title: PB CD34+ cells from PMF patient BG_5 (GEP)


title: PB CD34+ cells from PMF patient 5767 (GEP)

status: Public on Oct 01 2014

type: RNA

city: Modena

first: Rossella

last: Manfredini

address: Via Gottardi 100

department: Life Sciences

country: Italy

institute: Centre for Regenerative Medicine

description: Peripheral Blood CD34+ cells from PMF patient

hyb_protocol: Regarding GEP, fragmented cRNA was hybridized for 16 hr at 45C on Affymetrix HG-U219 array strips in GeneAtlas Hybridization Station. GeneChips were washed and stained using GeneAtlas Hybridization, Wash, and Stain Kit for 3’IVT Arrays, according to the standard protocol supplied by Affymetrix (GeneAtlas 3’ IVT Express Kit, P/N 702833 Rev. 4). As for miEP, tagged RNA was hybridized to the Affymetrix Genechip miRNA array 2.0 using manufacturer's recommendations (FlashTag™ Biotin HSR RNA Labeling Kit, P/N 703095 Rev. 1). The miRNA arrays were washed and stained by GeneChip Hybridization, Wash and Stain Kit (Affymetrix) with Fluidic Station 450 using fluidic script FS450_003.

scan_protocol: Affymetrix HG-U219 array strips were finally scanned using GeneAtlas Scanner.  Affymetrix Genechip miRNA arrays 2.0 were scanned using the Affymetrix GCS3000 7G Scanner.

data_processing: Gene expression data were imported into Partek Genomics Suite 6.6 (Partek, St Louis, Mo) as CEL files using default parameters. Raw data were preprocessed, including background correction, normalization, and summarization using robust multiarray average (RMA) analysis.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: PMF Peripheral Blood CD34+ Cells

label_protocol: Gene expression profiling (GEP) and miRNA expression profiling (miEP) were performed on the same RNA preparation. As regards GEP, biotinylated cRNA were prepared according to the standard GeneAtlas 3’IVT Express Kit protocol from 100ng of  total RNA (P/N 702833 Rev. 4, Affymetrix). Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) and Agilent 2100 Bioanalyzer were used to determine the cRNA concentration/quality as well as to optimize the cRNA fragmentation. NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) was used to evaluate the cRNA sample concentration.As for miEP, total RNA (100ng for samples) were labeled using the FlashTag® Biotin HSR kit (Affymetrix).

growth_protocol: CD34+ cells were purified from 30–50 ml of PB collected from PMF patients, from 150 ml of PB from G-CSF untreated healthy donors, or from 5 ml of BM aspirates, all obtained in preservative free heparin.  Mononuclear cells were separated over a Ficoll-Paque gradient (Lympholyte; Cederlane Labs) and processed through two sequential steps of immunomagnetic CD34  selection (Miltenyi Biotec, Bergisch Gladbach,Germany,http://www.miltenyibiotec.com). Purity of the isolated CD34+ cell population was evaluated by flow cytometry after labeling with PE-HPCA2 anti-CD34 monoclonal antibody (BD Biosciences) and was always > 95%.

extract_protocol: CD34+ cells were purified from Peripheral Blood of PMF patients and immediately  lysed in 700uL of QIAZOL Buffer (Qiagen, Valencia, CA, USA). Total RNA from CD34+ cells was extracted using miRNeasy Mini Kit (Qiagen, Valencia, CA, USA) in accordance with the manufacturer’s recommendations for Purification of Total RNA, Including Small RNAs, from Animal Cells. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit; Agilent Technologies, Waldbrunn, Germany) were used to determine the concentration and purity/integrity of RNA samples using Agilent 2100 Bioanalyzer. NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) was used to evaluate the RNA sample concentration, and 260/280 and 260/230 nm ratios were considered to verify the purity of total RNA.

tag: supplier

value: Vannucchi

tag: cell type

value: MPD

tag: disease

value: PMF

value: pos

tag: tissue

value: PB


title: PB CD34+ cells from PMF patient 5848 (GEP)


title: PB CD34+ cells from PMF patient 5807 (GEP)

value: neg


title: PB CD34+ cells from PMF patient 5715 (GEP)


title: PB CD34+ cells from PMF patient 5835 (GEP)


title: PB CD34+ cells from PMF patient 5786 (GEP)


title: PB CD34+ cells from PMF patient 5733 (GEP)


title: PB CD34+ cells from PMF patient 5724 (GEP)


title: Liver_Donor_E122

city: Murcia

first: Salam

last: Salloum-Asfar

state: Murcia

address: Ronda Garay, s/n

country: Spain

institute: Centro Regional de Hemodonación, Universidad de Murcia

hyb_protocol: standard manufacturer's protocol

scan_protocol: standard manufacturer's protocol

data_processing: Data are corrected by subtracting background and normalized to the statistical mean of all detectable transcripts. See manufacturer's website (http://www.lcsciences.com/).

source_name: Liver

label_protocol: standard manufacturer's protocol

growth_protocol: We extracted total RNA from human livers. A total of 400ng of total RNA were used for further protocol.

extract_protocol: Trizol

treatment_protocol: standard manufacturer's protocol

value: liver

tag: donor


title: Liver_Donor_711


title: Liver_Donor_664


title: Liver_Donor_662


title: Mad1 at 1 uM concentration and Max at 100 nM concentration

type: protein

city: Durham

first: Raluca

last: Gordan

state: NC

address: 101 Science Dr, CIEMAS 2179

department: Center for Genomic and Computational Biology

country: USA

institute: Duke University

hyb_protocol: Double-stranded microarrays were first pre-moistened in PBS / 0.01% Triton X-100 for 5 min and blocked with PBS / 2% (wt/vol) nonfat dried milk (Sigma) for 1 h. Microarrays were then washed once with PBS / 0.1% (vol/vol) Tween-20 for 5 min and once with PBS / 0.01% Triton X-100 for 2 min. Proteins were diluted to 200 or 100 nM in a 175-μl protein binding reaction containing PBS / 2% (wt/vol) milk / 51.3 ng/μl salmon testes DNA (Sigma) / 0.2 μg/μl bovine serum albumin (New England Biolabs). Preincubated protein binding mixtures were applied to individual chambers of a four-chamber gasket cover slip in a steel hybridization chamber (Agilent), and the assembled microarrays were incubated for 1 h at room temperature. Microarrays were again washed once with PBS / 0.5% (vol/vol) Tween-20 for 3 min, and then once with PBS / 0.01% Triton X-100 for 2 min. Alexa-488-conjugated rabbit polyclonal antibody to His (Invitrogen) was diluted to 50 μg/ml in PBS / 2% milk and applied to a single-chamber gasket cover slip (Agilent), and the assembled microarrays were again incubated for 1 h at 20°C. Finally, microarrays were washed twice with PBS / 0.05% (vol/vol) Tween-20 for 3 min each, and once in PBS for 2 min. After each hour-long incubation step, microarrays and cover slips were disassembled in a staining dish filled with 500 ml of the first wash solution. All washes were performed in Coplin jars on an orbital shaker at 125 r.p.m. Immediately following each series of washes, microarrays were rinsed in PBS (slowly removed over approximately 10 seconds) to ensure removal of detergent and uniform drying.

scan_protocol: Protein-bound microarrays were scanned to detect Alexa-488-conjugated antibody (488 nm ex, 522 nm em) using at least three different laser power settings to best capture a broad range of signal intensities and ensure signal intensities below saturation for all spots. Microarray TIF images were analyzed using GenePix Pro version 7.0 software (Molecular Devices), bad spots were manually flagged and removed, and data from multiple Alexa 488 scans of the same slide were combined using masliner (MicroArray LINEar Regression) software.

data_processing: To correct for any possible non-uniformities in protein binding, we adjusted the Alexa 488 signals according to their positions on the microarray. We calculated the median normalized intensity of the 15 x 15 block centered on each spot and divided the spot's signal by the ratio of the median within the block to the median over the entire chamber. The adjusted Alexa 488 signals are provided in the raw data files. Next, for each sequence represented on the array, we compute the median intensity over the 6 replicate spots (i.e. over probes with the same name but ending in o1_r1, o1_r2, o1_r3, o2_r1, o2_r2 and o2_r3). Median intensities are reported as the normalized signals for the sequences present on the array.

label: Alexa 488

molecule: protein

source_name: Human Mad1 and Max

label_protocol: Proteins were tagged with N-terminal His by cloning. Protein-bound arrays were incubated with Alexa-488-conjugated rabbit polyclonal antibody to His (Invitrogen).

growth_protocol: Plasmids were transformed into BL21 (DE3) expression strain of E. coli (New England BioLabs).  Overnight bacterial culture (5 mL) was diluted into 1 L LB (10 g BACTO Tryptone (BD); 5 g BACTO Yeast Extract (BD); 10 g NaCl; pH 7.5) and grown to OD 0.6 (600 nm visible light). Protein expression was then induced with 1 mM isopropyl β-D-1-thiogalactopyranoside (IPTG) for 3 hours at 37ºC. Cells were pelleted by centrifugation @ 12,000 rpm for 10 min and stored at -20ºC. Each pellet (from 1 L culture) was thawed in 15 ml lysis buffer (150 mM Tris-HCl, pH 8.0; 150 mM NaCl; 2 mM dithiothreitol (DTT); 1 tablet complete Mini, EDTA-free protease inhibitor cocktail (Roche, #11 836 170 001); 50 uM C4H10O6Zn (zinc acetate); 1 mg/ml chicken egg white lysozyme (Sigma, # L6876)) and subjected to two freeze-thaw cycles in dry ice/ethanol. To digest DNA, to each 15 ml lysis solution was added 10 uL recombinant, RNase-free DNAse I (Roche, #04 716 728 001, 10 U/ul), 30 uL 1 M MgCl2, and 2 mL 10% Triton X-100,  and digested at room temperature until solution was runny (~1 hr).  Solutions were centrifuged at 12,000 rpm for 25 min at 4ºC, and supernatant was used for protein purification.

extract_protocol: Full-length open reading frames were cloned into the Gateway pDEST17 (N-terminal His-tag) expression vector by recombinational cloning from previously created pENTR clones. All proteins were produced by over-expression in E. coli BL21 (DE3) cells (New England BioLabs), and purified by FPLC (AKTAprime plus) using HisTrap FF affinity columns (GE Healthcare). Anti-His Western blots were performed to assess protein quality and concentration.

tag: transcription factor

value: Mad1, Max

tag: protein concentration

value: 100nM Max, 1uM Mad1


title: c-Myc at 1 uM concentration and Max at 100 nM concentration

source_name: Human c-Myc and Max

value: c-Myc, Max

value: 100nM Max, 1uM c-Myc


title: Max at 100 nM dimer concentration

source_name: Human Max

value: Max

value: 100nM dimer


title: Medium 5216898024_F_1

city: Natanya

first: Tal

middle: Haim

last: Hasson

address: Hatrufa 12

department: Analytical R&D

country: Israel

institute: Teva Pharmaceuticals

description: Medium

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scan protocol

data_processing: This is a sister series to GSE40566. This GEO entry includes all samples including technical replicates. Background-corrected bead-level summarization was conducted using Illumina's Bead studio. Normalized version of the data was quantile normalized using R's preprocessCore package (normalize.quantilies function) and batch corrected using ComBat from the SVA package with Batch variable as batch and batchcovar as covariate

organism: Mus musculus

source_name: Spleen Cell Cultures

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

growth_protocol: Preparation of Mouse Spleen Cell Cultures: All experimental procedures conformed to accepted ethical standards for use of animals in research and were in accordance with Committee for the Care and Use of Experimental Animals guidelines and approved by the Teva Institutional Animal Care and Use Committee (Protocols #506 and #512). To stimulate induction of GA-reactive T cells, eight female 8- to 12-week-old F1 hybrid (SJL X BALB/C) mice (purchased from Harlan Biotech Israel, Rehovot, Israel) were inoculated with 100 µL of a 2.5 mg/mL solution of GA reference standard (GA-RS) in PBS to achieve an immunization dose of 250 µg GA-RS per mouse. Mice were housed in individually ventilated cages for 3 days after immunization, and on the third day, were sacrificed by cervical dislocation. Mouse spleens (SPL) were excised via side incision using sterile procedures, placed in sterile 50-mL CellStar polypropylene tubes (2 spleens/tube) containing RPMI 1640 without glutamine (Biological Industries, Beit Haemek, Israel), and placed on ice to prevent tissue degradation. Primary cultures of pooled SPL cells were collected as follows: SPL tissue in RPMI was filtered (70 µm nylon) and centrifuged at 300xg for 10 minutes at room temperature (RT). The precipitate was resuspended in Ack lysing buffer (Invitrogen, Carlsbad, CA) incubated for 3 minutes at RT, diluted 1:10 with RPMI, and centrifuged again at 200xg for 10 minutes at RT. The pellet was re-washed (10 mL RPMI), re-centrifuged (200xg, 10 minutes at RT), and then resuspended in enriched defined cell culture media (DCCM1). DCMM1 (Biological Industries, Beit Haemek, Israel) (96.7% v/v) was enriched with L-glutamine 2mM (1% v/v), MEM 2mM (1% v/v), sodium pyruvate 1 mM (1% v/v), antibiotic/antimycotic solution (0.2% v/v), and 2-mercaptoethanol (0.1% v/v). All SPL samples were pooled. Cell density and viability were assessed using the Trypan Blue Exclusion method (22) (hemacytometer, Sigma Z35,962-9). Viable cells were diluted with enriched DCCM1 to a concentration of 10 x 106 cells/mL.

extract_protocol: PerfectPure RNA Cultures CEKK kit 50 (5Prime GmbH, Hamburg, Germany) according to manufacturer’s instructions. RNA quality was assessed by the absorbance ratio at 260/280 nm and gel electrophoresis (Experionä, Bio-Rad, Hercules, CA).

treatment_protocol: Aqueous activator samples (125 µL per well of 80 µg/mL solutions of Verified GA, DM-GA, Unverified Glatiramoid [TV-5010 concentration was 40 µg/mL since 80 µg/mL was cytotoxic], Unverified Generic GA, MBP, and mannitol [the non-active excipient in Copaxone]) and medium samples were added to 96-well tissue culture plates (3 wells per sample).Viable SPL cells (125 µL 10x106 SPL cell/mL suspension) were added to the activator solutions and incubated for 24 hours at 37°C in a humidified incubator with a 5% CO2 atmosphere. Incubated samples were then centrifuged at 3000g x 5 minutes at RT, washed, diluted RNA stabilization solution (RNAlaterÒ solution, Applied Biosystems), and stored at 4°C.

tag: batch

tag: experiment

tag: batchcovar

value: Medium

tag: genetic background

value: SJL X BALB/C

value: spleen cell

tag: treatment


title: Glateramoid Edan 5216898024_E_1

description: Edan

value: Edan

value: Glateramoid Edan


title: Glateramoid TV-5010 5216898024_D_2

value: Glateramoid TV-5010


title: Medium 5216898024_F_2

description: Medium


title: Medium 5216898012_F_1

description: Medium


title: Glateramoid Shira 5216898024_B_2

description: Shira

value: Shira

value: Glateramoid Shira


title: Max at 50 nM dimer concentration

value: 50nM dimer


title: Glateramoid Shira 5216898024_B_1

description: Shira


title: GA RS 5216898024_A_1

description: GA RS

value: GA RS


title: Glateramoid Edan 5216898024_E_2

description: Edan


title: Medium 5216898012_F_2

description: Medium


title: GA RS 5216898024_A_2

description: GA RS


title: GA DP 5216898024_C_2

description: GA DP

value: GA DP


title: Glateramoid TV-5010 5216898024_D_1


title: Glateramoid Edan 5216898012_E_1

description: Edan


title: GA DP 5216898012_C_1

description: GA DP


title: GA DP 5216898012_C_2

description: GA DP


title: Appo2 5216898012_D_2

description: Appotex 2


title: GA DP 5216898024_C_1

description: GA DP


title: Appo2 5216898012_D_1

description: Appotex 2


title: Glateramoid Edan 5216898012_E_2

description: Edan


title: salivary gland infected rep-c

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

description: Gene expression data from_salivary gland infected rep-c

hyb_protocol: Hybridized at a constant temperature of 45◦C for approximately forty-eight hours using the Affymetrix 640 oven 500k approved

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

data_processing: The data were analyzed with GCOS 1.4 using Affymetrix default analysis with a scale filter for Ft genes setting and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

organism:
Plasmodium falciparum
Anopheles gambiae

source_name: salivary gland infected rep-c

label_protocol: RNA was amplified and labeled using two-rounds of linear amplification according to the manufacturer’s protocol (Affymetrix GeneChip® Two-Cycle cDNA Synthesis Kit)

growth_protocol: Anopheles gambiae mosquitoes were infected with Plasmodium falciparum (3D7) by allowing the mosquitoes to feed on infected mice.  The dissected tissues were immediately placed on RNAlater solution (Ambion Inc.) and stored at -80C until further processing.

extract_protocol: Three pools, each one containing whole organs from approximately 20 mosquitos were used for total RNA extraction using Trizol reagent (Invitrogen). For the infected organs we extracted the mosquito and parasite RNA simultaneously.

value: salivary gland

tag: infection

value: infected with P. falciparum


title: Appo1 5216898012_B_1

description: Appotex 1


title: GA RS 5216898012_A_1

description: GA RS


title: Appo1 5216898012_B_2

description: Appotex 1


description: Gene expression data from_salivary gland non-infected control rep-c

organism: Anopheles gambiae

value: control


title: salivary gland infected rep-b

description: Gene expression data from_salivary gland infected rep-b

source_name: salivary gland infected rep-b


title: salivary gland infected rep-a

description: Gene expression data from_salivary gland infected rep-a

source_name: salivary gland infected rep-a


description: Gene expression data from_salivary gland non-infected control rep-a


title: midgut infected rep-c

description: Gene expression data from_midgut infected rep-c

source_name: midgut infected rep-c

value: midgut


title: Medium 5216898008_F_1

description: Medium


description: Gene expression data from_salivary gland non-infected control rep-b


title: Medium 5216898008_F_2

description: Medium


title: midgut non-infected control rep-c

description: Gene expression data from_midgut non-infected control rep-c

source_name: midgut non-infected control rep-c


title: midgut infected rep-a

description: Gene expression data from_midgut infected rep-a

source_name: midgut infected rep-a


title: midgut infected rep-b

description: Gene expression data from_midgut infected rep-b

source_name: midgut infected rep-b


title: midgut non-infected control rep-b

description: Gene expression data from_midgut non-infected control rep-b

source_name: midgut non-infected control rep-b


title: 2hours-repI

city: Coventry

first: Nigel

middle: Paul

last: Dyer

address: Gibbet Hill Road

country: United Kingdom

institute: University of Warwick

hyb_protocol: standard Agilent protocol

scan_protocol: Scanned on an Agilent G2505C scanner.

data_processing: Data were extracted and normalized using Agilent Feature Extraction Software 10.7.3.1 with default parameter settings for gene expression two-color microarrays (protocol GE2_105_Dec08).

organism: Arabidopsis thaliana

source_name: wt

label_protocol: standard Agilent protocol

growth_protocol: Seedlings were grown on MS-agar plates for 2 weeks under 12 h-photoperiods before transfer to continuous light (LL).

extract_protocol: Total RNA was extracted from seedlings using the Plant RNeasy kit (Qiagen) and contaminating genomic DNA removed by treatment with DNaseI (SIGMA).

treatment_protocol: 17 h after transfer to constant light, 5 ml of (v/v) ethanol was added directly to the roots of the plants to induce expression of the transgene. Following this initial application, a 3 cm2 piece of filter paper soaked in ethanol was placed on the underside of the plate lid in order to maintain ethanol vapours. The filter paper was replaced at hourly intervals.

value: seedling

tag: genotype

value: wt

tag: time

value: 2 hours


title: 8hours-repI

value: 8 hours


title: GA RS 5216898012_A_2

description: GA RS

value: SJL X BALB/C

value: spleen cell


title: GA DP 5216898008_E_2

description: GA DP


title: 4hours-repI

value: 4 hours


title: GA DP 5216898008_C_1

description: GA DP


title: Glateramoid TV-5010 5216898008_D_1

value: Glateramoid TV-5010


title: 9hours-repS

value: 9 hours


title: GA DP 5216898008_C_2

description: GA DP


title: Glateramoid TV-5010 5216898008_D_2


title: 0hours-repI

value: 0 hours


title: 4hours-repS


title: GA DP 5216898008_E_1

description: GA DP


title: Medium 5216898004_F_2

description: Medium

value: Medium


title: Lateral Wall of C57 mice at 9 month group3

city: Omaha

first: David

last: He

state: Nebraska

address: 2500 California Plaza

department: Department of Biomedical Sciences

institute: Creighton University

description:
C57-9m-3
5 C57 9m SV 1 miRNA 01-08-13_(miRNA-1_0_2Xgain).CEL

hyb_protocol: The miR expression profile of the lateral wall of cochlear duct at different ages was determined by GeneChip microarray analysis (Affymetrix). Synthesis of cDNA, hybridization to chips, and washes were performed according to the manufacture’s protocol.

scan_protocol: GeneChips were scanned at 3 µm density with a GeneArray Scanner (Affymetrix).

data_processing: The data was normalized by Affy program “QC Tool”.  Mean fluorescence signal intensity for each probe was quartile normalized. The average of three mean signals for each gene probe was normalized to that for an added control oligonucleotide. Each gene probe was assessed for expression based on a Wilcoxon Rank-Sum test of the gene probe set signals compared to the distribution of signals from the background.

label: Biotin

source_name: C57BL/6J_cochlear lateral wall_9 month

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 250 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: CBA/J and C57BL/6J mice were used at the age of P21, 9m and 16m.

extract_protocol: Total RNA from approximately10 cochleae for each age group/stain was extracted and purified using the mirVana miRNA extraction Kit according to the manufacturer's instructions.

treatment_protocol: The lateral wall of the cochlear duct was isolated and stored at -20°C in RNAlater stabilization reagent. Total RNA including miRNAs was isolated using mirVana miRNA Isolation Kit (Ambion) and dissolved in 20-30 µl of RNase free water.

tag: strain

value: C57 BL/6J

tag: age

value: 9 month

tag: mice group

value: Lateral wall of cochlear duct

tag: molecule subtype

value: microRNA


title: 0hours-repS


title: Lateral Wall of C57 mice at 16 month group3

description:
C57-16m-3
C57 SV 16m 2 miRNA 5-1-13_(miRNA-1_0_2Xgain).CEL

source_name: C57BL/6J_cochlear lateral wall_16 month

value: 16 month


title: 2hours-repS


title: GA RS 5216898008_A_2

description: GA RS

tag: cell type

value: GA RS


title: Glateramoid Shira 5216898008_B_2

description: Shira

value: Shira

value: Glateramoid Shira


title: Lateral Wall of C57 mice at 9 month group1

description:
C57-9m-1
8 C57-9m 1 SV miRNA array 4-3-12_(miRNA-1_0_2Xgain).CEL

tag: tissue


title: GA DP 5216898004_E_1

description: GA DP

value: GA DP


title: Glateramoid Shira 5216898008_B_1

description: Shira


title: midgut non-infected control rep-a

description: Gene expression data from_midgut non-infected control rep-a

source_name: midgut non-infected control rep-a

value: midgut

value: control


title: GA DP 5216898004_E_2

description: GA DP

value: SJL X BALB/C

value: spleen cell


title: Lateral Wall of C57 mice at 16 month group1

description:
C57-16m-1
10 C57 16m-1 SV mRNA 2-14-13_(miRNA-1_0_2Xgain).CEL


title: GA RS 5216898008_A_1

description: GA RS


title: Medium 5216898004_F_1

description: Medium


title: Lateral Wall of C57 mice at postnatal 21 days group3

description:
C57-P21-3
C57 P21-2SV miRNA array 1-10-12_(miRNA-1_0_2Xgain).CEL

source_name: C57BL/6J_cochlear lateral wall_P21

value: Postnatal 21 days


title: Lateral Wall of C57 mice at 16 month group2

description:
C57-16m-2
C57 SV 16m 1 miRNA 5-1-13_(miRNA-1_0_2Xgain).CEL


title: Lateral Wall of C57 mice at 9 month group2

description:
C57-9m-2
10 C57-9m 2 SV miRNA array 4-3-12_(miRNA-1_0_2Xgain).CEL


title: Lateral Wall of C57 mice at postnatal 21 days group2

description:
C57-P21-2
C57 P21-1SV miRNA array 1-10-12_(miRNA-1_0_2Xgain).CEL


title: Appo2 5216898004_D_2

description: Appotex 2


title: Appo2 5216898004_D_1

description: Appotex 2


title: Lateral Wall of CBA mice at 16 month group2

description:
CBA-16m-2
6 CBA 16m SV mRNA 2-14-13_(miRNA-1_0_2Xgain).CEL

source_name: CBA/J_cochlear lateral wall_16 month

value: CBA/J


title: GA DP 5216898004_C_2

description: GA DP


title: Lateral Wall of CBA mice at 9 month group3

description:
CBA-9m-3
9m-SV-2 miRNA array 12-15-10_(miRNA-1_0_2Xgain).CEL

source_name: CBA/J_cochlear lateral wall_9 month


title: Appo1 5216898004_B_2

description: Appotex 1


title: Lateral Wall of CBA mice at 16 month group1

description:
CBA-16m-1
2 CBA16m 1 SV miRNA array 4-3-12_(miRNA-1_0_2Xgain).CEL


title: Lateral Wall of CBA mice at 16 month group3

description:
CBA-16m-3
CBA 16m-1SV miRNA array 1-10-12_(miRNA-1_0_2Xgain).CEL


title: Lateral Wall of C57 mice at postnatal 21 days group1

description:
C57-P21-1
1 C57 P21 SV 1 miRNA 01-08-13_(miRNA-1_0_2Xgain).CEL


title: Lateral Wall of CBA mice at 9 month group1

description:
CBA-9m-1
4 CBA 9m SV mRNA 2-14-13_(miRNA-1_0_2Xgain).CEL


title: Appo1 5216898004_B_1

description: Appotex 1


title: GA RS 5216898004_A_1

description: GA RS


title: Lateral Wall of CBA mice at postnatal 21 days group1

description:
CBA-P21-1
2 CBA P21 SV mRNA 2-14-13_(miRNA-1_0_2Xgain).CEL

source_name: CBA/J_cochlear lateral wall_P21


title: Medium 4763128060_F_1

description: Medium

source_name: Spleen Cell Cultures


title: Lateral Wall of CBA mice at postnatal 21 days group3

description:
CBA-P21-3
CBA P21-2SV miRNA array 1-10-12_(miRNA-1_0_2Xgain).CEL


title: Medium 4763128060_F_2

description: Medium


title: Lateral Wall of CBA mice at 9 month group2

description:
CBA-9m-2
9m-SV-1 miRNA array 12-15-10_(miRNA-1_0_2Xgain).CEL


title: Lateral Wall of CBA mice at postnatal 21 days group2

description:
CBA-P21-2
CBA P21-1SV miRNA array 1-10-12_(miRNA-1_0_2Xgain).CEL


title: GA DP 5216898004_C_1

description: GA DP


title: GA RS 5216898004_A_2

description: GA RS


title: GA DP 4763128060_E_2

description: GA DP


title: GA DP 4763128060_E_1

description: GA DP


title: ES_derived_airway_cells_stimulated_with_LPS_repl1

first: Mickie

last: Bhatia

state: Ontario

address: 1200 Main Street West

department: Stem Cell and Cancer Research Institute (SCC-RI)

country: Canada

institute: McMaster University

hyb_protocol: In accordance with manufacturer's protocols

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

data_processing: Data was normalized using Robust Multichip Averaging (RMA) algorithm using Partek Genomics Suite 6.6 software.

source_name: airway epithelium derived from ES stimulated with LPS

growth_protocol: Human CA2 ES cells adapted to mTeSR1 and grown on Matrigel were differentiated into airway cells by removal of bFGF and 2-step air liquid interface culture.

extract_protocol: Extraction of total RNA using total RNA purification kit (Norgen Biotek, Canada) was performed according to the manufacturer's instructions.

treatment_protocol: Innate immune challenge was performed with 5ug/ml LPS or 10ng/ml TNF-alpha for 5 hours.

value: airway epithelial cells differentiated from the ES line CA2

value: LPS


title: GA DM (SFC-962)  4763128060_D_1

description: GA DM

value: GA DM (SFC-962)


title: GA DM (SFC-962)  4763128060_D_2

description: GA DM


title: ES_derived_airway_cells_stimulated_with_TNF-alpha_repl2

source_name: airway epithelium derived from ES stimulated with TNF-alpha

label_protocol: In accordance with manufacturer's protocols

value: TNF-alpha


title: GA DP 4763128060_C_2

description: GA DP


title: Control_ES_derived_airway_cells_repl2

source_name: airway epithelium derived from ES

value: Control


title: GA DP 4763128060_C_1

description: GA DP


title: ES_derived_airway_cells_stimulated_with_TNF-alpha_repl1


title: ES_derived_airway_cells_stimulated_with_LPS_repl2


title: Generic B5 4763128060_B_2

description: GA Q

value: Generic B5


title: GA RS 4763128060_A_2

description: GA RS


title: secretory ameloblasts, biological repeat 1

city: Köln

first: Yulong

last: Niu

state: Nordrhein-Westfalen

address: Carl-von-Linne-Weg 10

department: Plant Microbe Interactions

country: Germany

institute: Max Planck Institute for Plant Breeding Research

description: human pooled SAB

hyb_protocol: Labeling, hybridization and scanning were performed according to Affymetrix recommendations (http://www.affymetrix.com/support/technical/byproduct.affx?product=hugene-1_0-st-v1).

data_processing: The raw data (CEL) were normalized by robust multi-array average (RMA) method provided by oligo R/Bioconductor package.

source_name: SAB

extract_protocol: RNA purification was done with RNeasy Plus Micro Kit and Rnase-Free DNase Set (Qiagen).

treatment_protocol: PAB and SAB were separately dissected and catapulted to AdhesiveCap containing beta-Mercaptoethanol supplemented RLT buffer. The caps containing buffer and cells were incubated upside down at room temperature for 30 min and then briefly centrifuged to collect the buffer and cells complex.

value: secretory ameloblasts

value: 18-22 weeks


title: secretory ameloblasts, biological repeat 3

description: human pooled SAB

scan_protocol: Labeling, hybridization and scanning were performed according to Affymetrix recommendations (http://www.affymetrix.com/support/technical/byproduct.affx?product=hugene-1_0-st-v1).


title: Medium 4763128059_F_2

description: Medium

value: Medium


title: Control_ES_derived_airway_cells_repl1


title: GA DM (SFC-962)  4763128059_D_1

description: GA DM


title: pre-ameloblasts, biological repeat 3

description: human pooled PAB

source_name: PAB

label_protocol: Labeling, hybridization and scanning were performed according to Affymetrix recommendations (http://www.affymetrix.com/support/technical/byproduct.affx?product=hugene-1_0-st-v1).

value: pre-ameloblasts


title: Generic B5 4763128060_B_1

description: GA Q


title: pre-ameloblasts, biological repeat 1

description: human pooled PAB


title: secretory ameloblasts, biological repeat 2

description: human pooled SAB


title: 801B.INV

city: East Melbourne

first: Dariush

last: Etemadmoghadam

address: St Andrew's Place

country: Australia

institute: Peter MacCallum Cancer Centre

description:
Sample name: 65661_INV
AlternateIDRawData: 801B.INV

hyb_protocol: Hybridization was performed according to the manufacturer’s instructions (Affymetrix, Santa Clara, CA).

scan_protocol: Arrays were washed using an Affymetrix fluidics stations and scanned using the Gene Chip Scanner 3000

data_processing: CEL files were produced using the Affymetrix® GeneChip® Command Console® Software (AGCC)

source_name: microdissected ovarian tumor

label_protocol: Affymetrix GeneChip® WT Terminal Labelling and Hybridization was performed according to the manufacturer’s protocol

extract_protocol: Total RNA was extracted from tumor cells using the AbsolutelyRNA microprep kit (Stratagene, Agilent Technologies, Santa Clara, CA, USA)

tag: patient

tag: disease state

value: LGSC

tag: component

value: Invasive


title: GA DP 4763128059_E_2

description: GA DP

tag: batch

value: GA DP


title: Medium 4763128059_F_1

description: Medium

tag: experiment

value: SJL X BALB/C


title: GA DP 4763128059_C_2

description: GA DP

tag: batchcovar

value: spleen cell


title: 51104.INV

description:
Sample name: 5899_INV
AlternateIDRawData: 51104.INV


title: 51104.LMP

description:
Sample name: 5899_SBT
AlternateIDRawData: 51104.LMP

value: Borderline


title: 801B.LMP

description:
Sample name: 65661_SBT
AlternateIDRawData: 801B.LMP


title: 460A.LMP

description:
Sample name: 65662_SBT
AlternateIDRawData: 460A.LMP


title: GA RS 4763128060_A_1

description: GA RS

tag: genetic background

value: GA RS


title: pre-ameloblasts, biological repeat 2

description: human pooled PAB


title: GA DP 4763128059_E_1

description: GA DP

tag: treatment


title: GA DM (SFC-962)  4763128059_D_2

description: GA DM


title: Generic B5 4763128059_B_1

description: GA Q


title: GA DP 4763128059_C_1

description: GA DP


title: 460A.INV

description:
Sample name: 65662_INV
AlternateIDRawData: 460A.INV


title: 428B.INV

description:
Sample name: 15043_INV
AlternateIDRawData: 428B.INV


title: Generic B5 4763128059_B_2

description: GA Q


title: GA RS 4763128059_A_1

description: GA RS


title: 428A.LMP

description:
Sample name: 15043_SBT
AlternateIDRawData: 428A.LMP


title: GA RS 4763128059_A_2

description: GA RS


title: 32054.LMP

description:
Sample name: 3960_SBT
AlternateIDRawData: 32054.LMP


title: Medium 4763646026_F_1

description: Medium


title: 34208.INV

description:
Sample name: 9128_INV
AlternateIDRawData: 34208.INV


title: Generic B2 4763646026_E_2

description: GA Q

value: Generic B2


title: Generic B2 4763646026_E_1

description: GA Q


title: Medium 4763646026_F_2

description: Medium


title: GA C-sample (1)  4763646026_D_1

description: GA C1

value: GA C-sample (1)


title: 32054.INV

description:
Sample name: 3960_INV
AlternateIDRawData: 32054.INV


title: 32023.INV

description:
Sample name: 2044_INV
AlternateIDRawData: 32023.INV


title: GA C-sample (1)  4763646026_D_2

description: GA C1


title: GA DP 4763646026_C_2

description: GA DP


title: 34208.LMP

description:
Sample name: 9128_SBT
AlternateIDRawData: 34208.LMP


title: 32023.LMP

description:
Sample name: 2044_SBT
AlternateIDRawData: 32023.LMP


title: Generic B4 4763646026_B_1

description: GA Q

value: Generic B4


title: CD4+ cells from peripheral blood from child I097

city: München

first: Olivia

last: Prazeres da Costa

state: Bavaria

address: Trogerstr. 30

department: Medical Microbiology, Immunology and Hygiene

institute: Technische Universität München

hyb_protocol: cRNA was hybridized to Affymetrix Human Gene 1.0 ST arrays.

scan_protocol: Affymetrix scanner 3000 7g.

data_processing: Data was normalized in R (v.2.14.) with the bioconductor package affy(v.1.32.0) and the function RMA.

source_name: CD4+ cells from peripheral blood_control

label_protocol: Total RNA (200 ng) was amplified and labeled with biotin using Affymetrix GeneChip Whole Transcript Sense Target Labeling Kit.

growth_protocol: CD4+ cells were isolated by depleting the non-CD4+ cells (human CD4+CD25high isolation kit, Miltenyi Biotec). The purity of the isolated cells was determined by Flow cytometry analysis and was above 90%.

extract_protocol: RNA from isolatedCD4+ cells was isolated using the RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions. The RNA quality and quantity was determined with Agilent Bioanalyzer chips (Bio-Rad Laboratories).

tag: group

value: healthy control (GK)

value: peripheral blood


title: Umod A227T_kidney_rep3

city: Neuherberg

first: Martin

last: Irmler

state: Bayern

address: Ingolstaedter Landstrasse 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum München GmbH

description: individual mutant mice were compared an analysed versus the mean of the corresponding wt

hyb_protocol: This hybridization mixture was placed on a prehybridised microarray, under a cover slip, placed into a hybridization chamber (Genetix) and immersed in a thermostatic bath at 42°C for at least 16 hours. After hybridization slides were washed in 40ml of 3x , 1x, 0.25x and 0.1x SSC at room temperature. For drying slides were placed in an empty 50 ml Falcon tube (Becton Dickinson, USA) and centrifuged at 4000m/s2.

scan_protocol: Dried slides were scanned with a GenePix 4000A microarray scanner and the images were analyzed using the GenePix Pro6.1 image processing software (Axon Instruments, USA)

data_processing: Normalisation with GenePix Pro 6.1: Ratio based normalized data in each image so that the mean of ratio of means of all of the features is equal to 1. The VALUE column contains the log2 ratio of the result file after normalisation

label_protocol: For labeling 20 µg of total RNA were used for reverse transcription and indirectly labeled with Cy3 or Cy5 fluorescent dye according the TIGR protocol (Hedge et al., 2000). Labeled cDNA was dissolved in 30 µl hybridization buffer (6x SSC, 0.5% SDS, 5x Denhardt’s solution and 50% formamide) and mixed with 30 µl of reference cDNA solution (pool from six control animals) labeled with the second dye.

extract_protocol: Total RNA was isolated just before processing for expression profiling. For preparation of total RNA individual organs were thawed in buffer containing chaotropic salt (RLT buffer, Qiagen) and homogenised using a Polytron homogeniser. Total RNA from individual samples was obtained according to manufacturer’s protocols using RNeasy Midi kits (Qiagen). The concentration was calculated from OD260/280 measurement and 2 µg RNA aliquots were run on a formaldehyde agarose gel to check for RNA integrity. The RNA was stored at -80°C in RNase free water (Qiagen).

tag: Sex

value: male

tag: genotype

value: Umod A227T

source_name: wt pool Umod A227T

value: wild type


title: Umod A227T_kidney_rep2


title: Umod A227T_kidney_rep1


title: GA DP 4763646026_C_1

description: GA DP


title: CD4+ cells from peripheral blood from child I083

source_name: CD4+ cells from peripheral blood_AA

value: allergic asthmatic (AA)


title: CD4+ cells from peripheral blood from child I068


title: Umod C93F_kidney_rep1

value: Umod C93F

source_name: wt pool Umod C93F


title: Umod A227T_kidney_rep4


title: Umod C93F_kidney_rep2


title: Umod C93F_kidney_rep3


title: CD4+ cells from peripheral blood from child I069


title: GA RS 4763646026_A_2

description: GA RS


title: Generic B4 4763646026_B_2

description: GA Q


title: Umod C93F_kidney_rep4


title: CD4+ cells from peripheral blood from child I095


title: GA RS 4763646026_A_1

description: GA RS


title: CD4+ cells from peripheral blood from child I082


title: CD4+ cells from peripheral blood from child I074


title: fld_macrophage_LPS_5h_rep4

city: Valladolid

first: Maria

middle: A.

last: Balboa

state: Valladolid

address: Sanz y Fores, 3

department: Innate Immunity

institute: Consejo Superior de Investigaciones Cientificas

hyb_protocol: Hybridization was performed according to the Agilent 60-mer oligo microarray processing protocol using the agilent Gene Expression Hybridization Kit. Briefly, 1.65 mg Cy3-labeled fragmented cRNA in hybridization buffer was hybridized overnight (17 hours, 65 oC) to Agilent  Whole Genome Oligo Microarrays 4x44K using agilent´s recommended hybridization chamber and oven.

scan_protocol: Fluorescence signals were detected using Agilent´s microarray Scanner System.

data_processing: The Agilent Feature Extraction Software was used to read out and process the microarray image files. Ratios were computed using the RosettaResolverTM software (Rosetta Inpharmatics). A common reference was computed by creating an artificial pool of all untreated samples in the analysis.

source_name: peritoneal macrophages

label_protocol: To produce Cyanine-3 (Cy3) labeled cRNA, RNA samples were amplified and labeled using the Agilent Low RNA Input Linear Amp Kit following the manufacturer´s protocol

growth_protocol: Cells were extracted from mice peritoneum and were plated at 2 x 106/well (six-well plates) in 2 ml RPMI 1640 medium with 10% heat-inactivated serum, 100 /ml penicillin, and 100 mg/ml streptomycin and allowed to adhere for 2 h in a humidified atmosphere of 5% CO2 at 37°C. Wells were washed extensively with PBS to remove nonadherent  cells. Adherent macrophages were used for experimentation.

extract_protocol: Total RNA was obtained by the Trizol method following the manufacturer´s recommendation.

treatment_protocol: Cells were untreated or treated with 100 ng/ml LPS for 5 hours in RPMI 1640 mdium without serum.

tag: gender

tag: strain

value: BALB/cByJ-Lpin1fld/J mice

value: fld

value: peritoneal macrophages

value: LPS for 5 hrs


title: CD4+ cells from peripheral blood from child I093


title: Medium 4763646012_F_2

description: Medium

value: Medium

value: SJL X BALB/C

value: spleen cell


title: Peripheral blood from child I063_NAA_LpA

description:
S1843_063_NAA_LpA
Gene expression data from peripheral blood of children (average age 8.4 years)

data_processing: Normalized data by RMA and imputated data corrected for labelling batch effect.

source_name: Peripheral blood_NAA_LpA

growth_protocol: Peripheral blood mononuclear cells (PBMCs) cells were isolated within 24 hours after blood withdrawal by density-gradient centrifugation with Ficoll-Hypaque (Amersham Bioscience, Uppsala, Sweden) after dilution in phosphate buffer saline (PBS, Gibco, Invitrogen, Karlsruhe, Germany). Cells were washed with RPMI 1640 and diluted to a concentration of 5x106 cells/ml in X-Vivo (Lonza, Cologne, Germany).

extract_protocol: RNA from isolated PBMCs and CD4+ cells was isolated using the RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions. The RNA quality and quantity was determined with Agilent Bioanalyzer chips (Bio-Rad Laboratories).

treatment_protocol: For RNA isolation, 2x10^6 cells were cultured (24-well plate; BD) in X-Vivo for 48 hours without stimulation, stimulated with plate-bound anti-CD3 (3µg/ml) plus soluble anti-CD28 (1µg/ml), lipid A (LpA, 0.1µg/ml) or peptidoglycan (Ppg, 1mg/ml) at 37°C. Cell pellets were used for RNA isolation.

value: Peripheral blood

tag: stimulation

value: LpA

value: non-allergic asthmatic (NAA)

tag: labelling batch

tag: batch year


title: Generic B2 4763646012_E_2

description: GA Q

tag: cell type

value: Generic B2


title: Medium 4763646012_F_1

description: Medium


title: fld_macrophage_LPS_5h_rep2

tag: tissue


title: Peripheral blood from child I063_NAA_328

description:
S1842_063_NAA_328
Gene expression data from peripheral blood of children (average age 8.4 years)

source_name: Peripheral blood_NAA_328

value: Peripheral blood mononuclear cells (PBMCs)

value: anti-CD3/CD28 (CD328)


title: fld_macrophage_untreated_rep4

value: male

value: untreated


title: fld_macrophage_LPS_5h_rep1


title: fld_macrophage_LPS_5h_rep3


title: Generic B2 4763646012_E_1

description: GA Q


title: fld_macrophage_untreated_rep2


title: control_macrophage_LPS_5h_rep2

value: heterozygotes


title: control_macrophage_LPS_5h_rep4


title: fld_macrophage_untreated_rep1


title: control_macrophage_untreated_rep3


title: GA C-sample (1)  4763646012_D_1

description: GA C1

value: GA C-sample (1)


title: Peripheral blood from child I063_NAA_M

description:
S1841_063_NAA_M
Gene expression data from peripheral blood of children (average age 8.4 years)

source_name: Peripheral blood_NAA_M

value: M (no stimulation)


title: Peripheral blood from child I040_NAA_LpA

description:
S1840_040_NAA_LpA
Gene expression data from peripheral blood of children (average age 8.4 years)


title: control_macrophage_LPS_5h_rep3

value: BALB/cByJ-Lpin1fld/J mice


title: Peripheral blood from child I040_NAA_328

description:
S1839_040_NAA_328
Gene expression data from peripheral blood of children (average age 8.4 years)


title: control_macrophage_LPS_5h_rep1

value: peritoneal macrophages


title: fld_macrophage_untreated_rep3

value: fld


title: GA DP 4763646012_C_1

description: GA DP

value: GA DP


title: Peripheral blood from child I040_NAA_M

description:
S1838_040_NAA_M
Gene expression data from peripheral blood of children (average age 8.4 years)


title: control_macrophage_untreated_rep4


title: control_macrophage_untreated_rep2


title: Peripheral blood from child I026_NAA_LpA

description:
S1837_026_NAA_LpA
Gene expression data from peripheral blood of children (average age 8.4 years)


title: GA DP 4763646012_C_2

description: GA DP

value: SJL X BALB/C


title: GA C-sample (1)  4763646012_D_2

description: GA C1

value: spleen cell


title: Generic B4 4763646012_B_1

description: GA Q

value: Generic B4


title: Peripheral blood from child I026_NAA_M

description:
S1835_026_NAA_M
Gene expression data from peripheral blood of children (average age 8.4 years)

value: Peripheral blood


title: Generic B4 4763646012_B_2

description: GA Q


title: Caco2_H2O2_rep biol2_rep tech2

city: Bagnols sur Cèze

first: Odette

last: Prat

address: Site de Marcoule

department: Life Science

country: France

institute: CEA

description: Gene expression after 72h exposure

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 µL 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried at ambiant atmosphere.

scan_protocol: Slides were scanned immediately after washing on the Axon genepix Scanner (4000B) using one color scan setting, Scan resolution 5 µm, Dye channel is set to 532 nm.

data_processing: The scanned images were analyzed with genespring software GX11 (Agilent technologies) using one-color technology  to obtain background subtracted and spatially detrended Processed Signal intensities.  Non-uniform outliers were excluded. The three last files were not considered for the data processing.

source_name: caco-2 cells, 24h,  treatment H2O2 21 µM

label_protocol: The RNAs were amplified and labeled with cyanine-3 fluorophore using a QuickAmp kit (Agilent), according to the supplier’s protocol. The efficiency of fluorescent labelling was controlled by UV spectroscopy (Nanodrop 1000)

growth_protocol: Caco-2 cells (ATCC, Manassas, VA, US) were cultured in Eagle's Minimum Essential Medium supplemented with 10% FCS (LGC Standards, Middlesex, UK) and penicillin/streptomycin (100 µg/mL) in a humidified incubator at 37 °C, and 5% CO2. The cells were used between passages 20 to 40. The cells were passaged weekly at a seeding concentration of 6x103 cells/cm2 and the medium was changed three times per week.

extract_protocol: The cells were centrifuged and RNA extracted using the RNeasy kit (Qiagen). The RNAs were quantified with the Nanodrop 1000 and their qualities analyzed on an Agilent Bioanalyzer 2100.

treatment_protocol: For microarray experiments, the cells were seeded in 6-well plates (to collect sufficient amounts of RNA) in the above medium at 5x104 cells/cm2 and allowed to differentiate for 21 days. The cells were exposed to 21.25 µg/mL for 72 h of all types of CeO2 NPs (3 mL/well), in duplicate. The cells were also exposed to hydrogen peroxide for 24 h at 20 µM, as a positive control. Control duplicates were achieved in the vehicle. Each condition of exposure to NPs was compared with a control, i.e. untreated cells (control 1 for NB and NB-DL, control 2 for NB-DA, control 3 for hydrogen peroxide and pristine CeO2). The cells were washed extensively to avoid co-extraction of nucleic acids with NPs adsorbed onto the cell surface, collected with trypsin and washed with PBS.

tag: microarray#

tag: block

tag: sample

value: Intestine

tag: cell line

tag: differentiation

value: 21 days


title: Caco2_H2O2_rep biol2_rep tech1

description: Gene expression after 72h exposure


title: Caco2_CeO2_rep biol2_rep tech2

description: Gene expression after 72h exposure

source_name: caco-2 cells, 72h,  treatment CeO2 21 µg/ml


title: Caco2_C3_rep biol2_rep tech2

description: Gene expression after 72h exposure

source_name: caco-2 cells, 72h, no treatment

value: CTRL 3


title: Peripheral blood from child I020_NAA_LpA

description:
S1834_020_NAA_LpA
Gene expression data from peripheral blood of children (average age 8.4 years)

value: Peripheral blood mononuclear cells (PBMCs)

value: LpA

value: non-allergic asthmatic (NAA)


title: Caco2_C3_rep biol2_rep tech1

description: Gene expression after 72h exposure


title: Peripheral blood from child I020_NAA_328

description:
S1833_020_NAA_328
Gene expression data from peripheral blood of children (average age 8.4 years)

value: anti-CD3/CD28 (CD328)


title: Medium 4763646030_F_1

description: Medium

source_name: Spleen Cell Cultures

tag: batch

tag: experiment

tag: batchcovar

value: Medium

tag: genetic background


title: Caco2_H2O2_rep biol1_rep tech2

description: Gene expression after 72h exposure


title: Medium 4763646030_F_2

description: Medium

tag: treatment


title: Caco2_CeO2_rep biol1_rep tech2

description: Gene expression after 72h exposure


title: Caco2_C3_rep biol1_rep tech2

description: Gene expression after 72h exposure


title: Caco2_CeO2_rep biol2_rep tech1

description: Gene expression after 72h exposure


title: control_macrophage_untreated_rep1

tag: gender

value: male

tag: genotype

value: heterozygotes

value: untreated


title: Control 3

city: Chicago

first: John

middle: C

last: Alverdy

state: IL

address: 5841 South Maryland Avenue

department: Surgery

institute: University of Chicago

description: Gene expression under control conditions

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Microarray slides were scanned using the 2500 GeneArray Scanner (Agilent Technologies).

data_processing:
Gene expression values were calculated using the gcrma function (v2.34.0) in the R (v3.0.2) Bioconductor affy package (v1.40.0).
Two-group comparison was conducted using Significance Analysis of Microarrays (SAM). The criteria for differentially expressed genes was set at false discover rate (FDR) <10% and fold change >1.5.

organism: Pseudomonas aeruginosa

source_name: Pseudomonas aeruginosa MPAO1, TY media

label_protocol: The cDNA synthesis, fragmentation, and labeling were performed according to the protocol for GeneChip Pseudomonas aeruginosa Genome Array (Affymetrix).

growth_protocol:
7-8 weeks old C57BL/6 mice weighing 18-22 grams were sacrificed and their fascia was collected. Samples were normalized by weight (20 mg) and homogenized into 1 mL of TY medium consisting of 10 g/L tryptone (EMD) and 5 g/L yeast extract (Sigma).
Pseudomonas aeruginosa MPAO1 culture grown overnight in TY medium was diluted (1:5,000) in fresh TY medium, and 10 uL of this inoculum was added to each 1 mL of fascia homogenate solution. Samples were incubated at 37°C for 12 hours.

extract_protocol: Total RNA was isolated using the Ribopure Bacteria Kit (Invitrogen).

treatment_protocol: Samples were preserved in 2 mL of RNA protect (Quiagen) to stabilize RNA. DNase I treatment was performed using DNA-free DNase kit (Ambion).

tag: strain


title: Caco2_C3_rep biol1_rep tech1

description: Gene expression after 72h exposure


title: Peripheral blood from child I026_NAA_328

description:
S1836_026_NAA_328
Gene expression data from peripheral blood of children (average age 8.4 years)

tag: stimulation

tag: group

tag: labelling batch


title: GA RS 4763646012_A_1

description: GA RS

tag: cell type

value: GA RS


title: Peripheral blood from child I088_NAA_LpA

description:
S1831_088_NAA_LpA
Gene expression data from peripheral blood of children (average age 8.4 years)

tag: tissue

tag: batch year


title: GA DP 4763646030_E_2

description: GA DP

value: GA DP


title: Caco2_CeO2_rep biol1_rep tech1

description: Gene expression after 72h exposure

tag: microarray#

tag: block

tag: sample


title: Peripheral blood from child I088_NAA_328

description:
S1830_088_NAA_328
Gene expression data from peripheral blood of children (average age 8.4 years)


title: Caco2_H2O2_rep biol1_rep tech1

description: Gene expression after 72h exposure

tag: cell line

tag: differentiation


title: Peripheral blood from child I020_NAA_M

description:
S1832_020_NAA_M
Gene expression data from peripheral blood of children (average age 8.4 years)

value: M (no stimulation)


title: Control 1


title: Control 2


title: Peripheral blood from child I011_AA_LpA

description:
S1828_011_AA_LpA
Gene expression data from peripheral blood of children (average age 8.4 years)

source_name: Peripheral blood_AA_LpA

value: allergic asthmatic (AA)


title: Fascia 3

description: Gene expression with fascia

source_name: Pseudomonas aeruginosa MPAO1, fascia homogenate in TY


title: Caco2_NBDA_rep biol2_rep tech2

description: Gene expression after 72h exposure

source_name: caco-2 cells, 72h,  treatment NB-DA 21 µg/ml

value: NB-DA


title: Fascia 2

description: Gene expression with fascia


title: Fascia 1

description: Gene expression with fascia


title: Caco2_NBDA_rep biol2_rep tech1

description: Gene expression after 72h exposure


title: Peripheral blood from child I011_AA_328

description:
S1827_011_AA_328_2
Gene expression data from peripheral blood of children (average age 8.4 years)

source_name: Peripheral blood_AA_328

value: Peripheral blood


title: GA RS (half dose) 4763646030_D_2

description: GA RS HD

tag: batch

tag: experiment

tag: batchcovar

value: SJL X BALB/C

value: spleen cell

value: GA RS (half dose)


title: GA DP 4763646030_E_1

description: GA DP

tag: genetic background

tag: treatment


title: Caco2_C2_rep biol2_rep tech1

description: Gene expression after 72h exposure

value: CTRL 2

value: Intestine

value: 21 days


title: GA RS (half dose) 4763646030_D_1

description: GA RS HD


title: Peripheral blood from child I059_AA_LpA

description:
S1825_059_AA_LpA
Gene expression data from peripheral blood of children (average age 8.4 years)

value: Peripheral blood mononuclear cells (PBMCs)

value: LpA


title: Peripheral blood from child I088_NAA_M

description:
S1829_088_NAA_M
Gene expression data from peripheral blood of children (average age 8.4 years)

value: non-allergic asthmatic (NAA)


title: Medium 4763646030_B_1

description: Medium

value: Medium


title: Caco2_C2_rep biol2_rep tech2

description: Gene expression after 72h exposure


title: Caco2_NB_rep biol2_rep tech2

description: Gene expression after 72h exposure

source_name: caco-2 cells, 72h,  treatment NB 21 µg/ml

value: NB


title: Caco2_NBDL_rep biol2_rep tech2

description: Gene expression after 72h exposure

source_name: caco-2 cells, 72h,  treatment NB-DL 21 µg/ml

value: NB-DL


title: GA RS 4763646030_C_1

description: GA RS

value: GA RS


title: GA RS 4763646030_C_2

description: GA RS


title: Peripheral blood from child I059_AA_328

description:
S1824_059_AA_328
Gene expression data from peripheral blood of children (average age 8.4 years)

value: anti-CD3/CD28 (CD328)


title: Caco2_NBDL_rep biol2_rep tech1

description: Gene expression after 72h exposure


title: Caco2_C1_rep biol2_rep tech2

description: Gene expression after 72h exposure

value: CTRL 1


title: GA DP 4763646030_A_2

description: GA DP

value: GA DP


title: Peripheral blood from child I011_AA_M

description:
S1826_011_AA_M
Gene expression data from peripheral blood of children (average age 8.4 years)

source_name: Peripheral blood_AA_M

value: Peripheral blood

value: M (no stimulation)

value: allergic asthmatic (AA)


title: Medium 4763646030_B_2

description: Medium

value: SJL X BALB/C

value: spleen cell


title: Peripheral blood from child I054_AA_M

description:
S1820_054_AA_M
Gene expression data from peripheral blood of children (average age 8.4 years)


title: HMLE-Twist, DMSO

city: Cambridge

first: Catherine

middle: A

last: Del Vecchio

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

description: Gene expression data from HMLE-Twist cells treated with DMSO

hyb_protocol: Standard Affymetrix protocol; hybridization was performed with high-throughput HG-U133A Plus 2.0 arrays

scan_protocol: Scanned using an Affymetrix HT Scanner

data_processing: The data were RMA-normalized using the open-source R-project statistical software with bioconductor packages.

source_name: HMLE-Twist breast cells after DMSO treatment

label_protocol: Standard Affymetrix protocol

growth_protocol: Cells were grown in a 1:1 mixture of DMEM+10%FBS, insulin, hydrocortisone and MEGM.

extract_protocol: Total RNA was extracted from culture plates for each cell type using an RNeasy Mini kit coupled with an RNase-free DNase set (Qiagen).

treatment_protocol: Cells were treated for 40uM Menadione for 2 hours or 1uM PERK inhibitor for 48 hours.

value: HMLE

tag: genotype

value: SV40ER, hTERT

tag: agent

value: DMSO


title: Peripheral blood from child I059_AA_M

description:
S1823_059_AA_M
Gene expression data from peripheral blood of children (average age 8.4 years)

value: Peripheral blood mononuclear cells (PBMCs)

tag: stimulation

tag: group


title: HMLE-Twist, Menadione

description: Gene expression data from HMLE-Twist cells treated with 40uM Menadione for 2 hours

source_name: HMLE-Twist breast cells after 40uM Menadione treatment

tag: cell type

value: Menadione


title: HMLE-Twist, PERKi

description: Gene expression data from HMLE-Twist cells treated with 1uM PERKi for 48 hours

source_name: HMLE-Twist breast cells after 1uM PERKi treatment

value: PERKi


title: Peripheral blood from child I054_AA_328

description:
S1821_054_AA_328
Gene expression data from peripheral blood of children (average age 8.4 years)

tag: tissue

tag: labelling batch


title: Caco2_C1_rep biol2_rep tech1

description: Gene expression after 72h exposure

tag: microarray#

value: Intestine

value: 21 days


title: Peripheral blood from child I045_AA_LpA

description:
S1819_045_AA_LpA
Gene expression data from peripheral blood of children (average age 8.4 years)

value: LpA

tag: batch year


title: Caco2_NB_rep biol2_rep tech1

description: Gene expression after 72h exposure

tag: block

tag: sample

value: NB


title: HMLE-shGFP, Menadione

description: Gene expression data from HMLE-shGFP cells treated with 40uM Menadione for 2 hours

source_name: HMLE-shGFP breast cells after 40uM Menadione treatment


title: GA RS (half dose) 4763646004_F_1

description: GA RS HD

value: GA RS (half dose)


title: Peripheral blood from child I045_AA_328

description:
S1818_045_AA_328
Gene expression data from peripheral blood of children (average age 8.4 years)

value: anti-CD3/CD28 (CD328)


title: Caco2_C2_rep biol1_rep tech2

description: Gene expression after 72h exposure

tag: cell line

tag: differentiation


title: HMLE-shGFP, DMSO

description: Gene expression data from HMLE-shGFP cells treated with DMSO

source_name: HMLE-shGFP breast cells after DMSO treatment


title: HMLE-shGFP, PERKi

description: Gene expression data from HMLE-shGFP cells treated with 1uM PERKi for 48 hours

source_name: HMLE-shGFP breast cells after 1uM PERKi treatment


title: GA DP 4763646030_A_1

description: GA DP

tag: batch

tag: experiment

value: GA DP


title: GA RS (half dose) 4763646004_F_2

description: GA RS HD

tag: batchcovar

tag: genetic background


title: GA RS 4763646004_E_2

description: GA RS

tag: treatment

value: GA RS


title: Caco2_NBDA_rep biol1_rep tech2

description: Gene expression after 72h exposure

value: NB-DA


title: GA RS 4763646004_E_1

description: GA RS

value: SJL X BALB/C


title: GL17

city: Rotterdam

first: Marieke

middle: van der

last: Linden

address: Dr. Molenwaterplein 50

department: Pediatric Oncology

country: Netherlands

institute: Erasmus MC

hyb_protocol: Labeled cRNA was then fragmented and hybridized to HU133plus2.0 GeneChips (Affymetrix) according to the manufacturer’s guidelines.

scan_protocol: Standard Affymetrix protocol

data_processing: Raw array data were collectively normalized using variance-stabilizing normalization 3 using Bioconductor and additionally corrected for batch effects using ComBat4

source_name: leukemic blasts

label_protocol: High-quality RNA was reverse transcribed using T7-linked oligo-dT primers, and the obtained cDNA was used as a template to synthesize biotinylated cRNA.

extract_protocol: All samples were freshly processed within 24 hours after sampling. Mononuclear cells were isolated by density gradient centrifugation using Lymphoprep (NycomedPharma), and non-leukemic cells were removed using immunomagnetic beads. All leukemia samples used in this study contained more than 90% leukemic cells, as determined morphologically on May-Grünwald-Giemsa (Merck)-stained cytospins. Total RNA and gDNA were extracted from a minimum of 5x106 leukemic cells using TRIzol reagent (Invitrogen Life Technologies) according to the manufacturer’s instructions with minor modifications. Quantification of DNA was performed using a spectrophotometer. Quantification and assessment of integrity of the extracted RNA was assessed using the Agilent 2100 Bio-analyzer (Agilent).

tag: mll status

value: wild-type

tag: gender

value: F

tag: age (months)

value: leukemic blasts


title: Caco2_NBDA_rep biol1_rep tech1

description: Gene expression after 72h exposure


title: Peripheral blood from child I039_AA_LpA

description:
S1816_039_AA_LpA
Gene expression data from peripheral blood of children (average age 8.4 years)

value: Peripheral blood

tag: cell type

tag: stimulation

tag: group

value: allergic asthmatic (AA)


title: GL16

value: M


title: GL15


title: Medium 4763646004_D_2

description: Medium

value: Medium

value: spleen cell


title: Peripheral blood from child I045_AA_M

description:
S1817_045_AA_M
Gene expression data from peripheral blood of children (average age 8.4 years)

tag: tissue

value: Peripheral blood mononuclear cells (PBMCs)

value: M (no stimulation)

tag: labelling batch


title: GA DP 4763646004_C_1

description: GA DP


title: Peripheral blood from child I039_AA_328

description:
S1815_039_AA_328
Gene expression data from peripheral blood of children (average age 8.4 years)

tag: batch year


title: Medium 4763646004_D_1

description: Medium


title: Caco2_C2_rep biol1_rep tech1

description: Gene expression after 72h exposure

source_name: caco-2 cells, 72h, no treatment

tag: microarray#

tag: block

tag: sample

value: Intestine

value: 21 days


title: GL13


title: Caco2_NBDL_rep biol1_rep tech2

description: Gene expression after 72h exposure

value: NB-DL

tag: cell line

tag: differentiation


title: GL14


title: Caco2_NB_rep biol1_rep tech2

description: Gene expression after 72h exposure

value: NB


title: Peripheral blood from child I037_AA_LpA

description:
S1813_037_AA_LpA
Gene expression data from peripheral blood of children (average age 8.4 years)

value: LpA


title: Caco2_NBDL_rep biol1_rep tech1

description: Gene expression after 72h exposure


title: GA RS 4763646012_A_2

description: GA RS

source_name: Spleen Cell Cultures

tag: batch

tag: experiment

tag: batchcovar

value: GA RS


title: GA RS (half dose) 4763646004_B_2

description: GA RS HD

tag: genetic background

value: SJL X BALB/C

tag: treatment

value: GA RS (half dose)


title: GL11

tag: mll status

value: wild-type

tag: gender

value: F

tag: age (months)


title: Peripheral blood from child I037_AA_328

description:
S1812_037_AA_328
Gene expression data from peripheral blood of children (average age 8.4 years)

value: Peripheral blood

tag: cell type

tag: stimulation

value: anti-CD3/CD28 (CD328)

tag: group


title: Peripheral blood from child I037_AA_M

description:
S1811_037_AA_M
Gene expression data from peripheral blood of children (average age 8.4 years)

tag: tissue

value: allergic asthmatic (AA)

tag: labelling batch

tag: batch year


title: Peripheral blood from child I039_AA_M

description:
S1814_039_AA_M
Gene expression data from peripheral blood of children (average age 8.4 years)


title: GL10

value: M

value: leukemic blasts


title: Caco2_C1_rep biol1_rep tech2

description: Gene expression after 72h exposure

tag: microarray#

tag: block

tag: sample


title: GA DP 4763646004_C_2

description: GA DP

tag: batch

value: spleen cell

value: GA DP


title: Peripheral blood from child I036_AA_LpA

description:
S1810_036_AA_LpA
Gene expression data from peripheral blood of children (average age 8.4 years)

value: Peripheral blood mononuclear cells (PBMCs)


title: GL9


title: Caco2_C1_rep biol1_rep tech1

description: Gene expression after 72h exposure

value: Intestine

tag: cell line

tag: differentiation

value: 21 days


title: Peripheral blood from child I036_AA_328

description:
S1809_036_AA_328
Gene expression data from peripheral blood of children (average age 8.4 years)


title: GA RS 4763646004_A_2

description: GA RS

tag: experiment

tag: batchcovar

tag: genetic background


title: Caco2_NB_rep biol1_rep tech1

description: Gene expression after 72h exposure

value: NB


title: GL12

tag: mll status

tag: gender


title: Peripheral blood from child I030_AA_LpA

description:
S1807_030_AA_LpA
Gene expression data from peripheral blood of children (average age 8.4 years)

tag: cell type

value: LpA


title: GA RS (half dose) 4763646004_B_1

description: GA RS HD

tag: treatment


title: GA RS 4763646004_A_1

description: GA RS

value: GA RS


title: RWPE-PCAT1 NT siRNA, replicate 1

city: Ann Arbor

last: Prensner

state: MI

address: 1400 E. Medical Center Drive, Room 7431 CCGC

department: Michigan Center for Translational Pathology

institute: University of Michigan

description: RWPE-PCAT1 cells transfected with non-targeting siRNA, RNA was harvested after 48 hours, replicate #1

hyb_protocol: Scanned on an Agilent G2565AA scanner.

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.

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

growth_protocol: RPMI-1640 media plus 10% FBS and 1% penicillin-streptomycin antibiotics.  Grown at 37 degrees C with 5% CO2.

extract_protocol: 10 µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label

treatment_protocol: Cells were in serum-free RPMI-1640.  siRNA was diluted to 20nM in Optimem with Oligofectamine.  Cells were treated with siRNA for 24 hours prior to replenishing 10% FBS and allowing for cell growth for 48 hours.

tag: age

value: < 20 cell passages from derivation


title: Peripheral blood from child I030_AA_328

description:
S1806_030_AA_328
Gene expression data from peripheral blood of children (average age 8.4 years)

tag: tissue

tag: stimulation

tag: group


title: Peripheral blood from child I030_AA_M

description:
S1805_030_AA_M
Gene expression data from peripheral blood of children (average age 8.4 years)

value: M (no stimulation)

tag: labelling batch

tag: batch year


title: Peripheral blood from child I036_AA_M

description:
S1808_036_AA_M
Gene expression data from peripheral blood of children (average age 8.4 years)


title: RWPE-PCAT1 NT siRNA, replicate 2

description: RWPE-PCAT1 cells transfected with non-targeting siRNA, RNA was harvested after 48 hours, replicate #2


title: GL8

value: wild-type

tag: age (months)


title: GL6

value: F


title: GL5


title: Du145-PCAT1 NT siRNA, replicate 1

description: Du145-PCAT1 cells transfected with non-targeting siRNA, RNA was harvested after 48 hours, replicate #1


title: TV-109 4682416087_F_1

description: TV Marker

tag: batch

value: SJL X BALB/C


title: GL7


title: Du145-PCAT1 NT siRNA, replicate 2

description: Du145-PCAT1 cells transfected with non-targeting siRNA, RNA was harvested after 48 hours, replicate #2

tag: cell line


title: TV-66 4682416087_E_1

description: TV Marker


title: GL4


title: TV-109 4682416087_F_2

description: TV Marker


title: TV-35 4682416087_D_1

description: TV Marker


title: Peripheral blood from child I083_AA_328

description:
S1803_083_AA_328
Gene expression data from peripheral blood of children (average age 8.4 years)

value: Peripheral blood

value: anti-CD3/CD28 (CD328)


title: RWPE-PCAT1 cMyc siRNA #3, replicate 1

description: RWPE-PCAT1 cells transfected with cMyc siRNA #3, RNA was harvested after 48 hours, replicate #1


title: GL2


title: RWPE-PCAT1 cMyc siRNA #4, replicate 1

description: RWPE-PCAT1 cells transfected with cMyc siRNA #4, RNA was harvested after 48 hours, replicate #1


title: TV-66 4682416087_E_2

description: TV Marker


title: TV-35 4682416087_D_2

description: TV Marker


title: Peripheral blood from child I083_AA_M

description:
S1802_083_AA_M
Gene expression data from peripheral blood of children (average age 8.4 years)

value: allergic asthmatic (AA)


title: Peripheral blood from child I083_AA_LpA

description:
S1804_083_AA_LpA
Gene expression data from peripheral blood of children (average age 8.4 years)


title: RWPE-PCAT1 cMyc siRNA #3, replicate 2

description: RWPE-PCAT1 cells transfected with cMyc siRNA #3, RNA was harvested after 48 hours, replicate #2


title: Peripheral blood from child I069_AA_LpA

description:
S1798_069_AA_LpA
Gene expression data from peripheral blood of children (average age 8.4 years)


title: GL3

value: M

value: leukemic blasts


title: GL1


title: GA DP 4682416090_F_1

description: GA DP

value: spleen cell

value: GA DP


title: RWPE-PCAT1 cMyc siRNA #4, replicate 2

description: RWPE-PCAT1 cells transfected with cMyc siRNA #4, RNA was harvested after 48 hours, replicate #2


title: Du145-PCAT1 cMyc siRNA #3, replicate 1

description: Du145-PCAT1 cells transfected with cMyc siRNA #3, RNA was harvested after 48 hours, replicate #1


title: Peripheral blood from child I069_AA_328

description:
S1797_069_AA_328
Gene expression data from peripheral blood of children (average age 8.4 years)

value: Peripheral blood mononuclear cells (PBMCs)


title: Peripheral blood from child I069_AA_M

description:
S1796_069_AA_M
Gene expression data from peripheral blood of children (average age 8.4 years)


title: GA RS 4682416087_C_1

description: GA RS


title: Du145-PCAT1 cMyc siRNA #4, replicate 1

description: Du145-PCAT1 cells transfected with cMyc siRNA #4, RNA was harvested after 48 hours, replicate #1


title: 20

city: San Francisco

first: Linda

last: Giudice

state: CA

address: 513 Parnassus Ave. HSE 1619

department: OBGYN and RS

institute: University of California, San Francisco

description: SAMPLE 148

hyb_protocol: Fragmented biotinylated cRNAs were hybridized overnight to a high density Affimetrix Human Genome (HG) U133 Plus 2.0 oligonucleotide microarray genechip containing 54600 probe sets (42203 annotated genes and 12397 expressed sequence tags [EST]) at the Gladstone Genomics Core Facility

scan_protocol: Fluorescent labeling and laser confocal scanning with a GeneChip Scanner 3000. Generated data were extracted for analysis using the Affymetrix Gene-Chip Operating Software and Microsoft Corp. (Redmond, WA) Excel/Mac2001 software.

data_processing: We imported all of the microarray data files into R and normalized them simultaneously. The normalization procedure consists of two steps executed with programs in the Bioconductor package GCRMA. First, we compute the probe affinities using the annotation file hgu133plus2cdf. Second, we normalize the data by setting two options and leaving the rest at default values. The affinity.info option is set to use the probe affinities computed in the first step. The type option is set to fullmodel which uses both the sequence information and mismatch probe model.

source_name: Non-Endometriosis_No Uterine Pelvic Pathology

label_protocol: Biotinylated-cRNA was then prepared using the Ambion MessageAmp II-Biotin Enhanced Kit according to manufacturer instructions.

extract_protocol: Total RNA was isolated from endometrial tissue using Trizol (Invitrogen, Carlsbad, CA, USA), according to the manufacturer’s instructions, followed by DNase treatment and purification with Qiagen RNeasy Plus Kit. The purity and quality of the RNA were assessed with Agilent 2100 Bioanalyzer. First and second strand cDNAs were prepared according to the Affymetrix microarray preparation protocol (Affymetrix).

value: Proliferative Endometrial tissue

tag: endometriosis/no endometriosis

value: Non-Endometriosis

tag: presence or absence of uterine/pelvic pathology

value: No Uterine Pelvic Pathology


title: 18

description: SAMPLE 146


title: GA RS 4682416087_C_2

description: GA RS

data_processing: This is a sister series to GSE40566. This GEO entry includes all samples including technical replicates. Background-corrected bead-level summarization was conducted using Illumina's Bead studio. Normalized version of the data was quantile normalized using R's preprocessCore package (normalize.quantilies function) and batch corrected using ComBat from the SVA package with Batch variable as batch and batchcovar as covariate

extract_protocol: PerfectPure RNA Cultures CEKK kit 50 (5Prime GmbH, Hamburg, Germany) according to manufacturer’s instructions. RNA quality was assessed by the absorbance ratio at 260/280 nm and gel electrophoresis (Experionä, Bio-Rad, Hercules, CA).

tag: experiment

tag: batchcovar

value: GA RS


title: 19

description: SAMPLE 147


title: Du145-PCAT1 cMyc siRNA #4, replicate 2

description: Du145-PCAT1 cells transfected with cMyc siRNA #4, RNA was harvested after 48 hours, replicate #2

value: < 20 cell passages from derivation


title: 34

description: SAMPLE 145

value: Mid-Secretory Endometrial tissue


title: Peripheral blood from child I068_AA_M

description:
S1793_068_AA_M
Gene expression data from peripheral blood of children (average age 8.4 years)

value: M (no stimulation)


title: Peripheral blood from child I068_AA_328

description:
S1794_068_AA_328
Gene expression data from peripheral blood of children (average age 8.4 years)


title: GA DP 4682416090_F_2

description: GA DP

tag: genetic background


title: 17

description: SAMPLE 144


title: Medium 4682416087_B_2

description: Medium

value: Medium


title: GA DM (SFC-961)  4682416087_A_2

description: GA DM

value: SJL X BALB/C

value: GA DM (SFC-961)


title: Peripheral blood from child I038_GK_LpA

description:
S1789_038_GK_LpA
Gene expression data from peripheral blood of children (average age 8.4 years)

source_name: Peripheral blood_control_LpA

value: Peripheral blood

value: LpA

value: healthy control (GK)


title: Du145-PCAT1 cMyc siRNA #3, replicate 2

description: Du145-PCAT1 cells transfected with cMyc siRNA #3, RNA was harvested after 48 hours, replicate #2


title: Peripheral blood from child I068_AA_LpA

description:
S1795_068_AA_LpA
Gene expression data from peripheral blood of children (average age 8.4 years)

source_name: Peripheral blood_AA_LpA

value: allergic asthmatic (AA)


title: Peripheral blood from child I038_GK_328

description:
S1788_038_GK_328
Gene expression data from peripheral blood of children (average age 8.4 years)

source_name: Peripheral blood_control_328

value: anti-CD3/CD28 (CD328)


title: Medium 4682416087_B_1

description: Medium

value: spleen cell


title: GA DM (SFC-961)  4682416087_A_1

description: GA DM


title: 49

description: SAMPLE 142

value: Uterine Pelvic Pathology


title: GA DP 4682416043_F_2

description: GA DP

value: GA DP


title: 71

description: SAMPLE 143

value: Late Secretory Endometrial tissue

value: Non-Endometriosis


title: 16

description: SAMPLE 141

value: Proliferative Endometrial tissue

value: No Uterine Pelvic Pathology


title: GA DP 4682416043_F_1

description: GA DP


title: 55

description: SAMPLE 140

value: Early Secretory Endometrial tissue


title: 33

description: SAMPLE 139

value: Mid-Secretory Endometrial tissue


title: sensory cortex of healthy mouse #4

city: Heidelberg - Melbourne

first: Stefan

last: Thiem

state: Victoria

address: 145 Studley Road

department: Cancer Research

institute: Olivia Newton-John Cancer Research Institute

description: Gene expression data from mouse sensory cortex control sample.

hyb_protocol: Standard Affymetrix 3' array hybridyzation protocol

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

data_processing: Expression data was analysed using Partek® genomics suite, Missouri, USA. Affymetrix® and Data was normalized using RMA (Bolstad et al 2003) and quantile normalization and adjusted for GC content.  Expression values were log transformed using base2 prior to differential expression analysis using a 2 way ANOVA on treatment and tissue.

source_name: sensory cortex, brain, healthy

label_protocol: 1 ug RNA was labeled following the standard Affymetrix biotin label protocol. The quantity of labelled product was ascertained using the Agilent Bioanalyser 2100 (NanoChip protocol).

growth_protocol: Animals were group housed.

extract_protocol: RNA was extracted using an RNeasy mini kit (QIAGEN Pty Ltd. Vic, AUS) as per manufacturer’s instructions. Total RNA was quality ascertained using the Agilent Bioanalyser 2100 (NanoChip protocol).

treatment_protocol: EAE was induced in 8-12 week old C57Bl/6 mice with 100μg MOG35-55 peptide injected subcutaneously in both rear flanks and 50μg into the tail base as well as an intraperitoneal injection of 400ng/100μl   Pertussis toxin on day 0 and 3. Control mice were housed in same cages as EAE mice.  For tissue collection, EAE (n=6) and healthy (n=4) mice (8-12 weeks) were euthanized and perfused with 20ml MT-PBS on day 21 following injection, followed by 10ml RNAlater, and forebrains were removed and placed into a cold metal brain matrix. The brains were cut into 1mm coronal slices and the motor and sensory cortex regions dissected with the help of a brain atlas.

tag: animal id number

tag: strain

value: sensory cortex

tag: gender

value: female

tag: injection age

value: 8-12 weeks

value: control

tag: eae grade (average)

tag: eae day

tag: chip processing date

tag: cohort


title: Peripheral blood from child I038_GK_M

description:
S1787_038_GK_M
Gene expression data from peripheral blood of children (average age 8.4 years)

source_name: Peripheral blood_control_M

tag: tissue

value: Peripheral blood

tag: cell type

value: Peripheral blood mononuclear cells (PBMCs)

tag: stimulation

value: M (no stimulation)

tag: group

tag: labelling batch

tag: batch year


title: sensory cortex of healthy mouse #3

tag: treatment


title: GA RS 4682416043_E_1

last: Hasson

address: Hatrufa 12

institute: Teva Pharmaceuticals

description: GA RS

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scan protocol

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

tag: batch

tag: experiment

tag: batchcovar

value: SJL X BALB/C

value: GA RS


title: GA FD (Base)  4682416043_D_1

description: GA FD

tag: genetic background

value: spleen cell

value: GA FD (Base)


title: Exp2 WT

city: Isehara

first: Akihide

last: Kamiya

state: Kanagawa

address: 143 Shimokasuya

country: Japan

institute: Tokai University

description: Gene expression data from E17.5 p57+/+ hepatic mesothelial and submesothlial cells.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45 degrees on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Single Array Analysis were calculated by  Microarray Suite version 5.0 (MAS5.0) with Affymetrix default setting and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: E17.5 p57+/+ mouse liver mesothelial and submesothelial cells

label_protocol: Biotinylated cRNA were synthesized by GeneChip 3'IVT Express Kit（Affymetrix) from 250 ng total RNA according to the manufacturer's instructions.  Biotinylated cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: Primary cell

extract_protocol: RNA was extracted using RNeasy Plus Mini (Qiagen; Venlo, The Netherlands).

treatment_protocol: E17.5 p57-/- or +/+ hepatic mesothelial and submesothelial cells were surgically isolated and their RNA was extracted by RNeasy Plus Mini kit (Qiagen).

value: liver

tag: strain

tag: developmental stage

value: Embryonic day 17.5

tag: genotype

value: wildtype


title: Peripheral blood from child I053_GK_LpA

description:
S1783_053_GK_LpA
Gene expression data from peripheral blood of children (average age 8.4 years)

value: LpA

value: healthy control (GK)


title: Exp1 KO

description: Gene expression data from E17.5 p57-/- hepatic mesothelial and submesothlial cells.

source_name: E17.5 p57-/- mouse liver mesothelial and submesothelial cells


title: sensory cortex of healthy mouse #1

tag: animal id number

tag: gender

tag: injection age

tag: eae grade (average)

tag: eae day


title: GA FD (Base)  4682416043_D_2

city: Natanya

first: Tal

description: GA FD

tag: cell type


title: Exp2 KO

tag: tissue


title: Peripheral blood from child I053_GK_328

description:
S1782_053_GK_328
Gene expression data from peripheral blood of children (average age 8.4 years)

tag: stimulation

value: anti-CD3/CD28 (CD328)

tag: group

tag: labelling batch


title: sensory cortex of healthy mouse #2

value: sensory cortex

tag: treatment

tag: chip processing date

tag: cohort


title: GA RS 4682416043_E_2

description: GA RS

tag: batch

tag: experiment

tag: batchcovar

tag: genetic background


title: Peripheral blood from child I053_GK_M

description:
S1781_05_GK_3_M
Gene expression data from peripheral blood of children (average age 8.4 years)

tag: batch year


title: 15

description: SAMPLE 136

value: Proliferative Endometrial tissue

tag: endometriosis/no endometriosis

value: Non-Endometriosis

tag: presence or absence of uterine/pelvic pathology

value: No Uterine Pelvic Pathology


title: Exp1 WT

tag: strain

tag: developmental stage

tag: genotype


title: 69

description: SAMPLE 137

tag: tissue

value: Mid-Secretory Endometrial tissue

value: Uterine Pelvic Pathology


title: 26

description: SAMPLE 135

value: Early Secretory Endometrial tissue


title: 54

description: SAMPLE 138


title: Peripheral blood from child I049_GK_LpA

description:
S1780_049_GK_LpA
Gene expression data from peripheral blood of children (average age 8.4 years)

value: Peripheral blood

tag: cell type

value: Peripheral blood mononuclear cells (PBMCs)

tag: stimulation


title: Peripheral blood from child I049_GK_328

description:
S1779_049_GK_328
Gene expression data from peripheral blood of children (average age 8.4 years)

tag: group

tag: labelling batch


title: GA FD (Heat)  4682416043_C_2

description: GA FD

value: SJL X BALB/C

value: spleen cell

tag: treatment

value: GA FD (Heat)


title: sensory cortex of EAE mouse #5

description: Gene expression data from mouse sensory cortex after EAE treatment.

source_name: sensory cortex, brain, EAE

tag: animal id number

tag: gender

value: female

tag: injection age

value: 8-12 weeks

value: EAE

tag: eae grade (average)

tag: eae day

tag: chip processing date

tag: cohort


title: GA DP 4682416090_E_1

description: GA DP

tag: batch

tag: experiment

tag: batchcovar

tag: genetic background

value: GA DP


title: sensory cortex of EAE mouse #4

tag: strain

tag: tissue


title: sensory cortex of EAE mouse #6


title: sensory cortex of EAE mouse #3


title: 13

description: SAMPLE 133

tag: endometriosis/no endometriosis

tag: presence or absence of uterine/pelvic pathology


title: Peripheral blood from child I049_GK_M

description:
S1778_049_GK_M_4
Gene expression data from peripheral blood of children (average age 8.4 years)

tag: cell type

tag: stimulation

value: M (no stimulation)

tag: group

value: healthy control (GK)

tag: labelling batch

tag: batch year


title: GA FD (Heat)  4682416043_C_1

description: GA FD

tag: treatment


title: sensory cortex of EAE mouse #2

tag: animal id number

value: sensory cortex

tag: gender

tag: injection age

tag: eae grade (average)

tag: eae day


title: Peripheral blood from child I048_GK_LpA

description:
S1777_048_GK_LpA
Gene expression data from peripheral blood of children (average age 8.4 years)

value: LpA


title: Peripheral blood from child I046_GK_LpA

description:
S1774_046_GK_LpA
Gene expression data from peripheral blood of children (average age 8.4 years)


title: 12

description: SAMPLE 132

value: Proliferative Endometrial tissue

value: Non-Endometriosis

value: No Uterine Pelvic Pathology


title: Generic B3 4682416043_B_1

description: GA Q

tag: batch

tag: experiment

tag: batchcovar

value: Generic B3


title: Generic B3 4682416043_B_2

description: GA Q

tag: genetic background


title: Peripheral blood from child I048_GK_328

description:
S1776_048_GK_328
Gene expression data from peripheral blood of children (average age 8.4 years)

tag: tissue

value: Peripheral blood

value: anti-CD3/CD28 (CD328)


title: Peripheral blood from child I046_GK_328

description:
S1773_046_GK_328
Gene expression data from peripheral blood of children (average age 8.4 years)

value: Peripheral blood mononuclear cells (PBMCs)


title: 147

description: SAMPLE 129

value: Mid-Secretory Endometrial tissue

tag: endometriosis/no endometriosis

value: Endometriosis

tag: endometriosis severity

value: Moderate/Severe


title: 117

description: SAMPLE 130


title: sensory cortex of EAE mouse #1

tag: strain

value: female

value: 8-12 weeks

tag: chip processing date

tag: cohort


title: Peripheral blood from child I046_GK_M

description:
S1772_046_GK_M
Gene expression data from peripheral blood of children (average age 8.4 years)

tag: cell type

tag: stimulation

tag: group

tag: labelling batch

tag: batch year


title: 146

description: SAMPLE 128


title: 70

description: SAMPLE 131

value: Late Secretory Endometrial tissue

tag: presence or absence of uterine/pelvic pathology

value: Uterine Pelvic Pathology


title: motor cortex of healthy mouse #2

description: Gene expression data from mouse motor cortex control sample.

source_name: motor cortex, brain, healthy

tag: animal id number

value: motor cortex

tag: gender

tag: injection age

tag: treatment

value: control

tag: eae grade (average)

tag: eae day


title: motor cortex of healthy mouse #3

tag: tissue


title: 101

description: SAMPLE 127

tag: endometriosis/no endometriosis

tag: endometriosis severity


title: Peripheral blood from child I082_GK_LpA

description:
S1771_082_GK_LpA
Gene expression data from peripheral blood of children (average age 8.4 years)

value: LpA

value: healthy control (GK)


title: GA DP 4682416090_E_2

description: GA DP

tag: batch

tag: experiment

tag: batchcovar

tag: genetic background

value: SJL X BALB/C

value: spleen cell

value: GA DP


title: GA DP 4682416090_D_1

description: GA DP

tag: cell type


title: GA DP 4682416090_D_2

description: GA DP


title: motor cortex of healthy mouse #4

tag: strain

tag: chip processing date

tag: cohort


title: motor cortex of EAE mouse #6

description: Gene expression data from mouse motor cortex after EAE treatment.

source_name: motor cortex, brain, EAE

tag: animal id number

value: EAE


title: GA RS 4682416043_A_1

description: GA RS

value: GA RS


title: 84

description: SAMPLE 126

value: Early Secretory Endometrial tissue

value: Minimal/Mild


title: Peripheral blood from child I082_GK_328

description:
S1770_082_GK_328
Gene expression data from peripheral blood of children (average age 8.4 years)

value: Peripheral blood

value: Peripheral blood mononuclear cells (PBMCs)

tag: stimulation

value: anti-CD3/CD28 (CD328)

tag: group

tag: labelling batch

tag: batch year


title: Peripheral blood from child I048_GK_M

description:
S1775_048_GK_M
Gene expression data from peripheral blood of children (average age 8.4 years)

value: M (no stimulation)


title: motor cortex of healthy mouse #1

tag: gender

value: female

tag: injection age

value: 8-12 weeks

tag: treatment

tag: eae grade (average)

tag: eae day


title: Medium 4682416090_C_2

description: Medium

tag: batch

tag: experiment

value: Medium


title: 87

description: SAMPLE 124

tag: tissue

tag: endometriosis/no endometriosis

value: Endometriosis

tag: endometriosis severity


title: 116

description: SAMPLE 125

value: Proliferative Endometrial tissue

value: Moderate/Severe


title: GA RS 4682416043_A_2

description: GA RS

tag: batchcovar

tag: genetic background

value: SJL X BALB/C

tag: cell type


title: Peripheral blood from child I097_GK_LpA

description:
S1768_097_GK_LpA
Gene expression data from peripheral blood of children (average age 8.4 years)

tag: stimulation

value: LpA

value: healthy control (GK)


title: Peripheral blood from child I082_GK_M

description:
S1769_082_GK_M
Gene expression data from peripheral blood of children (average age 8.4 years)

tag: group


title: Peripheral blood from child I066_GK_LpA

description:
S1786_066_GK_LpA
Gene expression data from peripheral blood of children (average age 8.4 years)

tag: labelling batch


title: Peripheral blood from child I097_GK_M

description:
S1766_097_GK_M
Gene expression data from peripheral blood of children (average age 8.4 years)

tag: batch year


title: Medium 4682416090_C_1

description: Medium

value: spleen cell


title: motor cortex of EAE mouse #2

tag: animal id number

tag: strain

value: motor cortex

tag: gender

value: EAE

tag: chip processing date

tag: cohort


title: Peripheral blood from child I095_GK_LpA

description:
S1765_095_GK_LpA
Gene expression data from peripheral blood of children (average age 8.4 years)


title: motor cortex of EAE mouse #4

tag: injection age

tag: treatment

tag: eae grade (average)

tag: eae day


title: Generic B4 4682416090_A_1

description: GA Q

tag: batch

tag: experiment

value: Generic B4


title: 11

description: SAMPLE 120

tag: tissue

tag: endometriosis/no endometriosis

value: Non-Endometriosis

tag: presence or absence of uterine/pelvic pathology

value: No Uterine Pelvic Pathology


title: GA DP 4682416090_B_2

description: GA DP

tag: batchcovar

tag: genetic background

tag: cell type

value: GA DP


title: Peripheral blood from child I097_GK_328

description:
S1767_097_GK_328
Gene expression data from peripheral blood of children (average age 8.4 years)

value: Peripheral blood

value: Peripheral blood mononuclear cells (PBMCs)

tag: stimulation

value: anti-CD3/CD28 (CD328)

tag: group

tag: labelling batch

tag: batch year


title: 148

description: SAMPLE 121

value: Unknown

tag: endometriosis severity


title: motor cortex of EAE mouse #3

tag: animal id number

tag: strain

tag: gender

value: female

tag: injection age

value: 8-12 weeks

tag: chip processing date

tag: cohort


title: Generic B4 4682416090_A_2

description: GA Q

tag: batch

tag: experiment

tag: treatment


title: Peripheral blood from child I095_GK_328

description:
S1764_095_GK_328
Gene expression data from peripheral blood of children (average age 8.4 years)

tag: tissue


title: GA DP 4682416090_B_1

description: GA DP

tag: batchcovar

tag: genetic background


title: GA DP 4682416019_F_2

description: GA DP

tag: cell type


title: motor cortex of EAE mouse #1

tag: eae grade (average)

tag: eae day


title: 10

description: SAMPLE 119

value: Proliferative Endometrial tissue

tag: endometriosis/no endometriosis

tag: presence or absence of uterine/pelvic pathology


title: motor cortex of EAE mouse #5

tag: animal id number


title: 14

description: SAMPLE 134


title: 9

description: SAMPLE 118


title: 99

description: SAMPLE 123

value: Endometriosis

tag: endometriosis severity

value: Minimal/Mild


title: Peripheral blood from child I093_GK_328

description:
S1761_093_GK_328
Gene expression data from peripheral blood of children (average age 8.4 years)

tag: stimulation

tag: group

value: healthy control (GK)

tag: labelling batch

tag: batch year


title: Peripheral blood from child I095_GK_M

description:
S1763_095_GK_M
Gene expression data from peripheral blood of children (average age 8.4 years)

value: M (no stimulation)


title: GA DP 4682416019_F_1

description: GA DP

tag: batch

value: SJL X BALB/C

value: spleen cell


title: Peripheral blood from child I093_GK_LpA

description:
S1762_093_GK_LpA
Gene expression data from peripheral blood of children (average age 8.4 years)

value: LpA


title: Peripheral blood from child I093_GK_M

description:
S1760_093_GK_M
Gene expression data from peripheral blood of children (average age 8.4 years)


title: 31

description: SAMPLE 116

value: Mid-Secretory Endometrial tissue

value: Non-Endometriosis


title: 6h, GDX + E2

city: Quebec

first: Ezequiel

middle: L

last: Calvo

state: Quebec

address: 2705 Boul. Laurier

department: Molecular Endocrinilogy

institute: CRCHUL

description:
Gene expression data from mammary gland tissue, 24h prior to necropsy.
Mammary gland tissue samples from all mice of the same group were collected, rapidly trimmed, snap-frozen in liquid nitrogen and stored at -80ºC prior to mRNA extraction.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C to the Affymetrix GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained according to the standard Affymetrix protocols in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix Scanner 3000 (Affymetrix).

data_processing: CEL files were extracted with GCOS 1.0 (Affymetrix). Data were analyzed with LimmaGUI software (Bioconductor) and normalized by RMA method.

source_name: mammary gland tissue

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 20 ug of total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA was isolated from cells using Trizol Reagent, according to the manufacturer’s protocol (Invitrogen).

treatment_protocol: E2 (0.05 µg mg/mouse) was injected subcutaneously 1, 3, 6, 12, 18 and 24 h prior to sacrifice in E2-treated groups. Two groups were retained as controls and received a vehicle solution.

tag: Female mice mammary gland tissue


title: GA RS 4682416019_E_1

description: GA RS

tag: experiment

tag: treatment

value: GA RS


title: Peripheral blood from child I074_GK_LpA

description:
S1759_074_GK_LpA
Gene expression data from peripheral blood of children (average age 8.4 years)

tag: tissue

value: Peripheral blood


title: GA RS 4682416019_E_2

description: GA RS

tag: batchcovar

tag: genetic background


title: 30

description: SAMPLE 115

value: No Uterine Pelvic Pathology


title: 29

description: SAMPLE 114


title: 32

description: SAMPLE 117


title: 18h, GDX + E2


title: 12h, GDX + E2


title: GA DP 4682416019_D_2

description: GA DP

tag: cell type

value: GA DP


title: 3h, GDX + E2


title: 24h, Control, GDX + vehicle 2


title: GA DP 4682416019_D_1

description: GA DP


title: 930301355b_N

city: Rochester

first: Zhifu

last: Sun

state: MN

address: 200 1st ST SW

department: HSR-BSI

institute: Mayo Clinic

description: FFPE

hyb_protocol: Fluorescently labelled cDNA PCR products were hybridized to the Illumina Sentrix BeadChip according to the manufacturer's protocol

scan_protocol: Scanned using the Illumina Bead Array Reader

data_processing: The microarray data was processed and normalized through BeadStudio software, version 3.0. (Illumina Inc.) using the quantile normalization method.

source_name: Lung normal

label_protocol: Biotinylated cDNA were prepared from 100-200ng total RNA using the DASL Assay (cDNA-mediated annealing, selection, extension and ligation)

extract_protocol: RNA was extracted using the miRNeasy FFPE kit (Qiagen Inc, Valencia, California, USA) using the manufacturer’s protocols. Quality control was performed with Agilent Bioanalyser

value: Normal


title: 930301349b_N

description: FFPE


title: Peripheral blood from child I074_GK_328

description:
S1758_074_GK_328
Gene expression data from peripheral blood of children (average age 8.4 years)

value: Peripheral blood mononuclear cells (PBMCs)

value: anti-CD3/CD28 (CD328)


title: 24h, GDX + E2


title: 53

description: SAMPLE 113

value: Early Secretory Endometrial tissue

value: Uterine Pelvic Pathology


title: 930301344b_N

description: FFPE


title: 1h, GDX + E2


title: 52

description: SAMPLE 112


title: 930301342b_N

description: FFPE


title: GA DP 4682416019_C_1

description: GA DP


title: 48

description: SAMPLE 111

value: Proliferative Endometrial tissue


title: 930301336b_N

description: FFPE


title: 86

description: SAMPLE 122

value: Endometriosis

value: Minimal/Mild


title: 47

description: SAMPLE 110


title: GA DP 4682416019_B_2

description: GA DP

value: SJL X BALB/C


title: GA DP 4682416019_C_2

description: GA DP

value: spleen cell


title: 46

description: SAMPLE 109


title: Peripheral blood from child I010_NAA_LpA

description:
S1314_010_NAA_LpA
Gene expression data from peripheral blood of children (average age 8.4 years)

source_name: Peripheral blood_NAA_LpA

value: LpA

value: non-allergic asthmatic (NAA)


title: Peripheral blood from child I074_GK_M

description:
S1757_074_GK_M
Gene expression data from peripheral blood of children (average age 8.4 years)

value: M (no stimulation)

value: healthy control (GK)


title: GA DP 4682416019_B_1

description: GA DP


title: 24h, Control, GDX + vehicle 1


title: GA RS 4682416019_A_1

description: GA RS

value: GA RS


title: 930301316a_T

description: FFPE

source_name: Lung carcinoid

value: Tumor


title: 45

description: SAMPLE 108

value: Non-Endometriosis


title: Peripheral blood from child I002_NAA_328

description:
S1310_002_NAA_CD3_28
Gene expression data from peripheral blood of children (average age 8.4 years)

source_name: Peripheral blood_NAA_328

value: Peripheral blood


title: Peripheral blood from child I002_NAA_LpA

description:
S1311_002_NAA_LpA
Gene expression data from peripheral blood of children (average age 8.4 years)

value: Peripheral blood mononuclear cells (PBMCs)


title: 920203783b_N

description: FFPE

value: Normal


title: Medium 4634633043_F_2

description: Medium

source_name: Spleen Cell Cultures

value: Medium


title: 930301322b_T

description: FFPE


title: GA RS 4682416019_A_2

description: GA RS


title: 44

description: SAMPLE 107

value: Uterine Pelvic Pathology