title: 170a


title: 175a

status: Public on Jun 28 2013

type: RNA

city: Odense C

first: Martin

middle: Jakob

last: Larsen

address: Sdr. Boulevard 29

department: Dept. of Clinical Genetics

country: Denmark

institute: Odense University Hospital

hyb_protocol: Hybridization and washing were performed according to manufacture’s recommendations in a low ozone environment.

scan_protocol: Scanned using a Agilent G2565CA Microarray scanner

data_processing: Scanned images were quantified using Agilent Feature Extraction Software (version 10.7.3.1). Bad quality features flagged during feature extraction were removed and the remaining data were pre-processed. Data were background corrected (normexp, offset=50), then within-array normalized by loess normalization method and between-array normalizatized by the quantile method. The normalized values were used to calculate log2 transformed Cy5/Cy3 ratios. Replicate probes were collapsed by calculating the median. Probes without gene symbol annotation were filtered out. In cases of multiple probes per gene symbol only the probe with the maximum mean (Cy5) intensity was kept. Missing expression values were imputed by k-nearest neighbors averaging (k = 10).

molecule: total RNA

organism: Homo sapiens

source_name: Breast tumor tissue

label_protocol: RNA was amplified and labeled using the Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion) according to the manufacturer’s protocol.

extract_protocol: Total RNA was extracted from freshly frozen tumor tissue using Trizol Reagent (Invitrogen) and RNeasy Micro Kit (Qiagen).

value: Premenopausal

tag: age

tag: who

value: Invasive ductal carcinoma

tag: grade

tag: group

value: LumB

tag: er

tag: pr

value: BRCA2 c.6486_6489delACAA, Exon11, p.(Lys2162Asnfs*5)

source_name: Universal Human Reference RNA (Stratagene)

tag: reference


title: 167a

value: Sporadic

value: Universal Human Reference RNA (Stratagene)


title: 164a

value: LumA


title: 163a


title: 156a


title: 162a


title: 155a

value: Postmenopausal


title: 137a

value: Medullary carcinoma

value: Basal


title: 158a


title: 172a


title: 140a

value: BRCA2 c.5754delT, Exon11, p.(His1918Glnfs*45)


title: 149a


title: 160a


title: 159a

value: Normal

value: BRCA1 c.181T>G, Exon5, p.(Cys61Gly)


title: 136a


title: 153a

value: BRCA1 c.2475delC, Exon11, p.(Asp825Glufs*21)


title: 143a


title: 150a


title: 165a


title: 125a

value: Perimenopausal


title: 129a


title: 124a


title: 128a


title: 122a


title: 119a


title: 131a


title: 139a


title: 118a

value: Invasive lobular carcinoma

value: BRCA1 c.1505delT, Exon11, p.(Leu502*)


title: 117a

value: Premenopausal


title: 114a

value: Invasive ductal carcinoma


title: 109a

value: LumB

value: BRCA2 c.1310_1313delAAGA, Exon10, p.(Lys437Ilefs*22)


title: 096a

value: Sporadic


title: 111a

value: Universal Human Reference RNA (Stratagene)


title: 102a

value: LumA


title: 106a

value: Postmenopausal


title: 092a


title: 095a


title: 085a

value: Other


title: 090a

value: Basal


title: 083a

value: Mucinous carcinoma


title: 077a


title: 075a

value: BRCA1 c.5213G>A, Exon20, p.(Gly1738Glu)


title: 080a


title: 068a


title: 067a


title: 074a


title: 116a


title: 093a

value: BRCA2 c.7617+1G>A, Splice mut, Exon15 skipping


title: 079a

value: Normal

value: BRCA2 c.145G>T, Exon3, p.(Glu49*)


title: 072a


title: 071a


title: 099a


title: 065a


title: 063a

value: BRCA2 c.6486_6489delACAA, Exon11, p.(Lys2162Asnfs*5)


title: 060a


title: 069a

value: Invasive lobular carcinoma


title: 059a


title: 084a


title: 048a

value: Premenopausal

value: BRCA1 c.5089T>C, Exon18, p.(Cys1697Arg)


title: 061a

value: Perimenopausal

value: Invasive ductal carcinoma


title: 053a

value: Sporadic


title: 057a

value: Universal Human Reference RNA (Stratagene)


title: 058a

value: LumA


title: 062a

value: Postmenopausal

value: LumB


title: 050a


title: 052a

value: BRCA2 c.6373delA, Exon11, p.(Thr2125Profs*12)


title: 047a

value: BRCA2 c.2808_2811delACAA, Exon11, p.(Ala938Profs*21)


title: 042a


title: 037a


title: 043a


title: 044a

value: Basal


title: 032a

value: BRCA1 c.5266dupC, Exon20, p.(Gln1756Profs*74)


title: 055a


title: 039a


title: 041a


title: 036a


title: 038a

value: Tubular carcinoma


title: 031a


title: 035a


title: 033a


title: 029a


title: 045a


title: 046a

value: BRCA1 c.2476delA, Exon11, p.(Thr826Glnfs*20)


title: 030a


title: 027a


title: 028a


title: 018a

value: Medullary carcinoma

value: BRCA1 c.5213G>A, Exon20, p.(Gly1738Glu)


title: 012a

value: BRCA1 c.5143A>C, Exon18, p.(Ser1715Arg)


title: 011a


title: 025a

value: Premenopausal


title: 015a

value: Perimenopausal


title: 014a

value: Invasive ductal carcinoma

value: Normal


title: 005a

value: Sporadic

value: Universal Human Reference RNA (Stratagene)


title: 007a


title: DFAT, Biological Replicate3

status: Public on Jun 12 2013

city: Itabashi

first: Yuji

last: Iribe

state: Tokyo

address: 30-1 Ohyaguchikamicho

department: Department of Medical Science

country: Japan

institute: Nihon University School of Medicine

description: Gene expression data of human DFAT cells established using adipose tissue from the donor 3.

hyb_protocol: The resulting cDNAs were hybridized to GeneChip Human Gene 1.0 ST Array (Affymetrix) in accordance with the protocols provided by Affymetrix.

scan_protocol: Scanning was done on the GeneChip Scanner3000.

data_processing: Expression data (CEL files) were extracted, normalized, and summarized using the robust multi-average (RMA) method with Bioconductor software based on R language. Linear regression analysis on normalized data was performed by R.

label: biotin

label_protocol: Total RNA (100 ng for each sample) was processed using GeneChip WT cDNA Synthesis and Amplification Kit (Affymetrix, Santa Clara, CA) and cDNA was then fragmented and labeled with biotin using GeneChip Terminal Labeling Kit (Affymetrix).

growth_protocol: Human subcutaneous adipose tissue was digested with collagenase. Digested tissues were centrifuged and two cellular fractions, a supernatant of mature adipocytes and a pellet of stromal vascular cells, respectively, were used for the establishment of DFAT cells and ADSCs, as described previously (Fernyhough ME et al., Cytotechnology, 2004;46:163-172, Matsumoto T et al., J Cell Physiol, 2008;215:210-222).

extract_protocol: Total RNA was extracted using RNeasy mini kit with on-column RNase-free DNase I treatment (Qiagen, Valencia, CA).

treatment_protocol: Freshly isolated (P0) DFAT cells and ADSCs were cryopreserved until subcultivation. The DFAT cells and ADSCs at Passage 5 were used for RNA extraction.

tag: individual

value: donor 3

tag: cell type

value: DFAT cell


title: DFAT, Biological Replicate1

description: Gene expression data of human DFAT cells established using adipose tissue from the donor 1.

value: donor 1


title: DFAT, Biological Replicate2

description: Gene expression data of human DFAT cells established using adipose tissue from the donor 2.

value: donor 2


title: ADSC, Biological Replicate1

description: Gene expression data of human adipose-derived stem/stromal cells established using adipose tissue from the donor 1.

data_processing: Expression data (CEL files) were extracted, normalized, and summarized with the robust multi-average (RMA) method using Bioconductor software based on R language. Linear regression analysis on normalized data was performed by R.

value: ADSC


title: ADSC, Biological Replicate3

description: Gene expression data of human adipose-derived stem/stromal cells established using adipose tissue from the donor 3.


title: S4-Th2

status: Public on Jun 01 2013

city: Xuzhou

first: Hui

last: Wang

state: Jiangsu

address: 209 Tongshan Rd

country: China

institute: Xuzhou Medical University

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a total volume of 25ul following the manufacturers instructions. On completion of the fragmentation reaction, 25ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4851A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent). Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Th2 cells, replicate 4

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 45ng total RNA using a LowInput QuickAmp Labeling Kit (Agilent Technologies, Palo Alto, Calif, USA) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Human primary Th1, Th2, Th17 and Treg cells were purified by flow cytometry sorting. Total RNA was extracted from naïve CD4+ T cells (NT), CD4+ T central memory T cells (TCM), Th1, Th2, Th17 and Treg subsets using a miRneasy Mini Kit (Qiagen, Valencia, CA, USA).

tag: tissue

value: whole blood


title: S4-Treg

source_name: Treg cells, replicate 4

value: Treg


title: S4-Naive T

source_name: Naïve T cells, replicate 4

value: Naive T


title: S1-Th2

source_name: Th2 cells, replicate 1


title: S1-Th17

source_name: Th17 cells, replicate 1


title: S4-Memory T

source_name: CD4+ T central memory cells, replicate 4

value: CD4+ T central memory


title: S4-Th1

source_name: Th1 cells, replicate 4


title: S4-Th17

source_name: Th17 cells, replicate 4


title: S1-Treg

source_name: Treg cells, replicate 1


title: ADSC, Biological Replicate2

description: Gene expression data of human adipose-derived stem/stromal cells established using adipose tissue from the donor 2.


title: S3-Memory T

source_name: CD4+ T central memory cells, replicate 3


title: S1-Th1

source_name: Th1 cells, replicate 1


title: S3-Naive T

source_name: Naïve T cells, replicate 3


title: S2-Th17

source_name: Th17 cells, replicate 2


title: S3-Th2

source_name: Th2 cells, replicate 3


title: S2-Treg

source_name: Treg cells, replicate 2


title: 019a

source_name: Breast tumor tissue

value: Postmenopausal

value: LumB


title: 004a

source_name: Universal Human Reference RNA (Stratagene)


title: S2-Th1

source_name: Th1 cells, replicate 2


title: S2-Th2

source_name: Th2 cells, replicate 2


title: S1-Memory T

source_name: CD4+ T central memory cells, replicate 1


title: S1-Naive T

source_name: Naïve T cells, replicate 1


title: S2-Memory T

source_name: CD4+ T central memory cells, replicate 2


title: S3-Th17

source_name: Th17 cells, replicate 3


title: S3-Treg

source_name: Treg cells, replicate 3


title: S3-Th1

source_name: Th1 cells, replicate 3


title: DIO-SS_7

status: Public on May 17 2013

city: Corvallis

first: Susan

middle: C.

last: Tilton

state: OR

address: 1007 ALS Bldg

department: AG Envr & Molec Toxicology

country: USA

institute: Oregon State University

description:
Gene expression data from diet induced obese mice exposed to sidestream smoke (SS)
619

hyb_protocol: Biotin-labeled cRNA (15 µg) was fragmented to a size range between 50-200 bases for array hybridization.  After hybridization, the arrays were washed and stained with streptavidin-phycoerythrin.

scan_protocol: The arrays were scanned at a resolution of 2.5 microns using an Affymetrix GeneChip Scanner 3000.

data_processing: Raw intensity data were quantile normalized by Robust Multi-Array Analysis (RMA) summarization and probes were subject to quality control to measure the efficiency of transcription, integrity of hybridization, and consistency of qualitative calls.

organism: Mus musculus

source_name: Diet induced obese mice exposed to sidestream smoke (SS), biological rep7

label_protocol: Complementary DNA was synthesized from 3 µg of total RNA in the presence of an oligo-dT primer containing a T7 RNA polymerase promoter, and an in vitro transcription reaction was performed in the presence of a mixture of biotin-labeled ribonucleotides to produce biotinylated cRNA from the cDNA template, according to manufacturer’s protocols (Affymetrix One-Cycle Target Labeling Kit).

growth_protocol: Control, i.e., nonobese or regular weight (RW) and diet-induced obese (DIO) male C57BL/6 mice at 13 weeks of age were purchased from the Jackson Laboratories (Bar Harbor, ME).  For this study, RW mice are defined as those mice fed a regular diet consisting of pelleted PMI® 5002 Certified Rodent Diet (PMI 5002 Rodent Diet®, Richmond, IN; ~5kcal% fat) throughout the study.  DIO mice were fed a high calorie/high fat diet consisting of pelleted D12492 Rodent Diet (Research Diets Inc., New Brunswick, NJ; 60kal% fat) throughout the study starting at six weeks of age for a total of nine weeks prior to the start of the 4-day LPS exposure study.

extract_protocol: Total RNA was collected using the RNeasy Kit (Qiagen, Valencia, CA).

treatment_protocol: Groups (N=6-8 biological replicates) of RW and DIO C57BL/6 mice (15-weeks old at start of exposures) were exposed to either filtered air (sham controls, SC), mainstream (MS) or sidestream (SS) cigarette smoke by nose-only inhalation exposure for 5 hr/day for a total of eight exposures over two weeks as follows: 5 consecutive days of exposure, followed by 2 days with no exposure, then three days of exposure, with necropsies occurring the day following the last exposure.

tag: strain

value: heart

tag: body weight

value: obese

tag: treatment

value: Sidestream smoke (SS)


title: DIO-SS_8

description:
Gene expression data from diet induced obese mice exposed to sidestream smoke (SS)
620

source_name: Diet induced obese mice exposed to sidestream smoke (SS), biological rep8


title: S2-Naive T

source_name: Naïve T cells, replicate 2


title: DIO-SS_6

description:
Gene expression data from diet induced obese mice exposed to sidestream smoke (SS)
606

source_name: Diet induced obese mice exposed to sidestream smoke (SS), biological rep6


title: DIO-SS_3

description:
Gene expression data from diet induced obese mice exposed to sidestream smoke (SS)
603

source_name: Diet induced obese mice exposed to sidestream smoke (SS), biological rep3


title: DIO-SS_4

description:
Gene expression data from diet induced obese mice exposed to sidestream smoke (SS)
604

source_name: Diet induced obese mice exposed to sidestream smoke (SS), biological rep4


title: DIO-SS_2

description:
Gene expression data from diet induced obese mice exposed to sidestream smoke (SS)
602

source_name: Diet induced obese mice exposed to sidestream smoke (SS), biological rep2


title: DIO-SS_1

description:
Gene expression data from diet induced obese mice exposed to sidestream smoke (SS)
601

source_name: Diet induced obese mice exposed to sidestream smoke (SS), biological rep1


title: 087a

source_name: Breast tumor tissue

value: Premenopausal

value: Invasive lobular carcinoma

source_name: Universal Human Reference RNA (Stratagene)


title: DIO-SS_5

description:
Gene expression data from diet induced obese mice exposed to sidestream smoke (SS)
605

source_name: Diet induced obese mice exposed to sidestream smoke (SS), biological rep5


title: 023a

value: Invasive ductal carcinoma

value: Sporadic

value: Universal Human Reference RNA (Stratagene)


title: RW-SS_7

description:
Gene expression data from regular weight mice exposed to sidestream smoke (SS)
520

source_name: Regular weight mice exposed to sidestream smoke (SS), biological rep7

value: regular weight


title: RW-SS_6

description:
Gene expression data from regular weight mice exposed to sidestream smoke (SS)
519

source_name: Regular weight mice exposed to sidestream smoke (SS), biological rep6


title: 070a

value: BRCA2 c.6601delT, Exon11, p.(Ser2201Leufs*5)


title: RW-SS_3

description:
Gene expression data from regular weight mice exposed to sidestream smoke (SS)
503

source_name: Regular weight mice exposed to sidestream smoke (SS), biological rep3


title: DIO-MS_6

description:
Gene expression data from diet induced obese mice exposed to mainstream smoke (MS)
419

source_name: Diet induced obese mice exposed to mainstream smoke (MS), biological rep6

value: Mainstream smoke (MS)


title: DIO-MS_4

description:
Gene expression data from diet induced obese mice exposed to mainstream smoke (MS)
405

source_name: Diet induced obese mice exposed to mainstream smoke (MS), biological rep4


title: DIO-MS_5

description:
Gene expression data from diet induced obese mice exposed to mainstream smoke (MS)
406

source_name: Diet induced obese mice exposed to mainstream smoke (MS), biological rep5


title: DIO-MS_3

description:
Gene expression data from diet induced obese mice exposed to mainstream smoke (MS)
403

source_name: Diet induced obese mice exposed to mainstream smoke (MS), biological rep3


title: RW-SS_1

description:
Gene expression data from regular weight mice exposed to sidestream smoke (SS)
501

source_name: Regular weight mice exposed to sidestream smoke (SS), biological rep1


title: RW-MS_7

description:
Gene expression data from regular weight mice exposed to mainstream smoke (MS)
319

source_name: Regular weight mice exposed to mainstream smoke (MS), biological rep7


title: DIO-MS_1

description:
Gene expression data from diet induced obese mice exposed to mainstream smoke (MS)
401

source_name: Diet induced obese mice exposed to mainstream smoke (MS), biological rep1


title: RW-SS_4

description:
Gene expression data from regular weight mice exposed to sidestream smoke (SS)
505

source_name: Regular weight mice exposed to sidestream smoke (SS), biological rep4


title: RW-MS_8

description:
Gene expression data from regular weight mice exposed to mainstream smoke (MS)
320

source_name: Regular weight mice exposed to mainstream smoke (MS), biological rep8


title: RW-SS_5

description:
Gene expression data from regular weight mice exposed to sidestream smoke (SS)
506

source_name: Regular weight mice exposed to sidestream smoke (SS), biological rep5


title: RW-MS_2

description:
Gene expression data from regular weight mice exposed to mainstream smoke (MS)
302

source_name: Regular weight mice exposed to mainstream smoke (MS), biological rep2


title: RW-MS_1

description:
Gene expression data from regular weight mice exposed to mainstream smoke (MS)
301

source_name: Regular weight mice exposed to mainstream smoke (MS), biological rep1


title: RW-MS_5

description:
Gene expression data from regular weight mice exposed to mainstream smoke (MS)
305

source_name: Regular weight mice exposed to mainstream smoke (MS), biological rep5


title: DIO-SC_8

description:
Gene expression data from diet induced obese mice exposed to filtered air (sham control, SC)
220

source_name: Diet induced obese mice exposed to filtered air (sham control, SC), biological rep8

value: control


title: RW-MS_3

description:
Gene expression data from regular weight mice exposed to mainstream smoke (MS)
303

source_name: Regular weight mice exposed to mainstream smoke (MS), biological rep3


title: DIO-SC_7

description:
Gene expression data from diet induced obese mice exposed to filtered air (sham control, SC)
219

source_name: Diet induced obese mice exposed to filtered air (sham control, SC), biological rep7


title: DIO-SC_4

description:
Gene expression data from diet induced obese mice exposed to filtered air (sham control, SC)
204

source_name: Diet induced obese mice exposed to filtered air (sham control, SC), biological rep4


title: RW-SS_2

description:
Gene expression data from regular weight mice exposed to sidestream smoke (SS)
502

source_name: Regular weight mice exposed to sidestream smoke (SS), biological rep2


title: RW-MS_6

description:
Gene expression data from regular weight mice exposed to mainstream smoke (MS)
306

source_name: Regular weight mice exposed to mainstream smoke (MS), biological rep6


title: RW-SC_8

description:
Gene expression data from regular weight mice exposed to filtered air (sham control, SC)
120

source_name: Regular weight mice exposed to filtered air (sham control, SC), biological rep8


title: DIO-SC_3

description:
Gene expression data from diet induced obese mice exposed to filtered air (sham control, SC)
203

source_name: Diet induced obese mice exposed to filtered air (sham control, SC), biological rep3


title: DIO-SC_5

description:
Gene expression data from diet induced obese mice exposed to filtered air (sham control, SC)
205

source_name: Diet induced obese mice exposed to filtered air (sham control, SC), biological rep5


title: DIO-MS_2

description:
Gene expression data from diet induced obese mice exposed to mainstream smoke (MS)
402

source_name: Diet induced obese mice exposed to mainstream smoke (MS), biological rep2


title: RW-SC_7

description:
Gene expression data from regular weight mice exposed to filtered air (sham control, SC)
119

source_name: Regular weight mice exposed to filtered air (sham control, SC), biological rep7


title: RW-SC_6

description:
Gene expression data from regular weight mice exposed to filtered air (sham control, SC)
106

source_name: Regular weight mice exposed to filtered air (sham control, SC), biological rep6


title: DIO-SC_6

description:
Gene expression data from diet induced obese mice exposed to filtered air (sham control, SC)
206

source_name: Diet induced obese mice exposed to filtered air (sham control, SC), biological rep6


title: RW-MS_4

description:
Gene expression data from regular weight mice exposed to mainstream smoke (MS)
304

source_name: Regular weight mice exposed to mainstream smoke (MS), biological rep4


title: RW-SC_2

description:
Gene expression data from regular weight mice exposed to filtered air (sham control, SC)
102

source_name: Regular weight mice exposed to filtered air (sham control, SC), biological rep2


title: RW-SC_5

description:
Gene expression data from regular weight mice exposed to filtered air (sham control, SC)
105

source_name: Regular weight mice exposed to filtered air (sham control, SC), biological rep5


title: DIO-SC_1

description:
Gene expression data from diet induced obese mice exposed to filtered air (sham control, SC)
201

source_name: Diet induced obese mice exposed to filtered air (sham control, SC), biological rep1


title: RW-SC_4

description:
Gene expression data from regular weight mice exposed to filtered air (sham control, SC)
104

source_name: Regular weight mice exposed to filtered air (sham control, SC), biological rep4


title: RW-SC_1

description:
Gene expression data from regular weight mice exposed to filtered air (sham control, SC)
101

source_name: Regular weight mice exposed to filtered air (sham control, SC), biological rep1


title: Patient 6, before second IFN-beta injection

status: Public on Apr 24 2013

city: Rostock

first: Michael

last: Hecker

address: Gehlsheimer Str. 20

department: Department of Neurology

country: Germany

institute: University of Rostock

description: Gene expression data from a multiple sclerosis patient treated with IFN-beta

hyb_protocol: Following fragmentation, 15 µg of cRNA were hybridized for 16 h at 45°C on Affymetrix HG-U133 Plus 2.0 arrays. The microarrays were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The raw probe-level signals were converted to expression values using the MAS5.0 algorithm and custom GeneAnnot-based chip definition files (version 2.2.0, available at http://www.xlab.unimo.it/GA_CDF). Data normalization was performed by a loess fit to the data with span=0.05 (using R package affy). Each chip yielded mRNA levels of 19,204 human genes.

label: Biotin

source_name: Peripheral blood mononuclear cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix 3' IVT protocol from 200 ng total RNA (Expression Analysis Technical Manual, Affymetrix).

growth_protocol: Patient blood samples were taken immediately before first IFN-beta injection as well as two days, four days and one month post therapy initiation.

extract_protocol: Peripheral blood mononuclear cells were separated using isopycnic centrifugation (Ficoll), and total RNA enriched with small RNAs was isolated using the mirVana miRNA isolation kit (Invitrogen) according to the manufacturers' protocols.

treatment_protocol: Patients were treated with subcutaneous IFN-beta-1b (Betaferon, Bayer HealthCare) at standard doses.

tag: diagnosis

value: relapsing-remitting multiple sclerosis

tag: gender

value: female

tag: age at ifn-beta therapy onset (baseline blood sampling)

tag: duration from diagnosis to therapy initiation (in months)

tag: edss at baseline

tag: edss after 1 year

tag: edss after 2 years

tag: number of relapses during the year prior to treatment

tag: number of relapses during 1-year follow-up

tag: number of relapses during 2-year follow-up

tag: completed months of ifn-beta therapy


title: Patient 4, 1 month after start of IFN-beta therapy

tag: completed years of ifn-beta therapy


title: Patient 4, before second IFN-beta injection


title: Patient 6, 1 month after start of IFN-beta therapy


title: Patient 6, before first IFN-beta injection


title: Patient 5, before first IFN-beta injection

value: clinically isolated syndrome


title: Patient 6, 1 month after start of IFN-beta therapy [TaqMan(r) Array Human MicroRNA B Cards v2.0]

description:
MS6_month_1
microRNA expression data from a multiple sclerosis patient treated with IFN-beta

data_processing:
Raw threshold cycle (Ct) values were computed using the SDS 2.3 and RQ Manager 1.2 software (Applied Biosystems), and undetermined data were set to Ct=45. To normalize the data, we first set the detection limit at Ct=38, and then converted the data to the linear scale using the equation 2^(-Ct)*10^9. Systematic differences in the time-course data of each patient were corrected by loess normalization using the R package affy. Finally, to reduce differences between the patients, we scaled the data so that the 95% quantile is the same for each patient.
Matrix non-normalized worksheet reports the raw Ct values. Matrix normalized worksheet reports the normalized expression data. Fold Change worksheet reports the log2 ratios of the microRNA expression levels during therapy compared to the pre-treatment levels (baseline).

label: FAM dye

label_protocol: Total RNA (120 ng) was reverse transcribed to cDNA using Megaplex RT Primers in combination with Megaplex PreAmp Primers for preamplification (Life Technologies). The real-time PCRs were performed with predesigned primers and TaqMan probes in 384-well plates with 45 cycles according to the manufacturer's instructions in a 7900HT Sequence Detection System (Applied Biosystems).


title: Patient 4, before first IFN-beta injection


title: Patient 5, 1 month after start of IFN-beta therapy


title: Patient 5, before third IFN-beta injection


title: Patient 6, before third IFN-beta injection


title: Patient 5, before second IFN-beta injection


title: Patient 1, 1 month after start of IFN-beta therapy


title: Patient 4, before third IFN-beta injection


title: Patient 3, before first IFN-beta injection


title: Patient 2, 1 month after start of IFN-beta therapy


title: Patient 2, before third IFN-beta injection


title: Patient 3, before third IFN-beta injection


title: Patient 2, before second IFN-beta injection


title: Patient 3, before second IFN-beta injection


title: Patient 2, before first IFN-beta injection


title: Patient 6, before third IFN-beta injection [TaqMan(r) Array Human MicroRNA B Cards v2.0]

description:
MS6_day_4
microRNA expression data from a multiple sclerosis patient treated with IFN-beta


title: Patient 3, 1 month after start of IFN-beta therapy


title: Patient 1, before second IFN-beta injection


title: Patient 6, before second IFN-beta injection [TaqMan(r) Array Human MicroRNA B Cards v2.0]

description:
MS6_day_2
microRNA expression data from a multiple sclerosis patient treated with IFN-beta


title: Patient 1, before third IFN-beta injection


title: Patient 6, before first IFN-beta injection [TaqMan(r) Array Human MicroRNA B Cards v2.0]

description:
MS6_baseline
microRNA expression data from a multiple sclerosis patient treated with IFN-beta


title: Patient 5, 1 month after start of IFN-beta therapy [TaqMan(r) Array Human MicroRNA B Cards v2.0]

description:
MS5_month_1
microRNA expression data from a multiple sclerosis patient treated with IFN-beta


title: Patient 6, before second IFN-beta injection [TaqMan(r) Array Human MicroRNA A Cards v2.0]


title: Patient 6, before third IFN-beta injection [TaqMan(r) Array Human MicroRNA A Cards v2.0]


title: Patient 6, before first IFN-beta injection [TaqMan(r) Array Human MicroRNA A Cards v2.0]


title: Patient 5, before third IFN-beta injection [TaqMan(r) Array Human MicroRNA B Cards v2.0]

description:
MS5_day_4
microRNA expression data from a multiple sclerosis patient treated with IFN-beta


title: Patient 5, 1 month after start of IFN-beta therapy [TaqMan(r) Array Human MicroRNA A Cards v2.0]


title: Patient 5, before second IFN-beta injection [TaqMan(r) Array Human MicroRNA A Cards v2.0]

description:
MS5_day_2
microRNA expression data from a multiple sclerosis patient treated with IFN-beta


title: Patient 5, before first IFN-beta injection [TaqMan(r) Array Human MicroRNA B Cards v2.0]

description:
MS5_baseline
microRNA expression data from a multiple sclerosis patient treated with IFN-beta


title: Patient 5, before first IFN-beta injection [TaqMan(r) Array Human MicroRNA A Cards v2.0]


title: Patient 4, before second IFN-beta injection [TaqMan(r) Array Human MicroRNA B Cards v2.0]

description:
MS4_day_2
microRNA expression data from a multiple sclerosis patient treated with IFN-beta


title: Patient 5, before third IFN-beta injection [TaqMan(r) Array Human MicroRNA A Cards v2.0]


title: Patient 5, before second IFN-beta injection [TaqMan(r) Array Human MicroRNA B Cards v2.0]


title: Patient 4, 1 month after start of IFN-beta therapy [TaqMan(r) Array Human MicroRNA B Cards v2.0]

description:
MS4_month_1
microRNA expression data from a multiple sclerosis patient treated with IFN-beta


title: Patient 4, 1 month after start of IFN-beta therapy [TaqMan(r) Array Human MicroRNA A Cards v2.0]


title: Patient 3, before third IFN-beta injection [TaqMan(r) Array Human MicroRNA B Cards v2.0]

description:
MS3_day_4
microRNA expression data from a multiple sclerosis patient treated with IFN-beta


title: Patient 3, 1 month after start of IFN-beta therapy [TaqMan(r) Array Human MicroRNA B Cards v2.0]

description:
MS3_month_1
microRNA expression data from a multiple sclerosis patient treated with IFN-beta


title: Patient 4, before first IFN-beta injection [TaqMan(r) Array Human MicroRNA B Cards v2.0]

description:
MS4_baseline
microRNA expression data from a multiple sclerosis patient treated with IFN-beta


title: Patient 4, before third IFN-beta injection [TaqMan(r) Array Human MicroRNA B Cards v2.0]

description:
MS4_day_4
microRNA expression data from a multiple sclerosis patient treated with IFN-beta


title: Patient 4, before third IFN-beta injection [TaqMan(r) Array Human MicroRNA A Cards v2.0]


title: Patient 6, 1 month after start of IFN-beta therapy [TaqMan(r) Array Human MicroRNA A Cards v2.0]


title: Patient 4, before second IFN-beta injection [TaqMan(r) Array Human MicroRNA A Cards v2.0]


title: Patient 3, before second IFN-beta injection [TaqMan(r) Array Human MicroRNA B Cards v2.0]

description:
MS3_day_2
microRNA expression data from a multiple sclerosis patient treated with IFN-beta


title: Patient 1, before first IFN-beta injection


title: Patient 3, 1 month after start of IFN-beta therapy [TaqMan(r) Array Human MicroRNA A Cards v2.0]


title: Patient 3, before first IFN-beta injection [TaqMan(r) Array Human MicroRNA B Cards v2.0]

description:
MS3_baseline
microRNA expression data from a multiple sclerosis patient treated with IFN-beta


title: Patient 3, before third IFN-beta injection [TaqMan(r) Array Human MicroRNA A Cards v2.0]


title: Patient 2, 1 month after start of IFN-beta therapy [TaqMan(r) Array Human MicroRNA B Cards v2.0]

description:
MS2_month_1
microRNA expression data from a multiple sclerosis patient treated with IFN-beta


title: Patient 2, before third IFN-beta injection [TaqMan(r) Array Human MicroRNA B Cards v2.0]

description:
MS2_day_4
microRNA expression data from a multiple sclerosis patient treated with IFN-beta


title: Patient 3, before second IFN-beta injection [TaqMan(r) Array Human MicroRNA A Cards v2.0]


title: Patient 4, before first IFN-beta injection [TaqMan(r) Array Human MicroRNA A Cards v2.0]


title: Patient 2, 1 month after start of IFN-beta therapy [TaqMan(r) Array Human MicroRNA A Cards v2.0]


title: Patient 2, before second IFN-beta injection [TaqMan(r) Array Human MicroRNA B Cards v2.0]

description:
MS2_day_2
microRNA expression data from a multiple sclerosis patient treated with IFN-beta


title: Patient 2, before first IFN-beta injection [TaqMan(r) Array Human MicroRNA B Cards v2.0]

description:
MS2_baseline
microRNA expression data from a multiple sclerosis patient treated with IFN-beta


title: Patient 2, before second IFN-beta injection [TaqMan(r) Array Human MicroRNA A Cards v2.0]


title: Patient 1, 1 month after start of IFN-beta therapy [TaqMan(r) Array Human MicroRNA B Cards v2.0]

description:
MS1_month_1
microRNA expression data from a multiple sclerosis patient treated with IFN-beta


title: Patient 2, before third IFN-beta injection [TaqMan(r) Array Human MicroRNA A Cards v2.0]


title: Patient 1, before third IFN-beta injection [TaqMan(r) Array Human MicroRNA B Cards v2.0]

description:
MS1_day_4
microRNA expression data from a multiple sclerosis patient treated with IFN-beta


title: Patient 2, before first IFN-beta injection [TaqMan(r) Array Human MicroRNA A Cards v2.0]


title: Patient 1, before third IFN-beta injection [TaqMan(r) Array Human MicroRNA A Cards v2.0]


title: Patient 1, before second IFN-beta injection [TaqMan(r) Array Human MicroRNA A Cards v2.0]

description:
MS1_day_2
microRNA expression data from a multiple sclerosis patient treated with IFN-beta


title: Patient 1, before first IFN-beta injection [TaqMan(r) Array Human MicroRNA B Cards v2.0]

description:
MS1_baseline
microRNA expression data from a multiple sclerosis patient treated with IFN-beta


title: Patient 1, before first IFN-beta injection [TaqMan(r) Array Human MicroRNA A Cards v2.0]


title: Patient 1, 1 month after start of IFN-beta therapy [TaqMan(r) Array Human MicroRNA A Cards v2.0]


title: Patient 1, before second IFN-beta injection [TaqMan(r) Array Human MicroRNA B Cards v2.0]


title: Patient 3, before first IFN-beta injection [TaqMan(r) Array Human MicroRNA A Cards v2.0]


title: Midtrimester_AF_sample_4_male_17_weeks

status: Public on Apr 23 2013

city: Medford

first: Heather

middle: C

last: Wick

state: MA

address: 161 College Ave

department: Department of Computer Science

institute: Tufts University

description: gene expression data from normal second trimester fetus

hyb_protocol: Arrays were washed and stained with streptavidin-phycoerythrin.

scan_protocol: Arrays were scanned on a GeneArray Scanner, using the GeneChip Microarray Suite 5.0 (Affymetrix, Santa Clara, CA).

data_processing: Normalization was performed with the threestep command from the AffyPLM package in BioConductor, using ideal-mismatch background/signal adjustment, quantile normalization, and the Tukey biweight summary method.  To obtain detection calls consistent with those produced by Affymetrix' 5.0 software, we used the mas5calls function from the Bioconductor affy package.

source_name: cell free mRNA from second trimester amniotic fluid

label_protocol: Samples were labeled using the Encore Biotin Module (NuGEN, San Carlos, CA)

extract_protocol: RNA was extracted from 5-10 mL AF.All samples were processed using the Qiagen Circulating Nucleic Acid kit with an on-column DNase digestion step to remove genomic DNA. The RNA was then purified and concentrated with the RNeasy MinElute Clean up kit and eluted in RNasefree water. RNA was converted to cDNA and amplified using the Ovation Pico WTA kit V2 and then purified with the QIAquick PCR Purification kit.

value: male

tag: Stage

value: second trimester


title: wt_on_rep1

status: Public on Apr 20 2013

city: Cambridge

first: Timothy

last: Newton

address: Addenbrooke's Hospital

country: United Kingdom

institute: University of Cambridge

description:
wt_on_15_11
Identified as an outlier and removed from further analysis

hyb_protocol: Hybridization was carried out following the beadchip manufacturer's instructions (Illumina)

scan_protocol: Illumina iScan  with iScan Control Software 1.3.10+

data_processing:
Raw data were pre-processed using R software (http://www.r-project.org) and the bioconductor (http://www.bioconductor.org) package lumi (Du et al., 2008).  Probes were removed from the data set where the Illimuna detection p-value was greater than 0.01.  The data were then transformed using the variance stabilisation transformation algorithm (VST) and normalised using the quantile normalisation method.  Differentially expressed genes for each condition (wild-type neuroserpin ‘on’ versus wild-type neuroserpin ‘off’, G392E neuroserpin ‘on’ versus G392E neuroserpin ‘off and Δ neuroserpin ‘on’ versus Δ neuroserpin ‘off’’) were identified by fitting linear models with the bioconductor R package limma (Smyth, 2004).  To account for multiple hypotheses testing, p-values were adjusted using the Benjamini & Hochberg False Discovery Rate (FDR) correction (Benjamini and Hochberg, 1995).  In order to assess the gene expression profiles at a pathway level, Gene Set Enrichment analysis (Subramanian et al., 2005) was performed on the normalised gene expression values for each group. Gene Set Enrichment analysis uses a priori defined gene sets to determine pathway differences between two phenotypic states.  Gene expression data is therefore evaluated at the pathway level rather than the single gene. Gene Set Enrichment analysis first ranks the genes according to their relative difference in gene expression.  The ranked list is then compared to gene sets (pathways) and an enrichment score (ES) is calculated for each gene.  When a gene is present in the gene set of interest, the running enrichment score is increased.  If the gene is absent the running enrichment score is decreased.  The enrichment statistic is the maximum deviation of the running enrichment score from zero.  Statistical significance is assessed by performing a permutation test procedure.  To account for the differences in gene set size, a normalised enrichment score (NES) is calculated.  Estimated significance levels are also adjusted for multiple hypothesis testing.  False Discovery Rate (FDR) is the estimated probability that a gene set with a given enrichment statistic represents a false-positive finding.  A total of 639 pathways (gene sets) were analysed from Kyoto Encyclopedia of Genes and Genomes, Reactome, and BioCarta databases (http://www.genome.jp/kegg/pathway.html, http://www.reactome.org/ and http://www.biocarta.com/genes/index.asp respectively). Gene sets containing less than 15 and greater than 500 genes were filtered out, along with gene sets containing no genes from the input data set.
Identified as an outlier and removed from further analysis

source_name: wt, 2 ug/ml doxycycline

label_protocol: Sample was labelled with biotin as part of the Ambion Total Prep kit (Ambion, UK) protocol.

growth_protocol: 250,000 Cells per well were grown in six well plates for 72 hours.  The cells were cultured in DMEM supplemented with 10% v/v Tet-free approved FBS (Clontech), 200 µg/ml Geneticin and 100 µg/ml Hygromycin B (both selective antibiotics from Invitrogen, Paisley, UK), at 37°C and 5% v/v CO2 in a humidified incubator.

extract_protocol: Cells were collected by trypsinisation and pelleted at 700 g for 10 min at 4⁰C.  RNA was isolated with Tri Reagent (Sigma).  RNA amplification was performed using Ambion Total Prep kit (Ambion, UK)

treatment_protocol: Neuroserpin expression was induced in 'on' samples with 2 ug/ml doxycycline 48 hours before collection.  'off' samples remained untreated.

tag: cell type

value: HeLa

tag: genotype/variation

value: Transfected with wild type Neuroserpin


title: wt_off_rep1

description:
wt_off_15_11
Identified as an outlier and removed from further analysis

source_name: wt, no doxycycline


title: Midtrimester_AF_sample_6_male_19_weeks


title: Midtrimester_AF_sample_5_male_17_weeks


title: wt_on_rep3

data_processing: Raw data were pre-processed using R software (http://www.r-project.org) and the bioconductor (http://www.bioconductor.org) package lumi (Du et al., 2008).  Probes were removed from the data set where the Illimuna detection p-value was greater than 0.01.  The data were then transformed using the variance stabilisation transformation algorithm (VST) and normalised using the quantile normalisation method.  Differentially expressed genes for each condition (wild-type neuroserpin ‘on’ versus wild-type neuroserpin ‘off’, G392E neuroserpin ‘on’ versus G392E neuroserpin ‘off and Δ neuroserpin ‘on’ versus Δ neuroserpin ‘off’’) were identified by fitting linear models with the bioconductor R package limma (Smyth, 2004).  To account for multiple hypotheses testing, p-values were adjusted using the Benjamini & Hochberg False Discovery Rate (FDR) correction (Benjamini and Hochberg, 1995).  In order to assess the gene expression profiles at a pathway level, Gene Set Enrichment analysis (Subramanian et al., 2005) was performed on the normalised gene expression values for each group. Gene Set Enrichment analysis uses a priori defined gene sets to determine pathway differences between two phenotypic states.  Gene expression data is therefore evaluated at the pathway level rather than the single gene. Gene Set Enrichment analysis first ranks the genes according to their relative difference in gene expression.  The ranked list is then compared to gene sets (pathways) and an enrichment score (ES) is calculated for each gene.  When a gene is present in the gene set of interest, the running enrichment score is increased.  If the gene is absent the running enrichment score is decreased.  The enrichment statistic is the maximum deviation of the running enrichment score from zero.  Statistical significance is assessed by performing a permutation test procedure.  To account for the differences in gene set size, a normalised enrichment score (NES) is calculated.  Estimated significance levels are also adjusted for multiple hypothesis testing.  False Discovery Rate (FDR) is the estimated probability that a gene set with a given enrichment statistic represents a false-positive finding.  A total of 639 pathways (gene sets) were analysed from Kyoto Encyclopedia of Genes and Genomes, Reactome, and BioCarta databases (http://www.genome.jp/kegg/pathway.html, http://www.reactome.org/ and http://www.biocarta.com/genes/index.asp respectively). Gene sets containing less than 15 and greater than 500 genes were filtered out, along with gene sets containing no genes from the input data set.


title: wt_on_rep2


title: 12hour_plusAkti_ rep1

status: Public on Mar 16 2013

city: Pittsburgh

first: Jing

last: Cheng

address: 3550 Terrace street

institute: University of Pittsburgh

description:
MouseRefSeq8
5773678020_E

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using cubic spline method

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

growth_protocol: The D10 Th2 T cell line was maintained in RPMI 1640, Supplemented with 10% heat-inactivated bovine growth serum (BGS; Hyclone), 2mM L-glutamine, 0.1mM nonessential amino acids, 50uM 2-ME, 100U/ml penicillin, 100ug/ml streptomycin and 25 IU/ml rhIL-2.

extract_protocol: RNA extraction was performed using a commercially available kit (RNeasy, Qiagen, Frederick,MD) according to the manufactures’ recommendations. RNA quality was confirmed based on a RNA integrity number >8 by use of an electrophoresis bioanalyzer (2100 Agilent Bioanalyser).

treatment_protocol: D10 T cells were left untreated or pretreated with 10uM Akti1/2 for 1h then stimulated with biotinylated anti-mCD3/CD28 and streptavidin for 0, 2, 6 and 12hs

value: Mouse Th2 cell line


title: Midtrimester_AF_sample_2_female_19_weeks


title: 6hour_plusAkti_ rep1

description:
MouseRefSeq8
5773678020_C


title: 12hour_plusAkti_ rep2

description:
MouseRefSeq8
5773678047_D


title: 6hour_plusAkti_ rep2

description:
MouseRefSeq8
5773678047_A


title: 12hour_minusAkti_ rep1

description:
MouseRefSeq8
5773678047_F


title: wt_off_rep3


title: 12hour_minusAkti_ rep2

description:
MouseRefSeq8
5773678020_G


title: 6hour_minusAkti_ rep2

description:
MouseRefSeq8
5773678047_E


title: wt_off_rep2


title: Midtrimester_AF_sample_3_female_18_weeks


title: 0hour_minusAkti_ rep1

description:
MouseRefSeq8
5773678020_D


title: 2hour_minusAkti_ rep2

description:
MouseRefSeq8
5773678047_H


title: 2hour_plusAkti_ rep2

description:
MouseRefSeq8
5773678047_B


title: 0hour_plusAkti_ rep2

description:
MouseRefSeq8
5773678047_C


title: 2hour_minusAkti_ rep1

description:
MouseRefSeq8
5773678020_B


title: 0hour_minusAkti_ rep2

description:
MouseRefSeq8
5773678047_G


title: 0hour_plusAkti_ rep1

description:
MouseRefSeq8
5773678020_A


title: 2hour_plusAkti_ rep1

description:
MouseRefSeq8
5773678020_F


title: 6hour_minusAkti_ rep1

description:
MouseRefSeq8
5773678020_H


title: DIO-SC_2

description:
Gene expression data from diet induced obese mice exposed to filtered air (sham control, SC)
202

source_name: Diet induced obese mice exposed to filtered air (sham control, SC), biological rep2

tag: strain

tag: tissue

value: heart

tag: body weight

value: obese


title: RW-SC_3

description:
Gene expression data from regular weight mice exposed to filtered air (sham control, SC)
103

source_name: Regular weight mice exposed to filtered air (sham control, SC), biological rep3

tag: treatment


title: bulk 454

status: Public on Feb 22 2013

type: genomic

city: Baltimore

first: Jerry

last: Guintivano

state: MD

address: 720 Rutland Avenue, Ross 1068

institute: Johns Hopkins University

description: 70_bulk 454-Batch1(P1F10)_7786915110_R06C02

hyb_protocol: Bisulfite-converted DNA was fragmented and hybridized to Illumina Infinium Human Methylation450 Beadchip Kit according to manfacturer's manual

scan_protocol: Polymer-coated chips were image-processed in Illumina's iScan scanner

data_processing: Data were extracted using Methylation Module of GenomeStudio v1.0 Software

label: Cy3, Cy5

molecule: genomic DNA

source_name: post mortem frontal cortex

label_protocol: Standard Illumina protocol

extract_protocol: All genomic DNA from nuclei was isolated with the MasterPure DNA Purification Kit (Epicentre Biotechnologies) according to manufacturer's instructions.

tag: suicide status (1 = suicide, 0 = no)

tag: diagnosis

value: Depression

tag: Sex

value: Male

tag: race

value: Caucasian

tag: age

tag: pmi


title: bulk 1363

description: 143_bulk 1363(P2F11)_7786915110_R05C02

value: Control

value: Female


title: bulk 1112

description: 139_bulk 1112(P2F7)_7786915110_R01C02


title: bulk 5444

description: 146_bulk 5444(P2G2)_7786915012_R02C01


title: bulk 5175

description: 147_bulk 5175(P2G3)_7786915012_R03C01


title: bulk 1103

description: 149_bulk 1103(P2G5)_7786915012_R05C01


title: bulk 4636

description: 137_bulk 4636(P2F5)_7786915110_R05C01


title: Mix8

value: mix


title: bulk 1551

description: 135_bulk 1551(P2F3)_7786915110_R03C01


title: bulk 1115

description: 138_bulk 1115(P2F6)_7786915110_R06C01


title: bulk 5234

description: 145_bulk 5234(P2G1)_7786915012_R01C01


title: Mix4


title: bulk 1228

description: 148_bulk 1228(P2G4)_7786915012_R04C01


title: Mix2


title: Mix6


title: Mix5


title: bulk 1944

description: 142_bulk 1944(P2F10)_7786915110_R04C02


title: Mix7


title: Mix9


title: Mix1


title: bulk 4643

description: 134_bulk 4643(P2F2)_7786915110_R02C01


title: bulk 1230

description: 133_bulk 1230(P2F1)_7786915110_R01C01


title: bulk 720

description: 136_bulk 720(P2F4)_7786915110_R04C01


title: 5444-N


title: bulk 1269

description: 141_bulk 1269(P2F9)_7786915110_R03C02


title: bulk 1613

description: 140_bulk 1613(P2F8)_7786915110_R02C02


title: Mix3


title: 1611-G


title: 1429-G


title: 1611-N


title: 5234-N


title: 5444-G


title: 5179-G


title: 5234-G


title: 454-G


title: 1473-N


title: 1230-N


title: 1054-N


title: 5179-N


title: bulk 5239

description: 150_bulk 5239(P2G6)_7786915012_R06C01


title: 5447-N


title: 1054-G


title: 5447-G


title: 240-G


title: 1112-G


title: 240-N


title: 5122-N


title: 1473-G


title: 1277-N


title: 5122-G


title: 1944-G


title: 1112-N


title: 1849-G


title: 454-N


title: 4637-G


title: 1849-N


title: 1269-N


title: 5078-G


title: 1944-N


title: 1429-N


title: 1269-G


title: 1613-G


title: 4903-N


title: 1277-G


title: 1363-G


title: 1363-N


title: 1613-N


title: 4782-G


title: 4903-G


title: 4782-N


title: 4637-N


title: 1230-G


title: 720-N


title: 720-G


title: 1497-G


title: 4919-G

value: African


title: 5078-N


title: 1271-G


title: 1579-G


title: 1298-G


title: 5376-N


title: 5086-N


title: 1454-N


title: 1739-N


title: 5376-G


title: 5124-G


title: 1271-N


title: bulk 5447

description: 69_bulk 5447-Batch1(P1F9)_7786915085_R03C02


title: 1454-G


title: 1497-N


title: 1298-N


title: 4919-N


title: 5124-N


title: 5239-N


title: 1489-G

value: Asian


title: 1579-N


title: 1103-G


title: 5086-G


title: 242-N


title: bulk 4782

description: 144_bulk 4782(P2F12)_7786915085_R04C02


title: 242-G


title: 590-N


title: 1489-N


title: 590-G


title: 1103-N


title: 5239-G


title: 4636-G


title: 1226-N


title: 1710-G


title: 1710-N


title: 5272-N


title: 5245-N


title: 1868-G


title: 165-G


title: 1551-G


title: 1115-G


title: 1226-G


title: 1115-N


title: 341-N


title: 341-G


title: 452-N


title: 1551-N


title: 5272-G


title: G9af/f BAT Cre-2

status: Public on Feb 01 2013

city: Bethesda

first: Kai

last: Ge

address: 50 South Dr Rm 4154

department: NIDDK

institute: NIH

hyb_protocol: standard Affymetrix hyb protocol

scan_protocol: standard Affymetrix scan protocol

data_processing: The data were normalized by Affymetrix Microarray Suite version 5.0 with default setting and global scaling, and no additional normalization is applied

source_name: G9af/f BAT Cre

label_protocol: standard Affymetrix label protocol

growth_protocol: Immortalized brown preadipocytes and all other cells were routinely cultured in DMEM plus 10% FBS.

extract_protocol: RNA was isolated by  trizol followed by purification

value: mixed C57/BL6-129

value: Immortalized brown preadipocytes

value: G9a knock out


title: 4643-N


title: G9af/f BAT Cre-1


title: 1228-N


title: 5245-G


title: 529-G


title: 813-G


title: 452-G


title: 529-N


title: 1739-G


title: 1868-N


title: 165-N


title: C. elegans btr-1 mutant versus wild type N2, on Bacillus thuringiensis DB27; Biological Replicate 3. Also Dye-swap 1.

status: Public on Jan 31 2013

city: Ipswich

first: Amit

last: Sinha

address: 240 County Road

institute: New England Biolabs

description: Biological replicate 3 of 3.

hyb_protocol: The labelled and fragmented cRNAs were hybridized to Agilent C. elegans oligonucleotide microarrays as per manufacturer's instructions.

scan_protocol: Scanned on a GenePix 4000B Microarray Scanner Images were quantified using GenePix Pro software  (version 6).

data_processing: The data was analyzed using the Bioconductor (Gentleman et al., 2004) package limma (Smyth, 397). Briefly, the array quality was assessed by checking for uniform background and foreground intensities over the entire array. The signal was background corrected using the "normexp" method (Ritchie et al., 2007). The arrays were lowess normalized individually ("normalizeWithinArrays" option), with differential weights assigned to probes and to positive control spike-ins which are expected to show no fold change (Smyth and Speed, 2003). This differential weighing of probes is particularly necessary to account for changes in the relative proportion of mRNA vs. total RNA. Without this differential weighing scheme, the fold change calculations can be erroneous (van de Peppel et al., 2003). The weight parameters were optimized based on MA-plots such that spike-in controls show their expected fold change values. lmFit function was used to fit a linear model to probe intensities across arrays, and differential expression was calculated by empirical Bayes method using the eBayes function (Smyth, 2004). Control of FDR was used employed as the multiple testing correction.

organism: Caenorhabditis elegans

source_name: C. elegans N2 strain young adults, exposed to Bacillus thuringiensis DB27

label_protocol: Equal amounts of total RNA (500ng to 1000ng) for 4 biological replicates from each stage was used to prepare Cy5- or Cy3- labelled cRNA using Quick Amp Labelling Kit (Agilent Technologies, Inc, Santa Clara, CA, USA), as per manufacturer's instructions. Based on the starting amounts of total RNA, appropriate dilutions of positive controls (Spike Mix-A and Spike-Mix B from Agilent) had been added to the reaction-mix before the RT reaction, as per manufacturer instructions.

growth_protocol: Synchronized populations of C. elegans (N2 strain) were obtained by hypochlorite treatment and allowed to grow to young adult stage on E. coli OP50 and were then exposed to Bacillus thuringiensis DB27 for 4 hours. For each biological replicate, about 200 young adult hermaphrodites were picked into 1mL of TRIzol (Invitrogen), and stored at -80C till RNA extraction.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions, and was purified further by Phenol:Chloroform:Isoamyl Alcohol precipitation.

tag: developmental stage

value: young adults

value: N2 Bristol

tag: bacteria

value: Bacillus thuringiensis DB27 for 4 hours

source_name: C. elegans nasp-1 / btr-1 young adults, exposed to Bacillus thuringiensis DB27

value: nasp-1 / btr-1 mutant


title: G9af/f BAT Vec-2

source_name: G9af/f BAT Vec

value: wild type


title: 4636-N


title: Neurons treated with supernatant prepared from U-9367-infected with JR-FL strain of HIV-1 (1) [miRNA]

status: Public on Dec 07 2012

city: Philadelphia

first: Bassel

middle: E

last: Sawaya

state: PA

address: 3307 N. Broad Street

department: Neurology

institute: Temple University

description: SAMPLE 7

hyb_protocol: RNA was labeled using the miRCURY LNATM miRNA, Hy5 Power Labeling Kit (Exiqon) as per manufacturer’s recommendations using Maui SC Hybridization Chambers (BioMicro Systems, Salt Lake City, UT).

scan_protocol: Array chips were scanned using Axon GenePix Scanner (Molecular Devices, Downingtown, PA) and Genepix 4000 image capture software (Molecular Devices, Downingtown, PA).

data_processing: Quantile normalization was used using JMP Genomics (JMP, Cary, NC) at Harvard Catalyst - Laboratory for Innovative Translational Technology (HC-LITT) and differentially regulated miRNAs were determined. Untreated cells were used as control.

source_name: Primary human Neurons

growth_protocol: Primary human neurons (HN) (5 x 105) purchased from ScienCell Research Laboratories (Carlsbad, CA) were grown in DMEM + 10% FBS on MatTek glass bottom plates treated with collagen (MatTek, Ashland, MA).

extract_protocol: Total RNA was isolated using Trizol (Invitrogen, Carlsbad, CA). 750 ng of total RNA was used for miRNA array analysis using miRCURY LNATM microRNA Array, v. 11.0 (Exiqon, Woburn, MA).

treatment_protocol: Cells were treated for 24hrs with 0.1 pg/cell as calculated by p24 ELISA, of supernatant isolated from U-937-infected with HIV-1 JR-FL

value: supernatant from HIV-infected U-937


title: G9af/f BAT Vec-1


title: HIV-1 Vpr (1) [miRNA]

description: SAMPLE 5

label_protocol: RNA was labeled using the miRCURY LNATM miRNA, Hy5 Power Labeling Kit (Exiqon) as per manufacturer’s recommendations using Maui SC Hybridization Chambers (BioMicro Systems, Salt Lake City, UT).

treatment_protocol: Cells were treated with Tat (10 ng/ml) kindly received from NIH (AIDS reagnets Bank) or 10 pg/ml of Vpr protein kindly received from Dr Eric Cohen, University of Montreal-Canada for 24 hours or control treatment.

value: Vpr


title: HIV-1 Tat (1)_HN [miRNA]

description: SAMPLE 3

value: Tat


title: Neurons treated with supernatant prepared from U-9367-infected with JR-FL strain of HIV-1 (2) [miRNA]

description: SAMPLE 8


title: C. elegans nasp-1 / btr-1 mutant versus wild type N2, on Bacillus thuringiensis DB27; Biological Replicate 2.

description: Biological replicate 2 of 3.


title: Control (2)_HN [miRNA]

description: SAMPLE 2

value: control


title: HIV-1 Vpr (2) [miRNA]

description: SAMPLE 6


title: Control (1)_HN [miRNA]

description: SAMPLE 1


title: Pancreatic_Islet_401.1089.1.1 [mirna]

status: Public on Nov 07 2012

city: La Jolla

first: Xiaoyan

last: Liao

state: CA

address: 200 W Arbor Street

department: Reproductive Medicine

institute: University of California, San Diego

hyb_protocol: The labeled product was hybridized to Illumina Human v2 MicroRNA Expression BeadChips according to the standard Illumina hybridization protocol.

scan_protocol: Scanned on a BeadArray Reader (Illumina, Inc.) according to the manufacturer's instructions.

data_processing: The data were filtered for detection pValue > 0.01 in GenomeStudio software v2010.3, and quantile normalised using CLC Bio.

source_name: Purified adult human beta islet cells

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

extract_protocol: Total RNA was purified using the MirVana RNA extraction kit (Ambion), quantified using the Ribogreen reagent (Lifetech, Inc.), and quality-controlled on a Bioanalyzer (Agilent).

tag: loring pipeline sample id

tag: loring pipeline stem cell matrix version

value: purified beta islet cells

value: adult

tag: gender

value: male

tag: patient id


title: Pancreatic_Islet_356.986.1.1 [mirna]

tag: cell type


title: PANCREAS_FETAL_220.422.1.1 [mirna]

source_name: Fetal pancreas

tag: tissue type

value: pancreas

value: fetal

tag: gestational age

value: unknown


title: Pancreatic_Islet_394.1066.1.1 [mirna]


title: 1740-N

value: Control

value: Female

value: African


title: Pancreatic_Islet_397.1069.1.1 [mirna]


title: PANCREAS_FETAL_220.417.1.1 [mirna]


title: HESC_Undiff_87.1665.3.1 [mirna]

description: HESC _Undiff_87.1665.3.1

source_name: embryonic stem cells, undifferentiated

tag: cell line

value: embryonic stem cells

tag: passage number

tag: differentiation stage

value: undifferentiated

value: female


title: 1546-N

tag: suicide status (1 = suicide, 0 = no)

tag: diagnosis

value: Depression


title: HESC_Diff_S5_325.984.18.1 [mirna]

description: HESC _Diff_S5_325.984.18.1

source_name: embryonic stem cells, differentiated; day 18

value: differentiated; day 18


title: HESC_Undiff_87.1663.1.1 [mirna]

description: HESC _Undiff_87.1663.1.1


title: HESC_Diff_S5_325.984.19.1 [mirna]

description: HESC _Diff_S5_325.984.19.1


title: HESC_Diff_S4_325.984.13.1 [mirna]

description: HESC _Diff_S4_325.984.13.1

source_name: embryonic stem cells, differentiated; day 15

value: differentiated; day 15


title: HESC_Diff_S5_87.926.3.1 [mirna]

description: HESC _Diff_S5_87.926.3.1


title: HESC_Diff_S3_87.925.1.1 [mirna]

description: HESC _Diff_S3_87.925.1.1

source_name: embryonic stem cells, differentiated; day 11

value: differentiated; day 11


title: HESC_Diff_S4_87.984.16.1 [mirna]

description: HESC _Diff_S4_87.984.16.1


title: HESC_Diff_S3_87.984.11.1 [mirna]

description: HESC _Diff_S3_87.984.11.1


title: HESC_Diff_S2_87.984.8.1 [mirna]

description: HESC _Diff_S2_87.984.8.1

source_name: embryonic stem cells, differentiated; day 7

value: differentiated; day 7


title: HESC_Diff_S1_325.984.1.1 [mirna]

description: HESC _Diff_S1_325.984.1.1

source_name: embryonic stem cells, differentiated; day 3

value: differentiated; day 3


title: HESC_Diff_S1_325.984.3.1 [mirna]

description: HESC _Diff_S1_325.984.3.1


title: HESC_Diff_S2_325.984.5.1 [mirna]

description: HESC _Diff_S2_325.984.5.1


title: HESC_Diff_S2_325.984.6.1 [mirna]

description: HESC _Diff_S2_325.984.6.1


title: 813-N

tag: Sex

tag: race

value: Caucasian


title: 1228-G

value: Male

tag: age

tag: pmi


title: 5175-G


title: 5121-N


title: Pancreatic_Islet_402.1090.1.1 [mirna]

value: purified beta islet cells

tag: developmental stage

value: adult


title: 4643-G


title: HESC_Diff_S1_325.984.2.1 [mirna]

description: HESC _Diff_S1_325.984.2.1

tag: loring pipeline sample id


title: 5175-N


title: HIV-1 Tat (2)_HN [miRNA]

description: SAMPLE 4

tag: treatment

value: Tat


title: 5121-G


title: 1546-G


title: Pancreatic_Islet_394.1066.1.1 [mRNA]

hyb_protocol: The labeled product was hybridized to Illumina HT-12 v4 arrays.

data_processing: The data were filtered for detection pValue > 0.01 and normalised using robust spline normalisation with lumi in R.

tag: loring pipeline stem cell matrix version

tag: gender

value: unknown


title: Pancreatic_Islet_356.986.1.1 [mRNA]

tag: cell type

value: male

tag: patient id


title: HESC_Diff_S5_325.984.18.1 [mRNA]

description: HESC _Diff_S5_325.984.18.1


title: PANCREAS_FETAL_220.417.1.1 [mRNA]

tag: tissue

value: pancreas

value: fetal

tag: gestational age


title: 1740-G

value: Control

value: Female

value: African


title: HESC_Undiff_87.1663.1.1 [mRNA]

description: HESC _Undiff_87.1663.1.1

tag: cell line

value: embryonic stem cells

tag: passage number

value: undifferentiated

value: female


title: PANCREAS_FETAL_220.422.1.1 [mRNA]


title: HESC_Undiff_87.1665.3.1 [mRNA]

description: HESC _Undiff_87.1665.3.1

tag: differentiation stage


title: Pancreatic_Islet_401.1089.1.1 [mRNA]


title: HESC_Undiff__87.1651.1.1 [mRNA]

description: HESC _Undiff_87.1651.1.1


title: Pancreatic_Islet_402.1090.1.1 [mRNA]


title: HESC_Diff_S4_325.984.13.1 [mRNA]

description: HESC _Diff_S4_325.984.13.1

value: differentiated; day 15


title: HESC_Diff_S3_87.984.11.1 [mRNA]

description: HESC _Diff_S3_87.984.11.1

value: differentiated; day 11


title: HESC_Diff_S4_87.984.16.1 [mRNA]

description: HESC _Diff_S4_87.984.16.1


title: Pancreatic_Islet_397.1069.1.1 [mRNA]


title: HESC_Diff_S5_87.926.3.1 [mRNA]

description: HESC _Diff_S5_87.926.3.1

value: differentiated; day 18


title: HESC_Diff_S2_87.984.8.1 [mRNA]

description: HESC _Diff_S2_87.984.8.1

value: differentiated; day 7


title: HCC1954_pERK1/2_T202Y204

status: Public on Oct 22 2012

type: protein

city: Heidelberg

first: Ulrike

last: Korf

address: Im Neuenheimer Feld 580

department: Molecular Genome Analysis

institute: German Cancer Research Center

description:
rabbit monoclonal
There are several sub-arrays on one slide. Each sub-array is incubated with one specific antibody, but one slide with 2 or 3 sub-arrays is stained with Fast Green FCF. Therefore, the number or rows differ between the antibody-files and the FCF-files.

hyb_protocol: Arrays were blocked using 50% Odyssey Blocking Puffer (LI-COR) in PBS. Primary antibodies were applied at a dilution of 1:300 and visualized by the application of Alexa680-labeled secondary antibodies (1:8000). Slides were washed with PBST between the incubation steps. Prior to scanning, arrays were wash once with MilliQ.

scan_protocol: Arrays were scanned using the Odyssey Infrared Imaging System (LI-COR), and signal intensities were determined using the GenePix Pro 5.0 analysis software.

data_processing:
Each biological sample was printed in triplicate on the array. One array was stained with Fast Green FCF to account for the total protein amount, a normalization factor for each spot was calculated, and antibody signals of each spot were normalized.
On-slide total protein quantification based on staining with Fast Green FCF served as basis for normalization of the signals derived from antibody incubation. A spot specific normalization factor was calculated by dividing the spot specific signal intensity by the mean of the signal intensities of all spots on this slide. The raw signal intensity of each spot was than divided by the normalization factor.

label: Alexa Fluor 680

molecule: protein

growth_protocol: Cells were seeded in 6-well plates, cultivated for 24h, and serum-starved for additional 24h.

extract_protocol: Medium was replaced by ice-cold PBS, transferred on ice, and cells were harvested manually by scraping in M-PER lysis buffer (Pierce, Bonn, Germany) containing protease inhibitor Complete Mini and phosphatase inhibitor PhosSTOP (Roche, Mannheim, Germany). Cells were lyzed for 20 min on an end-over-end shaker and lysates were cleared at 16,000 x g by centrifugation.

treatment_protocol: The inhibitors trastuzumab (10 ng/µL), pertuzumab (10 ng/µL), and erlotinib (1 µM) (Roche, Penzberg, Germany) were added to cells in starvation medium either alone or in combinations 1 h prior to stimulation with EGF or HRG (5 nM) for 0, 4, 8, 12, 16, 20, 30, 40, 50 and 60 min. After stimulation, medium was removed and ice-cold PBS was added to the plates.

tag: protein target

tag: phospho site

tag: antibody id


title: HESC_Diff_S1_325.984.2.1 [mRNA]

description: HESC _Diff_S1_325.984.2.1

value: differentiated; day 3


title: HESC_Diff_S2_325.984.6.1 [mRNA]

description: HESC _Diff_S2_325.984.6.1


title: HESC_Diff_S5_325.984.19.1 [mRNA]

description: HESC _Diff_S5_325.984.19.1


title: HESC_Diff_S1_325.984.1.1 [mRNA]

description: HESC _Diff_S1_325.984.1.1


title: pRPS6

growth_protocol: Cells were seeded in 6-well plates, cultivated for 24h prior to addition of the inhibitors.

treatment_protocol: The inhibitors trastuzumab (10 ng/µL), pertuzumab (10 ng/µL), and erlotinib (1 µM) (Roche, Penzberg, Germany) were added to cells in full growth medium either alone (erlotinib) or in combinations. After inhibition medium was removed and ice-cold PBS was added to the plates.


title: HCC1954_pAKT_S473

description:
rabbit polyclonal
There are several sub-arrays on one slide. Each sub-array is incubated with one specific antibody, but one slide with 2 or 3 sub-arrays is stained with Fast Green FCF. Therefore, the number or rows differ between the antibody-files and the FCF-files.

value: phospho-AKT


title: HESC_Diff_S3_87.925.1.1 [mRNA]

description: HESC _Diff_S3_87.925.1.1


title: SKBR3_pERK1/2_T202Y204

treatment_protocol: The inhibitors trastuzumab (10 ng/µL), pertuzumab (10 ng/µL), and erlotinib (1 µM) (Roche, Penzberg, Germany) were added to cells in starvation medium either alone or in combinations 1 h prior to stimulation with EGF or HRG (5 nM) for 0, 4, 8, 12, 16, 20, 30, 40, 50 and 60 min. After stimulation, medium was removed and ice-cold PBS was added to the plates.


title: HESC_Diff_S1_325.984.3.1 [mRNA]

description: HESC _Diff_S1_325.984.3.1


title: pRB

source_name: pRB

value: phospho-RB


title: MEF inactivated

status: Public on Sep 10 2012

city: Manhattan

first: Mark

middle: L

last: Weiss

state: KS

address: Coles Hall, Room 115

department: Anatomy and Physiology

institute: Kansas State University

description:
This Sample represents 2 technical replicates.
SAMPLES 3 & 4

data_processing:
The duplicate samples (technical replicates) were averaged. Normalization and all the data analysis were performed according to the manufacturer's instructions using the RT-PCR profiler instruction manual.
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)] and Ct_HKG = geometric mean of Gapdh and Ldha.
An Excel spreadsheet was used to calculate deltaCt, fold change, etc.
GSE30582_fold_change.txt': Fold Change file reports sample/control cell line. Specifically, average sample/MEF ratios for 2(-delta delta Ct) fold change. This file is linked to the GSE30582 record as a supplementary file.

label: SYBR Green

source_name: control, mitotically inactivated mouse embryonic fibroblasts

label_protocol: RT-PCR assays using a customized RT-PCR Profiler array (SABiosciences - Qiagen, Frederick, MD) following the manufacturer's instructions. Reverse transcription was performed from 1000 ng total RNA using the RT2 First Strand Kit (SA Biosciences). The focused array was run using Qiagen's RT2 qPCR Mastermix for the BioRad iQ5 thermal cycler (loading control dye). Quantitative real-time PCR were performed on a BioRad iCQ5 iCycler using Biorad iCycler IQ software version 3.1.7050. PCR program: 950C for 10 min, 40 cycles at 95 oC for 15 seconds and 60 oC for 60 seconds. Followed by melt point analysis.

extract_protocol: Total RNA was extracted with the Qiagen RNeasy Mini Kit using the manufacturer's protocol, followed by DNase I treatment. First-strand synthesis using the Qiagen's RT2 first strand kit. Samples were stored at -80C until use.

tag: strain

tag: differentiation status

value: mitotically inactivated by 6000 rads of gamma irradiation

tag: cdna id


title: Sick8_grp4_Q13LU

status: Public on Aug 02 2012

city: Ann Arbor

first: Celine

last: Berthier

state: MI

address: 1150 W. Medical Center Dr, MSRB2

institute: University of Michigan

description: Gene expression data from NZB/W nephritic kidney (36 weeks old, proteinuric)

hyb_protocol: standard Affymetrix protocol

scan_protocol: GeneChip arrays were scanned by GeneChip Scanner 3000 7G according to the Affymetrix Expression Analysis Technical Manual.

data_processing: The data were analyzed using GenePattern pipeline: RMA method and Mouse Entrez Gene custom CDF annotation version 10 were used for the normalization; and Combat for batch correction within the NZB/W mouse model and the NZW/BXSB mouse model.

source_name: Kidney from lupus NZB/W mouse (36 weeks old)

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

extract_protocol: Total RNA was isolated using Trizol and manufacturer's instructions

tag: disease status

value: Kidney from prenephritic mouse (36 weeks old, proteinuric)

value: Whole kidney


title: HeLa_normoxia_IL_siHexim

status: Public on Sep 21 2012

city: Tokyo

first: Olga

middle: Sergeevna

last: Safronova

address: Bunkyo-ku, Yushima, 1-5-45

department: Cellular Physiological Chemistry

institute: Tokyo Medical and Dental University

description: Gene expression in normoxic cells transfected with HEXIM1 siRNA and treated with IL-1beta for 1 hr.

hyb_protocol: Sample fragmentation was performed at 60°C for 30 minutes.On completion of the fragmentation reaction, samples were hybridized to Agilent SurePrint G3 Human GE microarrays (G4851A) at 65°C, 10rpm for 17 hours in a rotating hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2539A) using Scan Control, version A.8.5.1, Agilent Technologies software. Scanning parameters were as follow: Dye channel - green, Scan region - Agilent HD (61x21.6 mm), TIFF file dinamic range - 20bit, R/G PMT gain - 100%, Scan resolution 3um.

data_processing: The log2 transformed intensities were normalized on 75th percentile in each sample, and then turned into log-ratios against the control sample (N siScr).

source_name: HeLa, normoxia, IL-1 for 1 hr, HEXIM1 siRNA

label_protocol: cRNA was synthesized using T7 RNA polymerase and labeled with Cyanine 3 dye (Low input Quick Amp labeling kit, one-color,  Agilent Technologies) followed by purification with Rneasy mini kit (Qiagen).

growth_protocol: HeLa cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum.

extract_protocol: Total RNA was extracted with TRI-zol reagent (Invitrogen). Pooled RNA from two replicates was used per array. Total RNA was isolated using RNeasy mini kit (Qiagen). Double-stranded cDNA was synthesised from 100ng of totalRNA using poly dT primer.

treatment_protocol: HeLa cells were transfected with double-stranded siRNA oligonucleotides directed against HEXIM1 (Thermo Scientific Dharmacon; siHex) or control siRNA (Santa Cruz; siScr) and 48 hrs later treated for 1 hr with IL-1beta in normoxic (N IL-1) or hypoxic (H IL-1) (5% CO2, 0.5% O2, balanced with N2) environment.

value: HeLa


title: Sick10_grp4_V6LU


title: Sick9_grp4_E130


title: Sick1_grp4_E12RUK


title: Prot6_grp3_RA5RU

description: Gene expression data from NZB/W prenephritic kidney (23 weeks old, onset of proteinuria)

source_name: Kidney from lupus NZB/W mouse (23 weeks old)

value: Kidney from prenephritic mouse (23 weeks old, proteinuric)


title: Sick2_grp4_Clair2


title: Prot5_grp3_Q9RU


title: Sick4_grp4_Q60


title: HeLa_hypoxia_IL_siHexim

description: Gene expression in cells transfected with Hexim1 siRNA and treated with IL-1beta and hypoxia for 1 hr.

source_name: HeLa, hypoxia and IL-1 for 1 hr, HEXIM1 siRNA


title: HeLa_hypoxia_IL_siScr

description: Gene expression in cells transfected with control siRNA and treated with IL-1beta and hypoxia for 1 hr.

source_name: HeLa, hypoxia and IL-1 for 1 hr, control siRNA


title: Sick3_grp4_Claire1


title: Sick7_grp4_V4LL


title: Prot4_grp3_Q1LU


title: Sick5_grp4_Q6RU


title: Prot1_grp3_Green6LU


title: HeLa_normoxia_siScr

description: Gene expression in normoxic cells transfected with control siRNA.

source_name: HeLa, normoxia, control siRNA


title: Prot3_grp3_Q7LL


title: prot2_grp3_Q1RU


title: Sick6_grp4_V6RL


title: HESC_Undiff__87.1651.1.1 [mirna]

description: HESC _Undiff_87.1651.1.1

tag: loring pipeline sample id


title: 23wks10_grp2_Q3O

description: Gene expression data from NZB/W prenephritic kidney (23 weeks old, non-proteinuric)

value: Kidney from prenephritic mouse (23 weeks old, non-proteinuric)


title: 23wks8_grp2_Q3RL


title: 23wks7_grp2_Q3LU


title: 23wks5_grp2_Q2RU


title: 23wks6_grp2_Q1RL


title: 23wks9_grp2_Q1O


title: 23wks11_grp2_Q3RU


title: MUT_STP

status: Public on Jun 01 2012

first: Lydia

last: Freddolino

address: 1150 W. Medical Center Dr., MSRB 3 room 3315

department: Biological Chemistry

description: Two biological replicates (1-1, 1-2). Comparison of transposon insertion abundances in libraries grown under selective vs. reference conditions.

hyb_protocol: Agilent Gene Expression hybridization kit used following the manufacturer's instructions.

scan_protocol: Agilent Technologies Scanner G2505B US22502626 was used to scan the slide.

data_processing: Log ratios were extracted using Agilent Feature Extraction 9.5 with default settings. All replicate probes for each location were pooled across biological and technical replicates as appropriate for the Rosetta error model used by Feature Extraction, and Z-scores calculated from the pooled log ratios and log ratio errors [provided as a Sample supplementary file].

organism: Escherichia coli str. K-12 substr. MG1655

label_protocol: The T7 promoter on the transposon was used for in vitro transcription and labeling (Megascript; Ambion). Libraries grown in M9t/glucose were used as controls and were labeled with Cy5; whereas the target selections were labeled with Cy3.

growth_protocol: For RNA samples, WT or rho* cells were grown to mid-log phase in M9t/glucose.  WT or rho* transposon mutagenized libraries were grown overnight in the media indicated.

extract_protocol: Genomic DNA was extracted from the selected pools (DNeasy Blood & Tissue Kit, Qiagen). Each sample was then split in half, and each half digested with either HinP1 or MspI (3 hr at 37 C). After heat inactivation of the enzymes, the digestion products were combined and a Y-shaped linker was ligated to the DNA fragments. The samples were then purified using QIAquick PCR purification columns and used as template in a PCR containing a primer specific to the transposon and a primer specific to the Y-shaped linker.

tag: genotype/variation

value: rho*

tag: growth media

tag: culture age

value: overnight culture

source_name: rho* Transposon mutagenized library_M9t/glucose + streptomycin (1.25 mg/L)

value: M9t/glucose + streptomycin (1.25 mg/L)


title: MUT_AKG

source_name: rho* Transposon mutagenized library_M9t/glucose

source_name: rho* Transposon mutagenized library_M9t/AKG


title: MUT_NADM

source_name: rho* Transposon mutagenized library_M9t/NADM


title: WT_CML

value: WT

source_name: WT Transposon mutagenized library_M9t/glucose+chloramphenicol (1.875 mg/L)


title: WT_STP

source_name: WT Transposon mutagenized library_M9t/glucose + streptomycin (1.25 mg/L)


title: MUT_CML

source_name: rho* Transposon mutagenized library_M9t/glucose+chloramphenicol (1.875 mg/L)


title: RNA

description: Two biological replicates (1-1, 1-2). Comparison of gene expression between WT and rho* cells.

source_name: WT cells_mid-log-phase_M9t/glucose

label_protocol: A poly-A tail was added to the RNA samples using E. coli Poly(A) polymerase (NEB, M0276) for 15 minutes. Using an Agilent low input quick amp labeling kit, the rho* and WT samples were then labeled with Cy3 and Cy5, respectively.

extract_protocol: Total RNA was extracted using total RNA purification kit (Norgen Biotek, Cat 17200).

tag: growth phase

value: mid-log

source_name: rho* cells_mid-log-phase_M9t/glucose


title: WT_AKG

source_name: WT Transposon mutagenized library_M9t/glucose

source_name: WT Transposon mutagenized library_M9t/AKG


title: Y16wks3_grp1a_YM3

description: Gene expression data from NZB/W prenephritic kidney (16 weeks old, non-proteinuric)

source_name: Kidney from lupus NZB/W mouse (16 weeks old)

value: Kidney from prenephritic mouse

tag: tissue


title: Y16wks2_grp1a_YM2


title: 23wks1_grp2_Q2LL


title: Y16wks4_grp1a_NZBW


title: Y16wks8_grp1a_RA5RL


title: 23wks2_grp2_Q2LU


title: Y16wks5_grp1a_RA5LL


title: 23wks3_grp2_Q2O


title: Y16wks1_grp1a_redUL


title: Y16wks7_grp1a_RA5O


title: 23wks4_grp2_Q2RL


title: Y16wks6_grp1a_RA5LU


title: HeLa_normoxia_IL_siScr

description: Gene expression in normoxic cells transfected with control siRNA and treated with IL-1beta for 1 hr.

source_name: HeLa, normoxia, IL-1 for 1 hr, control siRNA


title: WT_NADM

source_name: WT Transposon mutagenized library_M9t/NADM


title: op1132_CNT (gene level)

status: Public on Apr 13 2012

city: Singapore

first: Michelle

middle: GK

last: Tan

address: 20 College Road

department: Clinical Translational Research

country: Singapore

institute: Singapore General Hospital

hyb_protocol: Samples were hybridized to Affymetrix GeneChip Human Exon 1.0 ST arrays at 45°C for 16 hours, then washed and stained in a Fluidics Station 450.

scan_protocol: GeneChips were scanned by a GCS3000 Scanner (Affymetrix).

data_processing:
CEL files were generated using Affymetrix GCOS software and exported to the Partek Genomics Suite V6.3. After GC content and Robust Multi-Chip analysis (RMA) background corrections, data across different batches were subject to quantile normalization. To facilitate analyses of expression analyses at the gene-level, log2 base normalized signal intensities of multiple probes on different exons were summarized into an expression value of all transcripts from the same gene.

Probe group file: HuEx-1_0-st-v2.r2.pgf
Meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps
Genome build: hg18

source_name: neocortex of control patient

label_protocol: Samples were fragmented and end-labeled using the WT Sense Target Labeling Kit (Affymetrix).

extract_protocol: Total RNA was isolated using Trizol reagents. Samples were first processed for rRNA depletion with the RiobMinus Human/Mouse Transcriptome Isolation Kit (Invitrogen). cDNA synthesis and amplification were then performed using the GeneChip Whole Transcript (WT) cDNA Synthesis and Amplification Kit (Affymetrix).

tag: age

tag: Sex

value: female

tag: pmi

value: control

value: neocortex


title: op107_AD (gene level)

source_name: neocortex of AD patient

value: Alzheimer's disease (AD)


title: op450_AD (gene level)

value: male


title: op1112_CNT (gene level)


title: op133_AD (gene level)


title: op340_AD (gene level)


title: op223_CNT (gene level)


title: op1151_CNT (gene level)


title: op80_AD (gene level)


title: op1146_CNT (gene level)


title: op91_AD (gene level)


title: op388_AD (gene level)


title: op346_CNT (gene level)


title: op9_CNT (gene level)


title: op417_AD (gene level)


title: op1044_CNT (gene level)


title: PDAC_Patient:GEO-PC-029_rep1

status: Public on Mar 31 2012

city: Sydney

first: Jianmin

last: Wu

state: NSW

address: 370 Victoria Street Darlinghurst

department: Cancer Division

country: Australia

institute: Garvan Institute of Medical Research

hyb_protocol: Amplified cRNA (750ng) was hybridized onto Illumina human HT-12 arrays (V4) as per manufacturer's instructions.

scan_protocol: Arrays were scanned on a Bead Array Reader (Illumina)

data_processing: Expression measurements were extracted using the GenomeStudio (version 2009.1) software, using no background correction or normalisation, and exported in two batches. This unnormalised data from two separate genome studio files were combined, retaining the 47215 probes in common, followed by variance-stabilising transformation (vst) and robust spline normalisation (rsn) using lumi (v2.4.0) in R (v 2.13.1)/Bioconductor (v2.8). Note that the vst-scale is very similar to the log2-scale for high levels (see Lin et al, NAR 36:e11). To obtain natural scale data, use inverseVST from lumi in R/Bioconductor. The 2 replicates from Patient ICGC-PC-027 were then averaged.

source_name: PDAC tumour RNA

label_protocol: mRNA samples (150ng/sample) were amplified and labeled using the Illumina TotalPrep RNA Amplification Kit (Life Technologies) as per manufacturer’s instructions. Amplified RNA was quantified using a NanoDrop (Thermo Scientific) and distribution of the amplified material was analysed in an 2100 Bioanalyzer (Agilent)

growth_protocol: Pancreas tissue was surgically removed from PDAC patients undergoing Whipple surgical resection.

extract_protocol: RNA was extracted from primary tissue using the Qiagen Allprep kit in accordance with the manufacturers instructions.

treatment_protocol: Tissue was immediately snap frozen in liquid nitrogen (for full protocol see APGI website: http://www.pancreaticcancer.net.au/).

value: Pancreas

tag: disease

value: PDAC (pancreatic ductal adenocarcinoma)


title: mES, p53-/-, Ctr, rep3

status: Public on Mar 05 2012

last: Huang

institute: National Cancer Institute

hyb_protocol: Samples were hybridized to the Affymetrix Mouse Gene ST 1.0 GeneChip.

scan_protocol: Arrays were scanned on the Affymetrix GeneChip scanner 3000.

data_processing:
Data were processed with Partek Genomics Suite v6.4. Signal intensities were RMA normalized.

Probe group file: MoGene-1_0-st-v1.r4.pgf
Meta-probeset file: MoGene-1_0-st-v1.r4.mps

source_name: mES, p53-/-, Ctr

label_protocol: Affymetrix Whole Transcript Sense Target Labeling kit per manufacturer’s protocol.

growth_protocol: Cells were grown in mESC growth medium, Knockout DMEM (KO-DMEM), 15% Fetal Bovine Serum, 100mM MEM non-essential amino acids, 0.1mM 2-mercaptoethanol, 2mM L-glutamine and 1X penicillin-streptomycin (All from Invitrogen) plus 1000 units/ml leukemia inhibitory factor (Lif, Millipore).

extract_protocol: RNAs were extracted using the RNeasy mini kit (Qiagen).

treatment_protocol: Cells were either untreated or treated with 0.5 micromolar adriamycin for 8 hours in growth medium.

tag: background/strain

tag: cell type

value: embryonic stem cells  (mES)

tag: genotype

tag: agent

value: untreated


title: mES, p53-/-, Adr, rep1

source_name: mES, p53-/-, Adr

value: adriamycin


title: DMSO_0.0_363

status: Public on Feb 03 2012

city: Midland

first: Craig

last: Rowlands

address: 1803 Bldg Washington Street

department: Toxicology & Environmental Research & Consulting

institute: The Dow Chemical Company

hyb_protocol: On each microarray, 1.65 ug of labeled cRNA was hybridized for 17 hours and subsequently washed per the Agilent protocol.

scan_protocol: Microarrays were scanned using the Agilent dual laser DNA microarray scanner, model G2565AA, with 5 µm resolution. The extended dynamic range option was used.

data_processing: Scanned images were processed with Agilent Feature Extraction software. Within Genespring, the data for each microarray were normalized to the median signal intensity of the microarray. Data were then log2 transformed.

organism: Rattus norvegicus

source_name: primary hepatocytes treated for 24h

label_protocol: For each sample, Alexa555-labeled cRNAs was generated from 500 ng of total RNA using the Epicentre TargetAMP 1-Round Aminoallyl-cRNA Amplification Kit per the vendor’s protocol (Epicentre Biotechnologies, Madison, WI). The Aminoallyl-cRNA was then purified using Qiagen RNeasy Mini Elute Kit.

growth_protocol: Primary cultures of rat hepatocytes were obtained from five individual 10-week-old female Sprague-Dawley rats.  Each individual rat was treated as a biological replicate.  Preplating cell viability, determined by trypan blue exclusion, ranged from 90 to 94% in rat hepatocytes. Following isolation, hepatocytes were resuspended in DMEM containing 5% fetal calf serum, insulin (4 ng/ml), and dexamethasone (1 nM).   The hepatocytes were then added to 24-well BioCoat (BD Biosciences) plates coated with collagen type 1 substratum and allowed to attach for 3–6 h at 37°C in a humidified chamber with 95% relative humidity and 5% CO2.  After attachment, the culture plates were swirled and the medium containing debris and unattached cells was aspirated.  Fresh, ice-cold, serum-free DMEM/Ham’s F12 medium containing 50 nM dexamethasone, 6.25 ng/ml insulin, 6.25 ng/ml transferrin, 6.25 ng/ml selenium (ITS+), and 0.25 mg/ml Matrigel was added to the culture plate and immediately returned to the humidified chamber. Serum-free medium was used since serum can significantly reduce the cellular uptake of TCDD. Medium was kept in the dark prior to use and was not changed during the incubation periods.

extract_protocol: Cells (24-well format) were washed with one volume of HBSS, lysed by addition of 0.35 ml of ABI Nucleic Acid Lysis Solution (Applied Biosystems, Foster City, CA), and frozen at -70 C.  Lysates were thawed and total RNA was isolated from each sample using an ABI 6100 Prepstation according to the manufacturer’s protocol.

treatment_protocol: Stock solutions of TCDD (100 µM) were diluted in DMSO and added to culture media (DMEM-Ham’s F12) to a final DMSO concentration of 0.1% .  The hepatocyte cultures were exposed for 24 h to the DMSO vehicle (0.1%) or one of the following TCDD concentrations: 0.00001, 0.0001, 0.001, 0.003, 0.01, 0.03, 0.1, 0.3, 1, 10, 100 nM. Cell viability was examined at the 24 h time point in the vehicle control hepatocytes and hepatocytes treated with 100 nM TCDD.  Viability was assessed by morphological appearance, LDH leakage (CytoTox-ONE, Promega, Madison, WI), ATP levels (CellTiterGlo, Promega), and phase contrast microscopy (LeCluyse et al., 2000; Meunier et al., 2000).  Cell viability end points did not demonstrate treatment-related cytotoxicity.

tag: strain

value: Sprague-Dawley

tag: gender

value: primary hepatocytes

tag: treatment

value: DMSO

tag: dose

tag: tcdd sample


title: DMSO_0.0_361


title: PDAC_Patient:GEO-PC-002_rep1


title: mES, p53-/-, Adr, rep2


title: PDAC_Patient:GEO-PC-027_rep2


title: PDAC_Patient:GEO-PC-009_rep1


title: DMSO_0.0_302


title: mES, p53-/-, Ctr, rep2


title: mES, p53-/-, Ctr, rep1


title: BM_CMP_WT_rep2

status: Public on Jan 07 2012

city: St. Louis

first: Amy

middle: M.

last: Becker

state: MO

address: 660 S. Euclide Ave.

department: Pathology and Immunology

institute: Washington University School of Medicine

description: replicate 2

data_processing: data analyzed using ArrayStar 4 (DNAstar) using quantiles-based normalization

source_name: mouse bone marrow

label_protocol: Biotinylated aRNA was prepared using the Nugen pico-amplification kit per manufacturer's instructions.

extract_protocol: RNA was extracted using the Qiagen Rneasy Kit per manufacturer's instructions.  RNA quality was accessed using the Agilent Bioanalyser.

value: bone marrow

value: IRF-8 wild type

value: common myeloid progenitors (Lineage-c-kithiSca-1-CD11c- CD34+ Flk2+CD16/32-CD115-)


title: BM_CMP_KO_rep1

description: replicate 1

value: IRF-8 knockout


title: BM_CMP_KO_rep2

description: replicate 2


title: HESC_Diff_S2_325.984.5.1 [mRNA]

description: HESC _Diff_S2_325.984.5.1

source_name: embryonic stem cells, differentiated; day 7

tag: loring pipeline sample id

tag: loring pipeline stem cell matrix version

tag: cell line

value: embryonic stem cells

tag: passage number

tag: differentiation stage

value: differentiated; day 7

value: female


title: mES, p53-/-, Adr, rep3


title: BM_ALP_WT_rep1

description: replicate 1

tag: tissue

value: all lymphoid progenitors (Lin-Ly6D-B220-c-kit+Flk2+IL7R+)


title: DMSO_0.0_277

tag: age


title: BM_ALP_WT_rep2

description: replicate 2


title: BM_CMP_WT_rep1

description: replicate 1


title: BM_ALP_KO_rep1

description: replicate 1


title: DMSO_0.0_293


title: BM_ALP_KO_rep2

description: replicate 2


title: GBM_B56

status: Public on Oct 31 2011

city: Aurora

first: Andrew

middle: M

last: Donson

state: CO

department: Pediatrics

institute: CU Anschutz Medical Campus

description: Gene expression data from surgical tumor sample of high grade astrocytoma

hyb_protocol: Following fragmentation, 11.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

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

data_processing: Microarray .CEL file data was background corrected and normalized using the gcRMA algorithm, resulting in log 2 expression values. The Affymetrix HG-U133 plus 2 microarray contains 54,675 probe sets including multiple probe sets for the same gene. In order to reduce error associated with multiple testing we used only a single probe set for each gene that possessed the highest gcRMA expression level across all our samples. This filtered list of the best expressed probe sets contained 20,722 genes.

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

extract_protocol:
Tumor samples were snap frozen in liquid nitrogen or transferred to RNAlater immediately after surgical removal as part of patient care. All samples were collected with appropriate IRB approval (COM-IRB#95-500).
RNeasy (Qiagen) extraction of total RNA was performed according to the manufacturer's instructions.

value: brain tumor (high grade astrocytoma)

tag: survival (months)


title: GBM_B17


title: GBM_B57


title: GBM_668


title: GBM_B10


title: GBM_B12


title: GBM_637


title: GBM_478


title: GBM_434


title: GBM_273


title: GBM_481


title: GBM_496


title: HUVEC_uninduced

status: Public on Dec 06 2011

city: Wien

first: Julia

last: Testori

address: Lazarettgasse 19

department: Vascular Biology and Thrombosis Research

country: Austria

institute: Medical University Vienna

description: Gene expression data

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: The data were analyzed using RMA (Robust multiarray average) Signal extraction and normalization.

source_name: HUVEC, starved, uninduced

label_protocol: Affymetrix protocol

growth_protocol: Endothelial cells were kept in complete EGM-2 Medium in dense culture without change of medium and before the stimulation in EGM-2 medium without growth factors over night.

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

value: Human umbilical vein endothelial cells

value: uninduced


title: GBM_309


title: GBM_391


title: GBM_281


title: HUVEC_VEGF_60min

description: Gene expression data

source_name: HUVEC, starved, 60min VEGF induced

treatment_protocol: Endothelial cells were induced for 60min with 100ng/ml VEGF-A.

value: VEGF

tag: time

value: 60 min


title: GBM_271


title: GBM_000


title: LCM_normal_lung_parenchyma94

status: Public on Apr 08 2011

city: Toronto

first: Ming-Sound

last: Tsao

country: Canada

institute: Ontario Cancer Institute/ Princess Margaret Hospital

description:
Whole-transcript expression profiling
Normal_lung94

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Raw data was pre-processed and normalized using RMA implemented in Affymetrix Expression console v1.1, expression values were summarized at the gene-core level based on NetAffx NA28 annotation library integrated in Affymetrix Expression console v1.1.

source_name: Normal lung

label_protocol: standard Affymetrix procedures

extract_protocol: Stromal tissue was isolated by Laser Capture Microdissection (LCM) using the CellCut Plus LCM (Molecular Machines & Industries, Glattbrugg, Switzerland) mounted on Olympus IX81 inverted microscope. Subsequently, RNA was isolated using Total RNA purification kit (Norgen Biotek, Canada) and RNA was amplified using RNA amplification kit (WT-OvationTM Pico RNA Amplification System Version 1.0, NuGEN, San Carlos, CA).

tag: Sex

value: F

tag: disease state

value: Normal lung

tag: histology

value: Normal lung parenchyma

tag: Stage


title: LCM_normal_lung_parenchyma192

description:
Whole-transcript expression profiling
Normal_lung192

value: M


title: LCM_normal_lung_parenchyma954

description:
Whole-transcript expression profiling
Normal_lung954


title: HUVEC_VEGF_150min

description: Gene expression data

source_name: HUVEC, starved, 150min VEGF induced

treatment_protocol: Endothelial cells were induced for 150min with 100ng/ml VEGF-A.

tag: cell type

value: 150 min


title: LCM_normal_lung_parenchyma927

description:
Whole-transcript expression profiling
Normal_lung927


title: LCM_normal_lung_parenchyma549

description:
Whole-transcript expression profiling
Normal_lung549


title: LCM_normal_lung_parenchyma727

description:
Whole-transcript expression profiling
Normal_lung727


title: LCM_normal_lung_parenchyma089

description:
Whole-transcript expression profiling
Normal_lung089


title: LCM_normal_lung_parenchyma491

description:
Whole-transcript expression profiling
Normal_lung491


title: HUVEC_VEGF_30min

description: Gene expression data

source_name: HUVEC, starved, 30min VEGF induced

treatment_protocol: Endothelial cells were induced for 30min with 100ng/ml VEGF-A.

tag: treatment

value: 30 min


title: LCM_normal_lung_parenchyma471

description:
Whole-transcript expression profiling
Normal_lung471


title: LCM_normal_lung_parenchyma690

description:
Whole-transcript expression profiling
Normal_lung690


title: LCM_primary_lung_tumor_stroma094

description:
Whole-transcript expression profiling
NSCLC_stroma094

source_name: primary lung cancer

value: primary lung cancer

value: Adenocarcinoma

value: III


title: LCM_primary_lung_tumor_stroma927

description:
Whole-transcript expression profiling
NSCLC_stroma927

value: I


title: LCM_primary_lung_tumor_stroma549

description:
Whole-transcript expression profiling
NSCLC_stroma549


title: LCM_normal_lung_parenchyma006

description:
Whole-transcript expression profiling
Normal_lung006


title: LCM_primary_lung_tumor_stroma954

description:
Whole-transcript expression profiling
NSCLC_stroma954

value: Squamous cell carcinoma


title: LCM_primary_lung_tumor_stroma971

description:
Whole-transcript expression profiling
NSCLC_stroma971

value: II


title: LCM_primary_lung_tumor_stroma746

description:
Whole-transcript expression profiling
NSCLC_stroma746


title: LCM_primary_lung_tumor_stroma727

description:
Whole-transcript expression profiling
NSCLC_stroma727


title: LCM_primary_lung_tumor_stroma471

description:
Whole-transcript expression profiling
NSCLC_stroma471


title: LCM_primary_lung_tumor_stroma089

description:
Whole-transcript expression profiling
NSCLC_stroma089


title: LCM_normal_lung_parenchyma935

description:
Whole-transcript expression profiling
Normal_lung935


title: LCM_primary_lung_tumor_stroma006

description:
Whole-transcript expression profiling
NSCLC_stroma006


title: LCM_normal_lung_parenchyma746

description:
Whole-transcript expression profiling
Normal_lung746


title: LCM_normal_lung_parenchyma971

description:
Whole-transcript expression profiling
Normal_lung971


title: LCM_primary_lung_tumor_stroma491

description:
Whole-transcript expression profiling
NSCLC_stroma491


title: LCM_normal_lung_parenchyma520

description:
Whole-transcript expression profiling
Normal_lung520


title: LCM_primary_lung_tumor_stroma690

description:
Whole-transcript expression profiling
NSCLC_stroma690


title: LCM_primary_lung_tumor_stroma935

description:
Whole-transcript expression profiling
NSCLC_stroma935

value: Combined small and large cell carcinoma and adenocarcinoma


title: LCM_primary_lung_tumor_stroma192

description:
Whole-transcript expression profiling
NSCLC_stroma192

value: Mixed large neuro- endocrine carcinoma and adenocarcinoma


title: PDAC_Patient:GEO-PC-070_rep1

value: Pancreas

tag: disease

value: PDAC (pancreatic ductal adenocarcinoma)


title: LCM_primary_lung_tumor_stroma520

description:
Whole-transcript expression profiling
NSCLC_stroma520