-5 mono-Reactive Dye Pack (Amersham Biosciences, Piscataway, NJ)

extract_protocol: Total RNA was isolated using RNAprotectTM bacteria reagent (Qiagen) and an RNeasy kit (Qiagen) according to the manufacturer’s protocol with an optional step of on-column DNase treatment with RNase-Free DNase (Qiagen). RNA concentration was measured with a NanoDrop ND-1000 (NanoDrop Technologies, Wilmington, DE).

tag: agent


title: Invasive TAM_replicate 5

status: Public on Dec 26 2009

city: Bronx

first: Laureen

last: Ojalvo

state: NY

address: Chanin 607, 1300 Morris Park Avenue

department: Developmental and Molecular Biology

institute: Albert Einstein College of Medicine

description: 7mer labeling for sample of invasive vs general TAMs (FVB)

hyb_protocol: Standard NimbleGen protocol was used (http://www.nimblegen.com/technology/index.html).

data_processing: Raw data files for each sample were normalized, background-corrected and saved to logarithmic scale using a Robust Multi-Array Analysis (RMA) as implemented by NimbleScan software, version 2.2.33

organism: Mus musculus

source_name: Invasive TAMs

label_protocol: 200ng of RNA from samples was re-suspended into 11 µl of RNase/DNase-free water, and a single round of linear amplification was performed by the in vitro transcription T7 promoter method as outlined by the manufacturer’s protocol (Ambion’s Message Amp T7 Kit; Ambion, Austin, TX). For microarray samples, a second round of linear amplification was performed with 200 ng of first round amplified material.  At all steps, yield and quality were established using spectrophotometry and an Agilent Bioanalyzer. Superscript III (Invitrogen) reverse transcriptase was used to prepare 5ug cDNA from amplified RNA.  Random primers (Invitrogen) were used to prime reaction.  Second-strand cDNA synthesis was performed using E. coli DNA Ligase (Invitrogen), E. coli DNA Polymerase 1 (Invitrogen) and T4 DNA Polymerase (Invitrogen).  RNase H (Invitrogen) treatment was additionally performed.  The reaction was stopped with 0.5M EDTA and then purified using a PCR purification kit (Qiagen) following manufacture’s protocol.  Samples were re-suspended to approximately 200ng/μl. Additional details can be found at http://www.nimblegen.com/technology/index.html.

extract_protocol: Total RNA was extracted from FACS sorted TAMs and splenic macrophages using RNeasy Micro Kits (Qiagen, Valencia, CA, USA) according to the manufacturer’s instruction.  Amplification-grade DNase 1 treatment was performed on the RNA elution column to remove potential genomic DNA contamination.  Approximate yields were 150ng, quality was determined using a nano-biosizing assay (Agilent Bioanalyzer; Agilent Technologies, Palo Alto, CA, USA).

tag: cell type

value: tumor-associated macrophages (TAMs)

tag: cell phenotype

value: invasive

tag: strain

value: FVB/NJ


title: General TAM_replicate 5

scan_protocol: Standard NimbleGen protocol was used (http://www.nimblegen.com/technology/index.html).

source_name: General TAMs

value: general


title: Invasive TAM_replicate 2


title: Invasive TAM_replicate 4


title: General TAM_replicate 1


title: General TAM_replicate 4


title: General TAM_replicate 2


title: TA adult rep3

status: Public on Dec 15 2009

city: Philadelphia

first: Ulrike

last: Zeiger

state: PA

address: 3700 Hamilton Walk

department: Physiology and PMI

institute: University of Pennsylvania

description: S06 - TA5 was hybridized and detected on the same chip as S05 - EOM5

hyb_protocol: Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies)9. On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://microrna.sanger.ac.uk/sequences/) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate.  The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry.  The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 µL 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C.  After hybridization detection used fluorescence labeling using tag-specific Cy3 and Cy5 dyes.

scan_protocol: Hybridization images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).

data_processing: Normalization across the four chips was carried out using a LOWESS (Locally-weighted Regression) method (5) on the background-subtracted data. A probe set was listed as detectable when signal was > 3x background standard deviations and if the signals from at least 50% of the repeating probes were above detection level. Data filtering removed miRNAs with normalized intensity values below a threshold value of 32 across all samples.

source_name: tibialis anterior_adult

label_protocol: The assay started from 2 to 5 µg total RNA sample, which was size fractionated using a YM-100 Microcon centrifugal filter (from Millipore) and the small RNAs (< 300 nt) isolated were 3’-extended with a poly(A) tail using poly(A) polymerase.  An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent dye staining; two different tags for fluorescence labeling using tag-specific Cy3 and Cy5 dyes were used for the two RNA samples in dual-sample experiments.

growth_protocol: muscle tissue was kept in RNAlater at -20 degrees

extract_protocol: Total RNA was isolated using mirVanaTM miRNA Isolation Kit (Ambion) and RNA quality control was performed using Bioanalyzer 2100 (Agilent Technologies Inc.)

tag: gender

value: male

tag: age

value: adult 10-13 weeks

tag: tissue

value: tibialis anterior


title: TA adult rep4

description: S07 - TA8 was hybridized and detected on the same chip as S08 - EOM8


title: TA adult rep1

description: S02 - TA1 was hybridized and detected on the same chip as S01 - EOM1


title: TA adult rep2

description: S03 - TA2 was hybridized and detected on the same chip as S04 - EOM2


title: EOM adult rep2

description: S04 - EOM2 was hybridized and detected on the same chip as S03 - TA2

source_name: extraocular muscle_adult

value: extraocular muscle


title: EOM adult rep1

description: S01 - EOM1 was hybridized and detected on the same chip as S02 - TA1


title: EOM adult rep3

description: S05 - EOM5 was hybridized and detected on the same chip as S06 - TA5


title: EOM adult rep4

description: S08 - EOM8 was hybridized and detected on the same chip as S07 - TA8


title: General TAM_replicate 3


title: Invasive TAM_replicate 3


title: B cell smoking-56

status: Public on Dec 25 2009

city: Xi'an

first: Feng

last: Pan

state: Shaanxi

address: Xian Ning West Road 28

department: School of life science and technology

country: China

institute: Xi'an Jiaotong University

description: Gene expression data from B cells isolated from healthy US white smoking females

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG133A Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: We use the Affymetrix Microarray Scanner by Hewlett-Packard 2500 and Microarray Suite 5.0 software for chip scanning and raw image generating.

data_processing: Microarray Suite 5.0 (MAS 5.0, Affymetrix, Santa Clara, CA, USA) software was used to generate array raw data in CEL files. A preselecting procedure adopted by our previous study (Xiao et al. 2008) was also used here. We selected a subset of 7,215 probe sets from a total of 22,283 for ~14,500 genes in the HG-133A array. Subsequent data analyses were performed on these selected probe sets. We applied multiple analytic approaches including mas5.0 algorithm (Affymetrix, Santa Clara, CA, USA), RMA (Robust Multiarray Algorithm), GCRMA (the improved GC-content adjusted RMA), and dChip for converting and normalizing our raw probe data to gene expression values.  Genes expressed differentially as determined by consensus using the 4 methods were extracted.

label: biotin

organism: Homo sapiens

source_name: circulating B cells in smoking woman

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Seventy milliliters of blood were drawn from each recruited female. B cell isolation from 70 ml whole blood was performed using a positive isolation method with Dynabeads® CD19 (Pan B) and DETACHaBEAD® CD19 (Dynal Biotech, Lake Success, NY, USA) following the manufacturer’s protocols. B cell purity was assessed by flow cytometry (BD Biosciences, San Jose, CA USA) with fluorescence labeled antibodies, PE-CD19 and FITC-CD45. The average purity was 96.3% with less than 1% deviation.

tag: menopausal

value: Post

value: B cell

tag: smoking

value: yes


title: Malme-3M neg ctrl II

status: Public on Dec 20 2009

city: Kingston

first: Harriet

last: Feilotter

state: Ontario

address: 88 Stuart St

department: Pathology and molecular department

country: Canada

institute: Queen's University

description: Biological replicate 2 of 2.

hyb_protocol: Successfully amplified and labeled samples were fragmented at 60°C for 30 minutes and hybridized to Agilent Human 4X44K Whole genome microarrays (Agilent, Santa Clara, CA) in a rotating oven  at 65°C for 17 hours following manufacturer's protocol.

scan_protocol: Images were scanned with Agilent scanner at 5µm resolution.

data_processing: All raw signal intensity was thresholded to 1, shifted to 75 percentile, and baseline to median of all samples.

source_name: Malme-3M cell line, control

label_protocol: 500 ng total RNA of each sample was mixed with 5 μL of a 5,000-fold dilution of Agilent's One-Color Spike-in RNA control (Agilent, Santa Clara, CA). The mixture was amplified and labeled using the One color, Quick Amp Labeling kit (Agilent, Santa Clara, CA). In short, mRNA was primed with an oligo(dT)primer containing a T7 RNA polymerase promoter to synthesize double-stranded cDNA, and the cDNA was then used as a template to generate Cy3-labeled cRNA in an in vitro transcription reaction.

growth_protocol: Metastatic melanoma cell lines Malme-3M were grown in RPMI medium 1640 (Hyclone) supplemented with 10% fetal bovine serum (Hyclone) at 37°C  and 5% CO2.

extract_protocol: Total RNA was harvested 24h after transfection using miRNeasy Mini kit (Ambion).

treatment_protocol: Malme-3M cells were seeded 100,000 cells/well in 6-well plate and transfected the following day with 5nM miRNA precursors (miR-193b or negative control) using Lipofectamine 2000 (Invitrogen).

tag: cell line

value: Metastatic melanoma

tag: transfection

value: negative control


title: Malme-3M miR193b II

description: Biological replicate 2 of 2.

source_name: Malme-3M cell line, miR-193b

value: miR-193b precursor


title: Malme-3M miR193b I

description: Biological replicate 1 of 2.


status: Public on Dec 10 2009

city: Maastricht

first: Ruben

last: Martherus

address: Universiteitssingel 50

department: Clinical Genomics

country: Netherlands

institute: Maastricht University

description: Cardiomyocytes_Pulsed-Blebbistatin_20090207.CEL

hyb_protocol: Following fragmentation, 11 ug of cRNA was hybridized for 16 hr at 45C on GeneChip Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix Gene Chip Scanner 7G

data_processing: Data processed using PLIER in Affymetrix Expression Console V 1.1 with default settings, further processed using BRB-tools (http://linus.nci.nih.gov/BRB-ArrayTools.html): Normalized using housekeeping genes (rat orthologues of housekeeping genes on Affymetrix HG U133 plus 2 array)

organism: Rattus norvegicus

source_name: Ventricular cardiomyocytes primary culture

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

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

value: Lewis

tag: developmental stage

value: 0-3 days neonatal

tag: treatment

value: Electrical stimulated for 3 days at 1Hz, 2 Volt/cm;Supplemented with blebbistatin 10 µmole/L


description: Cardiomyocytes_Pulsed-Blebbistatin_20090226.CEL


title: Cardiomyocytes_Pulsed_20090207

value: Electrical stimulated for 3 days at 1Hz, 2 Volt/cm


title: Malme-3M neg ctrl I

description: Biological replicate 1 of 2.


title: Cardiomyocytes_Pulsed_20090226


title: Invasive TAM_replicate 1

value: tumor-associated macrophages (TAMs)

value: invasive


description: Cardiomyocytes_Pulsed-Blebbistatin_20090131.CEL


title: Cardiomyocytes_Pulsed_20090131


title: Cardiomyocytes_Non-pulsed_20090207

value: untreated


title: Cardiomyocytes_Pulsed_20081009


title: Cardiomyocytes_Non-pulsed_20081009


title: Cardiomyocytes_Non-pulsed_20090131


title: Svev_lung1 Technical Replica 1

status: Public on Dec 01 2009

city: Cambridge

first: James

last: Abraham

state: MA

address: 75 Sidney Street

department: Bioinformatics

institute: AVEO Pharmaceuticals

description: Technical replica 1

hyb_protocol: Oligoarray control targets and hybridization buffer were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially

scan_protocol: Scanned on an Agilent G2505B scanner. Images were quantified using Agilent Feature Extraction Software (version A.7.5.1).

data_processing: Agilent Feature Extraction Software (v 7.5.1) was used for background subtraction and LOWESS normalization.

source_name: 129/SvEv lung RNA sample#1

label_protocol: 10 µg of total RNA were labeled with either Cy3 or Cy5 using Agilent Fluorescent Direct Label Kit following manufacturer's instructions

growth_protocol: Tumor RNA Lung tumors or normal lung tissue samples were harvested from either tumor bearing mice or control mice and snap frozen in liquid nitrogen immediatedly

extract_protocol: total RNA extracted using Qiagen RNAeasy mini spin column kit following manufacturer's instructions

tag: model

value: Tumor RNA Lung

source_name: Mouse Universal Reference RNA

value: Cell line


title: C57Bl6_lung1 Technical Replica 1

description: Technical replica 1

source_name: C57Bl6 lung RNA sample#1


title: Svev_lung3 Technical Replica 1

description: Technical replica 1

source_name: 129/SvEv lung RNA sample#3


title: Svev_lung1 Technical Replica 2

description: Technical replica 2


title: Svev_lung2 Technical Replica 1

description: Technical replica 1

source_name: 129/SvEv lung RNA sample#2


title: C57Bl6_lung1 Technical Replica 2

description: Technical replica 2


title: 33B3_lung1058 Technical Replica 1

description: Technical replica 1

source_name: Chimera lung RNA sample#2

value: Tumor RNA Lung HER2(V659E) with no induction


title: Svev_lung2 Technical Replica 2

description: Technical replica 2


title: 33B3_lung1060 Technical Replica 1

description: Technical replica 1

source_name: Chimera lung RNA sample#4


title: 33B3_lung1059 Technical Replica 1

description: Technical replica 1

source_name: Chimera lung RNA sample#3


title: C57Bl6_lung3 Technical Replica 1

description: Technical replica 1

source_name: C57Bl6 lung RNA sample#3


title: 33B3_lung1059 Technical Replica 2

description: Technical replica 2


title: C57Bl6_lung2 Technical Replica 2

description: Technical replica 2

source_name: C57Bl6 lung RNA sample#2


title: 33B3_lung1060 Technical Replica 2

description: Technical replica 2


title: Svev_lung3 Technical Replica 2

description: Technical replica 2


title: 33B3_lung1058 Technical Replica 2

description: Technical replica 2


title: C57Bl6_lung3 Technical Replica 2

description: Technical replica 2


title: 33B3_lung1057 Technical Replica 2

description: Technical replica 2

source_name: Chimera lung RNA sample#1


title: Tumor RNA LNorm2 Technical Replica 2

description: Technical replica 2

source_name: Normal lung RNA sample#2


title: Tumor RNA LNorm1 Technical Replica 2

description: Technical replica 2

source_name: Normal lung RNA sample#1


title: 33B3_lung1057 Technical Replica 1

description: Technical replica 1


title: Tumor RNA LK133 Technical Replica 2

description: Technical replica 2

source_name: Tumor RNA LK133

value: Tumor RNA Lung KRAS(G12V)

value: Tumor


title: Tumor RNA Lnorm3 Technical Replica 1

description: Technical replica 1

source_name: Normal lung RNA sample#3


title: Tumor RNA LNorm2 Technical Replica 1

description: Technical replica 1


title: Tumor RNA LNorm1 Technical Replica 1

description: Technical replica 1


title: C57Bl6_lung2 Technical Replica 1

description: Technical replica 1


title: Tumor RNA LK123 Technical Replica 2

description: Technical replica 2

source_name: Tumor RNA LK123


title: Tumor RNA LK133 Technical Replica 1

description: Technical replica 1


title: Tumor RNA Lnorm3 Technical Replica 2

description: Technical replica 2


title: Tumor RNA LK123 Technical Replica 1

description: Technical replica 1


title: Tumor RNA LK122 Technical Replica 1

description: Technical replica 1

source_name: Tumor RNA LK122


title: Tumor RNA LK105 Technical Replica 1

description: Technical replica 1

source_name: Tumor RNA LK105


title: Tumor RNA LK89 Technical Replica 2

description: Technical replica 2

source_name: Mouse Universal Reference RNA

source_name: Tumor RNA LK89


title: Tumor RNA LK97 Technical Replica 2

description: Technical replica 2

source_name: Tumor RNA LK97


title: Tumor RNA LK104 Technical Replica 2

description: Technical replica 2

source_name: Tumor RNA LK104


title: Tumor RNA LK96 Technical Replica 1

description: Technical replica 1

source_name: Tumor RNA LK96


title: Tumor RNA LK80 Technical Replica 2

description: Technical replica 2

source_name: Tumor RNA LK80


title: Tumor RNA LK105 Technical Replica 2

description: Technical replica 2


title: Tumor RNA LK70 Technical Replica 1

description: Technical replica 1

source_name: Tumor RNA LK70


title: Tumor RNA LK104 Technical Replica 1

description: Technical replica 1


title: Tumor RNA LK88 Technical Replica 2

description: Technical replica 2

source_name: Tumor RNA LK88


title: Tumor RNA LK51 Technical Replica 2

description: Technical replica 2

source_name: Tumor RNA LK51


title: Tumor RNA LK96 Technical Replica 2

description: Technical replica 2


title: Tumor RNA LK69 Technical Replica 1

description: Technical replica 1

source_name: Tumor RNA LK69


title: Tumor RNA LK88 Technical Replica 1

description: Technical replica 1


title: Tumor RNA LK54 Technical Replica 1

description: Technical replica 1

source_name: Tumor RNA LK54


title: Tumor RNA LK89 Technical Replica 1

description: Technical replica 1


title: Tumor RNA LK97 Technical Replica 1

description: Technical replica 1


title: Tumor RNA LK80 Technical Replica 1

description: Technical replica 1


title: Tumor RNA LK54 Technical Replica 2

description: Technical replica 2


title: Tumor RNA LK51 Technical Replica 1

description: Technical replica 1


title: Tumor RNA LK43 Technical Replica 2

description: Technical replica 2

source_name: Tumor RNA LK43


title: Tumor RNA LK70 Technical Replica 2

description: Technical replica 2


title: Tumor RNA LK43 Technical Replica 1

description: Technical replica 1


title: Tumor RNA LK42 Technical Replica 2

description: Technical replica 2

source_name: Tumor RNA LK42


title: Tumor RNA LK1 Technical Replica 2

description: Technical replica 2

source_name: Tumor RNA LK1


title: Tumor RNA LK1 Technical Replica 1

description: Technical replica 1


title: Tumor RNA LK3 Technical Replica 1

description: Technical replica 1

source_name: Tumor RNA LK3


title: Tumor RNA LK3 Technical Replica 2

description: Technical replica 2


title: Tumor RNA LH98 Technical Replica 1

description: Technical replica 1

source_name: Tumor RNA LH98

value: Tumor RNA Lung HER2(V659E)


title: Tumor RNA LH96 Technical Replica 1

description: Technical replica 1

source_name: Tumor RNA LH96


title: Tumor RNA LH97 Technical Replica 2

description: Technical replica 2

source_name: Mouse Universal Reference RNA

source_name: Tumor RNA LH97


title: Tumor RNA LH97 Technical Replica 1

description: Technical replica 1


title: Tumor RNA LK42 Technical Replica 1

description: Technical replica 1


title: Tumor RNA LH52 Technical Replica 2

description: Technical replica 2

source_name: Tumor RNA LH52


title: Tumor RNA LH98 Technical Replica 2

description: Technical replica 2


title: Tumor RNA LH52 Technical Replica 1

description: Technical replica 1


title: Tumor RNA LH95 Technical Replica 2

description: Technical replica 2

source_name: Tumor RNA LH95


title: Tumor RNA LH95 Technical Replica 1

description: Technical replica 1


title: Tumor RNA LH41 Technical Replica 2

description: Technical replica 2

source_name: Tumor RNA LH41


title: Tumor RNA LH96 Technical Replica 2

description: Technical replica 2


title: Tumor RNA LH48 Technical Replica 1

description: Technical replica 1

source_name: Tumor RNA LH48


title: Tumor RNA LH48 Technical Replica 2

description: Technical replica 2


title: Tumor RNA LH41 Technical Replica 1

description: Technical replica 1


title: Tumor RNA LH40 Technical Replica 1

description: Technical replica 1

source_name: Tumor RNA LH40


title: Tumor RNA LH39 Technical Replica 2

description: Technical replica 2

source_name: Tumor RNA LH39


title: Tumor RNA LH37 Technical Replica 2

description: Technical replica 2

source_name: Tumor RNA LH37


title: Tumor RNA LH40 Technical Replica 2

description: Technical replica 2


title: Tumor RNA LH39 Technical Replica 1

description: Technical replica 1


title: Tumor RNA LH37 Technical Replica 1

description: Technical replica 1


title: Tumor RNA LH32 Technical Replica 2

description: Technical replica 2

source_name: Tumor RNA LH32


title: Tumor RNA LH31 Technical Replica 2

description: Technical replica 2

source_name: Tumor RNA LH31


title: Tumor RNA LH36 Technical Replica 2

description: Technical replica 2

source_name: Tumor RNA LH36


title: Tumor RNA LH36 Technical Replica 1

description: Technical replica 1


title: Tumor RNA LH32 Technical Replica 1

description: Technical replica 1


title: Tumor RNA LH30 Technical Replica 1

description: Technical replica 1

source_name: Tumor RNA LH30


title: Tumor RNA LH31 Technical Replica 1

description: Technical replica 1


title: Tumor RNA LH30 Technical Replica 2

description: Technical replica 2


title: D1721/EGD-e Replicate 2

city: Würzburg

first: Regina

last: Stoll

address: Biozentrum, Am Hubland

country: Germany

institute: Lehrstuhl für Mikrobiologie

description: Biological replicate 2 of 3.

hyb_protocol: The slides were hybridized according to the manufacturers protocol (BF-BIOlabs)

scan_protocol: slides were scanned using Axon GenePix® 4300A (Molecular Devices) and analyzed using the Genepix Pro 6.0 software

data_processing:
The data are normalized based on the ratio of medians using the Genepix Pro 6.0 software.
NOTE: Submitter was unable to retrieve unnormalized Genepix files.

organism: Listeria monocytogenes EGD-e

source_name: L. monocytogenes EGD-e Dlmo1721 (mutant)

label_protocol: 30 µg of total RNA were primed with 9 µg Random primer at 70°C for 10 min, then reversed transcribed at 42°C for 2 h in the presence of 200 U SuperScript II RTase (Invitrogen), and 20 mM each dATP, dTTP, dGTP, with 16 µM dCTP, 50 nmol Cy3/Cy5-labelled dCTP

growth_protocol: Bacteria were grown  in MM + 10 mM glucose until OD600nm of 0.6.

extract_protocol: RNA from the L. monocytogenes strains grown to an OD600 of 0.6 was extracted using the RNeasy® Mini Kit (QIAGEN, Hilden, Germany) according to the manufacturer’s protocol. Residual DNA was removed on a column with RNase-free DNase (QIAGEN)

treatment_protocol: L. monocytogenes strains were grown under aerobic conditions in a defined minimal medium (MM; MM equates MWB without any additional carbon source (Premaratne et al., 1991)) supplemented with different sugars at 37°C.

tag: genotype/variation

value: prd deletion mutant Dlmo1721

source_name: L. monocytogenes EGD-e (wildtype)

value: wildtype


title: D1721/EGD-e Replicate 1

description: Biological replicate 1 of 3.


title: D0785/EGD-e Replicate 2

description: Biological replicate 2 of 3.

source_name: L. monocytogenes EGD-e Dlmo0785 (mutant)

value: prd deletion mutant Dlmo0785


title: D2683-5 D0027/EGD-e Replicate 1

description: Biological replicate 1 of 3.

source_name: L. monocytogenes EGD-e Dlmo2683-2685 Dlmo0027 (mutant)

growth_protocol: Bacteria were grown in MM + 10 mM glucose until OD600nm of 0.6

value: PTS deletion mutant Dlmo2683-2685 Dlmo0027


title: Tumor RNA LH29 Technical Replica 1

description: Technical replica 1

source_name: Tumor RNA LH29

source_name: Mouse Universal Reference RNA


title: D2683-5/EGD-e Replicate 3

description: Biological replicate 3 of 3.

source_name: L. monocytogenes EGD-e Dlmo2683-2685 (mutant)

value: PTS deletion mutant Dlmo2683-2685


title: D1721/EGD-e Replicate 3

description: Biological replicate 3 of 3.


title: D2683-5 D0027/EGD-e Replicate 2

description: Biological replicate 2 of 3.


title: Tumor RNA LH25 Technical Replica 1

description: Technical replica 1

source_name: Tumor RNA LH25


title: Tumor RNA LH29 Technical Replica 2

description: Technical replica 2


title: D0785/EGD-e Replicate 3

description: Biological replicate 3 of 3.


title: Tumor RNA LH25 Technical Replica 2

description: Technical replica 2


title: Tumor RNA LH26 Technical Replica 2

description: Technical replica 2

source_name: Tumor RNA LH26


title: Tumor RNA LH24 Technical Replica 2

description: Technical replica 2

source_name: Tumor RNA LH24


title: D2683-5 D0027/EGD-e Replicate 3

description: Biological replicate 3 of 3.


title: Tumor RNA LH24 Technical Replica 1

description: Technical replica 1


title: D2683-5/EGD-e Replicate 1

description: Biological replicate 1 of 3.


title: D2683-5/EGD-e Replicate 2

description: Biological replicate 2 of 3.


title: D0785/EGD-e Replicate 1

description: Biological replicate 1 of 3.


title: DManPTS D0027/EGD-e Replicate 3

description: Biological replicate 3 of 3.

source_name: L. monocytogenes EGD-e DManPTS Dlmo0027 (mutant)

value: PTS deletion mutant DManPTS Dlmo0027


title: Tumor RNA LH26 Technical Replica 1

description: Technical replica 1


title: DManPTS D0027/EGD-e Replicate 1

description: Biological replicate 1 of 3.


title: DManPTS D0027/EGD-e Replicate 2

description: Biological replicate 2 of 3.


title: DManPTS/EGD-e Replicate 3

description: Biological replicate 3 of 3.

source_name: L. monocytogenes EGD-e DManPTS (mutant)

value: PTS deletion mutant DManPTS


title: DManPTS/EGD-e Replicate 1

description: Biological replicate 1 of 3.


title: D0781-4/EGD-e Replicate 3

description: Biological replicate 3 of 3.

source_name: L. monocytogenes EGD-e Dlmo0781-0784 (mutant)

value: PTS deletion mutant Dlmo0781-0784


title: D0781-4/EGD-e Replicate 2

description: Biological replicate 2 of 3.


title: D0781-4/EGD-e Replicate 1

description: Biological replicate 1 of 3.


title: D0096-8/EGD-e Replicate 2

description: Biological replicate 2 of 3.

source_name: L. monocytogenes EGD-e Dlmo0096-0098 (mutant)

value: PTS deletion mutant Dlmo0096-0098


title: D0096-8/EGD-e Replicate 1

description: Biological replicate 1 of 3.


title: D0096-8/EGD-e Replicate 3

description: Biological replicate 3 of 3.


title: DManPTS/EGD-e Replicate 2

description: Biological replicate 2 of 3.


title: Col whole leaf, 5 d UI, biological rep 1

city: Berkeley

first: Mary

middle: C

last: Wildermuth

state: CA

address: 221 Koshland Hall MC3102

department: Plant and Microbial Biology

institute: University of California Berkeley

description: Gene expression data from 5d uninfected wild type whole mature leaves

hyb_protocol: Microarray hybridizations to Affymetrix Arabidopsis ATH1 GeneChips were performed according to the protocol given in the Affymetrix GeneChip Expression Analysis Technical Manual 701025 rev 1.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 7G at the Univeristy of California, Berkeley, functional genomics lab.

data_processing: Log2 (expression values) were extracted using robust multi-array analysis (RMA) implemented in the function rma() in the Bioconductor software package affy. Background correction was performed by correcting PM (perfect match) only, to reduce noise from signal intensity. Quantile normalization was performed to make the distributions of signal intensities uniform across chips. Quality assessment was done using the weights outputted from the linear model fitting function fitPLM() in the R package AffyExtensions.

organism: Arabidopsis thaliana

source_name: Col whole leaf uninfected 5d

label_protocol: Two-round and one-round target labeling was performed according to the protocols given in the Affymetrix GeneChip Expression Analysis Technical Manual 701025 rev 1. Quantity and quality of amplified RNA was determined by the A260/A280 ratio and by its profile on an Agilent 2100 Bioanalyzer.

growth_protocol: Arabidopsis seeds were stratified in 0.1% agarose for 3-5 days and planted in boxes containing Metromix 200 soil. Seeds were equally distributed in each box using a template, with 9 plants per box.  The flats (6 boxes per flat) were covered with plastic trays for 1 week and then uncovered. Flats were watered from below and fertilized at 2-1/2 weeks. Plants were grown in Percival AR66L growth chambers at 22°C, 70% RH, 12 h photoperiod with photosynthetically active radiation=180 µE m-2 s-1.

extract_protocol: Total RNA was extracted using the Picopure kit from Arcturus according to the manufacturer's instructions from LMD, whole leaf and leaf section scrape samples.  Samples were subject to on-column DNase digestion using  DNase I from Qiagen. RNA quality was determined by the A260/A280 ratio and by its profile on an Agilent 2100 Bioanalyzer.

treatment_protocol: At four weeks, a subset of boxes was infected with a light innoculum of G.orontii using a settling tower. Light innoculum is 2 half G.O.-infected leaves with conidia 10-14 dpi.  Infected plants were placed in a separate Percival growth chamber under the same conditions as the pathogen-free Percival. Infections were performed at 11:30 am to standardize experiments and minimize circadian effects. Samples were harvested at 5 dpi. An uninfected 5 d sample was also collected.  For each sample, four fully expanded mature leaves were excised per plant and transferred to Sorensen's buffer. Harvested leaves were microwave-fixed, dehydrated and embedded in paraffin. Embedded leaves were sectioned into 10 µm sections using a microtome prior to laser microdissection. Groups of epidermal and mesophyll cells surrounding G. orontii-infected cells were collected using the Leica AS LMD with 40XT objective from infected samples. In parallel, groups of epidermal and mesophyll cells were collected from uninfected samples. Whole leaves (3-4 fully expanded mature leaves) were also harvested for each sample and immediately frozen in liquid nitrogen. Two independent experiments were performed with triplicate samples collected within each experiment.  Two biological replicates were processed.

tag: genotype

value: wild type

value: 4 weeks old at time 0 (innoculation)

value: whole leaf


title: JCW27-TOPA-delta sir3 Vs JCW28-TOPA-delta sir3 0min (replicate 2)

city: Barcelona

first: Benjamin

last: Pina

address: Jordi Girona, 18

country: Spain

institute: IDAEA-CSIC

description: 27-TOPA-SIR3 Vs 28-TOPA-SIR3 0min (P2)

hyb_protocol: Microarray prehybridization was performed in 5x SSC (SSC: 150 mM NaCl, 15mM Na-citrate, pH 7.0), 0.1% SDS, 1%BSA at 42ºC for 45 min. (Fluka, Sigma-Aldrich, Buchs SG, Switzerland). Labeled cDNA was dried in a vacuum trap and used as probe after resuspension in 110 μl of hybridization solution (50% Formamide, 5xSSC, 0.1% SDS, 100 μg/ml salmon sperm from Invitrogen, Carlsbad, CA, USA). Hybridization and washing were performed in a Lucidea Slide Pro System (GE Healthcare, Uppsala, Sweden).

scan_protocol: GenePix 4000B fluorescence scanner and analyzed by Genepix® Pro 6.0 software (Axon Instruments, MDS Analytical Technologies, Toronto, Canada).

data_processing: Data was filtered according to spot quality. Only those spots with intensities at least twice the background signal and with at least 75% of pixels with intensities above background plus two standard deviations were selected for further calculations. Following these  criteria, over 70% of spots in each array were usually found suitable for further analysis. Ratio of medians was used to calculate the VALUEs.

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae strain JCW27-SIR3, 0min

label_protocol: 20 µg of total RNA were used for cDNA synthesis and labeling with Cy3-dUTP and Cy5-dUTP fluorescent nucleotides, following indirect labeling protocol (CyScribe postlabeling kit, GE-Healthcare). Labeling efficiency was evaluated by measuring Cy3 or Cy5 absorbance in Nanodrop Spectrophotometer.

growth_protocol: JCW27-TOPA-SIR3 and JCW28-TOPA-SIR3 cells were grown in LEU- SD media until logarithmic phase.

extract_protocol: Total RNA extracted by RiboPure RNA extraction kit (Ambion) following manufacturer's instructions.

treatment_protocol: Upon reaching logarithmic phase, cells were passed to 35C to inactivate top2. Samples were taken at 0 and 120min top2 inactivation (35C).

value: FY251 carrying null mutations delta top1 and NAT1:SIR3

value: Grown to log phase at 26C

source_name: Saccharomyces cerevisiae strain JCW28-SIR3, 0min

value: FY251 carrying null mutations delta top1 top2-4 and NAT1:SIR3


title: JCW27-TOPA-delta sir3 Vs JCW28-TOPA-delta sir3 0min (replicate 1)

description: 27-TOPA-SIR3 Vs 28-TOPA-SIR3 0min (P1)


title: JCW27-TOPA-delta sir3 Vs JCW28-TOPA-delta sir3 120min (replicate 2)

description: 27-TOPA-SIR3 Vs 28-TOPA-SIR3 120min (P2)

source_name: Saccharomyces cerevisiae strain JCW27-SIR3, 120min

value: After growth to log phase, 120min at 35C

source_name: Saccharomyces cerevisiae strain JCW28-SIR3, 120min


title: Tumor RNA LK122 Technical Replica 2

description: Technical replica 2

value: Cell line

source_name: Tumor RNA LK122

value: Tumor RNA Lung KRAS(G12V)

value: Tumor


title: JCW27-TOPA-delta sir3 Vs JCW28-TOPA-delta sir3 0min (replicate 3)

description: 27-TOPA-SIR3 Vs 28-TOPA-SIR3 0min (P3)


title: JCW27-TOPA-delta sir3 Vs JCW28-TOPA-delta sir3 120min (replicate 3)

description: 27-TOPA-SIR3 Vs 28-TOPA-SIR3 120min (P3)


title: JCW27-TOPA-delta sir3 Vs JCW28-TOPA-delta sir3 120min (replicate 1)

description: 27-TOPA-SIR3 Vs 28-TOPA-SIR3 120min (P1)


title: Col whole leaf, 5 dpi, biological rep 2

description: Gene expression data from 5d infected wild type whole mature leaves

source_name: Col whole leaf infected with Golovinomyces orontii 5d


title: eds16 laser microdissected, 5 dpi, biological rep 1

description: Gene expression data from 5d infected eds16 laser-microdessected leaves around the infection site without vascular bundle cells and lower epidermis

source_name: eds16 laser-microdissected leaf amplified infected with Golovinomyces orontii 5d

value: mutant

value: LMD leaf epidermal and mesophyll cells


title: Col laser microdissected, 5 d UI, biological rep 2

description: Gene expression data from 5d uninfected wild type laser-microdessected leaves around the infection site without vascular bundle cells and lower epidermis

source_name: Col laser-microdissected leaf uninfected 5d


title: JCW27-TOPA vs JCW28-TOPA 120min (replicate 2)

description: 27-TOPA Vs 28-TOPA 120min (P2)

source_name: Saccharomyces cerevisiae JCW27 strain, 120min

growth_protocol: JCW27-TOPA (delta top1) and JCW28-TOPA (delta top1 top2-4) cells were grown in LEU- SD media until logarithmic phase.

treatment_protocol: Upon reaching logarithmic phase, cells were passed to 35C to inactivate top2. Samples were taken at 0, 30 and 120min top2 inactivation (35C).

value: FY251 carrying null mutation delta top1

source_name: Saccharomyces cerevisiae JCW28 strain, 120min

value: FY251 carrying null mutations delta top1 and top2-4


title: eds16 laser microdissected, 5 dpi, biological rep 2


title: JCW27-TOPA vs JCW28-TOPA 30min (replicate 2)

description: 27-TOPA Vs 28-TOPA 30min (P2)

source_name: Saccharomyces cerevisiae JCW27 strain, 30min

value: After growth to log phase, 30min at 35C

source_name: Saccharomyces cerevisiae JCW28 strain, 30min


title: JCW27-TOPA vs JCW28-TOPA 120min (replicate 3)

description: 27-TOPA Vs 28-TOPA 120min (P3)


title: JCW27-TOPA vs JCW28-TOPA 30min (replicate 1)

description: 27-TOPA Vs 28-TOPA 30min (P1)


title: Tumor RNA LK69 Technical Replica 2

description: Technical replica 2

source_name: Mouse Universal Reference RNA

source_name: Tumor RNA LK69


title: JCW27-TOPA vs JCW28-TOPA 0min (replicate 1)

description: 27-TOPA Vs 28-TOPA 0min (P1)

source_name: Saccharomyces cerevisiae JCW27 strain, Omin

source_name: Saccharomyces cerevisiae JCW28 strain, Omin


title: JCW27-TOPA vs JCW28-TOPA 30min (replicate 3)

description: 27-TOPA Vs 28-TOPA 30min (P3)


title: JCW27-TOPA vs JCW28-TOPA 120min (replicate 1)

description: 27-TOPA Vs 28-TOPA 120min (P1)


title: JCW27-TOPA vs JCW28-TOPA 0min (replicate 2)

description: 27-TOPA Vs 28-TOPA 0min (P2)


title: JCW27-TOPA vs JCW28-TOPA 0min (replicate 3)

description: 27-TOPA Vs 28-TOPA 0min (P3)


title: Col laser microdissected, 5 dpi, biological rep 2

description: Gene expression data from 5d infected wild type laser-microdessected leaves around the infection site without vascular bundle cells and lower epidermis

source_name: Col laser-microdissected leaf amplified infected with Golovinomyces orontii 5d


title: NF1-affected #E1

status: Public on Nov 30 2009

city: Bethesda

first: Alexander

last: Pemov

state: MD

address: 49 Convent Drive

institute: National Institutes of Health

hyb_protocol: Amplified biotinylated cRNA (1.5 ug) were hybridized to HumanWG-6_v2 Sentrix BeadChips. In all steps, care was exercised to avoid batch effects. Samples were hybridized to the microarrays at 55ºC for 16-17 hours. Microarrays were washed to remove non-specifically bound cRNA, stained with 1 mg/mL Streptavidin-Cy3 (GE Healthcare, Piscataway, NJ, USA) and dried.

scan_protocol: Microarrays were scanned in BeadStation 500 scanner. Image acquisition and initial image analysis were done with Illumina BeadScan and BeadStudio applications.

data_processing:
Raw data from the Illumina BeadChips was corrected for background and quantile normalized using BeadExplorer (version 1.5.0), a Bioconductor module developed for quality control, normalization, annotation and exploration of Illumina BeadChip data. Average detection value was calculated for each transcript, and the transcripts with average detection values below 0.99 were excluded from further analysis.

Non-normalized data is available in the 'GSE18445_non-normalized_data.txt' file, which is linked to the Series GSE18445 record as a supplementary file.

source_name: European Cell and Culture Collection; LCL 89082417

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep RNA amplification kit (Ambion Inc., Austin, TX) per the manufacturer's instuctions.

growth_protocol: All NF1-affected and -unaffected banked lymphoblastoid cell lines (LCLs; Epstein-Barr virus (EBV)-transformed peripheral blood B-cell lymphocytes) from human kindred with neurofibromatosis type 1 were obtained from  the European Cell and Culture Collection “ECACC,” pedigree P0117; Salisbury, Wiltshire, United Kingdom).

extract_protocol: Trizol cell lysates were mixed with chloroform (1/5 of lysate volume), vortexed for one minute and centrifuged in a table-top centrifuge at 13,000 rpm for 15 min at 4ºC. The aqueous phase was used for RNA isolation. The aqueous phase was mixed with equal volume of 70% ethanol and immediately loaded onto RNeasy mini columns (Qiagen, Valencia, CA, USA), with subsequent steps performed as per the manufacturer’s protocol. The RNA quality was estimated on a 2100 Bioanalyzer, RNA 6000 Nano Chips (Agilent, Santa Clara, CA, USA). Samples with RNA integrity number (RIN) of 8.0 and above were used for further analysis.

treatment_protocol: None.

value: lymphoblastoid cells

tag: nf1-affectation status

value: Affected

tag: age (years)

value: Male


title: embryo replicate 2

city: Salt Lake City

first: Carl

last: Thummel

state: UT

department: Human Genetics

institute: University of Utah

description: biological replicate 2 of 4

hyb_protocol: Fluorescently labeled cRNA samples (825 ng each) were fragmented and combined with Agilent Hi-RPM Hybridization Buffer.  Microarray hybridizations were performed using Agilent SureHyb Hybridization chambers.  Hybridization chambers were loaded onto a rotisserie in an Agilent Hybridization oven and were incubated at 65ºC for 17 hours with a rotational speed of 10 rpm.  Following incubation, the microarray slide was washed for 1 minute each in Gene Expression Wash Buffer 1 (6X SSPE, 0.005% N-lauroylsarcosine; room temperature) and Gene Expression Wash Buffer (0.06X SSPE, 0.005% N-lauroylsarcosine; 31ºC) for 1 minute each.  Microarray slides were briefly dipped in a solution of acetonitrile and dried.

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505C Microarray Scanner.  The scanner performs simultaneous detection of Cyanine-3 and Cyanine-5 signal on the hybridized slide.  Data captured from the scanned microarray image is saved as a TIF file.

data_processing: TIF files generated from the scanned microarray image are loaded into Agilent Feature Extraction Software version 9.5.1.1.  The software automatically positions a grid and finds the centroid positions of each feature on the microarray.  This information is used to perform calculations that include feature intensities, background measurements and statistical analyses.  Data generated by the software is recorded as a tab-delimited text file.

organism: Drosophila melanogaster

source_name: w1118 embryos

label_protocol: The Agilent Two-Color Quick Amp Labeling Kit is used to generate fluorescently labeled cRNA for two-color microarray hybridizations.  Agilent RNA spike-in controls are combined with input total RNA samples (50 to 1000 ng).  The polyadenylated fraction of the total RNA sample is primed with oligo dT/T7 RNA polymerase promoter oligonucleotide sequences and cDNA synthesis is accomplished through the addition of MMLV-RT.   Following cDNA synthesis, T7 RNA polymerase and dye-labeled nucleotides are combined with the reaction mixture to simultaneously amplify the target material through the generation of cRNA and incorporate either cyanine 3-CTP or cyanine 5-CTP.  Fluorescently labeled, cRNA molecules are purified from the reaction mixture using the Qiagen RNeasy mini kit.  The concentration of the purified samples is determined using a NanoDrop ND-1000 spectrophotometer.

growth_protocol: Four-hour egg lays were collected on molasses agar plates supplemented with yeast paste and allowed to develop at 25ºC for 16 hours.

extract_protocol: Total RNA extracted using Tripure (Roche) following manufacturer's instructions and DNase treated using Qiagen Rneasy + DNase

source_name: DHR3 mutant embryos


title: embryo replicate 4

description: biological replicate 4 of 4


title: NF1-affected #E6

source_name: European Cell and Culture Collection; LCL 89082422

tag: cell type


title: NF1-unaffected #E2

source_name: European Cell and Culture Collection; LCL 89082418

value: Unaffected

value: Female


title: embryo replicate 1

description: biological replicate 1 of 4


title: embryo replicate 3

description: biological replicate 3 of 4


title: Wild type mouse #10

hyb_protocol: Amplified biotinylated cRNA (1.5 ug) were hybridized to Mouse Ref-6_v1 Sentrix BeadChips. In all steps, care was exercised to avoid batch effects. Samples were hybridized to the microarrays at 55ºC for 16-17 hours. Microarrays were washed to remove non-specifically bound cRNA, stained with 1 mg/mL Streptavidin-Cy3 (GE Healthcare, Piscataway, NJ, USA) and dried.

data_processing:
Raw data from the Illumina BeadChips was corrected for background and quantile normalized using BeadExplorer (version 1.5.0), a Bioconductor module developed for quality control, normalization, annotation and exploration of Illumina BeadChip data. Average detection value was calculated for each transcript, and the transcripts with average detection values below 0.99 were excluded from further analysis.

Non-normalized data is available in the 'GSE18447_non-normalized_data.txt' file, which is linked to the Series GSE18447 record as a supplementary file.

source_name: Spleen-derived B-cells from B6 mouse

growth_protocol: Six Nf1+/- B6 (three males, three females) and six wild-type (three males, three females) adult (“Nf1-Mouse-12”) mice from 5 litters of the same line were euthanized at the age of ~8 months with CO2.  The dissected spleens were homogenized with the tip of a syringe plunger (3 ml syringe, slip tip, BD Biosciences, Discovery Labware, Bedford, MA, USA) and passed through a 70 μm nylon cell strainer (BD Biosciences) and purified using the CD19 mouse microbeads (Miltenyi Biotec, Auburn, CA, USA) on the autoMACS Separator (Miltenyi Biotec) using the possel_d program, following the manufacturer’s directions. CD19+ and CD19- flow-through fractions were collected, and the purity was assessed by FACS on aliquots using GR1-FITC, B220-PE, CD3-PerCPCy5.5 and MAC1-APC antibodies (BD Pharmingen, San Diego, CA, USA). The remaining CD19+ and CD19- fractions were immediately lysed in 1 mL of the Trizol reagent (Invitrogen) and frozen at -80oC.

value: spleen-derived B cells

value: Wild type

tag: age (months)

value: adult

tag: sex


title: NF1-affected #E10

source_name: European Cell and Culture Collection; LCL 89082426

tag: gender


title: Wild type mouse #8

tag: strain


title: NF1-unaffected #E11

source_name: European Cell and Culture Collection; LCL 89082427


title: Wild type mouse #1


title: Nf1+/- heterozygous mouse #9

value: Nf1+/- heterozygote


title: Wild type mouse #5


title: NF1-unaffected #E7

source_name: European Cell and Culture Collection; LCL 89082423


title: Mammary_stage02_B

city: Viterbo

first: Alessio

last: Valentini

address: via San Camillo de Lellis

department: IBAF

country: Italy

institute: University of Tuscia

description: We analyzed the mammary transcriptome using biopsies from individuals of Gentile di Puglia and Sarda at two lactation stages to assess the differences between breeds, with the aim to identify genes controlling milk composition and their metabolic pathways.

hyb_protocol: The labeled aRNA was fragmented into 35- 200-base fragments and then hybridized onto the slide according to the Combimatrix’s instructions. Hybridization was performed overnight at 50°C.

scan_protocol: After hybridization, arrays were washed and scanned with a ScanArray Lite (Perkin Elmer) laser scanner. Microarray Imager 5.9.3 software was used to extract feature data from microarray fluorescence images.

data_processing: The saturated spots were flagged by the software Microarray Imager 5.9.3 (CombiMatrix). For each channel the mean of empty spots intensity (E) was calculated. Spots with signal to E ratio below 1.5 were filtered, together with flagged spots. We removed systematic bias in the data by applying the dye-swap normalization (Fang, Y.; Brass, A.; Hoyle, D.C.; Hayes, A.; Bashein, A.; Oliver, S.G.; Waddingtong, D.; Rattray, M. A model-based analysis of microarray experimental error and normalisation. Nucleic Acids Res. 2003, 31, e96.) that makes use of the reverse labelling in the two microarray replicates and the lowess normalization.

organism: Ovis aries

source_name: mammary gland stage 02 Sarda

label_protocol: RNA was quantified using a DTX fluorimeter (Beckman) using the Quant-iT kit (Invitrogen). Aliquots of 1 mg were amplified and Cy3/Cy5 labeled using the Kreatech Diagnostics (The Netherlands) kit.

extract_protocol: Tissues were subjected to RNA extraction with ice-cold TRIzol (Invitrogen) and using RNeasy Midi Kit columns (Qiagen). RNA integrity was assessed by electrophoretic analysis of 28S and 18S rRNA subunits. The purity of RNA and preliminary concentration were assessed with a spectrophotometer (GeneQuantpro). A260/A280 ratio was >1.9.

tag: tissue

value: mammary gland

tag: breed/lactation stage

value: Sarda sheep, taken 44 days after lambing (stage 02)

source_name: mammary gland stage 02 Gentile di Puglia

value: Gentile di Puglia sheep, taken 44 days after lambing (stage 02)


title: Nf1+/- heterozygous mouse #7


title: Nf1+/- heterozygous mouse #2


title: Mammary_stage01_B

source_name: mammary gland stage 01 Sarda

value: Gentile di Puglia sheep, taken at 6 days after lambing (stage 01)

source_name: mammary gland stage 01 Gentile di Puglia

value: Sarda sheep, taken at 6 days after lambing (stage 01)


title: Wild type mouse #3


title: Nf1+/- heterozygous mouse #4


title: Wild type mouse #12


title: Nf1+/- heterozygous mouse #6


title: Mammary_stage02_A


title: Mammary_stage01_A


title: Nf1+/- heterozygous mouse #11


title: Microdissected whole medulla, biological rep6

status: Public on Nov 24 2009

city: jupiter

first: howard

middle: t

last: petrie

state: FL

address: 130 scripps way

department: cancer biology

institute: the scripps research instititute

description: Gene expression data from mcirodissected whole thymic medulla from C57bl6/J male mice 4-6 weeks old.

hyb_protocol: Fragmentation/hybridization to MOE430v2.0 arrays (Affymetrix) were performed according to Affymetrix protocols.

scan_protocol: Imaging was performed on a Hewlett Packard GeneArray Scanner according to standard Affymetrix protocol.

data_processing: The data were analyzed using Affymetrix Expression Console version 1.0 based on Affymetrix MAS 5.0 analysis default settings.  Global scaling was applied and the trimmed mean target intensity of each array was arbitrarily set to 500.

label: Biotin

source_name: whole thymic medulla

label_protocol: Biotin-labeled cRNA probes were prepared as recommended by the manufacturer (Affymetrix), using oligo-dT primers, SuperScript, and BioArray High Yield RNA Transcript kits (Affymetrix).

extract_protocol: For microdissected tissues RNA was prepared using RNAqueous Micro kits (Ambion). For purified lymphoid cells RNA was prepared using RNeasy Mini Kits (Qiagen) according to recommended protocols.

value: Whole medulla

tag: cell phenotype

tag: age

value: 4-6 wks


title: Microdissected whole medulla, biological rep1


title: Microdissected whole medulla, biological rep2


title: Microdissected whole cortex, biological rep4

description: Gene expression data from mcirodissected whole thymic cortex from C57bl6/J male mice 4-6 weeks old.

source_name: whole thymic cortex

value: Whole cortex


title: Microdissected whole cortex, biological rep1


title: Microdissected whole medulla, biological rep7


title: Microdissected whole medulla, biological rep4


title: Microdissected whole medulla, biological rep5


title: Microdissected central cortical region, biological rep3

description: Gene expression data from mcirodissected central cortex thymus from C57bl6/J male mice 4-6 weeks old.

source_name: central cortex from thymus

value: Central cortex


title: Microdissected central cortical region, biological rep2


title: Microdissected whole cortex, biological rep3


title: Microdissected whole cortex, biological rep2


title: Microdissected whole medulla, biological rep3


title: Microdissected peri-medullary cortical region, biological rep2

description: Gene expression data from mcirodissected prei-medullary cortex thymus from C57bl6/J male mice 4-6 weeks old.

source_name: prei-medullary cortex from thymus

value: Peri-medullary cortex


title: Microdissected whole cortex, biological rep5


title: Sorted medullary thymocyte, biological rep3

description: Gene expression data from FACS sorted medullary lymphocytes from C57bl6/J male mice 4-6 weeks old.

source_name: medullary lymphocytes

value: medullary thymocyte

value: CD3hi AND CD45+


title: Microdissected central cortical region, biological rep1


title: Microdissected peri-medullary cortical region, biological rep3


title: Microdissected sub-capsular cortical region, biological rep2

description: Gene expression data from mcirodissected sub-capsular thymus from C57bl6/J male mice 4-6 weeks old.

source_name: sub-capsular thymic cortex

value: Sub-capsular cortex


title: Microdissected sub-capsular cortical region, biological rep1


title: Sorted medullary thymocyte, biological rep5


title: Sorted medullary thymocyte, biological rep2


title: Microdissected peri-medullary cortical region, biological rep1


title: Microdissected whole cortex, biological rep6


title: Sorted medullary thymocyte, biological rep4


title: Microdissected whole cortex, biological rep7


title: Microdissected sub-capsular cortical region, biological rep3


title: Sorted medullary thymocyte, biological rep1


title: Sorted cortical thymocyte, biological rep3

description: Gene expression data from FACS sorted cortical lymphocytes from C57bl6/J male mice 4-6 weeks old.

source_name: cortical lymphocytes

value: cortical thymocyte

value: CD3-/lo AND CD45+ AND (CD90+ OR CD117+)


title: Sorted cortical thymocyte, biological rep5


title: Sorted cortical thymocyte, biological rep4


title: LdP SAHM1 01

status: Public on Nov 12 2009

first: Raymond

last: Moellering

address: 12 Oxford Street

department: Chemistry and Chemical Biology

institute: Harvard University

hyb_protocol: Hybridization was performed according to standard protocols for Affymetrix Mouse 430 2.0 arrays.

scan_protocol: Arrays were scanned using a GenePix 4000B microarray scanner.

data_processing: Data was processed using GenePattern software available at the Broad Insititute. RMA processing was used with quantile normalization.

source_name: Diseased mice (received LdP-NOTCH1 transduced cells) treated with SAHM1

label_protocol: Biotinylated cRNA was generated using standard Affymetrix protocols.

growth_protocol: For bone marrow translplantation, 8-10 week-old  Tyrosinase-/- C57BL/6 mice were injected with 5-FU six days prior to bone marrow collection from femurs and tibiae of primary mice. After an overnight incubation in RPMI-1640 supplemented with 10% FBS, 10 ng/mL mIL-3, 20 ng/mL mIL-6 and 10 ng/mL mSCF, cells were spin-infected with an MSCV vector containing GFP and a mutant human NOTCH1 allele containing the L1601P and 2473AHP*Stop mutations, which are clinically apparent mutations in human T-ALL. Infection was confirmed by flow cytometry.  Transduced cells (1x106) were injected into the tail-vein of lethally irradiated syngeneic recipient mice. Animals were sacrificed 2-3 months post-transplant to obtain splenic T-ALL cells for secondary transplants and in vivo studies.

extract_protocol: Treated cells were centrifuged at 1000 rpm, washed with cold PBS and total RNA was extracted using a Qiagen Rneasy Kit according to manufacturers instructions.

treatment_protocol: Secondary recipients were monitored for established T-ALL by bio-luminescence imaging. After 20-30 days matched cohorts of diseased mice were treated with vehicle alone (5% DMSO in Hank's Buffered Saline Solution), 35 mg/kg SAHM1 once daily or 30 mg/kg SAHM1 twice daily, all by intraperitoneal injection. After five days of treatment mononuclear T-ALL cells were collected and analyzed for gene expression.

value: lymphoblast

tag: disease state

value: leukemia


title: Wild type salivary gland sporozoites biological replicate 2 technical replicate 1

status: Public on Nov 10 2009

city: Baltimore

first: Calvin

middle: Williams

last: Williams

address: HSF I Suite 380, 685 W. Baltimore St.

department: Microbiology and Immunology

institute: University of Maryland

hyb_protocol: 10ug labeled aRNA was fragmented using fragmentation reagents from Ambion. 1ug of fragmented Cy3 and Cy5 labeled aRNA. and mixed with polyA RNA (Invitrogen), 0.2% SDS, 20 mM Hepes, pH 7.2, in 3XSSC and applied underneath coverslips (Erie) onto microarray slides. Hybridization took place for 16 hours in a 65oC waterbath using hybridization chambers (Corning). After hybridization, microarrays were removed from the hybridization chambers and washed in 1X SSC with 0. 1% SDS for 2 min at room temperature , 0.2X SSC for 2min, 0.05X SSC for 1min twice and 0.01X SSC for 30 sec. Slides were dried using compressed air to remove excess fluid.

scan_protocol: Each microarray was scanned using a GenePix 4000A laser scanner and the array features (spots) were quantified using the GenePixPro 5.0 (Axon Instruments Inc.).

data_processing: A ratio-based normalization procedure using the Acuity 3.0 Microarray Informatics Software (Axon Instruments) was applied to the expression data. In each quad on each microarray, there are 6 positive control spots (containing olignucleotides from several P. yoelii genes). Arrays were normalized to yield a ratio of 1.0 for these spots. Each microarray also contained several negative control spots (each containing a randomized oligonucleotide). Genes were considered expressed if their expression was greater than or equal to 1.5 times the value of the mean fluorescence intensity (arithmetic) of these negative control spots calculated across all microarrays.

organism: Plasmodium yoelii

source_name: P. yoelii salivary gland sporozoites

label_protocol: Total RNA was subjected to one rounds of linear amplification using the Amino Allyl Message Amp II aRNA Amplification Kit (Ambion) according to manufaturer's directions.  The resultant amplified RNA (aRNA) was labeled with Cy3 or Cy5 (Amersham) to yield fluorescent Cy3 or Cy5 labeled aRNA.

extract_protocol: Total RNA from mixed blood stages was extracted using Trizol (Invitrogen) and DNase treated using Turbo-DNAfree (Ambion). Total RNA from all other samples was extracted using RNaqueous Micro kit (Ambion)and DNase treated using DNAfree (Ambion).

tag: extraction

value: Total RNA extracted using Rnaqueous Micro Kit (Ambion)

source_name: mixed blood stages

value: Total RNA extracted using Trizol


title: Wild type salivary gland sporozoites biological replicate 2 technical replicate 2


title: LdP SAHM1 03


title: Radiation attenuated sporozoites biological replicate 2 technical replicate 1

source_name: P. yoelii salivary gland sporozoite collected  after 12000rads of gamma irradiation


title: Radiation attenuated sporozoites biological replicate 2 dye swap 1


title: Wild type salivary gland sporozoites biological replicate 2 dye swap 1


title: LdP SAHM1 02


title: LdP Vehicle 02

source_name: Diseased mice (received LdP-NOTCH1 transduced cells) treated with vehicle


title: Radiation attenuated sporozoites biological replicate 2 technical replicate 2


title: LdP Vehicle 01


title: Sorted cortical thymocyte, biological rep1


title: LdP Vehicle 03


title: HPB-ALL_SAHM1_02

hyb_protocol: Hybridization was performed according to standard protocols for Affymetrix HG-U133 plus 2.0 arrays.

source_name: HPB-ALL cells treated with SAHM1

growth_protocol: T-ALL cells were grown in1640 RPMI with 10% FBS and 1% pen/strep.

treatment_protocol: Cells were cultured in 24-well plates and indicated with SAHM1 or the equivalent amount of DMSO for 24 hours.

value: T-cell

tag: cell line

value: HPB-ALL


title: Wild type salivary gland sporozoites biological replicate 1 dye swap 1


title: HPB-ALL_SAHM1_01


title: HPB-ALL_SAHM1_03


title: HPB-ALL_DMSO_02

source_name: HPB-ALL cells treated with DMSO


title: HPB-ALL_DMSO_03


title: HPB-ALL_DMSO_01


title: Sorted cortical thymocyte, biological rep2


title: Mycobacterium smegmatis

status: Public on Nov 15 2009

type: genomic

city: Toronto

first: Blair

last: Gordon

address: 1 King's College Circle

department: Molecular Genetics

institute: University of Toronto

hyb_protocol: 6.5 µg each of labeled ChIP cRNA and input cRNA were hybridized to a 241K M. tb H37Rv or M. smegmatis mc2155 whole genome tiling array

scan_protocol: Arrays were scanned on the Genepix Professional 4200A scanner as per manufacturer's protocol

data_processing: The value is log2R normalized using loess

molecule: genomic DNA

organism: Mycolicibacterium smegmatis

source_name: M. smegmatis MS8444  grown in vitro to OD 0.8-1.0

label_protocol: Input and ChIP DNA were amplified and labeled with monofunctional reactive Cy3 or Cy5 dyes based upon the T7 based protocol  (see: Liu, C.L., Schreiber, S.L. & Bernstein, B.E. (2003)  BMC Genomics  4, 19)

extract_protocol: Cultures (50 ml) of M. tb H37Rv/pLSR2-HA and M. smegmatis MS8444/pLSR2-HA  grown to an OD600 0.6-0.8 were treated with 1% formaldehyde and incubated for 15 min at RT. The cross-linking reaction was quenched with 1.25 mM glycine for 10 min. Cells were washed twice with ice-cold PBS and sonicated to generate DNA fragments of ~500-700 bp. Cell lysates were precipitated with an anti-HA antibody (Sigma H9658) using agarose protein G beads (Calbiochem).

tag: sample type

value: lsr2 coimmunoprecipitated DNA amplified to cRNA

value: Total DNA amplified to cRNA


title: Mycobacterium tuberculosis

organism: Mycobacterium tuberculosis H37Rv

source_name: M. tb H37Rv  grown in vitro to OD 0.8-1.0


title: Wild type salivary gland sporozoites biological replicate 1 technical replicate 2


title: 48hr infected hepatocytes biological replicate 2 technical replicate 2

source_name: P. yoelii infected hepatocytes collected 48hr after infection


title: 48hr infected hepatocytes biological replicate 2 technical replicate 1


title: Radiation attenuated sporozoites biological replicate 1 technical replicate 2


title: 24hr infected hepatocytes biological replicate 2 technical replicate 1

source_name: P. yoelii infected hepatocytes collected 24hr after infection


title: Wild type salivary gland sporozoites biological replicate 1 technical replicate 1


title: 24hr infected hepatocytes biological replicate 2 technical replicate2


title: 24hr infected hepatocytes biological replicate 1 technical replicate 2


title: 24hr infected hepatocytes biological replicate 4 technical replicate 1


title: 48hr infected hepatocytes biological replicate 2 dye swap 1


title: 24hr infected hepatocytes biological replicate 4 technical replicate 2


title: 6mMSB PC12

city: Valhalla

first: Bistra

last: Nankova

address: 95 Grassland Rd

institute: New York Medical College

description: gene expression data from PC12 cells treated for 48h with 6mM sodium butyrate

hyb_protocol: Following fragmentation in the presence of heat and Mg2+ the biotinilated cRNA is hybridized to Rat genome 230_2 array for 16 hours at 45C. The arry is washed and stained with streptavidin-phycoerythrin (SAPE) using fluidics station

scan_protocol: the array is scanned using GeneChip Scanner 3000

data_processing: The data were analyzed using Affymetrix GeneChipOperating Software and default setting. The comparison analyses follow the format Experimental_vbaselinechanges.txt and Experimental_vBaselinechanges2X.txt for probe sets shown to give a fold change of >_ 2 in gene expression between the two samples.

source_name: PC12 cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: PC12 cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% horse serum, 5% fetal bovine serum,50 ug/mL streptomycin, and 50 IU/m penicillin in a humidified atmosphere at 37°C and 10% CO2. Spraque-Dawley male (250- 280 grams) rats obtained from Taconic Farms (Germantown, NY) were housed 3 per cage and maintained under controlled conditions of a 12h light-dark cycle(lights on from 7 am to 7 pm) and 23+ 2 0C with food and tap water ad libitum.

extract_protocol: Total RNA from individual petridishes was isolated using RNAzol (Tel-Test, Inc., Friendswood, TX) and used for Northern blot analyses. For microarray analyses the samples from each experimental group were pooled (n=6) purified over Qiagen columns as recomended by Affymetrix and sent to Keck Microarray facility at Yale, New Haven, CT 06511 for RT and microarray analyses.

treatment_protocol: Two days before confluence, PC12 cells were treated with sodium butyrate (SB) in the media at two concentrations 1mM and 6mM for 48 hours. Control cells received vehicle. Rats were injected with SB (500 mg/kg in 0.5 ml) by i.p. injections every 12 hours for three consecutive times. Control animals received same volume of saline. The rats were sacrificed two hours after the last injection.

value: rat pheochromocytoma PC12 cells

tag: agent

value: 48h with 6mM sodium butyrate


title: Radiation attenuated sporozoites biological replicate 1 technical replicate 1


title: 48hr infected hepatocytes biological replicate 4 technical replicate 1


title: CPC12

description: gene expression data from control PC12 cells

value: control


title: Radiation attenuated sporozoites biological replicate 1 dye swap 1


title: 24hr infected hepatocytes biological replicate 1 technical replicate 1


title: 24hr infected hepatocytes biological replicate 3 technical replicate 1


title: 48hr infected hepatocytes biological replicate 1 technical replicate 1

label_protocol: Total RNA was subjected to one round of linear amplification using the Amino Allyl Message Amp II aRNA Amplification Kit (Ambion) according to manufacturer's directions.  The resultant amplified RNA (aRNA) was labeled with Cy3 or Cy5 (Amersham) to yield fluorescent Cy3 or Cy5 labeled aRNA.

extract_protocol: Total RNA from mixed blood stages was extracted using Trizol (Invitrogen) and DNase treated using Turbo-DNAfree (Ambion). Total RNA from all other samples was extracted using RNaqueous Micro kit (Ambion) and DNase treated using DNAfree (Ambion).

label_protocol: Total RNA was subjected to one round of linear amplification using the Amino Allyl Message Amp II aRNA Amplification Kit (Ambion) according to manufaturer's directions.  The resultant amplified RNA (aRNA) was labeled with Cy3 or Cy5 (Amersham) to yield fluorescent Cy3 or Cy5 labeled aRNA.


title: 48hr infected hepatocytes biological replicate 3 technical replicate 1


title: rat Control Adrenal Medulla

description: gene expression data from controls (PBS injected) rat adrenal medulla

source_name: rat adrenal medulla

value: Male

value: Sprague-Dawley

value: control (PBS injected)

value: rat adrenal medulla


title: 1mMSB PC12

description: gene expression data from PC12 cells treated for 48h with 1mM Sodium butyrate

value: 48h with 1mM Sodium butyrate


title: rat SBAdrenal Medulla

description: gene expression data from rat adrenal medulla following 3 ip injections of SB 500mg/kg

value: 3 ip injections of SB 500mg/kg


title: Patient 8-1

status: Public on Nov 09 2009

city: Berlin

first: Reinhard

last: Ullmann

department: Human Molecular Genetics

institute: MPIMG

description: Array CGH analysis of a female patient with pleomorphic/necrotic lobular intraepithelial neoplasia (LIN3), concurrent with intraepithelial lobular carcinoma (Patient 8-2).

hyb_protocol: Hybridization was done overnight at 42?C in a slide booster (Advalytix, Brunnthal, Germany). Detailed protocols are available at our website (Molecular Cytogenetics at the Max Planck Institute for Molecular Genetics)

scan_protocol: Slides were scanned at 10 ?m resolution using an Agilent scanner. PMT settings: 100/100

data_processing: TIFF images were analysed by Genepix 5.0 (Axon Instruments, Union City, CA) and raw intensities (gpr files) were imported into CGHPRO (Chen at al.,2005).Background intensities were not subtracted. Signal intensities were normalized by subgridd LOWESS. Aberrations were defined by Circular Binary Segmentation in combination with log2 ratio threshold of 0.15 and -0.15, respectively.

label: Alexa Fluor? 3

source_name: DNA isolated from laser captured microdissected formalin-fixed, paraffin-embedded tissue.

label_protocol: DNA was labelled by random priming according Invitrogens recommendation (Invitrogen BioPrime? Total Genomic Labeling System).Detailed protocols are available at our website (Molecular Cytogenetics at the Max Planck Institute for Molecular Genetics)

extract_protocol: Sections of formalin-fixed paraffin-embedded (FFPE) specimens cut at 7-8?m were mounted on special foil-coated slides (Molecular Devices, San Diego, USA). The sections were then deparaffinized with Xylene, processed in decreasing concentrations of ethanol and stained with haematoxylin. Lasercapture microdissection for both lesions was performed at multiple sites using Veritas Arcturus. Cells were digested in 10?l TE, pH 9, and 0.5?l proteinase K (20mg/ml) for 48h at 55?C. After inactivation of proteinase K at 99?C for 10min, the digest was stored at -20?C.  Without any further purification, the complete digest was used for whole genome amplification by means of the WGA (Whole Genome Amplification) kit from Sigma.

treatment_protocol: Whole genome amplification by GenomePlex (Sigma).

value: female

value: lobular intraepithelial neoplasia grade 3 (LIN3)

label: Alexa Fluor? 5

source_name: DNA pool isolated from laser captured microdissected formalin-fixed, paraffin-embedded healthy tissue.

value: mammary tissue without histomorphological changes obtained from reduction mammoplasty specimens


title: Patient 7-2

description: Array CGH analysis of a female patient with classic lobular intraepithelial neoplasia (LIN).

hyb_protocol: Hybridization was done overnight at 42degC  in a slide booster (Advalytix, Brunnthal, Germany). Detailed protocols are available at our website (Molecular Cytogenetics at the Max Planck Institute for Molecular Genetics)

scan_protocol: Slides were scanned at 10 um resolution using an Agilent scanner. PMT settings: 100/100

label: Alexa Fluor 3

source_name: test - DNA isolated from laser captured microdissected formalin-fixed, paraffin-embedded tissue.

label_protocol: DNA was labelled by random priming according Invitrogens recommendation (Invitrogen BioPrime Total Genomic Labeling System).Detailed protocols are available at our website (Molecular Cytogenetics at the Max Planck Institute for Molecular Genetics)

extract_protocol: Sections of formalin-fixed paraffin-embedded (FFPE) specimens cut at 7-8um were mounted on special foil-coated slides (Molecular Devices, San Diego, USA). The sections were then deparaffinized with Xylene, processed in decreasing concentrations of ethanol and stained with haematoxylin. Lasercapture microdissection for both lesions was performed at multiple sites using Veritas Arcturus. Cells were digested in 10ul TE, pH 9, and 0.5ul proteinase K (20mg/ml) for 48h at 55degC . After inactivation of proteinase K at 99degC  for 10min, the digest was stored at -20degC .  Without any further purification, the complete digest was used for whole genome amplification by means of the WGA (Whole Genome Amplification) kit from Sigma.

label: Alexa Fluor 5

source_name: reference - DNA pool isolated from laser captured microdissected formalin-fixed, paraffin-embedded healthy tissue.


title: Patient 8-2

description: Array CGH analysis of a female patient with intraepithelial lobular carcinoma (ILC), concurrent with pleomorphic/necrotic lobular intraepithelial neoplasia (Patient 8-1).

value: intraepithelial lobular carcinoma (ILC)


title: Patient 7-1 B

description: Array CGH analysis of a female patient with pleomorphic/necrotic lobular intraepithelial neoplasia (LIN3). Repeat of Patient 7-1.


title: Patient 1-1

description: Array CGH analysis of a female patient with pleomorphic/necrotic lobular intraepithelial neoplasia (LIN3) which is purely composed of signet-ring cells.


title: Patient 2-1

description: Array CGH analysis of a female patient with pleomorphic/necrotic lobular intraepithelial neoplasia (LIN3) which is purely composed of apocrine cells.


title: Patient 3

description: Array CGH analysis of a female patient with pleomorphic/necrotic lobular intraepithelial neoplasia (LIN3).


title: Patient 5


title: Patient 4


title: Patient 2-2

description: Array CGH analysis of a female patient with pleomorphic/necrotic lobular intraepithelial neoplasia (LIN3) which was composed purely of apocrine cells. Corresponding resected tumor to Patient 2-1.


title: Patient 1-2

description: Array CGH analysis of a female patient with pleomorphic/necrotic lobular intraepithelial neoplasia (LIN3) which was composed purely of signet-ring cells. Corresponding resected tumor to Patient 1-1.

extract_protocol: Sections of formalin-fixed paraffin-embedded (FFPE) specimens cut at 7-8um were mounted on special foil-coated slides (Molecular Devices, San Diego, USA). The sections were then deparaffinized with Xylene, processed in decreasing concentrations of ethanol and stained with haematoxylin. Lasercapture microdissection for both lesions was performed at multiple sites using Veritas Arcturus. Cells were digested in 10ul TE, pH 9, and 0.5ul proteinase K (20mg/ml) for 48h at 55degC . After inactivation of proteinase K at 99degC  for 10min, the digest was stored at -20°C.  Without any further purification, the complete digest was used for whole genome amplification by means of the WGA (Whole Genome Amplification) kit from Sigma.


title: Patient 7-1


title: Patient 7-2 B

description: Array CGH analysis of a female patient with classic lobular intraepithelial neoplasia (LIN). Repeat of Patient 7-2.

hyb_protocol: Hybridization was done overnight at 42°C in a slide booster (Advalytix, Brunnthal, Germany). Detailed protocols are available at our website (Molecular Cytogenetics at the Max Planck Institute for Molecular Genetics)

scan_protocol: Slides were scanned at 10 µm resolution using an Agilent scanner. PMT settings: 100/100

label: Alexa Fluor® 3

label_protocol: DNA was labelled by random priming according Invitrogens recommendation (Invitrogen BioPrime® Total Genomic Labeling System).Detailed protocols are available at our website (Molecular Cytogenetics at the Max Planck Institute for Molecular Genetics)

extract_protocol: Sections of formalin-fixed paraffin-embedded (FFPE) specimens cut at 7-8µm were mounted on special foil-coated slides (Molecular Devices, San Diego, USA). The sections were then deparaffinized with Xylene, processed in decreasing concentrations of ethanol and stained with haematoxylin. Lasercapture microdissection for both lesions was performed at multiple sites using Veritas Arcturus. Cells were digested in 10µl TE, pH 9, and 0.5µl proteinase K (20mg/ml) for 48h at 55°C. After inactivation of proteinase K at 99°C for 10min, the digest was stored at -20°C.  Without any further purification, the complete digest was used for whole genome amplification by means of the WGA (Whole Genome Amplification) kit from Sigma.

value: lobular intraepithelial neoplasia

label: Alexa Fluor® 5

tag: female mammary tissue without histomorphological changes obtained from reduction mammoplasty specimens


title: Patient 6


title: Near-shore Male 5, 15 Feb. 2009

status: Public on Nov 01 2009

city: Providence

first: Daniel

middle: James

last: Spade

state: RI

address: Box G-E5

department: Pathology and Laboratory Medicine

institute: Brown University

description: Testis total RNA from wild adult male queen conch (Strombus gigas) collected from a near-shore site in the middle Florida Keys (Tingler Island), 15 February 2009.

scan_protocol: Agilent 2505B DNA Microarray Scanner

data_processing:
Data analysis was performed using JMP Genomics v3.2. Quality flagging was used to remove any control spots or non-uniform spots, using the string:
%str( if ControlType ne 0 then _qFlag_ = -1;
else if (gIsFeatNonUnifOL) then _qFlag_ = 0;
else _qFlag_ = 1; ).
Following quality flagging, any rows with fewer than two data points for a location (treatment group, offshore or near-shore) were removed from the analysis. Finally, data were normalized by median-centering the signals within the array (sample).

organism: Aliger gigas

source_name: testis

label_protocol: Agilent Protocol: One-Color Microarray-Based Gene Expression Analysis, using Low RNA Input Linear Amplification Kit

extract_protocol:
Extracted with RNA STAT-60 (Tel-Test)
Reconstituted in RNAsecure (Ambion)
DNAse-treated with Turbo DNA-free (Ambion)
Followed manufacturer's protocols.

value: male;

tag: location

value: near-shore


title: Near-shore Male 1, 15 Feb. 2009

hyb_protocol: Agilent Protocol: One-Color Microarray-Based Gene Expression Analysis


title: Near-shore Male 4, 15 Feb. 2009


title: Offshore Male 3, 15 Feb. 2009

description: Testis total RNA from wild adult male queen conch (Strombus gigas) collected from an offshore site in the middle Florida Keys (Pelican Shoal), 15 February 2009.

data_processing:
Data analysis was performed using JMP Genomics v3.2.  Quality flagging was used to remove any control spots or non-uniform spots, using the string:
%str(           if ControlType ne 0 then _qFlag_ = -1;
else if (gIsFeatNonUnifOL) then _qFlag_ = 0;
else _qFlag_ = 1;        ).
Following quality flagging, any rows with fewer than two data points for a location (treatment group, offshore or near-shore) were removed from the analysis.  Finally, data were normalized by median-centering the signals within the array (sample).

label_protocol: Agilent Protocol:  One-Color Microarray-Based Gene Expression Analysis, using Low RNA Input Linear Amplification Kit

value: offshore


title: Offshore Male 1, 15 Feb. 2009

hyb_protocol: Agilent Protocol:  One-Color Microarray-Based Gene Expression Analysis


title: Offshore Male 2, 15 Feb. 2009


title: rumen_milk_day14_108

city: Beltsville

first: Erin

middle: E

last: Connor

address: 10300 Baltimore Avenue

department: Animal and Natural Resources Institute

institute: USDA-ARS, BARC

description: Gene expression data from bovine rumen epithelium around the weaning period under differential feeding

hyb_protocol: Single channel according to NimbleGen. See www.nimblegen.com

scan_protocol: At 5-uM resolution according to NimbleGen. See www.nimblegen.com

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Bos taurus

source_name: rumen, milk, day 14

label_protocol: Incorporation according to NimbleGen. See www.nimblegen.com

growth_protocol: Eighteen Holstein bull calves averaging 43.7+/-0.1 kg body weight and 1-2 d of age were used in the study. All calves were fed a commercial milk replacer (Cornerstone 22:20) until weaning at day 42 of age. The milk replacer consisted of 22.0% Crude Protein, 20.0% Crude Fat, 0.15% Crude Fiber, 0.75-1.25% Calcium (Ca), 0.70% Phosphorus (P), 30,000 IU/lb Vitamin A, 5000 IU/lb Vitamin D3, and 100 IU/lb Vitamin E. At weaning, calves were fed commercial milk replacer plus either orchard grass hay (milk + hay) or commercial calf starter (milk + grain). The calf starter (BelAir Calf Starter) consisted of 22.0% Crude protein, 4.0% Crude fat, and 5.5% Crude Fiber.

extract_protocol: Total RNA was isolated from rumen samples using TRIZOL Reagent (Invitrogen Corp., Carlsbad, CA). Samples were DNase-treated using the TURBO DNA-free kit (Ambion, Inc.) according to manufacturer's instructions, followed by column purification using the RNeasy Mini Kit (Qiagen, Valencia, CA). RNA quality was assessed using the BioAnalyzer 2100 (Agilent Technologies, Palo Alto, CA) and concentrations were determined using a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Rockland, DE).

treatment_protocol: Holstein bull calves (n = 18) were assigned randomly to dietary treatments of either commercial milk replacer only (milk), milk + hay, or milk + grain (commercial calf starter) and housed indoors in individual concrete pens. Calves fed milk only were sacrificed at either day 14 (n = 3) or day 42 (n = 3) of life. Calves fed milk + hay were fed milk replacer only until day 42 of life (weaning) and then were provided milk + hay thereafter and sacrificed on day 56 (n = 3) or day 70 (n = 3) of life. Calves fed milk + grain were fed milk replacer only until day 42 (weaning) and then were provided milk + grain thereafter and sacrificed on day 56 (n = 3) or day 70 (n = 3) of life. Rumen epithelial tissue was collected from each calf at slaughter and samples were immediately fixed in Ambion RNAlater (Ambion, Inc., Austin, TX), then stored at -80°C until RNA isolation.

tag: breed

value: Holstein bull calf

value: rumen epithelium

tag: development stage

tag: diet

value: milk diet


title: rumen_milk_day14_113


title: rumen_milk+grain_day56_116

source_name: rumen, milk+grain, day 56

value: milk + grain diet


title: 48hr infected hepatocytes biological replicate 1 technical replicate 2

value: Total RNA extracted using Rnaqueous Micro Kit (Ambion)

source_name: mixed blood stages

value: Total RNA extracted using Trizol


title: rumen_milk_day42_114

source_name: rumen, milk, day 42


title: rumen_milk_day14_118


title: rumen_milk+hay_day70_101

source_name: rumen, milk+hay, day 70

value: milk + hay diet


title: rumen_milk+grain_day70_112

source_name: rumen, milk+grain, day 70


title: rumen_milk+grain_day56_110


title: rumen_milk+hay_day70_111


title: rumen_milk+hay_day70_106


title: Young DG, biological rep8

first: Carlo

last: Colantuoni

address: 733 N Broadway

department: Neurology

institute: Johns Hopkins Univ. School of Medicine

description: this array/sample was omitted from the study as a result of quality control procedures

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Rat Genome 230 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: All quality control, normalization, differential expression, and exploratory analysis of microarray data were performed using the R statistical language (http://www.r-project.org/). The gcrma package in Bioconductor (http://www.bioconductor.org/) was used to normalize microarray data. Samples RHab-HCA-AIDG_21-1a-RAE230_2, RHab-HCA-AUDG_12-1a_2-RAE230_2, and RHab-HCA-YDG_8-1a_scan2-RAE230_2 were omitted from the study as a result of quality control procedures.

source_name: RNA from DG region of the hippocampus: Young

label_protocol: RNA samples were sent to the Johns Hopkins Microarray core facility for cRNA labeling, and hybridization to Affymetrix GeneChip Rat Genome 230 2.0 arrays using standard Affymetrix recommended procedures.

growth_protocol: Aged, male Long-Evans rats were obtained at 8-9 mo of age from Charles River Laboratories (Raleigh, NC) and housed in a vivarium at The Johns Hopkins University until 24-26 mo of age for the present experiments. Young rats at 6 months of age were tested alongside the aged rats. All rats were individually housed at 25°C and maintained on a 12 hr light/dark cycle. Food and water were provided ad libitum. The rats were examined for health and pathogen-free status throughout the experiments, as well as by necropsies at the time of sacrifice. All procedures were approved by the institutional animal care and use committee in accordance with the National Institutes of Health directive.

extract_protocol: All rats were sacrificed two weeks after completion of behavioral testing by rapid decapitation, and brains removed from the skull. The CA1, CA3 and DG regions of the hippocampus were microdissected from the hippocampus and total RNA was extracted by homogenization in Trizol reagent (Invitrogen) followed by application to Qiagen RNeasy columns.

treatment_protocol: There was no treatment. Three groups of rats were defined by age and cognitive staus: Young, Aged Unimpaired, and Aged Impaired. Behavioral assessment of memory function in a Morris water maze task was conducted as previously described (Gallagher et al., 1993). A learning index was generated from the proximity of the rat to the escape platform during probe trials interpolated throughout training and was used to define impairment in the rats. Low scores reflect good performance and aged rats performing within the range of young are designated aged unimpaired (AU) whereas those performing worse than young are considered aged impaired (AI).

tag: young (6 months old) male long-evans rats (charles river laboratories, raleigh, nc) were individually housed on a 12

value: 12-hr light/dark cycle with ad libitum access to food and water.


title: rumen_milk+grain_day70_107


title: rumen_milk+hay_day56_115

source_name: rumen, milk+hay, day 56


title: rumen_milk+grain_day70_102


title: Young DG, biological rep7

description: Hippocampal RNA


title: Young DG, biological rep5

description: Hippocampal RNA


title: Young DG, biological rep4

description: Hippocampal RNA


title: Young DG, biological rep6

description: Hippocampal RNA


title: Young DG, biological rep3

description: Hippocampal RNA


title: rumen_milk+hay_day56_104


title: rumen_milk+hay_day56_109


title: Young DG, biological rep2

description: Hippocampal RNA


title: Young DG, biological rep1

description: Hippocampal RNA


title: rumen_milk+grain_day56_105


title: rumen_milk_day42_117


title: Aged Unimpaired DG, biological rep2

source_name: RNA from DG region of the hippocampus: Aged Unimpaired

tag: aged (24-26 months old) cognitively unimpaired male long-evans rats (charles river laboratories, raleigh, nc) were individually housed on a 12


title: Aged Unimpaired DG, biological rep7

description: Hippocampal RNA


title: Aged Unimpaired DG, biological rep6

description: Hippocampal RNA


title: Aged Unimpaired DG, biological rep8

description: Hippocampal RNA


title: Young DG, biological rep9

description: Hippocampal RNA


title: Aged Unimpaired DG, biological rep1

description: Hippocampal RNA


title: Aged Unimpaired DG, biological rep4

description: Hippocampal RNA


title: Aged Unimpaired DG, biological rep3

description: Hippocampal RNA


title: Aged Impaired DG, biological rep5

source_name: RNA from DG region of the hippocampus: Aged Impaired

tag: aged (24-26 months old) cognitively impaired male long-evans rats (charles river laboratories, raleigh, nc) were individually housed on a 12


title: Aged Impaired DG, biological rep8

description: Hippocampal RNA


title: Aged Impaired DG, biological rep6

description: Hippocampal RNA


title: Aged Impaired DG, biological rep7

description: Hippocampal RNA


title: rumen_milk_day42_103

tag: tissue


title: Aged Impaired DG, biological rep2

description: Hippocampal RNA


title: Aged Impaired DG, biological rep4

description: Hippocampal RNA


title: Aged Impaired DG, biological rep3

description: Hippocampal RNA


title: Aged Impaired DG, biological rep1

description: Hippocampal RNA


title: tMDS12

city: Palo Alto

first: Kunju

middle: J

last: Sridhar

address: 3801 Miranda Ave, bldg 100, Rm E4-230

department: Hematology

institute: Stanford University

description: Bone Marrow Cd34+ from MDS subjects

hyb_protocol: After labeling, 20ug COT1 human DNA (2GIBCO-BRL), 20ug tRNA (GICO-BRL) along with 20X SSC and 10% SDS were added and the probe and the mixture was denatured by heating at 100oC for 2 mins. The entire probe mixture was placed on the array and overlaid with a cover slip. The arrays were then placed in a hybridization chamber (Die tech) and hybridized overnight at 65oC. Hybridized arrays were washed in successive buffers of 2X SSC with 0.1% SDS, 1X SSC and 0.5X SSC with gentle plunging for 2 minutes in each of the wash buffer.

scan_protocol: The arrays were scanned using Axon Genepix 4000 scanner (Axon Instruments, Foster City, CA) using Genepix software (10um scan).

data_processing: Log (base 2) of the ratio of the median of Channel 2  (635 nm) to Channel 1 (532 nm), default computed normalization procedure, see SMD website

source_name: RNA from 5 pooled Normal CD34+ cells

label_protocol: 3-6 ug of amplified RNA was labelled with Cy3 and Cy5 conjugated nucleotide using superscript II(Life technologies) and dN6 primers and dNTP's for 2hrs at 42oC, to make the cDNA probe. The probe was purifed using microcon YM-30 columns (Millipore, Bedford MA) with 20ug polyA RNA (Sigma).

extract_protocol: RNA was extracted using RNeasy Kit as per manufacturers instructions

value: bone marrow

tag: cell type

value: Normal CD34+

source_name: RNA from MDS CD34+ cells

value: MDS CD34+


title: Young CA3, biological rep7

description: Hippocampal RNA

data_processing: All quality control, normalization, differential expression, and exploratory analysis of microarray data were performed using the R statistical language (http://www.r-project.org/). The gcrma package in Bioconductor (http://www.bioconductor.org/) was used to normalize microarray data. Sample RHab-HCA-AUCA3_12-1a_2-RAE230_2 (originally loaded in GEO as GSM367861 and since removed) was omitted from the study as a result of quality control procedures.

source_name: RNA from CA3 region of the hippocampus: Young


title: Young CA3, biological rep5

description: Hippocampal RNA


title: Young CA3, biological rep3

description: Hippocampal RNA


title: Young CA3, biological rep1

description: Hippocampal RNA


title: tMDS11

description: Bone Marrow Cd34+ from MDS subjects


title: Young CA3, biological rep8

description: Hippocampal RNA


title: Young CA3, biological rep6

description: Hippocampal RNA


title: tMDS10

description: Bone Marrow Cd34+ from MDS subjects


title: Young CA3, biological rep2

description: Hippocampal RNA


title: Young CA3, biological rep4

description: Hippocampal RNA


title: iPS 6 input, methyl-depleted

first: Akiko

last: Doi

address: 855 N Wolfe St, Rangos 580

department: Medicine

institute: Johns Hopkins University School of Medicine

description: DNA methylation data from iPS cells

hyb_protocol: The labeled DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in NimbleGen Hybridization solution master mix. Arrays were hybridized in Maui hybridization stations for 16-20 h at 42C, and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/methylation_userguide_v5p0.pdf).

scan_protocol: Arrays were scanned on a GenePix 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/methylation_userguide_v5p0.pdf).

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 software (http://www.nimblegen.com/products/lit/methylation_userguide_v5p0.pdf).

source_name: Input fraction from MRC5-iPS7

label_protocol: 2 µg of DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy3 nonamers for the input (UT) fraction and Cy5 nonamers for the methyl-depleted (MD) fraction per manufacturer's protocol (http://www.nimblegen.com/products/lit/methylation_userguide_v5p0.pdf).

growth_protocol: iPS cells were cultured in hES medium (80% DMEM/F12, 20% KO Serum Replacement,10 ng/ml bFGF, 1 mM L-glutamine, 100 M nonessential amino acids, 100 M 2-mercaptoethanol, 50 U/ml penicillin, and 50 mg/ml streptomycin).

extract_protocol: Genomic DNA (gDNA) were isolated using DNeasy kit (Qiagen) according to the manufacturer’s protocol. For each sample, 5 µg of genomic DNA was sheared into 1.6-3kb DNA size fragments, digested with McrBC, and fractionated on a 1% agarose gel alongside the sheared input (UT) fraction to enrich for the methyl-depleted (MD) fraction. The UT and MD fractions were purified and whole genome amplified using the WGA2 kit (Sigma) according to the manufacturer's protocol.

treatment_protocol: no treatment

value: iPS cells derived from MRC5

source_name: Methyl-depleted fraction from MRC5-iPS7


title: Fibroblast 4 input, methyl-depleted

description: DNA methylation data from fibroblasts

source_name: Input fraction from PD

growth_protocol: Fibroblasts were grown in alpha-MEM containing 10 % inactivated fetal serum (IFS), 50 U/ml penicillin, 50 mg/ml streptomycin, and 1 mM L-glutamine.

value: AG20446 from Coriell

source_name: Methyl-depleted fraction from PD


title: Aged Unimpaired CA3, biological rep8

description: Hippocampal RNA

source_name: RNA from CA3 region of the hippocampus: Aged Unimpaired


title: tMDS9

description: Bone Marrow Cd34+ from MDS subjects

source_name: RNA from MDS CD34+ cells with del(5q)


title: iPS 5 input, methyl-depleted

description: DNA methylation data from iPS cells

source_name: Input fraction from SBDS-iPS3

value: iPS cells derived from SBDS

source_name: Methyl-depleted fraction from SBDS-iPS3


title: Fibroblast 2 input, methyl-depleted

description: DNA methylation data from fibroblasts

source_name: Input fraction from GD

value: GM00852A from Coriell

source_name: Methyl-depleted fraction from GD


title: tMDS8

description: Bone Marrow Cd34+ from MDS subjects


title: Aged Unimpaired CA3, biological rep6

description: Hippocampal RNA


title: tMDS5

description: Bone Marrow Cd34+ from MDS subjects


title: Young CA3, biological rep9

description: Hippocampal RNA


title: tMDS6

description: Bone Marrow Cd34+ from MDS subjects


title: Fibroblast 5 input, methyl-depleted

description: DNA methylation data from fibroblasts

source_name: Input fraction from SBDS

source_name: Methyl-depleted fraction from SBDS


title: tMDS3

description: Bone Marrow Cd34+ from MDS subjects


title: tMDS2

description: Bone Marrow Cd34+ from MDS subjects


title: Aged Unimpaired CA3, biological rep7

description: Hippocampal RNA


title: tMDS7

description: Bone Marrow Cd34+ from MDS subjects


title: iPS 1 input, methyl-depleted

description: DNA methylation data from iPS cells

source_name: Input fraction from DMD-iPS1

value: iPS cells derived from DMD

source_name: Methyl-depleted fraction from DMD-iPS1


title: Aged Impaired CA3, biological rep8

description: Hippocampal RNA

source_name: RNA from CA3 region of the hippocampus: Aged Impaired


title: Aged Unimpaired CA3, biological rep4

description: Hippocampal RNA


title: tMDS1

description: Bone Marrow Cd34+ from MDS subjects

source_name: RNA from 5 pooled Normal CD34+ cells

source_name: RNA from MDS CD34+ cells


title: Aged Unimpaired CA3, biological rep1

description: Hippocampal RNA


title: Aged Impaired CA3, biological rep7

description: Hippocampal RNA


title: Aged Impaired CA3, biological rep6

description: Hippocampal RNA


title: Fibroblast 3 input, methyl-depleted

description: DNA methylation data from fibroblasts

source_name: Input fraction from 551

value: Detroit 551 fetal skin fibroblast from ATCC

source_name: Methyl-depleted fraction from 551


title: iPS 3 input, methyl-depleted

description: DNA methylation data from iPS cells

source_name: Input fraction from 551-iPS5

value: iPS cells derived from 551

source_name: Methyl-depleted fraction from 551-iPS5


title: Fibroblast 6 input, methyl-depleted

description: DNA methylation data from fibroblasts

source_name: Input fraction from MRC5

value: 14 week old fetal lung fibroblast from ATCC

source_name: Methyl-depleted fraction from MRC5


title: sMDS23

description: Bone Marrow Cd34+ from MDS subjects


title: iPS 2 input, methyl-depleted

description: DNA methylation data from iPS cells

source_name: Input fraction from GD-iPS1

value: iPS cells derived from GD

source_name: Methyl-depleted fraction from GD-iPS1


title: sMDS22

description: Bone Marrow Cd34+ from MDS subjects


title: tMDS4

description: Bone Marrow Cd34+ from MDS subjects


title: sMDS18

description: Bone Marrow Cd34+ from MDS subjects


title: sMDS16

description: Bone Marrow Cd34+ from MDS subjects


title: sMDS17

description: Bone Marrow Cd34+ from MDS subjects