title: Cultured HSCs-LPS-24h-rep1

status: Public on Oct 31 2013

type: RNA

city: Pittsburgh

first: Stephen

middle: Alan Kenneth

last: Harvey

state: PA

address: 203 Lothrop St

department: Ophthalmology

country: USA

institute: University of Pittsburgh School of Medicine

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Rat Genome 230 2 array. GeneChips were washed and stained in an Affymetrix Fluidics Station 400.

scan_protocol: Stained microarrays were scanned with a Affymetrix GeneChip Scanner 3000

data_processing: The raw data obtained from microarray analysis were processed using Affymetrix GeneChip Operating Software (GCOS v 1.4) using software defaults, to assess the presence or absence of each transcript target sequence, its expression level, and then to make all relevant pair-wise statistical comparisons among samples. Expression levels were scaled to a target value of 500 using the software default (2% trimmed mean). Prior to scaling, global microarray signals were 279 ± 73 (mean ± SD, n = 11)

label: biotin

molecule: total RNA

organism: Rattus norvegicus

source_name: Cultured HSCs-LPS-24h-rep1

label_protocol: Total RNAs were amplified and labeled using Affymetrix products [catalog #s 900371 / 900431 / 900433 / 900449] now superseded by 3' IVT Express Kit (Affymetrix Inc., Santa Clara, CA)

growth_protocol: Isolated HSCs were plated at a density of 0.5 x 10^6 cells/cm^2, and the medium renewed after overnight culture and then on alternate days. The cells were used on day 7 of culture when the majority expressed α-sma but contained abundant retinoids

extract_protocol: Total RNA was isolated from cultured cells using an RNeasy Mini kit (Qiagen, Valencia, CA)

treatment_protocol: Cultured HSCs were treated with 10 ng / mL (final concentration) of LPS for 1h, 3h, 6h, 12h or 24h. Vehicle-treated controls were harvested at 1h or 24h.

tag: cell type

value: Primary cultured rat hepatic stellate cells

tag: gender

value: Male


title: E2 vs C2

city: Beijing

first: li

last: juan

address: East Street Fengtai District

country: China

institute: Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology

description: compare gene expression profiles of control cells

hyb_protocol: standard CapitalBio Methods

scan_protocol: Luxscan 10K (CapitalBio)

data_processing: After background correction and removal of bad spots, a space and intensity-dependent normalization based on a LOWESS program was employed. For each test and control sample, two hybridizations were performed by using fluorescent strategy and the geometric mean of lowess normalized log2 ratio (test/control).

organism: Homo sapiens

source_name: SH-SY5Y cells infected with HEV71

label_protocol: Fluorescent dye (Cy5 and Cy3-dCTP, GE Healthcare Cat. No. PA 55021/PA 53021) labeled DNA was produced through Eberwine's linear RNA amplification method and subsequent enzymatic reaction. The amplified RNA (aRNA) was purified with NucleoSpin Extract II (MN). We took a cDNA labeling approach with Klenow enzyme after reverse transcription.

growth_protocol: Human neuroblastoma cell line, SH-SY5Y cells were cultured in Dulbecco's modiﬁed Eagle's medium/F-12 (DMEM/F-12, Invitrogen), supplemented with 10% fetal bovine serum (FBS) (Gibco) at 37℃ with 5% CO2

extract_protocol: Stably infected cells and control cells were harvest, and total RNA was extracted with Trizol Reagent (Invitrogen) and ethanol precipitation.

treatment_protocol: SH-SY5Y cells were infected with HEV71 at 1m.o.i.. After 1h incubation, the cells were washed with PBS and refed with 2% containing medium. All experiments were done in duplication. At 12 h post-infection, adherent cells were harvested.

tag: cell line

tag: treatment

value: infected with HEV71 at 1m.o.i

source_name: SH-SY5Y cells non-infected with HEV71

value: non-infected


title: E1 vs C1


title: Cultured HSCs-control-24h-rep1

source_name: Cultured HSCs-control-24h-rep1


title: Cultured HSCs-LPS-3h-rep1

source_name: Cultured HSCs-LPS-3h-rep1


title: Cultured HSCs-LPS-1h-rep2

source_name: Cultured HSCs-LPS-1h-rep2


title: Cultured HSCs-LPS-24h-rep2

source_name: Cultured HSCs-LPS-24h-rep2


title: Cultured HSCs-control-1h-rep2

source_name: Cultured HSCs-control-1h-rep2


title: Cultured HSCs-LPS-1h-rep1

source_name: Cultured HSCs-LPS-1h-rep1


title: Cultured HSCs-control-24h-rep2

source_name: Cultured HSCs-control-24h-rep2


title: Normal T Cells-5

city: Baltimore

first: Amol

middle: Carl

last: Shetty

state: Maryland

address: 670 W. Baltimore Street, Floor 3

department: Institute for Genome Sciences

institute: University of Maryland Baltimore

description: Gene Expression Data from T Cells

hyb_protocol: Biotin labled RNA was hybridized for 16 hr at 45C on GeneChip miRNA 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Genechip Scanner 3000 and software AffyMetrix Genechip Command Console .

data_processing: The data were analyzed using the Partek Genomic Suite 6.6  to load the data before using the RMA algorithem to normalize all of the data

label: Biotin

source_name: T Cells

label_protocol: About 500 ng of total RNA was biotin labeled using Affymetrix propritary FlashTag Biotin HSR RNA labeling Kit that is covalently linked to biotin.

growth_protocol: All the leukemia cell lines were culture in vitro under appropriate cell cutlure conditions according to the supplier recommondataion. Normal mature hematopoietic cells were purifed from normal healthy donor peripheral blood using Ficoll gradiant centrifugation followed by FACS sorting.

extract_protocol: Cell were lysed in Trizol and total RNA was purifed using miRNAeasy kit  according to the manufacturer's instructions.

tag: phenotype

value: Normal

value: Normal T Cells


title: Normal T Cells-4

description: Gene Expression Data from T Cells


title: Normal T Cells-16

description: Gene Expression Data from T Cells


title: Normal T Cells-6

description: Gene Expression Data from T Cells


title: Normal T Cells-7

description: Gene Expression Data from T Cells


title: Normal T Cells-10

description: Gene Expression Data from T Cells


title: Normal T Cells-8

description: Gene Expression Data from T Cells


title: Normal T Cells-14

description: Gene Expression Data from T Cells


title: Normal T Cells-11

description: Gene Expression Data from T Cells


title: Normal T Cells-9

description: Gene Expression Data from T Cells


title: Normal T Cells-15

description: Gene Expression Data from T Cells


title: Normal T Cells-13

description: Gene Expression Data from T Cells


title: Normal T Cells-12

description: Gene Expression Data from T Cells


title: Cultured HSCs-LPS-12h-rep1

source_name: Cultured HSCs-LPS-12h-rep1


title: Cultured HSCs-control-1h-rep1

source_name: Cultured HSCs-control-1h-rep1


title: Normal T Cells-2

description: Gene Expression Data from T Cells


title: Normal T Cells-3

description: Gene Expression Data from T Cells


title: Normal T Cells-17

description: Gene Expression Data from T Cells


title: Normal T Cells-1

description: Gene Expression Data from T Cells


title: Cultured HSCs-LPS-6h-rep1

source_name: Cultured HSCs-LPS-6h-rep1


title: Primary T ALL sample-12

description: Gene Expression Data from T ALL Patient

source_name: T ALL Patient

value: Leukemia

tag: tissue

value: Primary T ALL sample


title: Primary T ALL sample-10 SP

description: Gene Expression Data from T ALL Patient


title: Primary T ALL sample-15

description: Gene Expression Data from T ALL Patient


title: Primary T ALL sample-11

description: Gene Expression Data from T ALL Patient


title: Primary T ALL sample-13

description: Gene Expression Data from T ALL Patient


title: Primary T ALL sample-6 BM

description: Gene Expression Data from T ALL Patient


title: Primary T ALL sample-8

description: Gene Expression Data from T ALL Patient


title: Primary T ALL sample-9

description: Gene Expression Data from T ALL Patient


title: Primary T ALL sample-4 SP2

description: Gene Expression Data from T ALL Patient


title: Primary T ALL sample-7 BM

description: Gene Expression Data from T ALL Patient


title: Primary T ALL sample-10

description: Gene Expression Data from T ALL Patient


title: MOLT16-4

description: Gene Expression Data from T ALL Cell Line

source_name: T ALL Cell Line


title: KARPAS45-4


title: Primary T ALL sample-1

description: Gene Expression Data from T ALL Patient


title: JURKAT-2

value: JURKAT


title: MOLT3-4


title: Primary T ALL sample-4 SP1

description: Gene Expression Data from T ALL Patient


title: CCRFCEM-4

value: CCRFCEM


title: JURKAT-4


title: CCRFCEM-3


title: MOLT16-3


title: KARPAS45-3


title: MOLT3-1


title: MOLT16-2


title: MOLT16-1


title: KARPAS45-2


title: CCRFCEM-2


title: MOLT3-2


title: MOLT3-3


title: JURKAT-3


title: Normal Monocytes-6

description: Gene Expression Data from Monocytes

source_name: Monocytes

value: Normal Monocytes


title: Normal Monocytes-5

description: Gene Expression Data from Monocytes


title: JURKAT-1


title: CCRFCEM-1


title: KARPAS45-1


title: NormalGranulocytes-12

description: Gene Expression Data from Granulocytes

source_name: Granulocytes

value: Normal Granulocytes


title: Normal Monocytes-1

description: Gene Expression Data from Monocytes


title: Normal Monocytes-4

description: Gene Expression Data from Monocytes


title: NormalGranulocytes-13

description: Gene Expression Data from Granulocytes


title: Normal Monocytes-3

description: Gene Expression Data from Monocytes


title: Normal Monocytes-2

description: Gene Expression Data from Monocytes


title: NormalGranulocytes-10

description: Gene Expression Data from Granulocytes


title: NormalGranulocytes-11

description: Gene Expression Data from Granulocytes


title: NormalGranulocytes-8

description: Gene Expression Data from Granulocytes


title: NormalGranulocytes-9

description: Gene Expression Data from Granulocytes


title: NormalGranulocytes-6

description: Gene Expression Data from Granulocytes


title: NormalGranulocytes-5

description: Gene Expression Data from Granulocytes


title: NormalGranulocytes-2

description: Gene Expression Data from Granulocytes


title: NormalGranulocytes-1

description: Gene Expression Data from Granulocytes


title: CD34+ HSPC-3

description: miRNA Expression Data from CD34+ HSPC

source_name: CD34+ HSPC

value: CD34+ HSPC


title: NormalGranulocytes-3

description: Gene Expression Data from Granulocytes


title: NormalGranulocytes-4

description: Gene Expression Data from Granulocytes


title: CD34+ HSPC-2

description: miRNA Expression Data from CD34+ HSPC


title: Primary B Cells-10

description: miRNA Expression Data from B Cells

source_name: B Cells

value: Primary B Cells


title: Primary B Cells-3

description: miRNA Expression Data from B Cells


title: Primary B Cells-4

description: miRNA Expression Data from B Cells


title: Primary B Cells-9

description: miRNA Expression Data from B Cells


title: Primary B Cells-11

description: miRNA Expression Data from B Cells


title: Primary B ALL sample - 43SP2

description: miRNA Expression Data from B ALL Patient

source_name: B ALL Patient

value: Primary B ALL sample


title: Primary B Cells-7

description: miRNA Expression Data from B Cells


title: Primary B Cells-5

description: miRNA Expression Data from B Cells


title: Primary B Cells-6

description: miRNA Expression Data from B Cells


title: Primary B Cells-1

description: miRNA Expression Data from B Cells


title: NormalGranulocytes-7

description: Gene Expression Data from Granulocytes


title: Primary B ALL sample - 43SP1


title: Primary B Cells-2

description: miRNA Expression Data from B Cells


title: Primary B Cells-8

description: miRNA Expression Data from B Cells


title: Primary B ALL sample - 48 SP


title: Primary B ALL sample - 47


title: Primary B ALL sample - 41


title: Primary B ALL sample - 50 SP


title: Primary B ALL sample - 46


title: Primary B ALL sample - 25 b


title: Primary B ALL sample - 21SP


title: Primary B ALL sample - 19-SP2


title: Primary B ALL sample - 23 SP


title: Primary B ALL sample - 23SP1


title: Primary B ALL sample - 21 BM


title: Primary B ALL sample - 30


title: Primary B ALL sample - 16


title: Primary B ALL sample - 42SP


title: Primary B ALL sample - 29


title: Primary B ALL sample - 42


title: Primary B ALL sample - 25 a


title: Primary B ALL sample - 4 SP


title: Primary B ALL sample - 5


title: Primary B ALL sample - 40


title: Primary B ALL sample - 21-SP2


title: Primary B ALL sample - 2 SP


title: SUPB15-4

description: miRNA Expression Data from B ALL Cell Line

source_name: B ALL Cell Line


title: Primary B ALL sample - 27


title: Primary B ALL sample - 17


title: Primary B ALL sample - 21


title: Primary B ALL sample - 23


title: RCHACV-4

value: RCHACV


title: Primary B ALL sample - 22


title: MUTZ5-4


title: RCHACV-3


title: REH-2

value: REH


title: KASUMI2-3


title: KOPN8-2


title: MHHCALL3-3


title: CD34+ HSPC-1

description: miRNA Expression Data from CD34+ HSPC


title: MHHCALL4-4


title: KASUMI2-4


title: NALM6-3


title: MHHCALL3-4


title: MHHCALL3-2


title: REH-4


title: KASUMI2-2


title: BALM6-4


title: KOPEN8-4


title: RCHACV-2


title: KOPN8-3


title: KOPN8-1


title: REH-3


title: REH-1


title: SUPB15-3


title: MHHCALL3-1


title: MHHCALL4-3


title: MHHCALL4-2


title: SUPB15-2


title: MUTZ5-3


title: MHHCALL4-1


title: RCHACV-1


title: KASUMI2-1


title: MUTZ5-2


title: MUTZ5-1


title: SUPB15-1


title: Primary AML sample - 9

description: miRNA Expression Data from AML Patient

source_name: AML Patient

value: Primary AML sample


title: Primary AML sample - 9 SP

description: miRNA Expression Data from AML Patient


title: Primary AML sample - 201 BM

description: miRNA Expression Data from AML Patient


title: NALM6-2


title: Primary AML sample - 14 BM

description: miRNA Expression Data from AML Patient


title: Primary AML sample - 42

description: miRNA Expression Data from AML Patient


title: Primary AML sample - 41

description: miRNA Expression Data from AML Patient


title: Primary AML sample - 44

description: miRNA Expression Data from AML Patient


title: Primary AML sample - 201

description: miRNA Expression Data from AML Patient


title: Primary AML sample - 39

description: miRNA Expression Data from AML Patient


title: Primary AML sample - 33

description: miRNA Expression Data from AML Patient


title: Primary AML sample - 28

description: miRNA Expression Data from AML Patient


title: Primary AML sample - 27

description: miRNA Expression Data from AML Patient


title: Primary AML sample - 14

description: miRNA Expression Data from AML Patient


title: Primary AML sample - 40

description: miRNA Expression Data from AML Patient


title: NALM6-1


title: Primary AML sample - 12

description: miRNA Expression Data from AML Patient


title: Primary AML sample - 3

description: miRNA Expression Data from AML Patient


title: Primary AML sample - 8

description: miRNA Expression Data from AML Patient


title: KASUMI1-2

description: miRNA Expression Data from AML Cell Line

source_name: AML Cell Line


title: ML2-4


title: KG1a-3


title: KASUMI1-3


title: MO7e-2


title: ML2-2


title: MO7e-3


title: KG1a-2


title: HL60-2


title: HL60-4


title: HL60-3


title: ML2-1


title: K562-2


title: HL60-1


title: ML2-3


title: K562-1


title: U937-2


title: K562-3


title: U937-4


title: U937-3


title: U937-1


title: KASUMI1-1


title: KG1a-1


title: BT474_lapatinib-resistant_rep1

city: Taichung

first: Wei-Chien

last: Huang

address: 9F, No.6, Hsueh-Shih Road

department: Graduate Institute of Cancer Biology

country: Taiwan

institute: China Medical University

description: gene expression in lapatinib-resistant BT474 cells

hyb_protocol: CyDye-labled cRNA (0.825 mg) was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer at 60oC for 30 minutes. Correspondingly fragmented labeled cRNA is then pooled and hybridized to Agilent Human Whole Genome Oligo 4×44 K Microarray at 60°C for 17 h.

scan_protocol: After washing and drying by nitrogen gun blowing, microarrays are scanned with an Agilent microarray scanner (Agilent Technologies, USA) at 535 nm for Cy3

data_processing: Scanned images are analyzed by Feature extraction 9.5.3 software (Agilent Technologies, USA), an image analysis and normalization software is used to quantify signal and background intensity for each feature, normalized the data by rank-consistency-filtering LOWESS method

source_name: BT474, lapatinib-resistant clone#6

label_protocol: 0.5 µg of total RNA were reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label

growth_protocol: SkBr3, BT474, and their lapatinib-resistant clone were cultured in Dulbecco’s modified Eagle’s medium (DMEM)/F12

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

treatment_protocol: To establish lapatinib-resistant cells, cancer cells were treated with increasing concentration of lapatinib up to 1  μM.

value: lapatinib

value: lapatinib-resistant breast cancer cells


title: SkBr-3_parental_rep1

description: gene expression in parental SkBr3 cells

value: Vehicle

value: breast cancer cells


title: SkB-3_lapatinib resistant_rep1

description: gene expression in lapatinib-resistant SkBr3 cells

source_name: SkB-3, lapainib-resistant clone#3


title: WT 1 hr Systemic

city: Riverside

first: Linda

middle: Lee

last: Walling

state: CA

address: 900 University Avenue

department: Botany and Plant Sciences

institute: University of California

hyb_protocol: All steps of microarray processing to obtain raw data (cDNA production, cDNA labeling, and microarray hybridization) were carried out by the TIGR Expression Profiling Service according to published methods (http://www.tigr.org/tdb/potato/microarray_SOPs.shtml).

scan_protocol: Spot data was extracted using GENEPIX (ver. 5.0 Pro: Axon Instruments, Union City, CA, USA) at TIGR.

data_processing:
A series of quality assessment routines were applied to the microarrays. This included ratio-intensity plots (also known as MA plots) within and between arrays and print tips, as well as distribution plots of intensities. Normalization and differential gene expression analysis steps were performed in R (http://www.r-project.org) using the LIMMA package. Here the data sets were normalized within arrays using the print-tip loess method. Background correction was omitted because it added too much variation to the data. In addition, arrays were normalized between arrays using quantile normalization. Within-array duplicate spot correlations were calculated and duplicate spots were weighted using the duplicateCorrection function of the LIMMA package.
Statistically significant differentially expressed genes (DEGs) among sample treatments, each with three biological replicates, were identified using the empirical Bayes method implemented in the LIMMA package. To control the false discovery rates (FDR) of candidate DEGs, their raw p-values were adjusted for multiple testing using the Benjamini & Hochberg method. As confidence threshold for DEGs, we used a log2 fold change (|FC|) ≥ 0.8 and an adjusted p < 0.05.

organism: Solanum lycopersicum

source_name: WT unwounded leaf tissue

growth_protocol: Solanum lycopersicum L. UC82 (wild-type) and P35S:LapA-SI plants were grown in a growth chamber with an 18-hr (28°C)/6-hr (24°C) light (300 μE)/dark cycle.

extract_protocol: RNAs were extracted using a hot phenol method. RNA for microarray analysis was further purified using the SV Total RNA Isolation System (Promega, Madison, WI USA). RNA was quantified and 260/280-nm absorbance ratios were measured using a Nano-Drop ND-1000 spectrophotometer. RNA quality was also ensured by checking for the presence of intact rRNA bands by 1.5% formaldehyde gel.

treatment_protocol: Three- to four-week-old plants were used in the wounding time-course studies. Plants were wounded by crushing the distal end of each leaflet of one lower leaf with a pair of needle-nosed pliers. Wounded leaves (local response) and all leaflets (typically 6-8 leaflets) from apical leaves (systemic response) were collected at designated times. The leaves of five plants at each time point were pooled together for RNA extractions. This experiment was repeated three times for microarray analysis.

tag: strain/background

tag: genotype/variation

value: WT

tag: age

value: 3-4 weeks

value: leaf

tag: time point

value: 0 hr

source_name: WT wounded leaf tissue, 1hr, systemic

value: wounding

value: 1 hr

tag: spatial response type

value: systemic


title: WT 0 hr

label_protocol: All steps of microarray processing to obtain raw data (cDNA production, cDNA labeling, and microarray hybridization) were carried out by the TIGR Expression Profiling Service according to published methods (http://www.tigr.org/tdb/potato/microarray_SOPs.shtml).


title: LapA-SI 8 hr Systemic

source_name: LapA-SI wounded leaf tissue, 8hr, systemic

value: LapA-SI

value: 8 hr


title: Rice seedlings roots_200 μM Cr(VI) Replicate 3

city: Tainan

first: Tsai-Lien

state: Taiwan

address: No.1, University Raod,

department: Life Sciences

institute: National Cheng Kung University

description: Biological replicate 3 of 3. Rice seedling roots with or without 200 μM-treated Cr(VI)

hyb_protocol: Correspondingly fragmented labeled cRNA is then pooled and hybridized to Agilent Rice Oligo 4×44K Microarray (Agilent Technologies, USA) at 60°C for 17 h.

scan_protocol: After washing and drying by nitrogen gun blowing, microarrays are scanned with an Agilent microarray scanner (Agilent Technologies, USA) at 535 nm for Cy3 and 625 nm for Cy5. Scanned images are analyzed by Feature extraction software 9.5.3 (Agilent Technologies, USA),

data_processing: An image analysis and normalization software is used to quantify signal and background intensity for each feature, substantially normalized the data by rank-consistency-filtering LOWESS method.

organism: Oryza sativa

source_name: Roots of rice seedlings were exposed to 200 μM Cr(VI)

label_protocol: 0.5 μg of total RNA was amplified by a Fluorescent Linear Amplification Kit (Agilent Technologies, USA) and labeled with Cy3-CTP or Cy5-CTP (CyDye, PerkinElmer, USA) during the in vitro transcription process rice roots after Cr(VI) treatment RNA was labeled by Cy5 and RNA from control RNA was labeled by Cy3. 0.825 μg of Cy-labled cRNA was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer (Agilent Technologies, USA) at 60oC for 30 minutes.

growth_protocol: 5-day-old seedlings

extract_protocol: Total RNA were extracted using QIAGEN RNeasy kit follwed by DNAse treatment. The RNA samples were further purified and concentrated by RNeasy MinElute Cleanup.

treatment_protocol: Control and rice seedlings were exposed to 200 μM Cr(VI)

tag: cultivar

value: 5 day

value: roots

value: 200 μM Cr(VI)

source_name: Rice seedlings roots were exposed to water

value: water


title: LapA-SI 8 hr Local

source_name: LapA-SI wounded leaf tissue, 8hr, local

value: local


title: LapA-SI 1 hr Local

source_name: LapA-SI wounded leaf tissue, 1hr, local


title: BT474_parental_rep1

description: gene expression in parental BT474 cells


title: Rice seedlings roots_200 μM Cr(VI) Replicate 1

description: Biological replicate 1 of 3. Rice seedling roots with or without 200 μM-treated Cr(VI)


title: WT 8 hr Local

source_name: WT wounded leaf tissue, 8hr, local


title: LapA-SI 0 hr

source_name: LapA-SI unwounded leaf tissue


title: WT 8 hr Systemic

source_name: WT wounded leaf tissue, 8hr, systemic


title: Rice seedlings roots_200 μM Cr(VI) Replicate 2

description: Biological replicate 2 of 3. Rice seedling roots with or without 200 μM-treated Cr(VI)


title: WT 1 hr Local

source_name: WT wounded leaf tissue, 1hr, local


title: LapA-SI 1 hr Systemic

source_name: LapA-SI wounded leaf tissue, 1hr, systemic


title: TE-8_control2

city: Houston

first: Sangbae

last: Kim

state: TX

address: 1 Baylor plaza

department: HGSC

institute: Baylor Colleage of Medicine

description:
TE8_con2
To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software.

hyb_protocol: Labeled, amplified material (750 ng per array) was hybridized to the Illumina HumanHT-12 V4.0 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.

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)

value: ESCC cell line TE-8

value: VTRNA1-1 ASO


title: TE-8_knockdown1

description:
TE8_kd1
To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software.

value: nc886 ASO


title: TE-1_knockdown1

description:
TE1_kd1
To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software.

value: ESCC cell line TE-1


title: TE-8_knockdown2

description:
TE8_kd2
To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software.


title: TE-1_control1

description:
TE1_con1
To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software.


title: TE-1_knockdown2

description:
TE1_kd2
To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software.


title: TE-8_control1

description:
TE8_con1
To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software.


title: TE-1_knockdown3

description:
TE1_kd3
To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software.


title: TE-8_control3

description:
TE8_con3
To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software.


title: TE-1_control3

description:
TE1_con3
To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software.


title: TE-8_knockdown3

description:
TE8_kd3
To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software.


title: Control_CD15 Sample 84 cell separation

city: London

first: Chloe

last: Bloom

address: The Ridgeway

country: United Kingdom

institute: MRC National Institute for Medical Research

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Background subtracted, normalised and log2 transformed for normalised values and non-normalised values have only had background subtraction

label_protocol: Biotinylated, amplified antisense cRNA were prepared using NuGEN WT-Ovation RNA Amplification and Encore BiotinIL Module.

growth_protocol: Direct ex vivo human blood frozen and purified leucocytes after RNA extraction frozen

extract_protocol: RNA was extracted using the Qiagen RNeasy Mini Kit.

treatment_protocol: Whole blood stored in Tempus, PBMCs obtained using Lymphoprep then leucocytes purified using Miltenyi whole blood MACS beads, neutrophils obtained after Lymphoprep and red blood cell lysis then Miltenyi MACS beads

tag: disease state

value: Control


title: Control_CD14 Sample 89 cell separation


title: HET-1A_knockdown1

description:
HET.1A_kd1
To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software.

value: nonmalignant cell line HET-1A


title: HET-1A_knockdown3

description:
HET.1A_kd3
To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software.


title: Control_Whole blood Sample 81 cell separation

source_name: Whole blood

value: whole blood


title: TE-1_control2

description:
TE1_con2
To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software.


title: TB_CD15 Sample 79 cell separation

value: TB


title: Sarcoid_CD14 Sample 88 cell separation

value: Sarcoid


title: Sarcoid_PBMC Sample 83 cell separation

source_name: PBMC

value: PBMC


title: HET-1A_knockdown2

description:
HET.1A_kd2
To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software.


title: HET-1A_control2

description:
HET.1A_con2
To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software.


title: Sarcoid_Whole blood Sample 87 cell separation


title: Control_Whole blood Sample 90 cell separation


title: Control_Whole blood Sample 85 cell separation


title: Sarcoid_CD14 Sample 82 cell separation


title: HET-1A_control3

description:
HET.1A_con3
To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software.


title: Sarcoid_CD15 Sample 80 cell separation


title: TB_CD14 Sample 86 cell separation


title: Sarcoid_CD4 Sample 78 cell separation


title: TB_Whole blood Sample 75 cell separation


title: Control_CD8 Sample 77 cell separation


title: HET-1A_control1

description:
HET.1A_con1
To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software.


title: TB_CD15 Sample 76 cell separation


title: Primary AML sample - 1

description: miRNA Expression Data from AML Patient

source_name: AML Patient

value: Leukemia

value: Primary AML sample


title: MO7e-1

description: miRNA Expression Data from AML Cell Line

source_name: AML Cell Line


title: TB_CD14 Sample 69 cell separation


title: Control_CD4 Sample 74 cell separation


title: Control_Whole blood Sample 67 cell separation


title: TB_PBMC Sample 59 cell separation


title: Control_CD15 Sample 72 cell separation


title: Control_CD14 Sample 62 cell separation


title: TB_CD15 Sample 50 cell separation


title: TB_CD15 Sample 64 cell separation


title: TB_Whole blood Sample 60 cell separation


title: Sarcoid_CD15 Sample 73 cell separation


title: TB_CD14 Sample 71 cell separation


title: Control_PBMC Sample 58 cell separation


title: Sarcoid_PBMC Sample 65 cell separation


title: TB_CD8 Sample 70 cell separation


title: TB_CD14 Sample 63 cell separation


title: Sarcoid_CD4 Sample 66 cell separation


title: TB_Whole blood Sample 48 cell separation


title: Control_CD4 Sample 56 cell separation


title: TB_CD4 Sample 57 cell separation


title: Sarcoid_CD8 Sample 52 cell separation


title: Sarcoid_CD14 Sample 53 cell separation


title: Sarcoid_Whole blood Sample 54 cell separation


title: TB_PBMC Sample 49 cell separation


title: TB_CD8 Sample 61 cell separation


title: TB_PBMC Sample 51 cell separation


title: Sarcoid_CD14 Sample 55 cell separation


title: TB_CD4 Sample 68 cell separation


title: Control_CD15 Sample 47 cell separation


title: Control_CD4 Sample 46 cell separation


title: Control_CD15 Sample 44 cell separation


title: Sarcoid_CD8 Sample 40 cell separation


title: TB_CD4 Sample 43 cell separation


title: Sarcoid_PBMC Sample 38 cell separation


title: Control_CD15 Sample 42 cell separation


title: Sarcoid_CD4 Sample 36 cell separation


title: Sarcoid_Whole blood Sample 41 cell separation


title: Sarcoid_CD14 Sample 34 cell separation


title: Control_CD14 Sample 45 cell separation


title: Control_CD8 Sample 32 cell separation


title: Control_PBMC Sample 30 cell separation


title: Sarcoid_PBMC Sample 26 cell separation


title: TB_CD8 Sample 33 cell separation


title: Control_PBMC Sample 29 cell separation


title: Control_CD14 Sample 22 cell separation


title: Control_CD14 Sample 28 cell separation


title: TB_Whole blood Sample 24 cell separation


title: Sarcoid_PBMC Sample 39 cell separation


title: Sarcoid_CD4 Sample 31 cell separation


title: TB_CD14 Sample 37 cell separation


title: Control_CD8 Sample 19 cell separation


title: Sarcoid_CD15 Sample 35 cell separation


title: Control_CD8 Sample 20 cell separation


title: Control_PBMC Sample 27 cell separation


title: Sarcoid_CD8 Sample 17 cell separation


title: TB_CD8 Sample 25 cell separation


title: Sarcoid_CD15 Sample 18 cell separation


title: Sarcoid_Whole blood Sample 23 cell separation


title: Sarcoid_CD15 Sample 21 cell separation


title: TB_CD4 Sample 15 cell separation


title: Control_CD8 Sample 8 cell separation


title: TB_CD4 Sample 9 cell separation


title: Control_CD4 Sample 16 cell separation


title: TB_PBMC Sample 6 cell separation


title: Sarcoid_CD8 Sample 11 cell separation


title: TB_Whole blood Sample 1 cell separation


title: Control_PBMC Sample 13 cell separation


title: Sarcoid_CD4 Sample 5 cell separation


title: Sarcoid_CD8 Sample 4 cell separation


title: Sarcoid Sample 13 2140 immunosuppressive treatment time pt. 2

data_processing:
The data were normalised using 75th percentile normalisation in GeneSpring 11.5
Background subtracted, normalised and log2 transformed for normalised values and non-normalised values have only had background subtraction

source_name: Whole Blood

label_protocol: Biotinylated, amplified cRNA were prepared using the Illumina CustomPrep RNA amplification kit

growth_protocol: Blood was taken into Tempus and frozen

extract_protocol: RNA was extracted using the MagMAX-96 Blood RNA Isolation Kit and globin reduced using GLOBINclear

treatment_protocol: Direct ex-vivo human blood

tag: treament

value: immunosuppressive treatment

tag: response

value: Inadequate

tag: time (d)

tag: subject


title: Sarcoid Sample 17 2100 immunosuppressive treatment time pt. 3

value: Good-response


title: Sarcoid Sample 11 2010 Pre-treatment time pt. 1

value: Pre-treatment


title: Control_Whole blood Sample 14 cell separation


title: TB_CD15 Sample 12 cell separation

tag: cell type


title: Sarcoid Sample 15 6009 Pre-treatment time pt. 1


title: Control_CD4 Sample 2 cell separation


title: Sarcoid Sample 16 2010 immunosuppressive treatment time pt. 2


title: TB_CD8 Sample 10 cell separation


title: Sarcoid Sample 12 6009 immunosuppressive treatment time pt. 2


title: Sarcoid Sample 14 2140 Pre-treatment time pt. 1


title: Sarcoid Sample 9 2100 Pre-treatment time pt. 1


title: Sarcoid Sample 10 6011 Pre-treatment time pt. 1


title: Sarcoid Sample 7 2099 Pre-treatment time pt. 1


title: Sarcoid Sample 8 2018 Pre-treatment time pt. 1


title: TB_PBMC Sample 3 cell separation


title: Sarcoid Sample 5 6011 immunosuppressive treatment time pt. 2


title: Sarcoid Sample 6 2099 immunosuppressive treatment time pt. 2


title: Sarcoid Sample 4 2099 immunosuppressive treatment time pt. 2


title: Sarcoid_Whole blood Sample 7 cell separation


title: Sarcoid Sample 3 2018 immunosuppressive treatment time pt. 2


title: Sarcoid Sample 2 2018 immunosuppressive treatment time pt. 3


title: Sarcoid Sample 95 training set

tag: gender

tag: ethnicity

value: Caucasian

value: Active Sarcoid


title: Control Sample 93 training set

value: F

value: Indian subcontinent


title: Sarcoid Sample 1 2100 immunosuppressive treatment time pt. 2


title: Cancer Sample 91 training set

value: M

value: lung cancer


title: Sarcoid Sample 94 training set


title: Pneumonia Sample 92 training set

value: Baseline


title: Control Sample 89 training set

value: Afro-Carribbean

value: Control

value: whole blood


title: TB Sample 87 training set

value: TB


title: TB Sample 81 training set


title: Sarcoid Sample 79 training set


title: Control Sample 85 training set


title: Control Sample 90 training set


title: Sarcoid Sample 82 training set


title: Control Sample 88 training set


title: Control Sample 84 training set


title: Pneumonia Sample 78 training set


title: Control Sample 86 training set


title: Sarcoid Sample 76 training set


title: Control Sample 77 training set


title: TB Sample 75 training set


title: TB Sample 74 training set


title: Control Sample 72 training set


title: Sarcoid Sample 80 training set


title: Control Sample 73 training set


title: Control Sample 68 training set


title: Control Sample 71 training set


title: Cancer Sample 66 training set


title: Control Sample 70 training set


title: TB Sample 69 training set


title: TB Sample 67 training set


title: Control Sample 60 training set


title: Control Sample 57 training set


title: TB Sample 61 training set


title: Control Sample 64 training set


title: Sarcoid Sample 58 training set


title: Control Sample 62 training set


title: Control Sample 65 training set


title: Sarcoid Sample 59 training set


title: Sarcoid Sample 56 training set


title: Sarcoid Sample 55 training set


title: Control Sample 51 training set


title: Pneumonia Sample 47 training set


title: Control Sample 54 training set


title: Control Sample 45 training set


title: Cancer Sample 53 training set


title: Sarcoid Sample 43 training set


title: Sarcoid Sample 50 training set

value: Non-active sarcoidosis


title: Sarcoid Sample 49 training set


title: TB Sample 52 training set


title: Sarcoid Sample 46 training set


title: Pneumonia Sample 63 training set


title: Sarcoid Sample 48 training set


title: Sarcoid Sample 42 training set


title: Control Sample 41 training set


title: TB Sample 44 training set


title: Cancer Sample 40 training set


title: TB Sample 39 training set


title: Cancer Sample 31 training set


title: Cancer Sample 34 training set


title: Control Sample 29 training set


title: Control Sample 37 training set


title: Control Sample 27 training set


title: Control Sample 32 training set


title: Pneumonia Sample 33 training set


title: Sarcoid Sample 25 training set


title: Control Sample 35 training set


title: TB Sample 28 training set


title: Sarcoid Sample 22 training set


title: Pneumonia Sample 36 training set


title: Sarcoid Sample 23 training set


title: Pneumonia Sample 38 training set


title: TB Sample 21 training set


title: Sarcoid Sample 19 training set


title: TB Sample 26 training set


title: Control Sample 20 training set


title: TB Sample 16 training set


title: Sarcoid Sample 24 training set


title: Control Sample 83 training set


title: Control Sample 11 training set


title: Control Sample 30 training set


title: Pneumonia Sample 18 training set

value: Middle Eastern


title: TB Sample 15 training set


title: Control Sample 12 training set


title: Control Sample 10 training set


title: Control Sample 14 training set


title: RE:CAKI_1_rep2

type: genomic

city: Princeton

first: Sudhir

last: Varma

state: NJ

address: 1215 Wessex Pl

institute: HiThru Analytics

description: Reference on Cy5 and RE:CAKI_1 on Cy3

data_processing:
Normalized data consists of log2 transformed sample/reference intensities. Raw data are the scan files from the Agilent scanner.
Log2 ratio of red/green (for arrays where sample=Cy5 and reference=Cy3) or green/red (where sample=Cy3 and reference=Cy5).

molecule: genomic DNA

source_name: Reference

label_protocol: Done according to array manufacturer's specifications.

growth_protocol: Cells grown in RPMI 1640 with 5% FBS (Bio Whittaker, not heat inactivated) and 1% L-glutamine. Cells not grown past 80% confluencey for attached cells, or 0.5 x 10^6 cells for suspended. Trypsinize (for attached cells) cells with 5 ml trypsin-EDTA per T162, for 15 min., at 37C. Spin down suspended cells, and resuspend in ~3ml growth media. Count cells. Pass 1x10^6 cells into new T162's w 30 ml media. Repeat growth cycle until desired amount of cells are available. Cells are not grown past passage 20.

extract_protocol: Genomic DNA was purified from cells using either the QIAamp DNA Blood Maxi Kit, or the Blood & Cell Culture DNA Maxi Kit (Qiagen Inc., Valencia, CA) according to manufacturer's instructions.  Quality was assessed by optical density 260/280 ratio using a spectrophotometer (Beckman-Coulter, Fullerton, CA) and by 0.8% agarose (SeaKem GTG, FMC BioProducts, Rockland, ME) gel electrophoresis in 1x TAE (Roche, Indianapolis, IN).

treatment_protocol: Untreated

tag: cell line

value: Reference

source_name: Clear cell carcinoma


title: Control Sample 5 training set


title: RE:RXF_393_rep2

description: RE:RXF_393 on Cy5 and Reference on Cy3

hyb_protocol: Done according to array manufacturer's specifications

source_name: hypernephroma


title: Cancer Sample 9 training set


title: LC:A549_rep8

description: LC:A549 on Cy5 and Reference on Cy3

scan_protocol: Done according to array manufacturer's specifications

source_name: Adenocarcinoma


title: Sarcoid Sample 4 training set


title: Cancer Sample 2 training set


title: TB Sample 7 training set


title: LC:NCI_H460_rep2

description: Reference on Cy5 and LC:NCI_H460 on Cy3

source_name: Large Cell Carcinoma


title: RE:RXF_393_rep1

description: Reference on Cy5 and RE:RXF_393 on Cy3


title: Sarcoid Sample 6 training set


title: CO:HCT_116_rep2

description: Reference on Cy5 and CO:HCT_116 on Cy3

source_name: carcinoma


title: Control Sample 1 training set


title: Sarcoid Sample 3 training set


title: LE:SR_rep2

description: LE:SR on Cy5 and Reference on Cy3

source_name: Lymphoma


title: BR:MDA_MB_231_rep2

description: Reference on Cy5 and BR:MDA_MB_231 on Cy3

source_name: Adenocarcinoma-mammary gland; breast; epithelial; metastatic site: pleural effusion;


title: CO:HT29_rep2

description: Reference on Cy5 and CO:HT29 on Cy3


title: CO:HCT_15_rep2

description: Reference on Cy5 and CO:HCT_15 on Cy3


title: ME:SK_MEL_2_rep2

description: ME:SK_MEL_2 on Cy5 and Reference on Cy3

source_name: Malignant melanotic melanoma


title: ME:UACC_257_rep2

description: Reference on Cy5 and ME:UACC_257 on Cy3

source_name: Melanotic melanoma


title: Control Sample 13 training set


title: ME:MDA_N_rep2

description: Reference on Cy5 and ME:MDA_N on Cy3

source_name: Ductal carcinoma-mammary gland; breast; duct; metastatic site: pleural effusion;


title: Pneumonia_Pre-treatment 2101

description: Sample 10

tag: treatment

value: pneumonia


title: ME:MDA_N_rep1

description: ME:MDA_N on Cy5 and Reference on Cy3


title: Pneumonia_Treated 2102

description: Sample 8

value: Treated with antibiotic

tag: tissue


title: LC:A549_rep7

description: Reference on Cy5 and LC:A549 on Cy3


title: Pneumonia_Treated 2121

description: Sample 9


title: Pneumonia_Treated 2105

description: Sample 6


title: LC:A549_rep5

description: Reference on Cy5 and LC:A549 on Cy3


title: Pneumonia_Treated 2101

description: Sample 7


title: LC:A549_rep4

description: LC:A549 on Cy5 and Reference on Cy3


title: Pneumonia_Pre-treatment 2105

description: Sample 5

value: Pre-treatment


title: Pneumonia_Pre-treatment 2121

description: Sample 4


title: TB Sample 102 test set

hyb_protocol: Standard IllumiNon-active sarcoidosis hybridization protocol

scan_protocol: Standard IllumiNon-active sarcoidosis scanning protocol

label_protocol: Biotinylated, amplified cRNon-active sarcoidosis were prepared using the IllumiNon-active sarcoidosis CustomPrep RNon-active sarcoidosis amplification kit

extract_protocol: RNon-active sarcoidosis was extracted using the MagMAX-96 Blood RNon-active sarcoidosis Isolation Kit and globin reduced using GLOBINclear


title: Pneumonia_Pre-treatment 2102

description: Sample 3


title: Pneumonia_Pre-treatment 2132

description: Sample 2


title: Pneumonia_Treated 2132

description: Sample 1


title: LE:HL_60_rep2

description: Reference on Cy5 and LE:HL_60 on Cy3

source_name: Pro myelocytic leukemia


title: LC:NCI_H226

description: LC:NCI_H226 on Cy5 and Reference on Cy3

source_name: Squamous cell carcinoma


title: LC:A549_rep6

description: Reference on Cy5 and LC:A549 on Cy3


title: LC:NCI_H460_rep1

description: LC:NCI_H460 on Cy5 and Reference on Cy3


title: TB Sample 98 test set

value: Black


title: TB Sample 96 test set


title: LC:NCI_H522_rep2

description: Reference on Cy5 and LC:NCI_H522 on Cy3


title: CNS:U251_rep2

description: Reference on Cy5 and CNS:U251 on Cy3

source_name: Glioblastoma


title: LC:A549_rep3

description: LC:A549 on Cy5 and Reference on Cy3


title: TB Sample 100 test set


title: TB Sample 101 test set


title: LE:CCRF_CEM_rep2

description: Reference on Cy5 and LE:CCRF_CEM on Cy3

source_name: ALL


title: LE:MOLT_4_rep2

description: Reference on Cy5 and LE:MOLT_4 on Cy3


title: BR:BT_549_rep2

description: Reference on Cy5 and BR:BT_549 on Cy3

source_name: Papillary infiltrating ductal carcinoma-mammary gland; breast


title: LC:NCI_H522_rep1

description: LC:NCI_H522 on Cy5 and Reference on Cy3


title: TB Sample 99 test set

source_name: Whole Blood


title: BR:BT_549_rep1

description: BR:BT_549 on Cy5 and Reference on Cy3

source_name: Reference


title: CO:SW_620_rep2

description: Reference on Cy5 and CO:SW_620 on Cy3

source_name: Carcinoma


title: LC:EKVX_rep2

description: Reference on Cy5 and LC:EKVX on Cy3


title: TB Sample 97 test set


title: TB Sample 94 test set

value: White


title: ME:UACC_257_rep1

description: ME:UACC_257 on Cy5 and Reference on Cy3


title: TB Sample 92 test set


title: Pneumonia Sample 90 test set

value: F

value: Pneumonia


title: OV:OVCAR_8_rep2

description: OV:OVCAR_8 on Cy5 and Reference on Cy3


title: TB Sample 93 test set

value: M

value: Indian subcontinent


title: ME:M14_rep2

description: ME:M14 on Cy5 and Reference on Cy3


title: Sarcoid Sample 91 test set


title: TB Sample 95 test set

value: SE Asian


title: ME:MDA_MB_435_rep2

description: ME:MDA_MB_435 on Cy5 and Reference on Cy3


title: Control Sample 8 training set

value: Caucasian


title: LE:RPMI_8226_rep2

description: LE:RPMI_8226 on Cy5 and Reference on Cy3

source_name: Myeloma


title: ME:LOXIMVI_rep2

description: ME:LOXIMVI on Cy5 and Reference on Cy3

source_name: Malignant amelanotic melanoma


title: LE:MOLT_4_rep1

description: LE:MOLT_4 on Cy5 and Reference on Cy3


title: Control Sample 89 test set

value: Control


title: Sarcoid Sample 17 training set

value: Active Sarcoid

value: whole blood


title: Pneumonia Sample 84 test set


title: LE:K_562_rep2

description: LE:K_562 on Cy5 and Reference on Cy3

source_name: CML


title: Control Sample 87 test set


title: Control Sample 88 test set


title: Control Sample 86 test set


title: PR:RC01_rep2

description: Reference on Cy5 and PR:RC01 on Cy3

source_name: Adenocarcinoma-prostate; metastatic site: bone;


title: LE:HL_60_rep1

description: LE:HL_60 on Cy5 and Reference on Cy3


title: Control Sample 85 test set


title: Control Sample 80 test set


title: Control Sample 83 test set


title: Control Sample 81 test set


title: RE:TK_10_rep2

description: Reference on Cy5 and RE:TK_10 on Cy3

source_name: Renal Spindle cell carcinoma


title: RE:UO_31_rep2

description: Reference on Cy5 and RE:UO_31 on Cy3

source_name: Renal cell carcinoma


title: LE:CCRF_CEM_rep1

description: LE:CCRF_CEM on Cy5 and Reference on Cy3


title: RE:SN12C_rep2

description: Reference on Cy5 and RE:SN12C on Cy3


title: Control Sample 79 test set


title: RE:786_0_rep2

description: Reference on Cy5 and RE:786_0 on Cy3

source_name: Adenocarcinoma


title: Cancer Sample 82 test set

value: lung cancer


title: CNS:SNB_19_rep2

description: Reference on Cy5 and CNS:SNB_19 on Cy3


title: Control Sample 77 test set


title: RE:ACHN_rep2

description: Reference on Cy5 and RE:ACHN on Cy3


title: RE:A498_rep2

description: Reference on Cy5 and RE:A498 on Cy3


title: Control Sample 74 test set


title: Sarcoid Sample 75 test set


title: Control Sample 78 test set


title: Sarcoid Sample 70 test set

value: Non-active sarcoidosis


title: PR:RC01_rep1

description: PR:RC01 on Cy5 and Reference on Cy3

value: Reference


title: LE:K_562_rep1

description: Reference on Cy5 and LE:K_562 on Cy3


title: Control Sample 73 test set


title: Sarcoid Sample 72 test set


title: Control Sample 71 test set


title: Control Sample 76 test set


title: CNS:SF_268_rep2

description: Reference on Cy5 and CNS:SF_268 on Cy3


title: LC:HOP_92_rep2

description: Reference on Cy5 and LC:HOP_92 on Cy3

source_name: Large cell


title: Control Sample 69 test set


title: CNS:SNB_75_rep2

description: Reference on Cy5 and CNS:SNB_75 on Cy3

source_name: Astrocytoma


title: Control Sample 68 test set


title: RE:UO_31_rep1

description: RE:UO_31 on Cy5 and Reference on Cy3


title: Cancer Sample 67 test set


title: Control Sample 65 test set


title: ME:SK_MEL_5_rep2

description: ME:SK_MEL_5 on Cy5 and Reference on Cy3

source_name: Malignant melanotic melanoma


title: LC:HOP_62_rep2

description: Reference on Cy5 and LC:HOP_62 on Cy3

source_name: adenocarcinoma


title: Sarcoid Sample 63 test set


title: Control Sample 66 test set


title: LC:A549_rep2

description: Reference on Cy5 and LC:A549 on Cy3


title: LC:NCI_H23_rep2

description: Reference on Cy5 and LC:NCI_H23 on Cy3


title: LC:NCI_H322M_rep2

description: Reference on Cy5 and LC:NCI_H322M on Cy3

source_name: Small cell Bronchioalveolar Carcinoma


title: BR:HS578T_rep2

description: Reference on Cy5 and BR:HS578T on Cy3

source_name: Carcinosarcoma-mammary gland; breast


title: Pneumonia Sample 61 test set


title: RE:TK_10_rep1

description: RE:TK_10 on Cy5 and Reference on Cy3


title: Control Sample 60 test set


title: Control Sample 62 test set


title: RE:SN12C_rep1

description: RE:SN12C on Cy5 and Reference on Cy3


title: PR:DU_145(ATCC)_rep1

description: PR:DU_145 on Cy5 and Reference on Cy3

source_name: Adenocarcinoma-prostate; metastatic site: brain; carcinoma


title: CNS:SNB_19_rep1

description: CNS:SNB_19 on Cy5 and Reference on Cy3

source_name: Glioblastoma


title: PR:DU_145(ATCC)_rep2

description: Reference on Cy5 and PR:DU_145 on Cy3

source_name: Reference


title: Control Sample 58 test set

source_name: Whole Blood


title: Control Sample 59 test set


title: PR:DU_145(DTP)_rep2

description: Reference on Cy5 and PR:DU_145 (DTP) on Cy3

value: PR:DU_145 (DTP)


title: PR:PC_3_rep2

description: Reference on Cy5 and PR:PC_3 on Cy3


title: Control Sample 56 test set

value: Middle Eastern


title: CO:SW_620_rep1

description: CO:SW_620 on Cy5 and Reference on Cy3

source_name: Carcinoma


title: Control Sample 55 test set


title: Control Sample 64 test set


title: OV:NCI_ADR_RES_rep2

description: Reference on Cy5 and OV:NCI_ADR_RES on Cy3


title: Pneumonia Sample 57 test set


title: OV:SK_OV_3_rep2

description: Reference on Cy5 and OV:SK_OV_3 on Cy3


title: RE:ACHN_rep1

description: RE:ACHN on Cy5 and Reference on Cy3


title: ME:MALME_3M_rep2

description: ME:MALME_3M on Cy5 and Reference on Cy3


title: Control Sample 54 test set


title: Control Sample 52 test set


title: Control Sample 50 test set


title: RE:A498_rep1

description: RE:A498 on Cy5 and Reference on Cy3


title: Sarcoid Sample 53 test set


title: Control Sample 47 test set


title: ME:MDA_MB_435_rep1

description: Reference on Cy5 and ME:MDA_MB_435 on Cy3

source_name: Ductal carcinoma-mammary gland; breast; duct; metastatic site: pleural effusion;


title: Control Sample 46 test set


title: RE:786_0_rep1

description: RE:786_0 on Cy5 and Reference on Cy3


title: OV:OVCAR_8_rep1

description: Reference on Cy5 and OV:OVCAR_8 on Cy3


title: Control Sample 51 test set


title: Sarcoid Sample 49 test set


title: Control Sample 48 test set


title: Cancer Sample 45 test set


title: ME:M14_rep1

description: Reference on Cy5 and ME:M14 on Cy3

source_name: Melanotic melanoma


title: ME:MALME_3M_rep1

description: Reference on Cy5 and ME:MALME_3M on Cy3


title: Cancer Sample 44 test set


title: ME:LOXIMVI_rep1

description: Reference on Cy5 and ME:LOXIMVI on Cy3

source_name: Malignant amelanotic melanoma


title: LE:RPMI_8226_rep1

description: Reference on Cy5 and LE:RPMI_8226 on Cy3

source_name: Myeloma


title: OV:IGROV1_rep1

description: OV:IGROV1 on Cy5 and Reference on Cy3

source_name: Cystoadenocarcinoma


title: Control Sample 39 test set


title: Cancer Sample 41 test set


title: Sarcoid Sample 34 test set


title: LE:SR_rep1

description: Reference on Cy5 and LE:SR on Cy3

source_name: Lymphoma


title: OV:OVCAR_5_rep2

description: Reference on Cy5 and OV:OVCAR_5 on Cy3

source_name: Adenocarcinoma


title: Control Sample 36 test set


title: OV:IGROV1_rep2

description: Reference on Cy5 and OV:IGROV1 on Cy3


title: Control Sample 42 test set


title: Control Sample 31 test set


title: Sarcoid Sample 40 test set


title: Control Sample 35 test set


title: Control Sample 30 test set


title: OV:OVCAR_3_rep2

description: OV:OVCAR_3 on Cy5 and Reference on Cy3


title: OV:OVCAR_4_rep2

description: Reference on Cy5 and OV:OVCAR_4 on Cy3


title: RE:CAKI_1_rep1

description: RE:CAKI_1 on Cy5 and Reference on Cy3

source_name: Clear cell carcinoma


title: Sarcoid Sample 43 test set


title: Cancer Sample 38 test set


title: ME:SK_MEL_28_rep1

description: ME:SK_MEL_28 on Cy5 and Reference on Cy3

source_name: Malignant melanotic melanoma


title: Control Sample 37 test set


title: Control Sample 33 test set


title: OV:OVCAR_5_rep1

description: OV:OVCAR_5 on Cy5 and Reference on Cy3


title: ME:SK_MEL_2_rep1

description: Reference on Cy5 and ME:SK_MEL_2 on Cy3


title: ME:UACC_62_rep2

description: ME:UACC_62 on Cy5 and Reference on Cy3


title: OV:OVCAR_4_rep1

description: OV:OVCAR_4 on Cy5 and Reference on Cy3


title: Control Sample 32 test set


title: ME:SK_MEL_28_rep2

description: Reference on Cy5 and ME:SK_MEL_28 on Cy3


title: Sarcoid Sample 29 test set


title: OV:OVCAR_3_rep1

description: Reference on Cy5 and OV:OVCAR_3 on Cy3


title: ME:UACC_62_rep1

description: Reference on Cy5 and ME:UACC_62 on Cy3


title: OV:SK_OV_3_rep1

description: OV:SK_OV_3 on Cy5 and Reference on Cy3


title: Control Sample 21 test set


title: Control Sample 27 test set


title: Cancer Sample 22 test set


title: PR:PC_3_rep1

description: PR:PC_3 on Cy5 and Reference on Cy3

source_name: Adenocarcinoma-prostate; metastatic site: bone;


title: Sarcoid Sample 20 test set


title: Sarcoid Sample 25 test set


title: PR:DU_145(DTP)_rep1

description: PR:DU_145 (DTP) on Cy5 and Reference on Cy3


title: CO:KM12_rep2

description: Reference on Cy5 and CO:KM12 on Cy3

source_name: Adenocarcinome


title: LC:NCI_H322M_rep1

description: LC:NCI_H322M on Cy5 and Reference on Cy3

source_name: Small cell Bronchioalveolar Carcinoma


title: Control Sample 15 test set


title: Sarcoid Sample 18 test set


title: OV:NCI_ADR_RES_rep1

description: OV:NCI_ADR_RES on Cy5 and Reference on Cy3


title: CNS:SF_539_rep2

description: Reference on Cy5 and CNS:SF_539 on Cy3

source_name: Glial cell neoplasm


title: Sarcoid Sample 24 test set


title: Control Sample 26 test set


title: Sarcoid Sample 19 test set


title: LC:NCI_H23_rep1

description: LC:NCI_H23 on Cy5 and Reference on Cy3


title: Sarcoid Sample 17 test set


title: Sarcoid Sample 16 test set


title: BR:MCF7_rep2

description: BR:MCF7 on Cy5 and Reference on Cy3

source_name: Adenocarcinoma-mammary gland; breast; metastatic site: pleural effusion;


title: CO:HCC_2998_rep2

description: Reference on Cy5 and CO:HCC_2998 on Cy3

source_name: Reference

source_name: carcinoma


title: Pneumonia Sample 28 test set

source_name: Whole Blood


title: Control Sample 23 test set


title: CO:COLO205_rep2

description: Reference on Cy5 and CO:COLO205 on Cy3


title: BR:HS578T_rep1

description: BR:HS578T on Cy5 and Reference on Cy3

source_name: Carcinosarcoma-mammary gland; breast


title: CNS:SNB_75_rep1

description: CNS:SNB_75 on Cy5 and Reference on Cy3

source_name: Astrocytoma


title: ME:SK_MEL_5_rep1

description: Reference on Cy5 and ME:SK_MEL_5 on Cy3


title: Control Sample 14 test set


title: Control Sample 12 test set


title: LC:HOP_62_rep1

description: LC:HOP_62 on Cy5 and Reference on Cy3

source_name: adenocarcinoma


title: BR:T47D_rep2

description: Reference on Cy5 and BR:T47D on Cy3

source_name: infiltrating ductal carcinoma


title: Control Sample 13 test set


title: Control Sample 9 test set


title: LC:EKVX_rep1

description: LC:EKVX on Cy5 and Reference on Cy3


title: LC:HOP_92_rep1

description: LC:HOP_92 on Cy5 and Reference on Cy3

source_name: Large cell


title: CO:KM12_rep1

description: CO:KM12 on Cy5 and Reference on Cy3


title: CNS:SF_295_rep2

description: Reference on Cy5 and CNS:SF_295 on Cy3

source_name: Glioblastoma


title: CO:HCT_15_rep1

description: CO:HCT_15 on Cy5 and Reference on Cy3

source_name: Adenocarcinoma


title: Sarcoid Sample 11 test set


title: LC:A549_rep1

description: LC:A549 on Cy5 and Reference on Cy3


title: Control Sample 8 test set


title: Sarcoid Sample 10 test set


title: CO:HCT_116_rep1

description: CO:HCT_116 on Cy5 and Reference on Cy3


title: Sarcoid Sample 7 test set


title: CO:COLO205_rep1

description: CO:COLO205 on Cy5 and Reference on Cy3


title: Sarcoid Sample 6 test set


title: CO:HT29_rep1

description: CO:HT29 on Cy5 and Reference on Cy3


title: CO:HCC_2998_rep1

description: CO:HCC_2998 on Cy5 and Reference on Cy3


title: CNS:SF_539_rep1

description: CNS:SF_539 on Cy5 and Reference on Cy3


title: BR:MCF7_rep1

description: Reference on Cy5 and BR:MCF7 on Cy3


title: Sarcoid Sample 5 test set


title: Cancer Sample 3 test set


title: CNS:U251_rep1

description: CNS:U251 on Cy5 and Reference on Cy3


title: Pneumonia Sample 4 test set


title: Sarcoid Sample 2 test set


title: CNS:SF_295_rep1

description: CNS:SF_295 on Cy5 and Reference on Cy3


title: CNS:SF_268_rep1

description: CNS:SF_268 on Cy5 and Reference on Cy3


title: Sarcoid Sample 1 test set


title: BR:T47D_rep1

description: BR:T47D on Cy5 and Reference on Cy3


title: BR:MDA_MB_231_rep1

description: BR:MDA_MB_231 on Cy5 and Reference on Cy3

source_name: Adenocarcinoma-mammary gland; breast; epithelial; metastatic site: pleural effusion;


title: seedling 6

city: Delhi

first: Pradeep

middle: Kumar

last: Burma

state: Delhi

address: Benito Juarez Road

department: Department of Genetics

country: India

institute: University of Delhi South campus

description: Gene expression of 21854 genes were analysed. Target for the reporter (RPTR_*) and spike controls (with Affx-r2-Tag_at) was not loaded  with the aim of negative control. Data for 24,138 probes are available.

hyb_protocol: Strandard Affymetrix protocol

scan_protocol: Scanner- GeneChip  Scanner 3000 with  GCOS software

data_processing: Algorithm- GC-RMA and Software- Genespring (Agilent)

organism: Gossypium hirsutum

source_name: Seedling

label_protocol: GeneChip  3  IVT Express Kit (Affymetrix catalog No.- 901228)

growth_protocol: Anthers were dissected from the cotton buds at  different stages of development, buds without anthers were stored separately, young leaf was harvested from one month old plant and seedling from 5days after germination was harvested.

extract_protocol: Anther dissections were done with fine pointed needle and immediately dipped in liquid Nitrogen. Total RNA was extracted from the dissected samples using SpectrumTM Plant Total RNA kit (Sigma Catalog no- STRN250). Quality of the total RNA was checked by bioanalyzer.

value: Seedling


title: seedling 5


title: seedling 7


title: Control Sample 41 validation set


title: Control Sample 40 validation set


title: Leaf 2

source_name: Leaf

value: Leaf


title: 8mm buds Flower parts 6

source_name: buds without anther

value: buds without anther


title: Leaf 3


title: Control Sample 42 validation set

value: F

value: White


title: Control Sample 39 validation set

value: Black


title: 8mm buds Anther 6

source_name: Anther

value: Anther


title: Control Sample 38 validation set

value: M

value: Central Asia


title: 8mm buds Anther 7


title: Control Sample 37 validation set

value: Control


title: 8mm buds Flower parts 5


title: Leaf 4


title: 8mm buds Flower parts 4


title: Sarcoid Sample 35 validation set


title: Sarcoid Sample 36 validation set

value: Active sarcoidosis


title: 7mm buds Flower parts 2


title: 8mm buds Anther 1


title: Control Sample 33 validation set

value: whole blood


title: Control Sample 34 validation set


title: 7mm buds Flower parts 1


title: Sarcoid Sample 31 validation set


title: 7mm buds Anther 3


title: Sarcoid Sample 32 validation set

value: Indian subcontinent


title: 7mm buds Anther 1


title: 5mm buds Flower parts 4


title: Sarcoid Sample 30 validation set


title: 5mm buds Flower parts 3


title: 006 d56

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

country: Germany

institute: Max-Planck-Institute for Infection Biology

description: study participant 6

hyb_protocol: After precipitation, purification and quantification the labeled samples were hybridized according to the supplier’s protocol (Agilent Technologies)

scan_protocol: Scanning of microarrays was performed with 5µm resolution 16 bit and extended range using a G2565CA high resolution laser microarray scanner (Agilent Technologies)

data_processing: Microarray image data were extracted and analyzed with the Image Analysis / Feature Extraction software G2567AA ( Agilent Technologies). The extracted MAGE-ML files were further analyzed with the Rosetta Resolver, Build 7.2.2.0 SP1.31 (Rosetta Biosoftware, Seattle, USA). The values are the 'gProcessedSignal' from the Agilent Technologies Feature Extraction and represent signal intensities left after multiplicatively detrended background subtraction. Arrays were normalized to the mean of trimmed positive non-flagged/non-control Reporters.

source_name: d56 post immunization

label_protocol: Total RNA labeling was performed with the one color Quick Amp Labeling Kit (Agilent Technologies)

extract_protocol: Total RNA from whole blood was isolated by the PAXgene protocol (PreAnalytiX)

treatment_protocol: PAXgene tubes were used for whole blood sampling.

value: PPD positive


title: 002 d56

description: study participant 2


title: 7mm buds Flower parts 3


title: 005 d56

description: study participant 5


title: 005 d168

description: study participant 5

source_name: d168 post immunization


title: 004 d56

description: study participant 4


title: 002 d168

description: study participant 2


title: 004 d168

description: study participant 4


title: 003 d56

description: study participant 3


title: Sarcoid Sample 29 validation set


title: Sarcoid Sample 27 validation set


title: 003 d168

description: study participant 3


title: 001 d168

description: study participant 1


title: Sarcoid Sample 28 validation set

value: Non-active sarcoidosis


title: 7mm buds Anther 2


title: 006 d168

description: study participant 6


title: Control Sample 26 validation set


title: 006 d28

description: study participant 6

source_name: d28 post immunization


title: 001 d56

description: study participant 1


title: Control Sample 25 validation set


title: 005 d28

description: study participant 5


title: 5mm buds Anther  3


title: 5mm buds Anther  4


title: Control Sample 24 validation set


title: 5mm buds Flower parts 2


title: 5mm buds Anther  1


title: 006 d14

description: study participant 6

source_name: d14 post immunization


title: 004 d28

description: study participant 4


title: 002 d28

description: study participant 2


title: Sarcoid Sample 23 validation set

source_name: Whole Blood


title: Control Sample 22 validation set


title: Control Sample 20 validation set


title: 001 d14

description: study participant 1


title: 003 d14

description: study participant 3


title: 005 d0

description: study participant 5

source_name: naive, pre-immunization


title: 004 d14

description: study participant 4


title: Control Sample 21 validation set


title: 003 d28

description: study participant 3


title: Control Sample 19 validation set


title: 005 d14

description: study participant 5


title: Control Sample 18 validation set


title: 002 d14

description: study participant 2


title: 001 d28

description: study participant 1


title: 006 d0

description: study participant 6


title: 004 d0

description: study participant 4


title: Control Sample 16 validation set


title: Control Sample 15 validation set


title: Sarcoid Sample 17 validation set


title: 002 d0

description: study participant 2


title: 003 d0

description: study participant 3


title: H3K27me1 Kc167 D.melanogaster Control Rep1

city: Toronto

first: DCC

last: modENCODE

state: Ontario

address: MaRS Centre, South Tower, 101 College Street, Suite 800

country: Canada

institute: Ontario Institute for Cancer Research

description: channel ch1 is input DNA;

hyb_protocol: 1. Prehybridize array for 1 hr in 200ml of 1xMES-Triton at 450C with 45 rpm rotation.   2. Incubate hybridization cocktail for 10min at 1000C then 10min at 450C. Spin at max speed for 3 min at RT. Transfer the supernatant to new tube. Spin for 3 more minutes use 200ml of resulted supernatant for hybridization.   3. Hybridize 18hr at 450C with 45 rpm rotation.   4. Use fluidics station EukGE-WS2v4 protocol (Affymetrix) for washing and staining.

scan_protocol: Standard Affymetrix Array Scanning Protocol was used

data_processing: M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

organism: Drosophila melanogaster

source_name: H3K27me1 Kc167 Control expt.1776 channel_1

extract_protocol:
1. Grow cell cultures in large T-flasks (175-225cm2) to a density of~5x106 cells/ml. Combine the content of 2-3 flasks in one. Immediately proceed with the following steps.   2. Add 37% formaldehyde (Sigma) to final concentration 1.8% directly to the culture incubate for 10min at 250C on a rotating or rocking platform.   3. Stop reaction by adding 1.25M glycine pH 7.0 to each culture to the final concentration of 125mM. Mix well, within next 5 min aliquot cell suspension into 50ml falcon tubes and accumulate them on ice.   4. Pellet fixed cells by spinning for 2? at 1500g, +40C. Use swinging bucket rotor.   5. Resuspend each pellet in 5ml of sterile 1xPBS, pool suspensions together.   6. Pellet the cells by spinning for 2? at 1500g, +40C.   7. Resuspend the cells in 10ml of ChIP wash A solution. Transfer suspension to a new 15ml Falcon tube. Wash fixed cells for 10min at +40C using rotating wheel. Pellet as above.   8. Thoroughly resuspend fixed cells in 10ml of  ChIP wash B solution, wash for 10min at +40C. Use rotating wheel.
After treatment with formaldehyde, Drosophila tissue culture cells were lysed with SDS and sonication (on ice) in the presence of protease inhibitors.  The resulting chromatin was treated with non-ionic detergents at physiological concentrations of monovalent cations.  Ribonucleic acid was removed by RNAse A, and the DNA was purified using SDS, proteinase K, and organic extraction, followed by ethanol precipitation.
1. Add 30ml of PAS (50% suspension in RIPA (-PMSF)) to 500ml of crosslinked chromatin. Incubate 1h at +40C.   2. Spin suspensions for 2min at top speed +40C. Transfer supernatants to new tubes. Add 5ml of 100mM PMSF solution in isopropanol to each 500ml aliquot of precleared chromatin.   3. Add appropriate amount of antibody to each reaction. Do not forget to set up no Ab control. Incubate for 15 hours at +40C on rotating weel.   4. Add 40ml of PAS (50% suspension in RIPA (-PMSF)), incubate 3h at +40C on rotating weel.   5. Wash the beads 5 times 10min each with 1ml of RIPA, then one time with 1ml of LiCl ChIP buffer and finally twice with 1ml of TE. To pellet the beads between washes spin samples for 20sec +40C at top speed. Do all the washes at +40C.   6. Resuspend the beads in 100ml TE add 1ml (final 50mg/ml) of RNAse A (10mg/ml) incubate 30min at +370C.   7. Add 7.5ml (final 0.5%) of 10% SDS and 3.8ml (final 0.5mg/ml) of Proteinase K (20mg/ml). Incubate overnight at +370C.   8. Transfer samples at +650C, incubate 6h.   9. Add 4.5ml of 5M NaCl (140mM final). Extract samples with 150ml of phenol-chloroform by vortexing for 30 sec, centrifuge for 10 min at RT, take 120ml of aqueous phase, back-extract organic phase with 150ml of TEN 140 (10mM Tris-HCl pH8.0; 1mM EDTA; 140mM NaCl). Take 150ml of aqueous phase. Combine aqueous phases (you will get 120ml + 150ml=270ml of solution).  10. Extract samples with 300ml of chloroform by vortexing for 30 sec, centrifuge for 5 min at RT. Transfer the upper aqueous phase into the new tube. Add 30ml of 3M NaAc pH 5.0 and 2ml of glycogen (5mg/ml) to aqueous phase. Precipitate DNA with 900ml of EtOH at -700C for 1h.  11. Spin for 10min, top speed at +40C. Wash the pellet in 300ml of 70%EtOH  12. Spin for 10min, top speed at +40C. If you plan to do qPCR analysis only dissolve the pellet in 150ml of pure H2O. If you plan to do both qPCR and microarray hybridization then first dilute DNA pellets in 12ml of pure H2O transfer 4ml of DNA solution to a new eppendorf tube and add 46ml of pure H2O. Use the latter for qPCR and the former for subsequent amplification and labeling. Store DNA solutions at -200C.  13. Prepare dilutions of DNA isolated from the original crosslinked chromatin (also called ?Input DNA? or simply ?Input?) following the chart below. Use the stock with concentration of 0.5% of input DNA per ml of solution (see: ?Isolation of ChIP Input DNA? protocol).

value: embryo-derived cell-line

tag: developmental stage

value: late embryonic stage

tag: genotype

value: se/e

tag: Sex

value: Female


title: H3K27me1 Kc167 D.melanogaster Experimental Rep2

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: H3K27me1;target name: H3K27me1;host: Rabbit;antigen: histone H3 containing the monomethylated  lysine 27 (H3K27me1) using a KLH-conjugated synthetic peptide.;clonal: Polyclonal;purified: Affinity;company: Other;catalog: pAb-045-050;short description: Rabbit polyclonal antibody raised against H3K27me1 using KLH conjugated peptide;channel ch1 is input DNA;

source_name: H3K27me1 Kc167 Experimental expt.2046 channel_1

label_protocol: 1. Prehybridize array for 1 hr in 200ml of 1xMES-Triton at 450C with 45 rpm rotation.   2. Incubate hybridization cocktail for 10min at 1000C then 10min at 450C. Spin at max speed for 3 min at RT. Transfer the supernatant to new tube. Spin for 3 more minutes use 200ml of resulted supernatant for hybridization.   3. Hybridize 18hr at 450C with 45 rpm rotation.   4. Use fluidics station EukGE-WS2v4 protocol (Affymetrix) for washing and staining.


title: H3K27me1 Kc167 D.melanogaster Experimental Rep1

source_name: H3K27me1 Kc167 Experimental expt.2047 channel_1


title: 001 d0

description: study participant 1


title: H3K27me1 ML-DmBG3-c2 D.melanogaster Control Rep2

description: channel ch1 is input DNA;

source_name: H3K27me1 ML-DmBG3-c2 Control expt.2041 channel_1

value: CNS-derived cell-line

value: third instar larval stage

value: y v f mal

value: Unknown


title: 507 d180

description: study participant 17

scan_protocol: Scanning of microarrays was performed with 5µm resolution, 16 bit and extended range using a G2565CA high resolution laser microarray scanner (Agilent Technologies)

source_name: d180 post immunization

extract_protocol: Total RNA from PBMCs was isolated by the TRIzol Reagent RNA preparation method (Invitrogen, Karlsruhe, Germany) using Glycogen as carrier

treatment_protocol: Cell preparation tubes (CPT) were used for PBMC isolation.

value: PBMC


title: 510 d180

description: study participant 20


title: Control Sample 13 validation set

value: F

value: White


title: Control Sample 11 validation set

value: M

value: Control


title: H3K27me1 ML-DmBG3-c2 D.melanogaster Experimental Rep2

source_name: H3K27me1 ML-DmBG3-c2 Experimental expt.2045 channel_1


title: H3K27me1 Kc167 D.melanogaster Control Rep2

description: channel ch1 is input DNA;

source_name: H3K27me1 Kc167 Control expt.1756 channel_1


title: H3K27me1 ML-DmBG3-c2 D.melanogaster Control Rep1

description: channel ch1 is input DNA;

source_name: H3K27me1 ML-DmBG3-c2 Control expt.1880 channel_1


title: Control Sample 14 validation set

value: whole blood


title: Control Sample 10 validation set

value: Black


title: H3K27me1 ML-DmBG3-c2 D.melanogaster Experimental Rep1

source_name: H3K27me1 ML-DmBG3-c2 Experimental expt.2044 channel_1


title: 506 d180

description: study participant 16

value: PPD positive


title: SU-HW HB Kc167 D.melanogaster Input Rep2

description: channel ch1 is input DNA;

source_name: SU-HW HB Kc167 Input expt.1750 channel_1


title: TB Sample 9 validation set

value: Indian subcontinent

value: TB


title: TB Sample 8 validation set


title: 503 d180

description: study participant 13


title: SU-HW HB Kc167 D.melanogaster ChIP Rep2

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: SU(HW)-HB;target name: SU(HW);host: Rabbit;antigen: Peptide based on aa 43-258 of the Su(HW) protein;clonal: Polyclonal;purified: Affinity;company: Lab;catalog: VP Lab;short description: Polyclonal Ab against SU(HW) protein;channel ch1 is input DNA;

source_name: SU-HW HB Kc167 ChIP expt.1869 channel_1

value: embryo-derived cell-line

value: late embryonic stage


title: 504 d180

description: study participant 14


title: SU-HW HB Kc167 D.melanogaster Input Rep1

description: channel ch1 is input DNA;

source_name: SU-HW HB Kc167 Input expt.1776 channel_1

value: se/e

value: Female


title: 502 d180

description: study participant 12


title: 501 d180

description: study participant 11


title: SU-HW HB Kc167 D.melanogaster ChIP Rep1

source_name: SU-HW HB Kc167 ChIP expt.1778 channel_1


title: TB Sample 6 validation set


title: TB Sample 5 validation set


title: Control Sample 12 validation set


title: 509 d180

description: study participant 19


title: TB Sample 4 validation set


title: 510 d57

description: study participant 20

source_name: d57 post immunization


title: 509 d57

description: study participant 19


title: RE:SN12C

description:
S1975150329
Renal cell carcinoma-poor differentiation

data_processing:
Probe intensities were normalized using the crlmmCopynumber method from Bioconductor's crlmm package (http://www.bioconductor.org/packages/release/bioc/html/crlmm.html). Log probe intensities were mean centered to have a mean of zero for each sample.
Normalized data consists of mean centered probe intensities (mean of each sample subtracted from the log probe intensities for the sample, to give a mean of zero for the sample). Non-normalized data is the copy number data from crlmmCopynumber method from Bioconductor's crlmm package (http://www.bioconductor.org/packages/release/bioc/html/crlmm.html).

label: biotin, dinitrophenyl

source_name: Renal cell carcinoma

label_protocol: Done according to array manufacturer's specifications. The labels are C-Bio and A-DNP. C and G nucleotides are biotin labeled and A and T nucleotides were dinitrophenyl labeled

tag: tissue of origin

value: Renal

tag: age

value: male

tag: prior treatment

tag: epithelial

value: yes

tag: ploidy

value: 3n, Triploid (69)

tag: p53 mutation

value: MT

tag: doubling time (hrs)

tag: contributing institute

value: MD Anderson Hospital and Tumor Institute

tag: contributing person

tag: reference


title: RE:UO_31

description:
S1975150442
Renal cell carcinoma-very poorly differentiated

tag: gender

value: female

value: WT

value: National Cancer Institute, NIH


title: 505 d180

description: study participant 15

value: PBMC

tag: cell type


title: RE:RXF_393

description:
S1975150319
hypernephroma-poor differentiation

source_name: hypernephroma

value: NCI/DCT/DTP

value: Contrib oncol 42, 1992


title: H3K4me3 (ab8580 lot1) ML-DmBG3-c2 CTCF RNAi D.melanogaster Input Rep2

description: channel ch1 is input DNA;

source_name: H3K4me3 (ab8580 lot1) ML-DmBG3-c2 CTCF RNAi Input expt.714 channel_1

extract_protocol:
The template for the dsRNA synthesis was PCR amplified from Drosophila genomic DNA using specific primers extended with 5? T7-promoter tails. The sequence of the T7-promoter tails is as follows: 5?- CTAATACGACTCACTATAGGGAG-3?. The amplicon was selected such that it is contained within single exon. Following PCR the template was purified using PCR purification Kit from Qiagen. 2.5ug of purified template was used to synthesize dsRNA with Ribomax T7 RNA transcription kit from Promega. The dsRNA was precipitated with ethanol, dissolved in 300ul of pure water, denatured by heating to 65C for 30min and re-annealed by slow cooling to room temperature.2x10^6cells were treated with 50ug of dsRNA in 25cm2 T-flask for 1 hour in serum-free Schneider?s media. They were further brought up 6ml of Schneider?s media supplemented with 10% FBS and grown to confluence (~4 days). The cells were passaged to a 75cm2 T-flask and treated the second time with 200ug of dsRNA as described above. Following the treatment the cells were grown to confluence in 15ml Schneider?s media. 1ml of resulted culture was taken for preparation of nuclear and cytoplasmic protein extracts and the rest was in vivo crosslinked with formaldehyde. The protocol typically yields about 7x10^7 crosslinked cells, which is enough for about 7 ChIPs. And the RNAi treated cells were treated with formaldehyde as in normal cultured cell.
After treatment with formaldehyde, Drosophila tissue culture cells were lysed with SDS and sonication (on ice) in the presence of protease inhibitors.  The resulting chromatin was treated with non-ionic detergents at physiological concentrations of monovalent cations.  Ribonucleic acid was removed by RNAse A, and the DNA was purified using SDS, proteinase K, and organic extraction, followed by ethanol precipitation.
1. Add 30ml of PAS (50% suspension in RIPA (-PMSF)) to 500ml of crosslinked chromatin. Incubate 1h at +40C.   2. Spin suspensions for 2min at top speed +40C. Transfer supernatants to new tubes. Add 5ml of 100mM PMSF solution in isopropanol to each 500ml aliquot of precleared chromatin.   3. Add appropriate amount of antibody to each reaction. Do not forget to set up no Ab control. Incubate for 15 hours at +40C on rotating weel.   4. Add 40ml of PAS (50% suspension in RIPA (-PMSF)), incubate 3h at +40C on rotating weel.   5. Wash the beads 5 times 10min each with 1ml of RIPA, then one time with 1ml of LiCl ChIP buffer and finally twice with 1ml of TE. To pellet the beads between washes spin samples for 20sec +40C at top speed. Do all the washes at +40C.   6. Resuspend the beads in 100ml TE add 1ml (final 50mg/ml) of RNAse A (10mg/ml) incubate 30min at +370C.   7. Add 7.5ml (final 0.5%) of 10% SDS and 3.8ml (final 0.5mg/ml) of Proteinase K (20mg/ml). Incubate overnight at +370C.   8. Transfer samples at +650C, incubate 6h.   9. Add 4.5ml of 5M NaCl (140mM final). Extract samples with 150ml of phenol-chloroform by vortexing for 30 sec, centrifuge for 10 min at RT, take 120ml of aqueous phase, back-extract organic phase with 150ml of TEN 140 (10mM Tris-HCl pH8.0; 1mM EDTA; 140mM NaCl). Take 150ml of aqueous phase. Combine aqueous phases (you will get 120ml + 150ml=270ml of solution).  10. Extract samples with 300ml of chloroform by vortexing for 30 sec, centrifuge for 5 min at RT. Transfer the upper aqueous phase into the new tube. Add 30ml of 3M NaAc pH 5.0 and 2ml of glycogen (5mg/ml) to aqueous phase. Precipitate DNA with 900ml of EtOH at -700C for 1h.  11. Spin for 10min, top speed at +40C. Wash the pellet in 300ml of 70%EtOH  12. Spin for 10min, top speed at +40C. If you plan to do qPCR analysis only dissolve the pellet in 150ml of pure H2O. If you plan to do both qPCR and microarray hybridization then first dilute DNA pellets in 12ml of pure H2O transfer 4ml of DNA solution to a new eppendorf tube and add 46ml of pure H2O. Use the latter for qPCR and the former for subsequent amplification and labeling. Store DNA solutions at -200C.  13. Prepare dilutions of DNA isolated from the original crosslinked chromatin (also called ?Input DNA? or simply ?Input?) following the chart below. Use the stock with concentration of 0.5% of input DNA per ml of solution (see: ?Isolation of ChIP Input DNA? protocol).

tag: cell line

value: CNS-derived cell-line

value: third instar larval stage

value: y v f mal

value: Unknown


title: TB Sample 3 validation set

source_name: Whole Blood

value: M

tag: ethnicity

value: Black

tag: disease state

value: TB

tag: tissue

value: whole blood


title: RE:A498

description:
S1975150388
Adenocarcinoma

source_name: Adenocarcinoma

value: Renal

value: yes

value: 3n, Triploid (69)


title: H3K4me3 (ab8580 lot1) ML-DmBG3-c2 CTCF RNAi D.melanogaster Input Rep1

description: channel ch1 is input DNA;

source_name: H3K4me3 (ab8580 lot1) ML-DmBG3-c2 CTCF RNAi Input expt.498 channel_1

tag: developmental stage

tag: genotype

tag: Sex


title: RE:TK_10

description:
S1975150480
Renal Spindle cell carcinoma

source_name: Renal Spindle cell carcinoma

tag: tissue of origin

tag: age

value: male

tag: prior treatment

value: 4n, Tetraploid (92)

value: MT

value: R.V.Clayman, Washington Univ.School of Medicine


title: H3K4me3 (ab8580 lot1) ML-DmBG3-c2 CTCF RNAi D.melanogaster ChIP Rep2

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: H3K4me3 (ab8580 lot1);target name: H3K4me3;host: Rabbit;antigen: Synthetic peptide conjugated to KLH derived from within residues 1 - 100 of Human Histone H3 tri methylated at K4.;clonal: Polyclonal;purified: Affinity;company: Abcam;catalog: 8580;reference: http://www.abcam.com/Histone-H3-tri-methyl-K4-antibody-ChIP-Grade-ab8580.html;short description: Histone H3 (tri methyl K4).;channel ch1 is input DNA;

source_name: H3K4me3 (ab8580 lot1) ML-DmBG3-c2 CTCF RNAi ChIP expt.751 channel_1


title: 507 d57

description: study participant 17

value: PBMC

value: PPD positive


title: Sarcoid Sample 2 validation set

value: F

value: Active sarcoidosis


title: 506 d57

description: study participant 16


title: RE:CAKI_1

description:
S1975150269
Clear cell carcinoma

source_name: Clear cell carcinoma

tag: epithelial

tag: source

value: Metastasis

tag: ploidy

tag: p53 mutation

value: WT

value: Memorial Sloan Kettering Cancer Center

value: J. Fogh

value: Human Tumor cells in vitro, pp 115-159, 1975


title: TB Sample 1 validation set

value: Indian subcontinent

value: TB

value: whole blood


title: TB Sample 7 validation set

value: White


title: PR:PC_3

description:
S1975150304
Adenocarcinoma-prostate; metastatic site: bone;

value: Prostate

value: male

value: yes

tag: doubling time (hrs)

tag: contributing institute

value: Pasadena Center for Medical Research

tag: contributing person

value: M.E. Kaighn

tag: reference


title: WT cells vs VF cells

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

description: Biological one replicate. Transcriptional profiling in WT cells and VF cells

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: ScanArray Express (PerkinElmer Japan Co., Ltd.) was used for scanning. Images were quantified using GenePix Pro version 6.0(Axon Instruments).

data_processing: F635 Median column as Red signal and F532 Median column as Green signal. Global normalized, background subtracted data obtained from log2 of processed Green signal/processed Red signal.

organism: Mus musculus

source_name: WT

label_protocol: cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: Cultured with RPMI medium containing 10% FBS and 2 ng/mL IL-3

treatment_protocol: Cultured with RPMI medimu containing 1% FBS for 12 hr.

tag: genotype/variation

value: Ba/F3 expressing wild type JAK2 (WT)

source_name: VF

value: Ba/F3 expressing JAK2 V617F mutant (VF)


title: 504 d57

description: study participant 14

value: PBMC

tag: cell type

value: PPD positive


title: 505 d57

description: study participant 15

tag: tissue


title: H3K4me3 (ab8580 lot1) ML-DmBG3-c2 CTCF RNAi D.melanogaster ChIP Rep1

source_name: H3K4me3 (ab8580 lot1) ML-DmBG3-c2 CTCF RNAi ChIP expt.466 channel_1

tag: cell line

value: CNS-derived cell-line

tag: developmental stage

value: third instar larval stage

value: y v f mal

value: Unknown


title: RE:786_0

description:
S1975150316
Adenocarcinoma

value: Renal

tag: gender

value: MT

value: R.D.Williams, Univ. of Iowa


title: RE:ACHN

description:
S1975150528
Renal cell carcinoma-poor to moderate differentiation

tag: tissue of origin

value: Rad/VB/CCNU/Mto/Pred

value: WT

value: Southern Research Inst. (T.F. Hogan, Middleton memorial VA hospital)


title: 1833 control, biological rep3

city: Chicago

first: Marsha

last: Rosner

state: IL

address: 929 East 57th Street

department: Ben May Department for Cancer Research

institute: University of Chicago

description: Gene expression data from metastatic triple-negative breast cancer cell line, biological  rep 3

hyb_protocol: The RNA quality control, cRNA ampliﬁcation, hybridization, and image scan were conducted in the Functional Genomics Facility at the University of Chicago.

data_processing: The data was analyzed using R (Version 2.13) using related packages (oligo and pd.hugene.1.0.st.v1) from Bioconductor (Version 2.5).  The quantiﬁed signals were normalized using Robust Multiarray Average (RMA).

source_name: 1833 control

growth_protocol: Stablely transfected 1833 cell lines were cultured in a complete medium consisting of DMEM supplemented with 10% (vol/vol) FBS, 50 U/mL penicillin, and 50 μg/mL streptomycin.

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

treatment_protocol: BACH1 depletion(shBACH1) and control were generated by transducing the cells with BACH1 shRNA or scrambled control in a pLKO.1 lentiviral vector (Open Biosystems). After transduction, cells were selected and maintained in 0.5 μg/mL puromycin.


title: 1833 shBACH1, biological rep3

description: Gene expression data from metastatic triple-negative breast cancer cell line depleted of BACH1 using shRNA, biological  rep 3

scan_protocol: The RNA quality control, cRNA ampliﬁcation, hybridization, and image scan were conducted in the Functional Genomics Facility at the University of Chicago.

source_name: 1833 shBACH1


title: 503 d57

description: study participant 13


title: 502 d57

description: study participant 12


title: Sarc (C)

city: Silver Spring

first: BIJU

last: ISSAC

state: MD

address: 503 Robert Grant Ave, Rm 2W123

department: Military HIV Research Program

institute: Walter Reed Army Institute of Research

description: control

hyb_protocol: target specific primers

data_processing:
The real-time PCR reactions were run  Roche Lightcycler 480 real-time PCR instrument. The data was analyzed using MultiD Genex (MultiD,  Gothenburg, Sweden) . Raw Data (Ct) were Inter-Plate calibrated. Outliers and negatives were filtered along with false positives. Missing values were filled/imputed. Data was normalized to global mean. The fold change (2^deltadelta CT) was computed between test and control after determining quantification and log convertions to base 2.
P value (BH corrected)<0.01

label: SYBR Green

source_name: chondrosarcoma

label_protocol: 20 ng of total RNA per panel was reverse transcribed using miRCURYLNA RTmicroPCR, polyadenylation and cDNA synthesis kit(Exiqon, Woburn,MA) For each sample the cDNA was diluted and each reaction was combined with SYBR Green Master Mix (Exiqon) and added to the Ready-to-Use PCR Panels.

growth_protocol: JJ012  cells were seeded on 60x15mm Petri dish at 5000000cells density.in seeding media of 5ml.

extract_protocol: Qiazol was added to each dish and the cells were subject to active lysis, . Lysates were frozen at -70 and total RNA was extracted with QiagenRNeasy  mini kit.

treatment_protocol: Cells were incubated 24 hours at 37Cin 5% CO2 incubator. After PRP-1 was added to the test dishes, while control remained untreated

value: JJ012 cell line

tag: treatment

value: control


title: 501 d57

description: study participant 11


title: 510 d29

description: study participant 20

source_name: d29 post immunization


title: OV:OVCAR_5

description:
S1975150435
Adenocarcinoma-well differentiated

value: Ovarian

tag: age

value: female

tag: prior treatment

value: yes

value: 2n+, Hyperdiploid (47-57)

value: National Cancer Institute, NIH

value: R. Ozols


title: 1833 shBACH1, biological rep1

description: Gene expression data from metastatic triple-negative breast cancer cell line depleted of BACH1 using shRNA, biological  rep 1

label_protocol: The RNA quality control, cRNA ampliﬁcation, hybridization, and image scan were conducted in the Functional Genomics Facility at the University of Chicago.


title: Sarc (A)

description: control


title: PR:DU_145(DTP)

description:
S1975150530
Derived from metastatic site: brain (patient with metastatic carcinoma of the prostate and a 3 year history of lymphocytic leukemia.)

source_name: Adenocarcinoma-prostate; metastatic site: brain; carcinoma

value: Prostate

value: male

value: Androgen independent and unresponsive to hormone therapy

tag: epithelial

tag: source

value: Metastasis

value: Washington University School of Medicine, Saint Louis, MO

value: K.R. Stone


title: OV:OVCAR_4

description:
S1975150526
Adenocarcinoma-moderate differentiation

value: CyPh/CsPt/Adr

tag: ploidy

tag: p53 mutation

value: T.C. Hamilton


title: OV:OVCAR_8

description:
S1975150529
Carcinoma-undifferentiated

source_name: Carcinoma

value: Ctx/Adr/CsPt/CyPh

value: MT

tag: doubling time (hrs)

tag: contributing institute


title: Sarc (B)

description: control

value: JJ012 cell line

value: control


title: 506 d29

description: study participant 16

value: PBMC

value: PPD positive


title: Sarc (F)

description: test

value: treated with antiproliferative cytostatic mTORC1 inhibitor PRP-1 cytokine


title: 507 d29

description: study participant 17


title: 1833 control, biological rep2

description: Gene expression data from metastatic triple-negative breast cancer cell line, biological  rep 2


title: OV:OVCAR_3_rep2

description:
S1975150308
Adenocarcinoma-moderate differentiation

value: Ovarian

value: female

value: yes

value: Ascites

value: National Cancer Institute, NIH

tag: contributing person

tag: reference


title: OV:NCI_ADR_RES

description:
S1975150507
Adenocarcinoma

value: K.Cowan, NCI


title: 509 d29

description: study participant 19

tag: cell type


title: 1833 shBACH1, biological rep2

description: Gene expression data from metastatic triple-negative breast cancer cell line depleted of BACH1 using shRNA, biological  rep 2


title: Sarc (D)

description: test


title: 1833 control, biological rep1

description: Gene expression data from metastatic triple-negative breast cancer cell line, biological  rep 1


title: 505 d29

description: study participant 15

tag: tissue


title: 502 d29

description: study participant 12


title: Sarc (E)

description: test


title: 503 d29

description: study participant 13


title: OV:IGROV1

description:
S1975150479
Cystoadenocarcinoma-poor differentiation

source_name: Cystoadenocarcinoma

value: Rad

value: Institute Gustave Roussy, France


title: OV:OVCAR_3_rep1

description:
S1975150418
Adenocarcinoma-moderate differentiation

value: CyPh/CsPt/Adr


title: 501 d29

description: study participant 11

source_name: naive, pre-immunization


title: 504 d29

description: study participant 14


title: OV:SK_OV_3

description:
S1975150531
Adenocarcinoma-very poorly differentiated

value: Thiotepa

value: Memorial Sloan Kettering Cancer Center

value: Human Tumor Cells in vitro, pp. 115-159, 1975


title: 510 d0

description: study participant 20


title: PR:RC01

description:
S1975150434
Drug resistant variant of DU145(ATCC)

source_name: Adenocarcinoma-prostate; metastatic site: bone;

value: Prostate

value: male

value: Androgen independent and unresponsive to hormone therapy

value: Metastasis

value: Washington University School of Medicine, Saint Louis, MO

value: K.R. Stone


title: 507 d0

description: study participant 17

value: PBMC

value: PPD positive


title: ME:UACC_257

description:
S1975150278
Melanotic melanoma

source_name: Melanotic melanoma

value: Melanoma

value: no

value: 3n+, Hypertriploid (70-80)

value: WT

value: University of Arizona

value: A. Leibovitz, UACC


title: 505 d0

description: study participant 15


title: 504 d0

description: study participant 14


title: 506 d0

description: study participant 16


title: PR:DU_145(ATCC)

description:
S1975150452
Derived from metastatic site: brain (patient with metastatic carcinoma of the prostate and a 3 year history of lymphocytic leukemia.)

value: yes


title: ME:UACC_62

description:
S1975150327
Melanotic melanoma


title: 503 d0

description: study participant 13


title: 502 d0

description: study participant 12


title: ME:SK_MEL_28_rep1

description:
S1975150525
Malignant melanotic melanoma

source_name: Malignant melanotic melanoma

value: 4n-, Hypotetraploid (81-91)

value: MT

value: Memorial Sloan Kettering Cancer Center

value: T. Takahashi


title: 501 d0

description: study participant 11


title: ME:SK_MEL_28_rep2

description:
S1975150438
Malignant melanotic melanoma

value: male


title: ME:SK_MEL_2

description:
S1975150432
Malignant melanotic melanoma

value: Metastasis

value: G. Trempe; L.J. Old

value: Human Tumor Cells in vitro, pp 115-159, 1975


title: 110 d180

description: study participant 10

source_name: d180 post immunization

value: PBMC

value: PPD negative


title: 509 d0

description: study participant 19

value: PPD positive


title: 109 d180

description: study participant 9


title: 108 d180

description: study participant 8


title: ME:MALME_3M

description:
S1975150431
Malignant melanotic melanoma

value: Melanoma

value: no

value: J. Fogh


title: 106 d180

description: study participant 6


title: ME:M14

description:
S1975150512
Melanotic melanoma

value: D.H. Kern, John Wayne Cancer Clinic, UCLA School of Medicine


title: ME:MDA_MB_435

description:
S1975150527
Ductal carcinoma-mammary gland; breast; duct; metastatic site: pleural effusion;

value: female

value: Pleural effusion

value: 2n+, Hyperdiploid (47-57)

value: R. Cailleau


title: 107 d180

description: study participant 7


title: ME:MDA_N

description:
S1975150433
Ductal carcinoma-mammary gland; breast; duct; metastatic site: pleural effusion;

value: MT


title: 105 d180

description: study participant 5


title: ME:LOXIMVI

description:
S1975150672
Malignant amelanotic melanoma

source_name: Malignant amelanotic melanoma

value: WT

value: Norsk Hydro's Institut, Norway


title: 206381 treated -2

city: Ann Arbor

first: David

last: Miller

state: MI

address: 3560B MSRB II, 1150 W. Medical Center Dr.

department: Internal Medicine

institute: University of Michigan

hyb_protocol: Hybridization with Affymetrix Human Genome U133 Plus 2.0 Genechips conducted by commecial vendor (SeqWright DNA Technology Services, Houston TX).

scan_protocol: Image capture done by commecial vendor with Affymetrix 7G scanner (SeqWright DNA Technology Services, Houston TX).

data_processing: Primary data analysis done by commecial vendor using Mas5.0 algorithm (SeqWright DNA Technology Services, Houston TX).

source_name: BE(2)-C neuronal cells

label_protocol: RNA labelled by commecial vendor (SeqWright DNA Technology Services, Houston TX).

growth_protocol: BE(2)-C neuronal cells grown in DMEM (high glucose formulation) with 0.1 mM non-essential amino acids, 10 U/ml penicillin, 10 ug/ml streptomycin, and 5% bovine growth serum at 37C in 5% CO2.

extract_protocol: Total RNA harvested using Trizol with subsequent purification using RNAsy (both according to the manufacturer's instructions).  Quantity/purity examined by A260/280 and non-denaturing gel electrophorises with EtBr staining.

treatment_protocol: Cells incubated with either DMSO or 25 uM 205432/206381 for 24 h.


title: LE:SR

description:
S1975150650
Lymphoma

source_name: Lymphoma

value: Leukemia

value: male

value: Y

value: Program Resources, Inc.

value: W.J. Urba, Program Resources, Inc.


title: 104 d180

description: study participant 4

value: PBMC

value: PPD negative


title: 103 d180

description: study participant 3


title: 102 d180

description: study participant 2