title: Normal mouse liver (mouse #1)

status: Public on Sep 28 2011

city: Bethesda

first: Daekwan

last: Seo

address: 37 Convent Dr. Rm 4140

department: NCI

institute: NIH

description:
WT1-3we-Cy3-543

Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.

hyb_protocol: Before the hybridization, oligonucleotide microarrays were pretreated with a 5xSSC, 1% BSA, 0.1% SDS blocking solution. The samples were applied on the microarray slides in a hybridization mix containing 25% formamide, 0.1% SDS, and 5xSSC in 28 ul final volume. After overnight incubation, the slides were washed in a 1xSSC 0.1% SDS solution for 2 minutes and then consecutively in 1xSSC and 0.2xSSC solutions.

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243]

data_processing: Dataset extraction/normalization/filtration was performed using the mAdb database (NIH). Spot signal calculation: Median spot intensity - Median background intensity. Normalization: 50th percentile (median).  Filtration: Bad/not found spots, spots with diameter less than 30 um or more than 250 um, spots with a signal intensity below 2 x SD of background intensity for any of the 2 fluorescent channels were excluded. Only genes with a value in >10% arrays were selected for further data analysis. For each spot, log2 transformed intensity value was used for further data analysis.

source_name: Normal mouse liver, 3 weeks

label_protocol: Total RNA was used to synthesize fluorescently labeled (Amersham Biosciences) cDNA probes. Briefly, 20 ug RNA were denaturated with 4 ug (d)T20 primer at 70degrees C for 5 minutes, chilled on ice, and incubated for 1 hour at 42degrees C in a 50-ul reaction mix containing 10 ul 10x First-Strand buffer (Invitrogen), 2.5 ul 20x deoxynucleotide triphosphate (dNTP) mix (10 mM dATP, dGTP, and CTP; 4 mM dTTP; and 6 mM aminoallyl-dUTP; Sigma-Aldrich), 5 ul of 0.1 M DTT, 2 ul SuperScript II (Invitrogen) reverse transcriptase, and 1 ul SUPERaseIn (Ambion ). After digestion with 4 U RNase H (Ambion Inc.) at 37degrees C for 20 minutes, the samples were cleaned up with a MinElute PCR Purification Kit (Qiagen). The eluted cDNA samples were concentrated by Speed Vac (Global Medical Instrumentation Inc.) and resolved in 20 ul 0.1 M NaHCO3 solution. The Cy3 and Cy5 dyes (Amersham Biosciences) were also dissolved in 20 ul of water. For the coupling reaction, 2 ul of dye was added to each sample, and the mix was left in a dark box for an hour. Labeled cDNA was purified again with a MinElute kit (Qiagen), and Cy3- and Cy5-labeled target and reference samples were combined.

growth_protocol: All experiments were conducted according to the National Institutes of Health (NIH) guidelines for animal care and following a study protocol approved by the National Cancer Institute (NCI) Animal Care and Use Committee. Mice had free access to food and water.

extract_protocol: Total RNAs were purified using a CsCl gradient-density centrifugation method.

treatment_protocol: Liver samples from male animals were collected at various time-points ranging from 3 weeks to 18 months. Tissue samples were divided into two parts; one was fixed in 10% formalin for histological evaluation and the other was used for RNA analysis.

tag: strain/background

value: wild-type

value: 3 weeks

value: liver

tag: histology

value: normal

tag: sample id

source_name: Reference RNA

value: 3 months

value: reference


title: Normal mouse liver (mouse #7)

type: RNA

state: MD

country: USA

description:
Hi-WT7NL-Cy3-267

Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.

molecule: total RNA

organism: Mus musculus

source_name: Normal mouse liver, 3 months

tag: genotype

tag: gender

value: male

tag: age

tag: tissue

tag: strain

tag: sample type


title: Normal mouse liver (mouse #3)

description:
WT3-3we-Cy3-547

Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.


title: Normal mouse liver (mouse #4)

description:
WT4-3we-Cy3-549

Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.


title: Normal mouse liver (mouse #3)-replicate

description:
WT3-3we-Cy5-548

Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.


title: Normal mouse liver (mouse #9)-replicate

description:
Hi-WT9NL-Cy5-272

Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.


title: Normal mouse liver (mouse #9)

description:
Hi-WT9NL-Cy3-271

Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.


title: Normal mouse liver (mouse #2)-replicate

description:
WT2-3we-Cy5-546

Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.


title: Normal mouse liver (mouse #10)-replicate

description:
WT5-3we-Cy5-552

Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.


title: Normal mouse liver (mouse #4)-replicate

description:
WT4-3we-Cy5-550

Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.


title: Normal mouse liver (mouse #6)-replicate

description:
Hi-WT6NL-Cy5-266

Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.


title: Normal mouse liver (mouse #10)

description:
WT5-3we-Cy3-551

Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.


title: Normal mouse liver (mouse #6)

description:
Hi-WT6NL-Cy3-265

Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.


title: Normal mouse liver (mouse #8)-replicate

description:
Hi-WT8NL-Cy5-270

Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.


title: Tgfa, tumor 6T-replicate

description:
Hi-TGA6T-Cy5-468

Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.

source_name: Tgfa, tumor, 18 months

value: Tgfa transgenic

value: 18 months

value: hepatocellular carcinoma (HCC)


title: Normal mouse liver (mouse #7)-replicate

description:
Hi-WT7NL-Cy5-268

Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.


title: Normal mouse liver (mouse #1)-replicate

description:
WT1-3we-Cy5-544

Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.


title: Normal mouse liver (mouse #2)

description:
WT2-3we-Cy3-545

Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.


title: Normal mouse liver (mouse #8)

description:
Hi-WT8NL-Cy3-269

Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.


title: Tgfa, tumor 5T-replicate

description:
Hi-TGA5T-Cy5-466

Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.


title: Tgfa, tumor 6T

description:
Hi-TGA6T-Cy3-467

Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.


title: Normal mouse liver (mouse #5)

description:
Hi-WT5NL-Cy3-263

Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.


title: Tgfa, tumor 4T-replicate

description:
Hi-TGA4T-Cy5-464

Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.


title: Tgfa, tumor 4T

description:
Hi-TGA4T-Cy3-463

Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.


title: Normal mouse liver (mouse #5)-replicate

description:
Hi-WT5NL-Cy5-264

Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.


title: Tgfa, tumor 3T

description:
Hi-TGA3T-Cy3-461

Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.


title: Tgfa, tumor 1T-replicate

description:
Hi-TGA1T-Cy5-458

Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.


title: Tgfa, tumor 1T

description:
Hi-TGA1T-Cy3-457

Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.


title: Tgfa, tumor 3T-replicate

description:
Hi-TGA3T-Cy5-462

Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.


title: Tgfa, tumor 2T-replicate

description:
Hi-TGA2T-Cy5-460

Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.


title: Myc/Tgfa, tumor 9T1-replicate

description:
Hi-MA9T1-Cy5-42

c-Myc/Tgfa double-transgenic mice were produced by crossing homozygous B6CBA Alb/c-Myc and B6CBAxCD1 Mt/Tgfα single transgenic mice.
Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.

source_name: Myc/Tgfa, tumor, 9 months

value: c-Myc/Tgfa double-transgenic

value: 9 months


title: Tgfa, tumor 2T

description:
Hi-TGA2T-Cy3-459

Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.


title: Tgfa, tumor 5T

description:
Hi-TGA5T-Cy3-465

Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.


title: Myc/Tgfa, tumor 8T5-replicate

description:
Hi-MA8T5-Cy5-40

c-Myc/Tgfa double-transgenic mice were produced by crossing homozygous B6CBA Alb/c-Myc and B6CBAxCD1 Mt/Tgfα single transgenic mice.
Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.


title: Myc/Tgfa, tumor 8T5

description:
Hi-MA8T5-Cy3-39

c-Myc/Tgfa double-transgenic mice were produced by crossing homozygous B6CBA Alb/c-Myc and B6CBAxCD1 Mt/Tgfα single transgenic mice.
Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.


title: Myc/Tgfa, tumor 9T1

description:
Hi-MA9T1-Cy3-41

c-Myc/Tgfa double-transgenic mice were produced by crossing homozygous B6CBA Alb/c-Myc and B6CBAxCD1 Mt/Tgfα single transgenic mice.
Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.


title: Myc/Tgfa, tumor 6T1-replicate

description:
Hi-MA6T1-Cy5-296

c-Myc/Tgfa double-transgenic mice were produced by crossing homozygous B6CBA Alb/c-Myc and B6CBAxCD1 Mt/Tgfα single transgenic mice.
Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.


title: Myc/Tgfa, tumor 3T1-replicate

description:
Hi-MA3T1-Cy5-144

c-Myc/Tgfa double-transgenic mice were produced by crossing homozygous B6CBA Alb/c-Myc and B6CBAxCD1 Mt/Tgfα single transgenic mice.
Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.


title: Myc/Tgfa, tumor 5T3-replicate

description:
Hi-MA5T3-Cy5-148

c-Myc/Tgfa double-transgenic mice were produced by crossing homozygous B6CBA Alb/c-Myc and B6CBAxCD1 Mt/Tgfα single transgenic mice.
Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.


title: Myc/Tgfa, dysplastic liver (3 weeks) 34

description:
Hi-MA34L-Cy3-541

c-Myc/Tgfa double-transgenic mice were produced by crossing homozygous B6CBA Alb/c-Myc and B6CBAxCD1 Mt/Tgfα single transgenic mice.
Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.

source_name: Myc/Tgfa, dysplastic liver, 3 weeks

value: mild hepatocyte dysplasia


title: Myc/Tgfa, tumor 7T1-replicate

description:
Hi-MA7T1-Cy5-160

c-Myc/Tgfa double-transgenic mice were produced by crossing homozygous B6CBA Alb/c-Myc and B6CBAxCD1 Mt/Tgfα single transgenic mice.
Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.


title: Myc/Tgfa, tumor 5T3

description:
Hi-MA5T3-Cy3-147

c-Myc/Tgfa double-transgenic mice were produced by crossing homozygous B6CBA Alb/c-Myc and B6CBAxCD1 Mt/Tgfα single transgenic mice.
Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.


title: Myc/Tgfa, dysplastic liver (3 weeks) 33-replicate

description:
Hi-MA33L-Cy5-540

c-Myc/Tgfa double-transgenic mice were produced by crossing homozygous B6CBA Alb/c-Myc and B6CBAxCD1 Mt/Tgfα single transgenic mice.
Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.


title: Myc/Tgfa, tumor 3T1

description:
Hi-MA3T1-Cy3-143

c-Myc/Tgfa double-transgenic mice were produced by crossing homozygous B6CBA Alb/c-Myc and B6CBAxCD1 Mt/Tgfα single transgenic mice.
Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.


title: UHRR-9

status: Public on Sep 29 2011

city: Toronto

first: Dong-Yu

last: Wang

address: 610 University Ave

country: Canada

institute: UHN-PMH-OCI

description: replicate 9

hyb_protocol: 750 ng of labeled cRNA were applied to Illimuna whole-genome gene expression HumanRef-8 v2 BeadChips for a overnight hybridization at 58°C.

scan_protocol: Signal is developed with streptavidin-Cy3 and the BeadChip is scanned with the Illumina BeadArray Reader.

data_processing: Image data were processed by BeadStudio software using background subtraction and Quantile normalization.

label: Biotin

organism: Homo sapiens

source_name: Stratagene Universal Human Reference RNA (Catalog #740000)

label_protocol: 250 ng of total RNA were converted to cDNA, followed by an in vitro transcription amplification step to generate biotin-labeled cRNA using the Ambion Illumina TotalPrep RNA Amplification Kit (Applied Biosystems, Austin, TX).

extract_protocol: Statagene Universal Reference RNA

value: Reference RNA


title: Primary MG calcium D14_Biological Replicate 3

city: Boston

first: David

middle: A

last: Sullivan

state: MA

address: 20 Staniford Street

institute: Schepens Eye Research Institute

description: replicate 3

hyb_protocol: cRNA/hybridization buffer mixtures were incubated at 65°C for 5 minutes, followed by brief centrifugation to collect.  The mixtures were added to BeadChips and then BeadChips inserted into hybridization chambers, and hybridization was carried out at 58°C for 16-18 hours at rocking speed set to 5.  BeadChips were washed and stained in the following steps:  1) 55°C for 10 minutes static in HighTemp Wash Buffer in a Hybex waterbath, 2) ambient temperature shaking for 5 minutes in E1BC wash buffer, 3) ambient temperature shaking for 10 minutes in ethanol, 4) ambient temperature shaking for 2 minutes in E1BC buffer, 5) ambient temperature for 10 minutes rocking in Block E1 buffer, 6) ambient temperature for 10 minutes rocking in Block E1 buffer containing 1ug/ml Cy3-streptavidin, and 7) ambient temperature shaking for 5 minutes in E1BC buffer.

scan_protocol: BeadArrays were dried in a centrifuge for 4 minutes and scanned using a BeadArray scanner.  Illumina BeadScan software was used to produce .idat, .xml, and .tif files for each array on a slide and .sdf files for each barcode on a slide of 12 arrays.  Raw data were extracted using Illumina BeadStudio software v 3.   Following quality assessment, data from the replicate beads on each array were summarized into raw intensity values with and without background subtraction in an Excel report containing the project description (sample key), gene identifiers and corresponding probe IDs, table of detection p-values, tables of normalized data with and without background subtraction, array quality control metrics, and array quality control metric cut-offs and definitions.

data_processing: The data were normalised using background subtraction and cubic spline normalization. Normalized hybridization intensity values were adjusted by adding a constant such that the lowest intensity value for any sample equaled 16

source_name: Primary cultured meibomian gland epithelial cells

label_protocol: Biotinylated cRNA were prepared using a MessageAmp™ II-based protocol (Ambion Inc., Austin, TX) and one round of amplification. The cRNA yields were quantified by UV spectrophotometry and the distribution of transcript sizes was assessed using the Agilent Bioanalyzer 2100 capillary electrophoresis system.  Labeled cRNA was used to probe HumanHT-12 v3 Expression BeadChips.

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

tag: cell type

tag: condition

value: calcium D14


title: Myc/Tgfa, dysplastic liver (3 weeks) 33

description:
Hi-MA33L-Cy3-539

c-Myc/Tgfa double-transgenic mice were produced by crossing homozygous B6CBA Alb/c-Myc and B6CBAxCD1 Mt/Tgfα single transgenic mice.
Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.


title: Myc/Tgfa, tumor 7T1

description:
Hi-MA7T1-Cy3-159

c-Myc/Tgfa double-transgenic mice were produced by crossing homozygous B6CBA Alb/c-Myc and B6CBAxCD1 Mt/Tgfα single transgenic mice.
Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.


title: Myc/Tgfa, tumor 4T3

description:
Hi-MA4T3-Cy3-145

c-Myc/Tgfa double-transgenic mice were produced by crossing homozygous B6CBA Alb/c-Myc and B6CBAxCD1 Mt/Tgfα single transgenic mice.
Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.


title: Primary MG KGM D14_Biological Replicate 3

description: replicate 3

value: Primary cultured meibomian gland epithelial cells

value: KGM D14


title: Myc/Tgfa, surrounding tissue 4

description:
Hi-MA4ST-Cy3-123

c-Myc/Tgfa double-transgenic mice were produced by crossing homozygous B6CBA Alb/c-Myc and B6CBAxCD1 Mt/Tgfα single transgenic mice.
Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.

source_name: Myc/Tgfa, surrounding tissue, 9 months

value: severe hepatocyte dysplasia

value: wild-type


title: Myc/Tgfa, tumor 6T1

description:
Hi-MA6T1-Cy3-295

c-Myc/Tgfa double-transgenic mice were produced by crossing homozygous B6CBA Alb/c-Myc and B6CBAxCD1 Mt/Tgfα single transgenic mice.
Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.

value: liver


title: Myc/Tgfa, surrounding tissue 3

description:
Hi-MA3ST-Cy3-121

c-Myc/Tgfa double-transgenic mice were produced by crossing homozygous B6CBA Alb/c-Myc and B6CBAxCD1 Mt/Tgfα single transgenic mice.
Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.

value: normal


title: Primary MG calcium D14_Biological Replicate 1

description: replicate 1


title: Myc/Tgfa, surrounding tissue 3-replicate

description:
Hi-MA3ST-Cy5-122

c-Myc/Tgfa double-transgenic mice were produced by crossing homozygous B6CBA Alb/c-Myc and B6CBAxCD1 Mt/Tgfα single transgenic mice.
Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.

value: 3 months


title: Myc/Tgfa, tumor 4T3-replicate

description:
Hi-MA4T3-Cy5-146

c-Myc/Tgfa double-transgenic mice were produced by crossing homozygous B6CBA Alb/c-Myc and B6CBAxCD1 Mt/Tgfα single transgenic mice.
Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.

value: reference


title: Myc/Tgfa, dysplastic liver (3 weeks) 32-replicate

description:
Hi-MA32L-Cy5-538

c-Myc/Tgfa double-transgenic mice were produced by crossing homozygous B6CBA Alb/c-Myc and B6CBAxCD1 Mt/Tgfα single transgenic mice.
Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.

value: male

value: 3 weeks


title: Primary MG KGM D14_Biological Replicate 2

description: replicate 2


title: Primary MG KGM D14_Biological Replicate 1

description: replicate 1


title: Myc/Tgfa, dysplastic liver (3 weeks) 34-replicate

description:
Hi-MA34L-Cy5-542

c-Myc/Tgfa double-transgenic mice were produced by crossing homozygous B6CBA Alb/c-Myc and B6CBAxCD1 Mt/Tgfα single transgenic mice.
Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.


title: Myc/Tgfa, dysplastic liver (3 weeks) 32

description:
Hi-MA32L-Cy3-537

c-Myc/Tgfa double-transgenic mice were produced by crossing homozygous B6CBA Alb/c-Myc and B6CBAxCD1 Mt/Tgfα single transgenic mice.
Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.


title: Myc/Tgfa, dysplastic liver (3 weeks) 30-replicate

description:
Hi-MA30L-Cy5-534

c-Myc/Tgfa double-transgenic mice were produced by crossing homozygous B6CBA Alb/c-Myc and B6CBAxCD1 Mt/Tgfα single transgenic mice.
Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.


title: Myc/Tgfa, surrounding tissue 4-replicate

description:
Hi-MA4ST-Cy5-124

c-Myc/Tgfa double-transgenic mice were produced by crossing homozygous B6CBA Alb/c-Myc and B6CBAxCD1 Mt/Tgfα single transgenic mice.
Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.


title: Myc/Tgfa, dysplastic liver (3 weeks) 31-replicate

description:
Hi-MA31L-Cy5-536

c-Myc/Tgfa double-transgenic mice were produced by crossing homozygous B6CBA Alb/c-Myc and B6CBAxCD1 Mt/Tgfα single transgenic mice.
Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.


title: Primary MG serum D14_Biological Replicate 3

description: replicate 3

value: serum D14


title: Myc/Tgfa, dysplastic liver (3 weeks) 31

description:
Hi-MA31L-Cy3-535

c-Myc/Tgfa double-transgenic mice were produced by crossing homozygous B6CBA Alb/c-Myc and B6CBAxCD1 Mt/Tgfα single transgenic mice.
Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.


title: Myc/Tgfa, tumor 2T2-replicate

description:
Hi-MA2T2-Cy5-140

c-Myc/Tgfa double-transgenic mice were produced by crossing homozygous B6CBA Alb/c-Myc and B6CBAxCD1 Mt/Tgfα single transgenic mice.
Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.

value: hepatocellular carcinoma (HCC)


title: Primary MG serum D14_Biological Replicate 2

description: replicate 2


title: Primary MG undifferentiated_Biological Replicate 2

description: replicate 2

value: undifferentiated


title: Primary MG undifferentiated_Biological Replicate 1

description: replicate 1


title: hTERT MG undifferentiated_Biological Replicate 3

description: replicate 3

source_name: hTERT immortalized meibomian gland epithelial cells


title: Myc/Tgfa, surrounding tissue 2-replicate

description:
Hi-MA2ST-Cy5-120

c-Myc/Tgfa double-transgenic mice were produced by crossing homozygous B6CBA Alb/c-Myc and B6CBAxCD1 Mt/Tgfα single transgenic mice.
Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.

value: c-Myc/Tgfa double-transgenic

value: 9 months


title: Myc/Tgfa, surrounding tissue 2

description:
Hi-MA2ST-Cy3-119

c-Myc/Tgfa double-transgenic mice were produced by crossing homozygous B6CBA Alb/c-Myc and B6CBAxCD1 Mt/Tgfα single transgenic mice.
Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.


title: Myc/Tgfa, dysplastic liver (3 months) 23

description:
Hi-MA23L-Cy3-377

c-Myc/Tgfa double-transgenic mice were produced by crossing homozygous B6CBA Alb/c-Myc and B6CBAxCD1 Mt/Tgfα single transgenic mice.
Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.

source_name: Myc/Tgfa, dysplastic liver, 3 months


title: Myc/Tgfa, dysplastic liver (3 weeks) 30

description:
Hi-MA30L-Cy3-533

c-Myc/Tgfa double-transgenic mice were produced by crossing homozygous B6CBA Alb/c-Myc and B6CBAxCD1 Mt/Tgfα single transgenic mice.
Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.

value: mild hepatocyte dysplasia


title: Myc/Tgfa, dysplastic liver (3 months) 24-replicate

description:
Hi-MA24L-Cy5-380

c-Myc/Tgfa double-transgenic mice were produced by crossing homozygous B6CBA Alb/c-Myc and B6CBAxCD1 Mt/Tgfα single transgenic mice.
Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.


title: hTERT MG KGM D14_Biological Replicate 3

description: replicate 3

value: hTERT immortalized meibomian gland epithelial cells


title: hTERT MG KGM D14_Biological Replicate 2

description: replicate 2


title: hTERT MG calcium D14_Biological Replicate 2

description: replicate 2

value: calcium D14


title: Myc/Tgfa, dysplastic liver (3 months) 22-replicate

description:
Hi-MA22L-Cy5-376

c-Myc/Tgfa double-transgenic mice were produced by crossing homozygous B6CBA Alb/c-Myc and B6CBAxCD1 Mt/Tgfα single transgenic mice.
Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.


title: Myc/Tgfa, dysplastic liver (3 months) 24

description:
Hi-MA24L-Cy3-379

c-Myc/Tgfa double-transgenic mice were produced by crossing homozygous B6CBA Alb/c-Myc and B6CBAxCD1 Mt/Tgfα single transgenic mice.
Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.


title: hTERT MG KGM D14_Biological Replicate 1

description: replicate 1

value: KGM D14


title: hTERT MG calcium D14_Biological Replicate 3

description: replicate 3


title: Primary MG serum D14_Biological Replicate 1

description: replicate 1

value: Primary cultured meibomian gland epithelial cells


title: Myc/Tgfa, tumor 2T2

description:
Hi-MA2T2-Cy3-139

c-Myc/Tgfa double-transgenic mice were produced by crossing homozygous B6CBA Alb/c-Myc and B6CBAxCD1 Mt/Tgfα single transgenic mice.
Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.

value: wild-type


title: hTERT MG calcium D14_Biological Replicate 1

description: replicate 1


title: Myc/Tgfa, dysplastic liver (3 months) 21-replicate

description:
Hi-MA21L-Cy5-374

c-Myc/Tgfa double-transgenic mice were produced by crossing homozygous B6CBA Alb/c-Myc and B6CBAxCD1 Mt/Tgfα single transgenic mice.
Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.

value: liver

value: severe hepatocyte dysplasia


title: Primary MG calcium D14_Biological Replicate 2

description: replicate 2


title: Myc/Tgfa, dysplastic liver (3 months) 21

description:
Hi-MA21L-Cy3-373

c-Myc/Tgfa double-transgenic mice were produced by crossing homozygous B6CBA Alb/c-Myc and B6CBAxCD1 Mt/Tgfα single transgenic mice.
Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.

value: 3 months

value: normal


title: Primary MG undifferentiated_Biological Replicate 3

description: replicate 3


title: Myc/Tgfa, dysplastic liver (3 months) 22

description:
Hi-MA22L-Cy3-375

c-Myc/Tgfa double-transgenic mice were produced by crossing homozygous B6CBA Alb/c-Myc and B6CBAxCD1 Mt/Tgfα single transgenic mice.
Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.

value: male

value: reference


title: Myc/Tgfa, dysplastic liver (3 months) 23-replicate

description:
Hi-MA23L-Cy5-378

c-Myc/Tgfa double-transgenic mice were produced by crossing homozygous B6CBA Alb/c-Myc and B6CBAxCD1 Mt/Tgfα single transgenic mice.
Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.


title: hTERT MG serum D14_Biological Replicate 2

description: replicate 2

value: serum D14


title: hTERT MG undifferentiated_Biological Replicate 2

description: replicate 2


title: hTERT MG serum D14_Biological Replicate 3

description: replicate 3


title: hTERT MG serum D14_Biological Replicate 1

description: replicate 1


title: Myc/Tgfa, dysplastic liver (3 months) 20

description:
Hi-MA20L-Cy3-371

c-Myc/Tgfa double-transgenic mice were produced by crossing homozygous B6CBA Alb/c-Myc and B6CBAxCD1 Mt/Tgfα single transgenic mice.
Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.


title: Myc/Tgfa, tumor 1T1-replicate

description:
Hi-MA1T1-Cy5-142

c-Myc/Tgfa double-transgenic mice were produced by crossing homozygous B6CBA Alb/c-Myc and B6CBAxCD1 Mt/Tgfα single transgenic mice.
Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.

value: hepatocellular carcinoma (HCC)


title: Myc/Tgfa, dysplastic liver (3 months) 20-replicate

description:
Hi-MA20L-Cy5-372

c-Myc/Tgfa double-transgenic mice were produced by crossing homozygous B6CBA Alb/c-Myc and B6CBAxCD1 Mt/Tgfα single transgenic mice.
Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.


title: hTERT MG undifferentiated_Biological Replicate 1

description: replicate 1

value: undifferentiated


title: Myc/Tgfa, surrounding tissue 18-replicate

description:
Hi-MA18ST-Cy5-128

c-Myc/Tgfa double-transgenic mice were produced by crossing homozygous B6CBA Alb/c-Myc and B6CBAxCD1 Mt/Tgfα single transgenic mice.
Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.

value: c-Myc/Tgfa double-transgenic


title: T CD8 Tim, IL7 treated, rep2

city: Lyon

first: erwan

last: ventre

address: 21, avenue Tony Garnier

country: France

institute: INSERM U851

hyb_protocol: Fragmentation and Hybridation of 15 µg cRNA on GeneChip Mouse Genome 430 2.0 Array (Affymetrix)

scan_protocol: Microarrays were scanned using GeneChip Scanner 3000 7G

data_processing: The data was analysed with GeneSpring GX software and affy and limma Bioconductor/R packages. The R scripts were directly called by the GeneSpring editor. The data preprocessing included probe summarization (RMA technology) and quantile normalization. All comparisons of mRNA expression levels between the groups were performed using LIMMA method (moderated t-statistics).

label: biotin

source_name: mRNAs isolated from Tim CD8 memory cells incubated with IL7 for 20h in vitro

label_protocol: 50ng of RNA was amplified using MessageAmp II kit (Ambion) and labelled using IVT labeling kit (Affymetrix)

growth_protocol: TIM memory cells were generated immunizing twice naïve F5 mice with the NP68 peptide. Memory cells were analysed at day 45.

extract_protocol: F5 Naive CD8 T cells and F5 TIM memory CD8 T cells were sorted from the spleen using flow cytometry. RNAs were extracted using RNeasy kit (Qiagen)

treatment_protocol: Sorted naive cells and TIM memory cells were incubated 20 hours at a concentration of 3.106 cells/mL in presence or absence of IL-7 at a concentration of 10 ng/mL and/or IL-4 at a concentration of 20 ng/mL.

tag: treatment

value: incubated with IL7 for 20h in vitro


title: Myc/Tgfa, tumor 1T1

description:
Hi-MA1T1-Cy3-141

c-Myc/Tgfa double-transgenic mice were produced by crossing homozygous B6CBA Alb/c-Myc and B6CBAxCD1 Mt/Tgfα single transgenic mice.
Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.

value: 9 months


title: Myc/Tgfa, surrounding tissue 17-replicate

description:
Hi-MA17ST-Cy5-126

c-Myc/Tgfa double-transgenic mice were produced by crossing homozygous B6CBA Alb/c-Myc and B6CBAxCD1 Mt/Tgfα single transgenic mice.
Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.


title: T CD8 Tim, medium, rep2

source_name: mRNAs isolated from Tim CD8 memory cells incubated 20h in vitro

value: incubated 20h in vitro


title: Myc/Tgfa, dysplastic liver (3 months) 19-replicate

description:
Hi-MA19L-Cy5-370

c-Myc/Tgfa double-transgenic mice were produced by crossing homozygous B6CBA Alb/c-Myc and B6CBAxCD1 Mt/Tgfα single transgenic mice.
Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.


title: Myc/Tgfa, dysplastic liver (3 months) 19

description:
Hi-MA19L-Cy3-369

c-Myc/Tgfa double-transgenic mice were produced by crossing homozygous B6CBA Alb/c-Myc and B6CBAxCD1 Mt/Tgfα single transgenic mice.
Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.


title: chronic pancreatitis 1

city: Bochum

first: Stephan

last: Hahn

address: Universitaetsstrasse 150

department: MGO

country: Germany

institute: Ruhr-University Bochum

description: miRNA expression

hyb_protocol: The hybridization mixture [10X GE blocking agent (4.5 ul), 2X Hi-RPM hybridization buffer (22.5ul)] along with labeled miRNA sample was heated for 5 min at 100 °C and immediately cooled to 0 °C. Each 45 mL sample was hybridized onto a microarray at 55 °C for 21 h. Slides were washed 5 min in GE wash buffer 1 at RT and again for 5 min in GE wash buffer 2 at 37 °C, followed by an acetonitrile wash for 10 sec at RT to dry the slides completely.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B ) using one color scan setting for 8x15k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%, No XDR).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol miRNA_107_Sep09 and Grid: 019118_D_F_20100604) to obtain background subtracted and spatially detrended Processed Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: chronic pancreatitis, pancreas,xenograft, fresh frozen, macrodissected

label_protocol: miRNA labeling was performed as described in Agilent miRNA microarray protocol version 2.0 using Agilent miRNA labeling kit. 100 ng of total RNA was dephosphorylated with calf intestine alkaline phosphatase for 30 min at 37°C. Denaturation was performed by adding DMSO and incubating at 100°C for 6 min and immediately transferred to ice water bath. Ligation was performed with pCp-Cy3 at 16 °C for 2 h. The labeled samples were dried completely in a vaccum concentrator and resuspended in 18 ul of nuclease free water.

extract_protocol: RNA isolation from microdissected cells was performed using the RNAqueous-Micro kit (Ambion); RNA from macrodisected cryostat sections was isolated using the mirVana PARIS RNA Isolation Kit (Ambion). In all instances RNA isolation was performed according to the manufacturer’s instructions. Total-RNA concentration and purity of total-RNA samples was measured with the NanoDrop 1000 spectrophotometer (NanoDrop Technologies/Thermo Scientific). Furthermore, total-RNA used for microarray analyses were further quantified using the Qubit RNA Assay kit (Invitorgen)


title: chronic pancreatitis 2

description: miRNA expression

value: chronic pancreatitis, pancreas,xenograft, fresh frozen, macrodissected


title: Myc/Tgfa, surrounding tissue 17

description:
Hi-MA17ST-Cy3-125

c-Myc/Tgfa double-transgenic mice were produced by crossing homozygous B6CBA Alb/c-Myc and B6CBAxCD1 Mt/Tgfα single transgenic mice.
Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.


title: T CD8 Tim, IL7 treated, rep1

value: Tim CD8 memory cells incubated with IL7 for 20h in vitro


title: Myc/Tgfa, surrounding tissue 18

description:
Hi-MA18ST-Cy3-127

c-Myc/Tgfa double-transgenic mice were produced by crossing homozygous B6CBA Alb/c-Myc and B6CBAxCD1 Mt/Tgfα single transgenic mice.
Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.


title: Cancer 4

description: miRNA expression

source_name: Cancer cells, pancreas,xeograft, fresh frozen, microdissected


title: Myc/Tgfa, tumor 16T1-replicate

description:
Hi-MA16T1-Cy5-10

c-Myc/Tgfa double-transgenic mice were produced by crossing homozygous B6CBA Alb/c-Myc and B6CBAxCD1 Mt/Tgfα single transgenic mice.
Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.


title: Cancer 5

description: miRNA expression

value: Cancer cells, pancreas,xeograft, fresh frozen, microdissected


title: Myc/Tgfa, tumor 15T1

description:
Hi-MA15T1-Cy3-7

c-Myc/Tgfa double-transgenic mice were produced by crossing homozygous B6CBA Alb/c-Myc and B6CBAxCD1 Mt/Tgfα single transgenic mice.
Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.

value: wild-type


title: Myc/Tgfa, tumor 14T-replicate

description:
Hi-MA14T-Cy5-46

c-Myc/Tgfa double-transgenic mice were produced by crossing homozygous B6CBA Alb/c-Myc and B6CBAxCD1 Mt/Tgfα single transgenic mice.
Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.

value: liver


title: T CD8 Tim, medium, rep1

value: Tim CD8 memory cells incubated 20h in vitro


title: T CD8 Tim, IL4 and IL7 treated, rep2

source_name: mRNAs isolated from Tim CD8 memory cells incubated with IL4 and IL7, for 20h in vitro


title: chronic pancreatitis 3

description: miRNA expression


title: chronic pancreatitis 4

description: miRNA expression


title: Myc/Tgfa, tumor 15T1-replicate

description:
Hi-MA15T1-Cy5-8

c-Myc/Tgfa double-transgenic mice were produced by crossing homozygous B6CBA Alb/c-Myc and B6CBAxCD1 Mt/Tgfα single transgenic mice.
Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.

value: 3 months


title: Myc/Tgfa, tumor 14T

description:
Hi-MA14T-Cy3-45

c-Myc/Tgfa double-transgenic mice were produced by crossing homozygous B6CBA Alb/c-Myc and B6CBAxCD1 Mt/Tgfα single transgenic mice.
Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.

value: normal


title: Myc/Tgfa, tumor 16T1

description:
Hi-MA16T1-Cy3-9

c-Myc/Tgfa double-transgenic mice were produced by crossing homozygous B6CBA Alb/c-Myc and B6CBAxCD1 Mt/Tgfα single transgenic mice.
Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.

value: male


title: T CD8 Tim, IL4 treated, rep2

source_name: mRNAs isolated from Tim CD8 memory cells incubated with IL4 for 20h in vitro

value: incubated with IL4 for 20h in vitro


title: T CD8 Tim, IL4 and IL7 treated, rep1

value: Tim CD8 memory cells incubated with IL4 and IL7, for 20h in vitro


title: Myc/Tgfa, tumor 13T2

description:
Hi-MA13T2-Cy3-23

c-Myc/Tgfa double-transgenic mice were produced by crossing homozygous B6CBA Alb/c-Myc and B6CBAxCD1 Mt/Tgfα single transgenic mice.
Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.

value: hepatocellular carcinoma (HCC)

value: reference


title: T CD8 Naive, IL4 and IL7 treated, rep2

source_name: mRNAs isolated from Naïve CD8 memory cells incubated with IL4 and IL7, for 20h in vitro


title: Cancer 3

description: miRNA expression


title: Myc/Tgfa, tumor 13T2-replicate

description:
Hi-MA13T2-Cy5-24

c-Myc/Tgfa double-transgenic mice were produced by crossing homozygous B6CBA Alb/c-Myc and B6CBAxCD1 Mt/Tgfα single transgenic mice.
Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.

value: c-Myc/Tgfa double-transgenic

source_name: Reference RNA


title: Myc/Tgfa, tumor 11T1-replicate

description:
Hi-MA11T1-Cy5-44

c-Myc/Tgfa double-transgenic mice were produced by crossing homozygous B6CBA Alb/c-Myc and B6CBAxCD1 Mt/Tgfα single transgenic mice.
Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.


title: Cancer 1

description: miRNA expression


title: Cancer 2

description: miRNA expression


title: Myc/Tgfa, tumor 10T1-replicate

description:
Hi-MA10T1-Cy5-5

c-Myc/Tgfa double-transgenic mice were produced by crossing homozygous B6CBA Alb/c-Myc and B6CBAxCD1 Mt/Tgfα single transgenic mice.
Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.


title: T CD8 Naive, IL7 treated, rep2

source_name: mRNAs isolated from Naïve CD8 memory cells incubated with IL7, for 20h in vitro

value: incubated with IL7, for 20h in vitro


title: T CD8 Tim, IL4 treated, rep1

value: Tim CD8 memory cells incubated with IL4 for 20h in vitro


title: Myc/Tgfa, tumor 10T1

description:
Hi-MA10T1-Cy3-6

c-Myc/Tgfa double-transgenic mice were produced by crossing homozygous B6CBA Alb/c-Myc and B6CBAxCD1 Mt/Tgfα single transgenic mice.
Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.

value: 9 months


title: Myc/Tgfa, tumor 11T1

description:
Hi-MA11T1-Cy3-43

c-Myc/Tgfa double-transgenic mice were produced by crossing homozygous B6CBA Alb/c-Myc and B6CBAxCD1 Mt/Tgfα single transgenic mice.
Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.


title: T CD8 Naive, IL4 and IL7 treated, rep1

value: Naïve CD8 memory cells incubated with IL4 and IL7, for 20h in vitro


title: Ductal 4

description: miRNA expression

source_name: Ductal cells, pancreas, fresh frozen, microdissected


title: c-Myc, tumor 7T3, RNA-136, Cy3

description:
Hi-M7T3-Cy3-181

Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.

source_name: c-Myc, tumor, 18 months

value: c-Myc transgenic

value: 18 months


title: c-Myc, tumor 8T1

description:
Hi-M8T1-Cy3-183

Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.

value: wild-type


title: T CD8 Naive, IL7 treated, rep1

value: Naïve CD8 memory cells incubated with IL7, for 20h in vitro


title: Ductal 3

description: miRNA expression

value: Ductal cells, pancreas, fresh frozen, microdissected


title: Acinar 4

description: miRNA expression

source_name: Acinar cells, pancreas, fresh frozen, microdissected


title: T CD8 Tim, ex vivo, biological rep4

source_name: mRNAs isolated from Tim CD8 memory cells

value: Tim CD8 memory cells


title: Ductal 2

description: miRNA expression


title: Ductal 1

description: miRNA expression


title: c-Myc, tumor 7T3-replicate

description:
Hi-M7T3-Cy5-182

Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.

value: liver

value: 3 months

value: normal


title: Acinar 3

description: miRNA expression

value: Acinar cells, pancreas, fresh frozen, microdissected


title: c-Myc, tumor 8T1-replicate

description:
Hi-M8T1-Cy5-184

Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.

value: male

value: hepatocellular carcinoma (HCC)


title: c-Myc, tumor 7T1

description:
Hi-M7T1-Cy3-167

Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.

value: reference


title: T CD8 Tim, ex vivo, biological rep1


title: c-Myc, tumor 6T2-replicate

description:
Hi-M6T2-Cy5-166

Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.


title: Acinar 2

description: miRNA expression


title: T CD8 Tim, ex vivo, biological rep3


title: c-Myc, tumor 5T2-replicate

description:
Hi-M5T2-Cy5-162

Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.


title: c-Myc. tumor 7T1-replicate

description:
Hi-M7T1-Cy5-168

Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.


title: c-Myc, tumor 6T1

description:
Hi-M6T1-Cy3-163

Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.


title: c-Myc, tumor 5T2

description:
Hi-M5T2-Cy3-161

Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.


title: WT mast cell rep3 vs p85α-KO mast cell rep3

city: Indianapolis

first: Raghuveer

last: Mali

state: Indiana

address: 1044 W Walnut St., R4 169

department: Pediatrics

institute: Indiana University School of Medicine

description: KIT and IgE receptor-double positive cells

hyb_protocol: WT and p85α-/- cDNAs labeled with fluorescent dye cy3 or cy5 was simultaneously hybridized overnight (17 hours, 65oC) to an Agilent whole-mouse genome oligo microarray 4 × 44K. In order to avoid differential incorporation of the 2 dyes into target samples, dye incorporation rate was carefully monitored. To avoid breakdown of cy5 by ozone, an ozone-free microarray facility in Miltenyi Biotech was maintained with specially installed ozone extractors.

scan_protocol: Subsequently, microarrays were washed and signals were detected using Agilents DNA microarray scanner.

data_processing: Agilent Feature Extraction Software (FES) was used to read out and process the microarray image files. The software determines feature intensities and ratios (including background subtraction and normalization), rejects outliers and calculates statistical confidences (p-values). A quantile normalization procedure was used to adjust for the difference in probe intensity.distribution across different chips. For our analysis, we included genes that showed a fold-change > 1.5 and p < 0.05.

source_name: WT bone marrow derived mast cell progenitors

label_protocol: 250 ng of WT and p85α-/- cDNAs was labeled with fluorescent dye cy3 or cy5.

growth_protocol: LDMNCs were harvested from 3 independent WT and p85α-/- mice and cultured in IMDM supplemented with 10% fetal bovine serum, 2% penicillin/streptomycin, and 10 ng/mL of IL-3 for 7 days. Cells were collected by centrifugation, resuspended in 200 μL PBS containing 0.2% BSA, and then incubated with 5 µg of anti-PE-KIT and anti-FITC-IgE antibody for 30 min at 4°C. Cells were washed with PBS containing 0.2% BSA to remove any unbound antibodies. The mast cell population that demonstrated double expression of KIT and IgE receptors was then sorted and collected.

extract_protocol: Frozen mast cells stimulated with SCF (100 ng/mL) from 3 independent WT and p85α-/- mice (as described above) were sent to Miltenyi Biotech to carry out the microarray analysis. Due to smaller sample size (<10,000 cells), super-amplification technology was used for the analysis. This amplification was based on a global PCR protocol using mRNA-derived cDNA. mRNA was isolated via magnetic bead technology. Amplified cDNA from the mRNA samples was quantified and quality was evaluated by capillary electrophoresis on an Agilent 2100 Bioanalyzer platform (Agilent Technologies; Santa Clara, CA).

treatment_protocol: The sorted KIT and IgE receptor double positive cells from WT and p85α-/- mice were stimulated with SCF (100 ng/mL) for 48 hours, after which, they were pelleted, frozen immediately and stored at -80oC until further use for microarray analysis.

value: Mast cell progenitors

tag: genotype/variation

value: wild type

source_name: p85α KO bone marrow derived mast cell progenitors

value: p85α KO


title: c-Myc, tumor 6T1-replicate

description:
Hi-M6T1-Cy5-164

Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.


title: WT mast cell rep2 vs p85α-KO mast cell rep2


title: Individual 18

status: Public on Sep 27 2011

city: Philadelphia

first: Leonard

middle: C.

last: Edelstein

state: PA

address: 1015 Walnut St.

department: Medicine/Hematology

institute: Thomas Jefferson University

hyb_protocol: Samples were hybridzied using Tecan hybridization stations in which the hybridization and washing steps are fully automated.

scan_protocol: Samples were scanned on Agilent G2505B Microarray Scanners operated in an ozone-free environment to avoid bleaching of the fluorescent labels. Image analysis was done with ImaGene.

data_processing: Data were background subtracted and LOWESS normalized using the Bioconductor LIMMA package.

source_name: Human platelets, hyporeactivity

label_protocol: RNA was labeled with the miRCURY LNA™ microRNA Power Labeling Kit.

extract_protocol: RNA was extracted from lymphocyte-depleted platelets using Trizol following the manufacturer's protocol.

value: platelets

tag: disease state

value: healthy

tag: platelet reactivity to 1.5 um epinephrine

value: hypo

source_name: Common reference

tag: composition

value: mixture of all the samples pooled together


title: Individual 16

source_name: Human platelets, hyperreactivity

value: hyper


title: Individual 19


title: Acinar 1

description: miRNA expression


title: c-Myc, tumor 6T2

description:
Hi-M6T2-Cy3-165

Reference sample described in PMID 17006931: Coulouarn et al., Hepatology. 2006 Oct;44(4):1003-11. Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis.

value: c-Myc transgenic

value: 18 months

value: wild-type


title: Individual 17


title: Follicular lymphoma FL12

first: Yuelin

middle: Jack

last: Zhu

address: 9000 Rockville Pike

department: Genetics Branch, Center for Cancer Research

institute: NCI

hyb_protocol: Hybridization and washing were performed according to the manufacturer's directions.

scan_protocol: Scanning was performed according to the manufacturer's directions.

data_processing:
Expression data were normalized by the VST-RSN method using the lumi R package available at Bioconductor.

Processed data was not provided for this Sample.

source_name: follicular lymphoma

label_protocol: Biotinylated cRNA was prepared using the Ambion TotalPrep RNA Amplification Kit starting with 200 ng total RNA.

extract_protocol: Total RNA was extracted using the Qiagen Kit.  Purification was performed on RNeasy columns according to the manufacturer’s instructions.

value: follicular lymphoma

tag: tissue processing

value: frozen


title: T CD8 Tim, ex vivo, biological rep2

value: Tim CD8 memory cells


title: chronic pancreatitis 5

description: miRNA expression

source_name: chronic pancreatitis, pancreas,xenograft, fresh frozen, macrodissected


title: WT mast cell rep1 vs p85α-KO mast cell rep1


title: T CD8 Naive, ex vivo, biological rep2

source_name: mRNAs isolated from Naïve CD8 memory cells

value: Naïve CD8 memory cells


title: T CD8 Naive, ex vivo, biological rep1


title: castlemans disease FH9

source_name: Castlemans disease

value: Castlemans disease tumor


title: Individual 15

value: reference


title: Individual 14


title: Individual 13


title: Individual 2


title: Individual 1


title: Follicular lymphoma FL11


title: Individual 4


title: Individual 3


title: Individual 6


title: Individual 8


title: Individual 9


title: Individual 10


title: Individual 7


title: Individual 11


title: Individual 5


title: Individual 12


title: Follicular lymphoma FL10


title: 25ERNEGTumor3

city: La Jolla

first: Steven

last: Head

state: CA

address: 10550 N Torrey Pines Rd

institute: The Scripps Research Institute

description: 25ERNEGTumor3: Human primary breast carcinoma negative tumor, replicate #3.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on the v4 GeneChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with RMA Express using the default settings (Background Adjust - Yes, Normalization - Quantile, Summarization Method - Median Polish, Store Residuals - unchecked).

source_name: Human primary breast carcinoma ER negative tumor

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 0.5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

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

tag: Sex

value: unknown

tag: estrogen receptor status

value: ER-

value: Breast Cancer


title: 64ERNEGTumor4

description: 64ERNEGTumor4: Human primary breast carcinoma negative tumor, replicate #4.

value: female


title: Follicular lymphoma FL9


title: 57ERNEGTumor2

description: 57ERNEGTumor2: Human primary breast carcinoma negative tumor, replicate #2.


title: 22ERNEGTumor1

description: 22ERNEGTumor1: Human primary breast carcinoma negative tumor, replicate #1.


title: Reactive lymph node FH10

source_name: reactive lymph node

value: reactive lymph node


title: Follicular lymphoma FL8


title: Reactive lymph node FH5


title: 48ERNEGTumor5

description: 48ERNEGTumor5: Human primary breast carcinoma negative tumor, replicate #5.


title: Follicular lymphoma FL7


title: Follicular lymphoma FL5


title: 67ERNEGTumor6

description: 67ERNEGTumor6: Human primary breast carcinoma negative tumor, replicate #6.


title: Follicular lymphoma FL4


title: Follicular lymphoma FL3


title: 16ERPOSTumor1

description: 16ERPOSTumor1: Human primary breast carcinoma positive tumor, replicate #1.

source_name: Human primary breast carcinoma ER positive tumor

value: ER+


title: 61ERNEGTumor7

description: 61ERNEGTumor7: Human primary breast carcinoma negative tumor, replicate #7.


title: 44ERNEGTumor8

description: 44ERNEGTumor8: Human primary breast carcinoma negative tumor, replicate #8.


title: 47ERNEGTumor9

description: 47ERNEGTumor9: Human primary breast carcinoma negative tumor, replicate #9.


title: 20ERNEGTumor10

description: 20ERNEGTumor10: Human primary breast carcinoma negative tumor, replicate #10.


title: Reactive lymph node FH3


title: 76ERPOSTumor2

description: 76ERPOSTumor2: Human primary breast carcinoma positive tumor, replicate #2.


title: 14ERPOSTumor4

description: 14ERPOSTumor4: Human primary breast carcinoma positive tumor, replicate #4.


title: 15ERPOSTumor5

description: 15ERPOSTumor5: Human primary breast carcinoma positive tumor, replicate #5.


title: B-CLL sample 7

city: Houston

first: Aaron

middle: E

last: Foster

state: TX

address: 2130 W Holcombe Blvd

department: Product Discovery

institute: Bellicum Pharmaceuticals

hyb_protocol: Hybridization performed per Miltenyi Biotec's standard MACS Molecular Agilent hybridization protocol

scan_protocol: Scanned on an Agilent G2505B scanner; Images were quantified using Agilent Feature Extraction Software (v.9.1)

data_processing: Agilent Feature Extraction Software (v.9.1) was used for background subtraction

source_name: CD5+CD19+ SP B-CLL

label_protocol: 250 ng of each of the cDNAs were used as template for Cy3 and Cy5 labeling which was performed according to Miltenyi Biotec’s undisclosed protocol

extract_protocol: Miltenyi Biotec SuperAmp extraction, amplification and purification

tag: tumor location

value: PBMC

tag: sorting selection

value: SP

source_name: CD5+CD19+ non-SP B-CLL

value: non-SP


title: B-CLL sample 9


title: B-CLL sample 5


title: Ta_anaerob_3

city: Martinsried (Planegg)

first: István

last: Nagy

address: Am Klopferspitz 18

department: Dept. of Structural Biology

institute: Max Planck Institute of Biochemistry

description: Thermoplasma acidophilum DSM 1728 cultured under anaerobic condition. It is the third of three biological replicates used in this experiment, each from separate cultures.

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

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

organism: Thermoplasma acidophilum DSM 1728

source_name: Thermoplasma acidophilum cultured under anaerobic condition

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: T. acidophilum DSM 1728 was cultured as described earlier with minor modification (Robb, F. T. and Place, A. R., Archaea: A Laboratory Manual, Thermophiles. 1995: Cold Spring Harbor Laboratory Press. 60-61). For aerobic cultures, pH was adjusted to 1.6 with H2SO4 (96%). 500 ml medium in a 1000 ml flask was inoculated with 2% starter culture and it was shaken at 120 rpm at 59 °C. Cell growth was stopped at the late-exponential growth phase (2 days).

extract_protocol: Total RNA of T. acidophilum was isolated with the RNeasy Protect Bacteria Kit (Qiagen). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer

treatment_protocol: For anaerobic cultures, cells were grown in medium, which was modified as follows: the pH was adjusted to 2.0 with H2SO4 (96%), 0.4% (w/v) S0 was added, the medium was heated at 100 °C for 30 min to sterilize the sulfur, and oxygen content was reduced by adding 1.2 g/l Na2S∙xH2O (x=7-9). Cell cultures were placed into a plastic beaker – to prevent corrosion – that was positioned in a Parr bomb 1.2 l metal container. The gas phase was filled with 80% N2/20% CO2 (pressure 2.5 kp/cm2) and the culture was agitated continuously at 300 rpm with a magnetic stirrer. Cells were grown at 59 °C for 4 days until late-exponential phase.

tag: growth protocol

value: anaerobic


title: 53ERPOSTumor3

description: 53ERPOSTumor3: Human primary breast carcinoma positive tumor, replicate #3.


title: Rfa1 ChIP from sub1D cells, replicate 2

type: genomic

city: Worcester

first: Oliver

last: Rando

address: 364 Plantation St.

institute: UMass Medical School

description:
Sample name: TS_4
YF1675 cells (isogenic to BY4741 but bearing a deletion of the Sub1 gene)  were grown to an OD of 0.5 in YPDextrose. Cells were crosslinked with formaldehyde (2%), and cell pellets were lysed by bead beating. Chromatin pellets were sonicated, and then subjected to immunoprecipitation with 1.5 ul  polyclonal Rfa1 antibody from Steven Brill.  As a reference, DNA was obtained from the input chromatin prior to antibody addition.
Raw data file: Agilent11003-4-sub1-rfa1-3f5

hyb_protocol: Amplified, labeled ChIP DNA were mixed, purified by microcon, and hybridized to the microarrays in Agilent hyb buffer for 16 hours at 65 degrees.

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000B fluorescent scanner at 5 micron resolution and image intensity data were extracted and analyzed with GenePix Pro 5.1 analysis software.

data_processing: After background correction and removal of flagged values, data was block normalized by dilation and log base 2 ratios (Cy5/Cy3) were calculated to produce the values given in the data table.

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: input

label_protocol: DNA was Klenow-labeled using Cy3-dCTP or Cy5-dCTP. The Cy5 and Cy3 labelled cDNAs were combined and purified with a Qiagen MinElute ERC cleanup kit.

extract_protocol: After immunoprecipitations, DNA was isolated via Pronase digestion and phenol:chloroform extraction, and was amplified by Round A-Round B PCR.

tag: genotype

value: sub1 deletion mutant

tag: chip antibody

value: input

source_name: Rfa1 ChIP

tag: chip antibody purveryor

value: Rabbit polyclonal antibody was a gift from Steven Brill (Department of Molecular Biology and Biochemistry, Rutgers University). SJ Brill and B Stillman, Genes Dev. 1991 5:1589-1600.


title: B-CLL sample 1

tag: patient


title: Rfa1 ChIP from sub1D cells, replicate 1

description:
Sample name: TS_3
YF1675 cells (isogenic to BY4741 but bearing a deletion of the Sub1 gene)  were grown to an OD of 0.5 in YPDextrose. Cells were crosslinked with formaldehyde (2%), and cell pellets were lysed by bead beating. Chromatin pellets were sonicated, and then subjected to immunoprecipitation with 1.5 ul  polyclonal Rfa1 antibody from Steven Brill.  As a reference, DNA was obtained from the input chromatin prior to antibody addition.
Raw data file: Agilent11003-3-sub1-rfa1-5f3

tag: strain


title: Ta_anaerob_2

description: Thermoplasma acidophilum DSM 1728 cultured under anaerobic condition. It is the second of three biological replicates used in this experiment, each from separate cultures.


title: B-CLL sample 8


title: 69ERPOSTumor7

description: 69ERPOSTumor7: Human primary breast carcinoma positive tumor, replicate #7.


title: B-CLL sample 3


title: B-CLL sample 4


title: B-CLL sample 6


title: B-CLL sample 2


title: Total RNA transcriptome R.conorii 4

city: Marseille

first: Aurélie

last: Renvoisé

address: 27 bd Jean Moulin

institute: Urmite

description: Concerning the raw data, the experiments were performed using dual colors labeling system. But the data corresponding to each channel were afterwards analyzed independently. For sample 4, data corresponding to Cy5 labelling were considered.

hyb_protocol: Hybridizations were performed for 17h at 62°C as previously described (Renesto et al, Plos One 2008)

scan_protocol: Slides were scanned using Agilent scanner (Agilent Technologies, CA, USA) with a 3 µm resolution and a 20 bit format. Data were extracted by Feature Extraction TM software (10.5.1.1 version, Agilent)

data_processing:
Data were normalized  using MIDAS software (Microarray Data Analysis System) (http://www.tm4.org/midas.html). Signal were transformed in log2 scale and local background signal were substracted. Negative values were considered as 0. FInally global normalization was applied to our datas.
Data were analyzed using Excel 2003 (Microsoft). A cut-off value defined as 2-standard deviation obtained for background intensities was then applied.

label: d-CTP Cy5

organism: Rickettsia conorii str. Malish 7

source_name: Transcriptome of R.conorii containing fraction of small RNA

label_protocol: Using the previously obtained RNA, cDNA synthesis was performed with M-MLV reverse transcriptase (Invitrogen) following the manufacturer’s instructions. 1µg cDNA was labelled with Cy3-dCTP and Cy5-dCTP (GE Healthcare) using BioPrime DNA labeling System (Invitrogen). Labelled cDNA was purified using Minelute Reaction Cleanup kit (Qiagen). The levels of Cy3-dCTP and Cy5-dCTP incorporation were quantified by absorbance measurement at 550 nm and 650 nm, respectively, on Nanodrop (ThermoFisher)

growth_protocol: XTC cells were infected by R.conorii (malish 7) for 4 days at 28°C. Cells were harvested and treated by trypsin to lyse the eukaryotic cells. Bacteria were purified by renograffin gradient

extract_protocol: Samples were diluted in 200 µl TE pH 7.8, and then incubated for 10 min at room temperature in the presence of lysozyme (10 mg/ml). The obtained supernatants were then treated following the miRNeasy purification kit protocol (Qiagen). Enriched fractions of small RNAs (<200 nt), as well as total RNA containing small RNAs were obtained. RNA samples were systematically treated by TURBO DNA Free kit (Ambion) and the presence of residual DNA was systematically checked by real time PCR. Final RNA was then characterized using small RNA chips (Agilent) combined with Bioanalyzer Agilent 2100.

value: malish 7


title: 72ERPOSTumor8

description: 72ERPOSTumor8: Human primary breast carcinoma positive tumor, replicate #8.


title: resistant cell, biological rep 2

city: Nashville

first: Bo

last: Lu

state: TN

address: 1301 22nd Avenue South

department: Radiation Oncology

institute: Vanderbilt University Medical Center

description: expression data of cisplatin resistant cell rep 2

hyb_protocol: Affymetrix reagent kits

scan_protocol: .CEL files were scanned using Affymetrix GeneChip Scanner 3000 7G.

data_processing: Raw data was processed using Affymetrix Expression Console with RMA normalization.

source_name: cisplatin resistant cell derived from H460

label_protocol: Affymetrix reagent kits

growth_protocol: DMEM with 10% FBS, 1% penicilin streptomycin

extract_protocol: Trizol followed by Qiagen coloumn clean up

tag: tissue type

value: lung

tag: cell type


title: resistant cell, biological rep 3

description: expression data of cisplatin resistant cell rep 3

value: cisplatin resistant cell derived from H460


title: Ta_anaerob_1

description: Thermoplasma acidophilum DSM 1728 cultured under anaerobic condition. It is the first of three biological replicates used in this experiment, each from separate cultures.


title: Rfa1 ChIP from wild-type cells, replicate 2

description:
Sample name: TS_2
BY4741 cells  were grown to an OD of 0.5 in YPDextrose. Cells were crosslinked with formaldehyde (2%), and cell pellets were lysed by bead beating. Chromatin pellets were sonicated, and then subjected to immunoprecipitation with 1.5 ul  polyclonal Rfa1 antibody from Steven Brill.  As a reference, DNA was obtained from the input chromatin prior to antibody addition.
Raw data file: Agilent11003-2-wt-rfa1-3f5

value: WT


title: 13ERPOSTumor6

description: 13ERPOSTumor6: Human primary breast carcinoma positive tumor, replicate #6.


title: Total RNA transcriptome R.conorii 2

description: Concerning the raw data, the experiments were performed using dual colors labeling system. But the data corresponding to each channel were afterwards analyzed independently. For sample 2, data corresponding to Cy3 labelling were considered.

label: d-CTP Cy3


title: H460 cell, biological rep 3

description: expression data of H460 rep 3

source_name: parental H460 cell

value: parental H460 cell


title: Ta_aerob_3

description: Thermoplasma acidophilum DSM 1728 cultured under aerobic condition. It is the third of three biological replicates used in this experiment, each from separate cultures.

source_name: Thermoplasma acidophilum cultured under aerobic condition

value: aerobic


title: 63ERPOSTumor9

description: 63ERPOSTumor9: Human primary breast carcinoma positive tumor, replicate #9.

value: Breast Cancer


title: Total RNA transcriptome R.conorii 3

description: Concerning the raw data, the experiments were performed using dual colors labeling system. But the data corresponding to each channel were afterwards analyzed independently. For sample 3, data corresponding to Cy5 labelling were considered.


title: Ta_aerob_2

description: Thermoplasma acidophilum DSM 1728 cultured under aerobic condition. It is the second of three biological replicates used in this experiment, each from separate cultures.


title: Rfa1 ChIP from wild-type cells, replicate 1

description:
Sample name: TS_1
BY4741 cells  were grown to an OD of 0.5 in YPDextrose. Cells were crosslinked with formaldehyde (2%), and cell pellets were lysed by bead beating. Chromatin pellets were sonicated, and then subjected to immunoprecipitation with 1.5 ul  polyclonal Rfa1 antibody from Steven Brill.  As a reference, DNA was obtained from the input chromatin prior to antibody addition.
Raw data file: Agilent11003-1-wt1-rfa1-5f3.gpr


title: Ta_aerob_1

description: Thermoplasma acidophilum DSM 1728 cultured under aerobic condition. It is the first of three biological replicates used in this experiment, each from separate cultures.


title: resistant cell, biological rep 1

description: expression data of cisplatin resistant cell rep 1


title: Total RNA transcriptome R.conorii 1

description: Concerning the raw data, the experiments were performed using dual colors labeling system. But the data corresponding to each channel were afterwards analyzed independently. For sample 1, data corresponding to Cy3 labelling were considered.


title: H460 cell, biological rep 2

description: expression data of H460 rep 2


title: H460 cell, biological rep 1

description: expression data of H460 rep 1


title: DU145 lacZ_3

status: Public on Sep 26 2011

first: Timothy

last: Thompson

state: Texas

address: 1515 Holcombe Blvd.

department: Genitourinary Medical Oncology

institute: MD Anderson Cancer Center

description: To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software. The whole 48803 probes on the Human-12 beadChip ver. 3 were used.

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

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

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

source_name: DU145 lacZ

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

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

tag: cell line


title: LNCaP GLIPR1_1

source_name: LNCaP GLIPR1

value: LNCaP


title: DU145 lacZ_1


title: DU145 GLIPR1_1

source_name: DU145 GLIPR1


title: VCaP lacZ_1

source_name: VCaP lacZ

value: VCaP


title: CaP GLIPR1_2

source_name: VCaP GLIPR1


title: LNCaP lacZ_1

source_name: LNCaP lacZ


title: LNCaP lacZ_2


title: VCaP lacZ_2


title: LNCaP lacZ_3


title: VCaP GLIPR1_1


title: LNCaP GLIPR1_2


title: VCaP GLIPR1_3


title: DU145 lacZ_2


title: VCaP lacZ_3


title: A97

city: New York

first: Yupu

last: Liang

state: NY

address: 1230 York Avenue

institute: The Rockefeller University

description: Genomic DNA from an MPM tumor for aCGH analysis.

hyb_protocol: Labelled cDNA was hybridized to the arrays at 20rpm at 65C for 40 hours following Agilent instructions.

scan_protocol: Slides were scanned using the Agilent Scanner with the standard protocols.

data_processing: The normalization is done through gcNormalization developed at MSKCC (http://cbio.mskcc.org/CGCC/methods_091022.pdf). The 'methods_091022.pdf' file is also linked to the Series record as a supplementary file.

source_name: Mesothelioma tumor, Sarc

label_protocol: Standard Agilent Cy5/Cy3 labeling protocols were used with 3ug of DNA.

extract_protocol: DNA was extracted using the Qiagen DNeasy Blood & Tissue Kit according to the manufacturer's instructions.

tag: tissue

value: malignant pleural mesothelioma (MPM)

tag: subtype

value: Sarc

source_name: Promega normal reference

tag: disease state

value: normal

tag: sample type

value: reference


title: A8


title: A92

source_name: Mesothelioma tumor, biphasic

value: biphasic


title: DU145 GLIPR1_3


title: A99

source_name: Mesothelioma tumor, epi

value: epi


title: LNCaP GLIPR1_3


title: A89


title: DU145 GLIPR1_2


title: A79


title: A90


title: A78


title: A73


title: A76


title: A75


title: A62


title: A69


title: A91


title: A7


title: A61


title: A6


title: A59


title: A42


title: A50


title: A32


title: A41


title: A49


title: A43


title: A52


title: A36


title: A33


title: A3


title: A46


title: A4


title: A20


title: A58


title: A37


title: A40


title: A44


title: A111


title: A28


title: A18


title: A53


title: A112


title: A17


title: miRNA_PBMCs_PRE exercise_12

city: Irvine

first: Shlomit

last: Radom-Aizik

address: 101 Academy

institute: University of California, Irvine

description: miRNA expression before-exercise

hyb_protocol: Cy3-labeled RNA from each sample was hybridized to an Agilent Human miRNA Version 2 Microarray.

scan_protocol: The hybridized array was then washed and scanned according to Agilent specifications and data was extracted from the scanned image using Feature Extraction version 10.2 (Agilent Technologies).

data_processing: The results were analyzed using GeneSpring GX 10.0.2 Software (Agilent Technologies, Inc).

source_name: Human PBMCs before exercise

label_protocol: One hundred ng of total RNA was labeled with the fluorescent dye Cyanine 3-pCp (Cy3) using the miRNA Labeling Reagent and Hybridization Kit (Agilent Technologies, Palo Alto, CA) following the manufacturer’s protocol.

extract_protocol: PBMCs were isolated from EDTA treated peripheral blood using OptiPrep Density Gradient Medium (SIGMA). Total RNA was extracted using TRIzol® (Gibco BRL Life Technologies, Rockville, MD).

treatment_protocol: Blood sample was drawn before and immediately after 30 min of exercise.

value: PBMCs

tag: exercise state

value: 30 before


title: miRNA_PBMCs_PEAK exercise_12

description: miRNA expression after-exercise

source_name: Human PBMCs after 30 min bout of exercise

value: 30 after


title: miRNA_PBMCs_PRE exercise_11

description: miRNA expression before-exercise


title: miRNA_PBMCs_PEAK exercise_11

description: miRNA expression after-exercise


title: miRNA_PBMCs_PRE exercise_10

description: miRNA expression before-exercise


title: miRNA_PBMCs_PEAK exercise_10

description: miRNA expression after-exercise


title: A108


title: miRNA_PBMCs_PEAK exercise_09

description: miRNA expression after-exercise


title: miRNA_PBMCs_PEAK exercise_08

description: miRNA expression after-exercise


title: miRNA_PBMCs_PRE exercise_07

description: miRNA expression before-exercise


title: miRNA_PBMCs_PRE exercise_09

description: miRNA expression before-exercise


title: A11


title: miRNA_PBMCs_PEAK exercise_07

description: miRNA expression after-exercise


title: miRNA_PBMCs_PRE exercise_06

description: miRNA expression before-exercise


title: miRNA_PBMCs_PEAK exercise_06

description: miRNA expression after-exercise


title: A105


title: miRNA_PBMCs_PRE exercise_05

description: miRNA expression before-exercise


title: miRNA_PBMCs_PRE exercise_08

description: miRNA expression before-exercise


title: miRNA_PBMCs_PRE exercise_04

description: miRNA expression before-exercise


title: A107


title: miRNA_PBMCs_PEAK exercise_04

description: miRNA expression after-exercise


title: A109


title: A104


title: miRNA_PBMCs_PEAK exercise_05

description: miRNA expression after-exercise


title: miRNA_PBMCs_PRE exercise_03

description: miRNA expression before-exercise


title: miRNA_PBMCs_PEAK exercise_03

description: miRNA expression after-exercise


title: miRNA_PBMCs_PRE exercise_02

description: miRNA expression before-exercise


title: A71


title: miRNA_PBMCs_PEAK exercise_02

description: miRNA expression after-exercise


title: miRNA_PBMCs_PRE exercise_01

description: miRNA expression before-exercise


title: A102


title: A30


title: A27


title: SYTSSX2-expressing, replicate 1

first: Josiane

last: Eid

address: 2220 Pierce Avenue

institute: Vanderbilt University

hyb_protocol: Sample cDNA was hybridized to Affymetrix Human Gene 1.0 ST array according to manufacturer's protocol.

scan_protocol: The arrays were scanned according to manufacturer's protocol (Affymetrix).

data_processing: The samples were normalized by RMA using Affymetrix GCOS and Expression Console software.

source_name: SYTSSX2-infected hMSCs, 48 hours post-infection

label_protocol: 5.5 ug cDNA was fragmented and end-labeled using WT terminal labeling kit (Affymetrix) according to manufacturer's protocol.

growth_protocol: Cells were maintained in alpha-MEM supplemented with 20% FBS, 1% L-glutamine, and 1% penicillin/streptomycin at 37˚C, 5% CO2.

extract_protocol: Four days post-infection, total RNA was extracted using Rneasy Mini Kit (Qiagen) according to manufacturer's protocol.

treatment_protocol: Cells were infected with pOZ- or SYTSSX2-containing retrovirus for 6h at 37˚C.  The medium was changed to fresh growth medium, and cells were allowed to grow for 48h at 37˚C.  Positive cells were selected and allowed to grow 48 hours after selection.

value: human bone marrow-derived MSCs


title: Treg+OX86 rep1

city: Milan

first: Paola

last: Pittoni

state: Italy

address: Via Amadeo, 42

department: Dept. Experimental Oncology

country: Italy

institute: IRCCS Istituto Nazionale dei Tumori

description:
Sample name: 5511141042_B
replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with Illumina BeadStudio Gene Expression Module v3

source_name: mouse spleen Treg

label_protocol: Biotinylated cRNA were prepared with the Ambion Illumina RNA TotalPrep amplification kit

extract_protocol: RNA was purified with AMBION mirVANA kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: age

tag: protocol

value: o.n. activation with anti-CD3 + OX86


title: A100


title: Treg+iso rep2

description:
Sample name: 5511141042_C
replicate 2

value: o.n. activation with anti-CD3 + rat IgG


title: SYTSSX2-expressing, replicate 2


title: miRNA_PBMCs_PEAK exercise_01

description: miRNA expression after-exercise


title: Treg+OX86 rep2

description:
Sample name: 5511141042_D
replicate 2


title: vector control, replicate 1

source_name: pOZ-infected hMSCs, 48 hours post-infection


title: SYTSSX2-expressing, replicate 2

hyb_protocol: Sample cDNA was hybridized to Affymetrix Mouse Gene 1.0 ST array according to manufacturer's protocol.

source_name: SYTSSX2-infected C2C12 cells, 48 hours post-infection

growth_protocol: Cells were grown in DMEM supplemented with 10% FBS at 37˚C, 5% CO2

extract_protocol: Total RNA was extracted using Rneasy Mini Kit (Qiagen) according to manufacturer's protocol.

treatment_protocol: Cells were infected with pOZ- or SYTSSX2-containing retrovirus for 6h at 37˚C.  The media was changed to fresh DMEM + 10% FBS, and cells were allowed to grow for 48h at 37˚C.

value: C2C12 myoblasts


title: Treg+iso rep1

description:
Sample name: 5511141042_A
replicate 1


title: vector control, replicate 2


title: Cohyb_H13_D0 vs D21_GE_B

first: Robert

last: Waterland

address: 1100 Bates St.,

institute: Baylor College of Medicine

hyb_protocol: Hybridization of the arrays was carried out according to the Agilent Two-Color Microarray-Based Gene Expression (Quick Amp Labeling) Protocol (version 6.5, 2010)

scan_protocol: Scanned on an Agilent Technologies Scanner G2505B scanner. Images were quantified using Agilent Feature Extraction Software (version 9.1.3.1).

data_processing: Agilent Feature Extraction Software (9.1.3.1) was used for background subtraction and LOWESS normalization.

source_name: RNA extracted from undifferentiated hESCs (one biological replicate)

label_protocol: Amplified cRNA was labelled from each sample with either Cy3 or Cy5 according to the Agilent Two-Color Microarray-Based Gene Expression (Quick Amp Labeling) Protocol (version 6.5, 2010)

extract_protocol: Total RNA was extracted by Qiagen Rneasy Mini Kit (Cat. No. 74104)

value: embryonic stem cell

tag: differentian stage

source_name: RNA extracted from hESCs with 21 days after undirected differentiation (one biological replicate)


title: A101


title: vector control, replicate 2

source_name: pOZ-infected C2C12 cells, 48 hours post-infection


title: SYTSSX2-expressing, replicate 1


title: Cohyb_H13_D0 vs D21_Methy_B

hyb_protocol: Hybridization of the arrays was carried out according to the Agilent Chip-on-chip mammalian protocol (version 9.1, 2006)

data_processing: Agilent Feature Extraction Software (9.1.3.1) was used for background subtraction and LOWESS normalization. Probe ratios within one SmaI interval were averaged and the median of the P value log10 ratios of the probes within one SmaI interval was calculated.

source_name: genomic DNA extracted from undifferentiated hESCs (one biological replicate)

label_protocol: 2µg of the digested and amplified DNA was labelled from each sample with either Cy3 or Cy5 according to the Agilent Chip-on-chip mammalian protocol (version 9.1, 2006)

extract_protocol: Total DNA was extracted by standard phenol-chloroform isolation

source_name: genomic DNA extracted from hESCs with 21 days after undirected differentiation (one biological replicate)


title: Cohyb_H13_D0 vs D90_Methy_B

source_name: genomic DNA extracted from hESCs with 90 days after undirected differentiation (one biological replicate)


title: Cohyb_H13_D0 vs D90_GE_B

source_name: RNA extracted from hESCs with 90 days after undirected differentiation (one biological replicate)


title: Cohyb_H13_D0 vs D90_Methy_A

source_name: genomic DNA extracted from undifferentiated hESCs

source_name: genomic DNA extracted from hESCs with 90 days after undirected differentiation


title: MCF-7ADR_multi-step_doxorubicin_selected_subline_rep_2

first: Suresh

middle: V.

last: Ambudkar

address: 37 Convent Dr., Room 2120

institute: National Cancer Institute, NIH

description: Doxorubicin-selected subline biological replicate 2

hyb_protocol: The biotinylated complementary RNA was fragmented for 35 minutes at 94C in fragmentation buffer from the labelling kit (Enzo, Farmingdale, NY) and then hybridized to the Affymetrix GeneChip U133A 2.0 arrays (Santa Clara, CA) for 16 hours at 45C. Each probe array was then washed and stained before being scanned.

scan_protocol: Each probe array was scanned twice with the GeneArray Scanner, according to the manufacturers procedures (Affymetrix, Santa Clara, CA).

data_processing: The CEL files for hybridizations of the MCF-7/ADR cells and the MCF-7 cells were log2-transformed by use of RMA Express (Bioinformatics 2003 19(2):185-193 and Biostatistics 2003 4(2):249-264). Microarray data for the expression of 14,500 genes from MCF-7 and MCF-7/ADR were filtered with BRB-ArrayTools (version 3.8.0) (developed by Dr. Richard Simon and BRB-ArrayTools Development Team from the Biometric Research Branch at the National Cancer Institute, NIH, Bethesda, MD). The array data were filtered by use of the exclusion parameters, spot intensities that were less than 10 and genes with a P value for the log-ratio variation that was greater than .01, and a total of 4976 genes were identified for further analysis. These 4976 genes were clustered by use of the Euclidean distance and complete linkage (Supplementary Figure 1, available online). The resulting dendrogram indicated that, for all experimental conditions, the duplicate microarrays form clusters, suggesting that the results were reproducible. A two-sample t test (with random variance model) was used to perform a class comparison and determine the statistically significant genes expressed between the MCF-7 and MCF-7/ADR cells. The univariate test random variance model parameters were a equals 1.68165, b equals 14.3422, and Kolmogorov–Smirnov statistic equals 0.03998. The nominal statistical significance level of each univariate test was .001. The first 419 genes listed were statistically significant at the nominal .001 level in the univariate test with a spot intensity fold change of 10. Genes with a spot intensity fold increase of greater than 10 are shown in Supplementary Table 1 (available online), and genes with spot intensity fold decrease of greater than –10 are shown in Supplementary Table 2 (available online).

source_name: MCF 7 cell line drug resistant cell subline

label_protocol: Isolated total RNA from the MCF-7 parental cells and MCF-7/ADR cells was used with the GeneChip Sample Cleanup Module to prepare biotinylated eukaryotic complementary RNA to hybridize to the GeneChip expression probe arrays, according to the manufacturers protocol (Qiagen).

extract_protocol: RNA was isolated from approximately 1 million MCF-7 and MCF-7/ADR cells grown in two six-well plates. The medium and any detached cells were first removed from the wells, and total RNA was isolated from the cells that remained attached to the culture dish by use of the Qiagen RNeasy kit (Valencia, CA) by the manufacturers protocol. RNA was quantitated by use of a NanoDrop micro-volume spectrophotometer (Thermo Scientific, Wilmington, DE) and then the integrity of the mRNA was verified with an Agilent BioAnalyzer (Santa Clara, CA).

treatment_protocol: MCF-7 cells were maintained in DMEM supplemented with 10 percent fetal calf serum, penicillin (100 units/mL), and streptomycin (100 ug/ml)

tag: treatment

value: Multi-step doxorubicin-selected subline


title: Cohyb_H13_D0 vs D21_GE_A

source_name: RNA extracted from undifferentiated hESCs

source_name: RNA extracted from hESCs with 21 days after undirected differentiation


title: vector control, replicate 1


title: Cohyb_H13_D0 vs D21_Methy_A

source_name: genomic DNA extracted from hESCs with 21 days after undirected differentiation


title: MCF-7ADR_multi-step_doxorubicin_selected_subline_rep_1

description: Doxorubicin-selected subline biological replicate 1


title: Cohyb_H1_D0 vs D90_GE_B


title: Cohyb_H1_D0 vs D90_Methy_B


title: Cohyb_H1_D0 vs D21_GE_B

source_name: RNA extracted from uhESCs with 21 days after undirected differentiation (one biological replicate)


title: MCF-7_parental_cell_rep_2

description: MCF 7 parental cell line Control biological replicate 2

source_name: MCF 7 parental cell line

value: Control


title: Cohyb_H1_D0 vs D21_Methy_B


title: Cohyb_H1_D0 vs D90_GE_A

source_name: RNA extracted from hESCs with 90 days after undirected differentiation


title: Cohyb_H1_D0 vs D90_Methy_A


title: MCF-7_parental_cell_rep_1

description: MCF 7 parental cell line Control biological replicate 1


title: Cohyb_H13_D0 vs D90_GE_A