title: QD655_24hr-1

source_name: HepG2 cell line with QD655 treatment at 24hr


title: DLBCL_DS-41_Specimen 42

status: Public on Dec 01 2015

type: genomic

city: Rutherford

first: Jane

last: Houldsworth

state: NJ

address: 201 Route 17 North

country: USA

institute: Cancer Genetics, Inc.

description: DLBCL_DS-41_Specimen 42 as test DNA and Promega normal DNA as reference

hyb_protocol: Oligoarray hybridization buffer, block (both from Agilent In Situ Hybridization Kit Plus), and Cot-1 DNA (Life Technologies) were added to each sample prior to application to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization for 24 hours, slides were washed sequentially as described by the manufacturer.

scan_protocol: Scanned on an Agilent Technologies Scanner G2505B.

data_processing: Data extraction was performed using Feature Extraction Version 10.7.3.1 (Agilent Technologies).

molecule: genomic DNA

organism: Homo sapiens

source_name: Human DLBCL specimen

label_protocol: Genomic DNA samples were labeled using the Agilent Genomic DNA Enzymatic Labeling Kit, according to the manufacturer's protocol, except that 1μg of DNA was used per 25μl labeling reaction mix.

extract_protocol: Extraction of genomic DNA was performed using Qiagen DNeasy Blood and Tissue kit according to the manufacturer's instructions.

tag: disease state

value: diffuse large B-cell lymphoma

tag: treatment

value: R-CHOP or R-CHOP like immuno-chemo therapy

source_name: Reference human genome DNA equimixture of normal male and normal female (Promega).

tag: sample type

value: reference


title: first visit [7305]

type: RNA

city: Decatur

first: Aliza

middle: P.

last: Wingo

state: GA

address: 1670 Clairmont Rd

department: Psychiatry

institute: Atlanta VAMC/Emory University

hyb_protocol: Illumina BeadArray protocol

scan_protocol: Illumina's BeadArray protocol and GenomeStudio (Gene expression module)

data_processing: The raw log2 transformed probes were normalized by ANOVA fitting technical effects of date of hybridization and RIN score. The reason why there are so many missing probes in the normalized dataset is because they are below the expression threshold and so not included in the normalization process.

molecule: total RNA

source_name: whole peripheral blood

label_protocol: Illumina BeadArray protocol

extract_protocol: Total RNA was extracted from whole peripheral blood using Norgen protocol and kits. Quality control was performed using Agilent's Bioanalyzer

tag: Sex

value: male

tag: age

tag: comorbid ptsd and depression status

tag: rin

tag: hybridization batch

value: V

tag: principal component 1

tag: principal component 2

tag: principal component 3

tag: principal component 4

tag: principal component 5

tag: tissue

value: whole peripheral blood


title: DLBCL_DS-41_Specimen 45

description: DLBCL_DS-41_Specimen 45 as test DNA and Promega normal DNA as reference


title: first visit [7366]


title: BMI1 overexpressed Human hepatic stem cells(BMI-OE-HpSCs)P10_3

city: Yokohama City

first: Yasuharu

last: Ueno

state: Kanagawa

address: 3-9  Fuku-ura, Kanazawa-ku

department: Graduate School of Medicine

country: Japan

institute: Yokohama City University

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent High-Resolution Microarray Scanner using one color scan setting for 4x44k v2 array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the One-Color Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNeasy Mini column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the RNeasy Mini Purification kit (QIAGEN, Valencia, CA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: BMI1 introduced Human Hepatic Stem Cells


title: Human hepatic stem cells(HpSCs)P0_1

value: Human Hepatic Stem Cells isolated from fetal liver cells


title: QD655_4hr-2

city: Miaoli County

first: Chieh Hua

last: Lin

address: 35, Keyan Road, Zhunan Town

department: Division of Biostatistics and Bioinformatics

country: Taiwan

institute: National Health Research Institutes

hyb_protocol: The labeled cDNA was hybridized to Human 46K cDNA array at 42°C for 12-16 hrs in 0.25 ml formamide, 20X SSC, 10% SDS and 10 mg/ml salmon sperm DNA. The array chip was washed once in 2× SSC with 0.1% SDS for 5 min at 42°C and once in 0.1X SSC with 0.1% SDS for 10 min at room temperature. Finally, the array was washed four times (1 min each time) in 0.1X SSC.

scan_protocol: The arrays were scanned on a GenePix 4000B scanner and analyzed with the GenePix software (Axon Instruments)

data_processing: The signal intensity was corrected by subtracted the background median from foreground mean. Then, the genes were kept with fluorescence signal intensities greater than intensity 250. After that, the raw data of fluorescence ratios (Cy5:Cy3) was adjusted by log transformation (base 2).

source_name: HepG2 cell line with QD655 treatment at 4hr

label_protocol: cRNA was prepared by Roche cDNA Synthesis kit and Microarray RNA Target Synthesis kit from 1 μg total RNA. 1 μg cRNA from QD-treated cell and Universal Human Reference RNA (Stratagene, La Jolla, CA), was reverse transcribed to Cy3- or Cy5-labeled cDNA, respectively, with CyScribe Post-Labeling Kit (Amersham Biosciences, Piscataway, NJ)

growth_protocol: Human hepatoblastoma HepG2 cells were cultured in Dulbecco Minimum Essential Media (DMEM) supplemented with 10% fetal bovine serum.

extract_protocol: Total RNA were extracted using the RNeasy kit (Qiagen)

treatment_protocol: The cultured cells were treated with 50 nM QD655 and QD705 separately. Total cellular RNA were harvested from 4, 8, 12, 24 and 48 hr QD-treated and untreated cells.

tag: cell line

tag: time point

tag: agent

source_name: Stratagene’s Universal Human Reference RNA

value: pooled from 10 humal cell lines


title: QD655_4hr-1


title: first visit [7326]


title: first visit [7275]

value: female


title: Human hepatic stem cells(HpSCs)P10_2


title: DLBCL_DS-41_Specimen 44

description: DLBCL_DS-41_Specimen 44 as test DNA and Promega normal DNA as reference

tag: disease state


title: control_48hr-2

source_name: HepG2 cell line without treatment at 48hr


title: first visit [7262]


title: control_48hr-1


title: DLBCL_DS-41_Specimen 39 2

description: DLBCL_DS-41_Specimen 39 as test DNA and Promega normal DNA as reference

tag: treatment


title: first visit [7243]


title: DLBCL_DS-41_Specimen 40

description: DLBCL_DS-41_Specimen 40 as test DNA and Promega normal DNA as reference

tag: sample type


title: DLBCL_DS-41_Specimen 3

description: DLBCL_DS-41_Specimen 3 as test DNA and Promega normal DNA as reference


title: DLBCL_DS-41_Specimen 39 1


title: first visit [7236]

tag: Sex


title: DLBCL_DS-41_Specimen 38

description: DLBCL_DS-41_Specimen 38 as test DNA and Promega normal DNA as reference


title: Case 5

city: San Francisco

first: Iwei

last: Yeh

state: California

address: 1701 Divisadero St. Ste 280

department: Dermatology

institute: UCSF

description: Case 5

hyb_protocol: After the labelling process the refernce and the sample DNA are cleaned to remove unused primers and unincorporated dyes. Then the sample and the reference DNA are combined together and incubated in a hybridization mix containing Cot-1 and bolcking agents. This mixture is hybridized onto an Agilent catalog 4X180K array (Agilent Technologies). The array is hybridized in a hybridization oven for 40hrs at 65°C.  After the hybridization, the array is washed and scanned according to the manufacturer’s protocol.

scan_protocol: The arrays are scanned at 3µ using the DNA Microarray Scanner G2505C with SureScan - High Resolution Technology (Agilent Technologies).

data_processing: Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).

source_name: melanocytic tumors_FFPE

label_protocol: 1ug of reference and sample DNA was labeled with CY3/CY5 dyes respectively using the Bioprime Total FFPE genomic labeling system (Life Technologies) according to manufacturer's protocol.

growth_protocol: Patient-derived tumors.

extract_protocol: Manual micro-dissection of the umor bearing region was performed on 5-10-µm paraffin sections using a stereo-microscope to avoid significant normal cell contamination. Deparafinization was performed with Safeclear and ethanol.  After digestion with proteinase K at 55 degrees for 2 days, phenol/chloroform extraction was performed.

treatment_protocol: No treatment.

tag: age (yrs)

tag: diagnosis

value: Spitz tumor

tag: met copy number transition

value: FALSE

tag: gain distal 7q

value: TRUE

source_name: Human Genomic DNA: Male

value: reference sample

tag: sample info.

value: male DNA from Promega (Cat # G1471)


title: first visit [7239]

tag: age

tag: comorbid ptsd and depression status

tag: rin

tag: hybridization batch

tag: principal component 1

tag: principal component 2


title: Case 6

description: Case 6


title: control_12hr-2

source_name: HepG2 cell line without treatment at 12hr

tag: cell line

tag: time point


title: first visit [7241]

tag: principal component 3

tag: principal component 4

tag: principal component 5

tag: tissue


title: control_8hr-2

source_name: HepG2 cell line without treatment at 8hr

tag: agent

tag: sample type


title: first visit [7178]

tag: Sex


title: Case 3

description: Case 3

tag: age (yrs)

tag: diagnosis

tag: met copy number transition

tag: gain distal 7q


title: first visit [7216]

tag: age

tag: comorbid ptsd and depression status

tag: rin


title: Case 2

description: Case 2

value: melanoma, spitzoid

tag: sample info.


title: control_24hr-2

source_name: HepG2 cell line without treatment at 24hr

tag: cell line


title: control_12hr-1

tag: time point


title: first visit [7190]

tag: hybridization batch

tag: principal component 1

tag: principal component 2

tag: principal component 3


title: control_24hr-1

tag: agent


title: DLBCL_DS-41_Specimen 37

description: DLBCL_DS-41_Specimen 37 as test DNA and Promega normal DNA as reference

tag: disease state

tag: treatment

tag: sample type


title: DLBCL_DS-41_Specimen 34

description: DLBCL_DS-41_Specimen 34 as test DNA and Promega normal DNA as reference


title: control_4hr-2

source_name: HepG2 cell line without treatment at 4hr


title: DLBCL_DS-41_Specimen 32

description: DLBCL_DS-41_Specimen 32 as test DNA and Promega normal DNA as reference


title: DLBCL_DS-41_Specimen 36

description: DLBCL_DS-41_Specimen 36 as test DNA and Promega normal DNA as reference


title: control_8hr-1


title: Case 1

description: Case 1

tag: Sex

tag: age (yrs)

tag: diagnosis


title: QD655_24hr-2


title: first visit [7058]

tag: age

tag: principal component 4

tag: principal component 5

tag: tissue


title: first visit [7059]

tag: comorbid ptsd and depression status

tag: rin


title: DLBCL_DS-41_Specimen 30

description: DLBCL_DS-41_Specimen 30 as test DNA and Promega normal DNA as reference


title: strain ssrAB, planktonic hypoxic growth, rep 2

city: Rochester

first: Paul

last: Dunman

state: NY

address: 601 Elmwood Avenue

department: Microbiology and Immunology

institute: University of Rochester

description: Gene expression data from hypoxically grown S. aureus strain USA300-LAC (delta ssrA)

hyb_protocol: 1.5 ug of RNA were hybrized for 16 hr at 45C on an S. aureus Affymetrix GeneChip.  GeneChips were washed and stained in an Affymetrix Fluidics Station using ProKaryotic GE-wash2 protocol.

scan_protocol: GeneChips were scanned in an Affymetrix 7G GeneArray Scanner

data_processing: The data were analyzed with Microarray Suite version 5.0 using Affymetrix default analysis settings.

label: Biotin

organism: Staphylococcus aureus

source_name: Staphylococcus aureus

label_protocol: 10 micrograms of each sample was labeled per Affymetrix (Santa Clara, CA) instructions for prokaryotic arrays (reverse transcribed, DNase I fragmentation and 3' biotinylated).

growth_protocol: S. aureus strain USA300-LAC or isogenic ssrA mutant cells were grown to mid-exponential phase (Optical Density 600nm of 0.5) in trypic soy broth at 37C with aeration (180 rpm in a rotary shaker).  Cells were then continued to grow for 1 hr during either: 1. aerobic conditions (37C at 180 rpm in an orbital shaker) or 2. hypoxic conditions (37C in a tight capped conical tube).

extract_protocol: Culture samples were mechanically disrupted in a Bullet Blender (Next Advance; Averill Park, NY) using 0.5 mm RNase-free zirconium oxide beads.  Following disruption, total bacterial RNA was precipitated using isopropyl alcohol precipitation, washed with 70% ethanol and resuspended in deionized water.

treatment_protocol: An equal volume of ice cold acetone:ethanol (1:1) was added to inactivate bacterial ribonucleases

tag: sample

value: Whole cell

tag: genotype

value: ssrAB (strain USA300-Lac with delta_ssrA )

tag: growth phase

value: Hypoxic growth


title: DLBCL_DS-41_Specimen 31

description: DLBCL_DS-41_Specimen 31 as test DNA and Promega normal DNA as reference

value: diffuse large B-cell lymphoma

value: R-CHOP or R-CHOP like immuno-chemo therapy

value: reference


title: strain ssrAB, planktonic aerobic growth, rep 1

description: Gene expression data from aerobically grown S. aureus strain USA300-LAC (delta ssrA)

value: Aerobic growth


title: DLBCL_DS-41_Specimen 28

description: DLBCL_DS-41_Specimen 28 as test DNA and Promega normal DNA as reference


title: first visit [7052]

tag: hybridization batch

value: V

tag: principal component 1

tag: principal component 2

tag: principal component 3

value: whole peripheral blood


title: first visit [7144]


title: DLBCL_DS-41_Specimen 26

description: DLBCL_DS-41_Specimen 26 as test DNA and Promega normal DNA as reference

tag: disease state

tag: treatment

tag: sample type


title: first visit [7155]

tag: Sex


title: control_4hr-1

tag: cell line

tag: time point

tag: agent

value: pooled from 10 humal cell lines


title: strain ssrAB, planktonic aerobic growth, rep 2


title: first visit [7032]

value: female

tag: age

tag: principal component 4

tag: principal component 5

tag: tissue


title: strain ssrAB, planktonic hypoxic growth, rep 1

tag: sample

tag: genotype


title: DLBCL_DS-41_Specimen 25

description: DLBCL_DS-41_Specimen 25 as test DNA and Promega normal DNA as reference


title: DLBCL_DS-41_Specimen 35

description: DLBCL_DS-41_Specimen 35 as test DNA and Promega normal DNA as reference


title: DLBCL_DS-41_Specimen 2

description: DLBCL_DS-41_Specimen 2 as test DNA and Promega normal DNA as reference


title: Control rat 3

city: Brasília

first: Rolando

middle: Andre Rios

last: Villacis

state: DF

address: Asa Norte

department: Genetics and Morphology

country: Brazil

institute: University of Brasília - UnB

description:
CT_3_soleus
Gene expression data from skeletal muscle of control rats, without cardiac cachexia.

hyb_protocol: Standard protocol, using the Affymetrix GeneChip Hybridization, Wash and Stain Kit.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip® Scanner 3000 7G, and the .CEL files were generated using the Affymetrix GeneChip Command Console (AGGC) software.

data_processing: The data were normalized using the Robust Multi-chip Average (RMA) algorithm and analyzed with the default options of AltAnalyze software v2.0.8.

label: biotin

organism: Rattus norvegicus

source_name: Soleus muscle without cardiac cachexia

label_protocol: Standard protocol (starting with 200ng of total RNA), using the Ambion WT Expression Kit and the Affymetrix GeneChip WT Terminal Labeling and Controls Kits.

growth_protocol: Not applicable.

extract_protocol: RNA was extracted with the Trizol reagent (Invitrogen) according to the manufacturer's instructions.

treatment_protocol: A heart failure was induced in three male Wistar rats (250-300g body weight) on the 60th day of life by a single intra-peritoneal (60 mg/kg) injection of monocrotaline (MCT, Sigma-Aldrich, Germany). Simultaneously, three controls rats with the same age received saline injections. After the 30th day of treatment (total of 90 days of life), the animals injected with monocrotaline developed overt heart failure and both groups of animals (test and controls) were euthanized. Soleus muscles were immediately excised, frozen in liquid nitrogen and stored at -80 °C.

tag: strain/background

value: Wistar

tag: disease status

value: control

value: skeletal (soleus) muscle

tag: gender

value: male

value: 90 days


title: Control rat 1

description:
CT_1_soleus
Gene expression data from skeletal muscle of control rats, without cardiac cachexia.


title: strain USA300-Lac, planktonic hypoxic growth, rep 1

description: Gene expression data from hypoxically grown S. aureus strain USA300-LAC

value: Wild type (strain USA300-Lac)

tag: growth phase


title: strain USA300-Lac, planktonic hypoxic growth, rep 2

value: Whole cell


title: Control rat 2

description:
CT_2_soleus
Gene expression data from skeletal muscle of control rats, without cardiac cachexia.


title: strain USA300-Lac, planktonic aerobic growth, rep 2

description: Gene expression data from aerobically grown S. aureus strain USA300-LAC


title: delta dapZ with pBAD DapZ GU (sample 1)

type: mixed

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

country: Germany

institute: Max-Planck-Institute for Infection Biology

hyb_protocol: Labeled samples were mixed and hybridized to 8x15K custom-commercial microarrays overnight at 65ºC using 1x Hi hybridization buffer together with blocking buffer according to the supplier`s recommendations (Agilent Technologies). Washing of the hybridized arrays was done with the SSC protocol according supplier`s protocol (Agilent Technologies).

scan_protocol: Scanning of microarrays was performed with 5 µm resolution and extended range using a DNA microarray laser scanner (Agilent Technologies).

data_processing: Raw microarray image data were analyzed with the Image Analysis / Feature Extraction software G2567AA (Version A.10.5.1, Agilent Technologies). To compensate for unequal dye incorporation, data centering to zero was performed for each individual microarray on the slide separately. Microarray data were analysed using GeneSpring 7.3 (Agilent) and genes were considered to be differentially expressed if they displayed ≥2-fold changes in both replicates and were statistically significantly different (Student's t-test; p<0.05)

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

source_name: delta dapZ with pBAD DapZ GU

label_protocol: Total RNA was labelled by random priming according to the protocols described at the IFR (Institute of Food Research, Norwich) website (www.ifr.ac.uk/safety/microarrays/protocols.html). Briefly, 10 µg RNA were reverse transcribed and labeled with Cy3-conjugated dCTP (Pharmacia) using 200 units of StrataScript and random octamers (Invitrogen).

extract_protocol: Salmonella RNA was isolated using the Promega SV total RNA purification kit

tag: strain background

value: S.typhimurium SL1344 dapZ deletant

tag: transformed with

value: pBAD DapZ GU plasmid (DapZ variant that lacks the GcvB-like R1 region)

source_name: wild type

label_protocol: Chromosomal DNA (400 ng) was labeled with Cy5-dCTP using the Klenow fragment.

extract_protocol: Genomic DNA isolated using the Qiagen 'Genomic DNA' Kit (Cat. No.: 19060 for the buffer kit; 10243 for the columns)

value: S.typhimurium SL1344

tag: genotype/variation

value: Wild type


title: Rat 2 with CC

description:
CC_6_soleus
Gene expression data from skeletal muscle of rats with cardiac cachexia.

source_name: Soleus muscle with cardiac cachexia

value: cardiac cachexia


title: strain USA300-Lac, planktonic aerobic growth, rep 1

value: Aerobic growth


title: Rat 3 with CC

description:
CC_21_soleus
Gene expression data from skeletal muscle of rats with cardiac cachexia.


title: DLBCL_DS-41_Specimen 22

description: DLBCL_DS-41_Specimen 22 as test DNA and Promega normal DNA as reference

source_name: Human DLBCL specimen

tag: disease state

value: diffuse large B-cell lymphoma

tag: treatment

value: R-CHOP or R-CHOP like immuno-chemo therapy

tag: sample type

value: reference


title: delta dapZ with pBAD DapZ GU (sample 2)


title: delta dapZ with pBAD-ctr (sample 2)

source_name: delta dapZ with pBAD-ctr

tag: trasnformed with

value: pBAD-ctr plasmid (negative control)


title: first visit [7017]

source_name: whole peripheral blood

tag: Sex

value: female

tag: age

tag: comorbid ptsd and depression status

tag: rin

tag: hybridization batch

value: V

tag: principal component 1

tag: principal component 2

tag: principal component 3

value: whole peripheral blood


title: Case 4

description: Case 4

tag: age (yrs)

tag: diagnosis

value: Spitz tumor

tag: met copy number transition

value: TRUE

tag: gain distal 7q

value: reference sample

tag: sample info.

value: male DNA from Promega (Cat # G1471)


title: delta dapZ with pBAD-ctr (sample 1)

tag: strain background

value: S.typhimurium SL1344 dapZ deletant

tag: genotype/variation


title: first visit [7030]

tag: principal component 4

tag: principal component 5

tag: tissue


title: P7526

city: East Melbourne

first: Kylie

middle: L

last: Gorringe

state: Victoria

address: St Andrew's Pl

department: Research Division

country: Australia

institute: Peter MacCallum Cancer Centre

hyb_protocol: standard affymetrix protocol

scan_protocol: standard affymetrix protocol

data_processing:
standard affymetrix protocol
Copy number values were obtained against a baseline of normal DNA samples. Raw data is only available for the single file run on OncoScan v3. The rest are available in 2 matrix files, and have slightly different numbers of probes. Each sample has 5 columns: Copy A, Copy B, Copy number, Allele ratio and Allelic difference.

source_name: DCIS FFPE tissue

label_protocol: standard affymetrix protocol

extract_protocol: up to 40x 10 micron FFPE sections were needle microdissected for epithelial cells. Total genomic DNA was isolated using the DNeasy Blood and Tissue Kit (Qiagen) using a modified protocol: Wu L, Patten N, Yamashiro CT, Chui B (2002) Extraction and amplification of DNA from formalin-fixed, paraffin-embedded tissues. Appl Immunohistochem Mol Morphol 10 (3):269-274

treatment_protocol: retrospective cases received standard care

tag: file name

value: DCIS

tag: grade

value: High

tag: er status

value: Positive

tag: recurrence status

value: Primary with recurrence

tag: her2 copy number status

value: Negative

value: Low

tag: size (mm)

tag: age at initial diagnosis


title: DLBCL_DS-41_Specimen 20

description: DLBCL_DS-41_Specimen 20 as test DNA and Promega normal DNA as reference

tag: disease state

value: diffuse large B-cell lymphoma

tag: treatment

value: R-CHOP or R-CHOP like immuno-chemo therapy

source_name: Reference human genome DNA equimixture of normal male and normal female (Promega).

tag: sample type


title: DLBCL_DS-41_Specimen 23

description: DLBCL_DS-41_Specimen 23 as test DNA and Promega normal DNA as reference

value: reference


title: A15322

value: Non-Recurrence


title: DLBCL_DS-41_Specimen 18

description: DLBCL_DS-41_Specimen 18 as test DNA and Promega normal DNA as reference


title: first visit [6937]

tag: Sex

value: male

tag: age

tag: comorbid ptsd and depression status

tag: rin

tag: hybridization batch

value: V

tag: principal component 1

tag: principal component 2

tag: principal component 3


title: first visit [6798]

value: T

tag: principal component 4

tag: principal component 5

tag: tissue

value: whole peripheral blood


title: Rat 1 with CC

description:
CC_4_soleus
Gene expression data from skeletal muscle of rats with cardiac cachexia.

tag: strain/background

value: Wistar

tag: disease status

value: cardiac cachexia

value: skeletal (soleus) muscle

tag: gender

value: 90 days


title: first visit [7005]


title: first visit [7019]

value: female


title: first visit [6778]

value: U


title: first visit [6771]


title: delta dapZ with pBAD DapZ (sample 2)

source_name: delta dapZ with pBAD DapZ

tag: strain background

value: S.typhimurium SL1344 dapZ deletant

tag: transformed with

value: pBAD DapZ plasmid (wild-type DapZ)

value: S.typhimurium SL1344

tag: genotype/variation

value: Wild type


title: first visit [6848]

tag: Sex


title: A21181

tag: file name

value: DCIS

tag: grade

value: High

tag: er status

value: Positive

tag: recurrence status

tag: her2 copy number status

value: Low

tag: size (mm)

tag: age at initial diagnosis


title: control rep3

city: Oviedo

first: Francisco

last: Moris

address: Edificio Cientifico Tencológico, Campus El Cristo

country: Spain

institute: EntreChem SL

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Total RNA was extracted from purified cell populations using RNeasy Mini Kit (Qiagen, Valencia, CA, USA) according to the manufacturer’s instructions. The RNA integrity was assessed using Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA). Labelling and hybridizations were performed according to protocols from Affymetrix. Briefly, 100 ng of total RNA were amplified and labeled using the WT Plus reagent kit (Affymetrix) and then hybridized to Human Gene 2.0 ST Array (Affymetrix). Washing and scanning were performed using GeneChip System of Affymetrix (GeneChip Hybridization Oven 645, GeneChip Fluidics Station 450 and GeneChip Scanner 7G).

data_processing: The data were processed using the dChip software (Dana Farber Cancer Institute, Boston, MA)

source_name: TNBC cell line

label_protocol: cRNA was labelled using the BioArray RNA labeling kit (Enzo Life Sciences, Farmingdale, NY

growth_protocol: MDA-MB-231 cells were grown in DMEM with 10% of FBS and added to a final concentration of 500.000 cells/plate.

extract_protocol: RNA was extracted and purified using the Rneasy Mini Kit (Qiagen)

treatment_protocol: cells were treated with 500 nM EC-70124 for 24h

tag: cell line

tag: treatment

value: control


title: DLBCL_DS-41_Specimen 19

description: DLBCL_DS-41_Specimen 19 as test DNA and Promega normal DNA as reference

tag: disease state

value: diffuse large B-cell lymphoma

value: R-CHOP or R-CHOP like immuno-chemo therapy

tag: sample type

value: reference


title: control rep2


title: DLBCL_DS-41_Specimen 1

description: DLBCL_DS-41_Specimen 1 as test DNA and Promega normal DNA as reference


title: first visit [6801]

tag: age

tag: comorbid ptsd and depression status

tag: rin

tag: hybridization batch

value: T

tag: principal component 1

tag: principal component 2

tag: principal component 3

tag: principal component 4

tag: principal component 5

tag: tissue

value: whole peripheral blood


title: DLBCL_DS-41_Specimen 14

description: DLBCL_DS-41_Specimen 14 as test DNA and Promega normal DNA as reference


title: first visit [6800]

tag: Sex


title: DLBCL_DS-41_Specimen 13

description: DLBCL_DS-41_Specimen 13 as test DNA and Promega normal DNA as reference


title: control rep1


title: A18439

tag: file name

tag: grade

tag: er status

tag: recurrence status

value: Non-Recurrence

tag: her2 copy number status

value: Negative

tag: size (mm)


title: untreated mice gDNA

city: Frankfurt am Main

first: Klaus

last: Scholich

state: Hessen

address: Theodor Stern Kai 7

department: Clinical Pharmacology

institute: Hospital of Goethe University

description: DRG from untreated mice

data_processing:
25 ng cDNA per reaction were used to generate Ct values. 6 ng genomic DNA (gDNA)  were used with  the same primer pair as standard to calculate gene copy number per nanogram RNA. PCR reactions were performed by using LyghtCycler 480 II (Roche) and data anaylsis was done by using LightCycler
Gene copy number was calculated by the formula: (gDNA (ng)/P)*2e(gDNA Ct - cDNA Ct)/cDNA (ng), where P= 3,28 pg.

label: FAM/Dark Quencher

organism: Mus musculus

source_name: dorsal root ganglia

label_protocol: RNA isolation and transcription was performed with the RNeasy kit (Qiagen). Quantitative PCR was done by using specific primers designed with the Roche's online tool. PCR program: 5°C for 5 min, followed by 45 cycles of 95°C for 5 s, 60°C for 10 s, and 72°C for 1 s.

growth_protocol: 6-8 week male mice

extract_protocol: total RNA

treatment_protocol: untreated

tag: gender

value: male

tag: strain


title: TCR-stimulated Temra replicate4

city: Kyoto

first: Ruka

last: Setoguchi

address: Yoshidakonoe-cho

institute: Kyoto University

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
CEL files were read into Affymetrix Expression Console and normalized probeset level expression values were calculated with RMA method.
affymetrix-algorithm-name = rma-gene-default
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.2.1.20

source_name: TCR-stimulated Temra

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Peripheral blood was obtained from healthy volunteers (aged 30-65 years).

extract_protocol: Total RNA was isolated from sorted cells or cultured cells for 2 days with Trizol (Invitrogen) and RNeasy Mini Kit (Qiagen)

treatment_protocol: IL-15 (Peprotec) was used for stimulation of human CD8+ T cell-subsets at 10 ng/mL. TCR stimulation was performed using anti-CD3 and anti-CD28 mAb-coated beads (Invitrogen).

tag: subject status

value: healthy volunteers aged 30-65 yr

value: peripheral blood

tag: cell type

value: CCR7-CD45RA+ CD8+ T cells; TEMRA

tag: sample group

value: stimulated with anti-CD3/CD28 coated beads for 2 days


title: A18418

value: DCIS

tag: age at initial diagnosis


title: EC-70124 500nM 24h rep1

tag: cell line

tag: treatment


title: untreated mice cDNA

description: DRG from untreated mice


title: DLBCL_DS-41_Specimen 17

description: DLBCL_DS-41_Specimen 17 as test DNA and Promega normal DNA as reference

tag: disease state

tag: sample type


title: TCR-stimulated Temra replicate3

tag: tissue


title: first visit [6828]

tag: Sex

value: female

tag: age

tag: comorbid ptsd and depression status

tag: rin

tag: hybridization batch

tag: principal component 1

tag: principal component 2

tag: principal component 3

tag: principal component 4

tag: principal component 5


title: DLBCL_DS-41_Specimen 16

description: DLBCL_DS-41_Specimen 16 as test DNA and Promega normal DNA as reference


title: A21180

tag: file name

tag: grade

value: High

tag: er status

value: Positive

tag: recurrence status

tag: her2 copy number status

tag: size (mm)


title: DLBCL_DS-41_Specimen 15

description: DLBCL_DS-41_Specimen 15 as test DNA and Promega normal DNA as reference

tag: disease state

tag: treatment

tag: sample type


title: delta dapZ with pBAD DapZ (sample 1)

tag: strain background

value: S.typhimurium SL1344 dapZ deletant

tag: transformed with

value: pBAD DapZ plasmid (wild-type DapZ)

value: S.typhimurium SL1344

tag: genotype/variation

value: Wild type


title: DLBCL_DS-41_Specimen 12

description: DLBCL_DS-41_Specimen 12 as test DNA and Promega normal DNA as reference

value: diffuse large B-cell lymphoma

value: R-CHOP or R-CHOP like immuno-chemo therapy

value: reference


title: A17461

tag: tissue

value: Low

value: Non-Recurrence

value: Negative

tag: age at initial diagnosis


title: first visit [6753]

tag: Sex

tag: age

tag: comorbid ptsd and depression status

tag: rin

tag: hybridization batch

value: U

tag: principal component 1

tag: principal component 2

tag: principal component 3

value: whole peripheral blood


title: DLBCL_DS-41_Specimen 10

description: DLBCL_DS-41_Specimen 10 as test DNA and Promega normal DNA as reference


title: Liver_Control_rep4

city: Hangzhou

first: Kunkai

last: Su

address: 79 Qingchun Road

country: China

institute: Zhejiang University

description: 10-month-old male beagle canines were purchased from the ANNIMO Science and Technology Ltd (Nanjing, China, Certificate No. SCXK (Su) 2010-0002)

hyb_protocol: The Hy3TM-labeled samples were hybridized on the miRCURYTM LNA Array (v.18.0) (Exiqon) according to array manual

scan_protocol: The slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).

data_processing: Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities>=30 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. After normalization, differentially expressed miRNAs with statistical significance were identified through Volcano Plot filtering.

organism: Canis lupus familiaris

source_name: Liver

label_protocol: The miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling

growth_protocol: All dogs were raised in Pathogen-free room and the room was maintained at a constant temperature of 23±1℃ with a 12 h light/dark cycle. Food and water were available ad libitum in the home cages.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and miRNeasy mini kit (QIAGEN) according to manufacturer’s instructions, which efficiently recovered all RNA species, including miRNAs. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis

treatment_protocol: Canines were sacrificed at 11 days after initiation of the treatment. Livers were excised immediately after sacrifice. Part of the livers were immediately snap-frozen in liquid nitrogen and kept at -80°C for total RNA isolation and microRNA microarray analysis.

value: Liver

value: PharMaceutical starch (3 mg/kg/day)


title: first visit [6759]

value: male

value: T

tag: principal component 4

tag: principal component 5


title: DLBCL_DS-41_Specimen 11

description: DLBCL_DS-41_Specimen 11 as test DNA and Promega normal DNA as reference

tag: disease state

tag: treatment


title: TCR-stimulated Temra replicate2

tag: subject status

value: healthy volunteers aged 30-65 yr

value: peripheral blood

tag: cell type

value: CCR7-CD45RA+ CD8+ T cells; TEMRA

tag: sample group

value: stimulated with anti-CD3/CD28 coated beads for 2 days


title: EC-70124 500nM 24h rep2

tag: cell line


title: Liver_Control_rep3

tag: tissue


title: Liver_Control_rep2


title: A11312

tag: file name

value: DCIS

tag: grade

value: High

tag: er status

value: Positive

tag: recurrence status

tag: her2 copy number status

tag: size (mm)

tag: age at initial diagnosis


title: IL-15- stimulated Temra replicate4

source_name: IL-15- stimulated Temra

value: cultured with IL-15 (10 ng/mL) for 2 days


title: IL-15- stimulated Temra replicate2


title: EC-70124 500nM 24h rep3


title: A14385

value: Low


title: A10211

value: Non-Recurrence


title: first visit [6731]

tag: Sex

value: female

tag: age

tag: comorbid ptsd and depression status

tag: rin

tag: hybridization batch

tag: principal component 1

tag: principal component 2

tag: principal component 3


title: first visit [6729]

value: U

tag: principal component 4

tag: principal component 5


title: IL-15- stimulated Temra replicate3

tag: subject status

tag: tissue

tag: cell type

tag: sample group


title: TCR-stimulated Temra replicate1


title: A15125

tag: file name

tag: grade

tag: er status

tag: recurrence status

tag: her2 copy number status

value: Negative


title: Liver_AAI_rep4

value: Liver

tag: treatment

value: Aristolochic Acid I (3 mg/kg/day)


title: A14854

tag: size (mm)

tag: age at initial diagnosis


title: first visit [6711]

tag: Sex

value: male

tag: age

tag: comorbid ptsd and depression status

tag: rin

tag: hybridization batch

tag: principal component 1

value: whole peripheral blood


title: first visit [6748]

tag: principal component 2

tag: principal component 3

tag: principal component 4

tag: principal component 5

tag: tissue


title: Liver_AAI_rep3


title: A15874

tag: file name

tag: grade

tag: er status

value: NK


title: first visit [6683]


title: first visit [6682]

value: T


title: unstimulated Temra replicate4

description: unstimulated Temra 4

source_name: unstimulated Temra

tag: subject status

value: healthy volunteers aged 30-65 yr

value: peripheral blood

tag: cell type

value: CCR7-CD45RA+ CD8+ T cells; TEMRA

tag: sample group

value: cultured without stimulation for 2 days


title: Liver_AAI_rep2

tag: treatment


title: unstimulated Temra replicate3

description: unstimulated Temra 3


title: A13433

description: recurrence of A15661

source_name: IDC FFPE tissue

value: IDC

value: High

value: Positive

tag: recurrence status

value: Recurrence

tag: her2 copy number status

tag: size (mm)

tag: age at initial diagnosis


title: first visit [6678]

tag: Sex

value: female

tag: age

tag: comorbid ptsd and depression status

tag: rin

tag: hybridization batch

tag: principal component 1


title: IL-15- stimulated Temra replicate1

tag: tissue

value: cultured with IL-15 (10 ng/mL) for 2 days


title: Liver_Control_rep1

value: PharMaceutical starch (3 mg/kg/day)


title: unstimulated Temra replicate2

description: unstimulated Temra 2


title: first visit [6656]

value: U

tag: principal component 2

tag: principal component 3

tag: principal component 4

tag: principal component 5


title: unstimulated Temra replicate1

description: unstimulated Temra 1

tag: subject status

tag: cell type

tag: sample group


title: ex vivo Temra replicate4

description: ex vivo Temra 4

source_name: ex vivo Temra

value: ex-vivo isolated


title: first visit [6610]


title: A15661

tag: file name

value: DCIS

tag: grade

value: Low

tag: er status

tag: recurrence status

value: Primary but nonclonal recurrence

tag: her2 copy number status

value: Negative


title: Liver_AAI_rep1

value: Liver

tag: treatment

value: Aristolochic Acid I (3 mg/kg/day)


title: first visit [6648]

tag: Sex

tag: age

tag: comorbid ptsd and depression status

tag: rin

value: whole peripheral blood


title: ex vivo Temra replicate3

description: ex vivo Temra 3

value: healthy volunteers aged 30-65 yr

tag: tissue

value: peripheral blood

value: CCR7-CD45RA+ CD8+ T cells; TEMRA


title: A15675

value: High

value: Positive

value: Primary with recurrence

tag: size (mm)

tag: age at initial diagnosis


title: first visit [6596]

value: female

tag: hybridization batch

value: T

tag: principal component 1

tag: principal component 2

tag: principal component 3

tag: principal component 4

tag: principal component 5


title: A17030

tag: file name

tag: grade

tag: er status

value: Equivocal

value: NK


title: first visit [6569]

value: male

value: U


title: first visit [6565]


title: A12149

value: DCIS

tag: recurrence status

tag: her2 copy number status


title: A20410


title: A017210

value: Negative


title: A17661

description: recurrence of A15675

value: Recurrence


title: A027898

description: recurrence of A017210


title: A11044C

value: Non-recurrence


title: first visit [6564]

tag: Sex

tag: age

value: whole peripheral blood


title: first visit [6563]

tag: comorbid ptsd and depression status

tag: rin


title: YCC3_NTC siRNA, Biological Replicate 2

city: Madurai

first: Kumaresan

last: Ganesan

state: Tamil Nadu

address: School of Biological Sciences,

department: Genetics

country: India

institute: Madurai Kamaraj University

description: Gene expression data of YCC3 gastric cancer cell line treated with non-targeting control siRNA - Replicate 2

hyb_protocol: The fragmented and labelled cDNA were hybridized for 16 hrs at 45°C with Affymetrix Human Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Scanning was done on an Affymetrix GeneChip Scanner 3000.

data_processing: Gene level normalized expression signals were calculated from Affymetrix CEL files by RMA, in Affymetrix Expression Console version 1.1.

source_name: Non-targeting control siRNA treated YCC3 gastric cancer cells - Replicate 2

label_protocol: 500 ng of total RNA was used to generate fragmented and biotin labelled sense cDNA using Ambion WT Expression kit (Affymetrix).

growth_protocol: YCC3 gastric cancer cell line were seeded in 6 well culture plates and maintained in MEM with 10% FBS in a humidified incubator at 37˚C and 5% CO2.

extract_protocol: 48 hrs after transfection, the total RNA was isolated from the cells using Trizol (Invitrogen).

treatment_protocol: Upon reaching 70-80% confluency, the cells were transfected with CTNNB1 siRNA or with Non-targeting control siRNA (Dharmacon)

tag: cell line


title: YCC3_NTC siRNA, Biological Replicate 3

description: Gene expression data of YCC3 gastric cancer cell line treated with non-targeting control siRNA - Replicate 3

source_name: Non-targeting control siRNA treated YCC3 gastric cancer cells - Replicate 3


title: A17460J

tag: tissue

tag: size (mm)

tag: age at initial diagnosis


title: A16033C


title: YCC3_CTNNB1 siRNA, Biological Replicate 2

description: Gene expression data of YCC3 gastric cancer cell line treated with CTNNB1 siRNA - Replicate 2

source_name: CTNNB1 siRNA treated YCC3 gastric cancer cells - Replicate 2


title: ex vivo Temra replicate2

description: ex vivo Temra 2

tag: subject status

value: healthy volunteers aged 30-65 yr

tag: cell type

tag: sample group

value: ex-vivo isolated


title: DLBCL_DS-66_Specimen USC83

description: DLBCL_DS-66_Specimen USC83 as test DNA and Promega normal DNA as reference

source_name: Human DLBCL specimen

tag: disease state

value: diffuse large B-cell lymphoma

tag: treatment

value: R-CHOP or R-CHOP like immuno-chemo therapy

tag: sample type

value: reference


title: YCC3_CTNNB1 siRNA, Biological Replicate 1

description: Gene expression data of YCC3 gastric cancer cell line treated with CTNNB1 siRNA - Replicate 1

source_name: CTNNB1 siRNA treated YCC3 gastric cancer cells - Replicate 1


title: DLBCL_DS-66_Specimen USC85

description: DLBCL_DS-66_Specimen USC85 as test DNA and Promega normal DNA as reference


title: first visit [6562]

source_name: whole peripheral blood

tag: hybridization batch

tag: principal component 1

tag: principal component 2

tag: principal component 3

tag: principal component 4

tag: principal component 5


title: DLBCL_DS-66_Specimen USC84

description: DLBCL_DS-66_Specimen USC84 as test DNA and Promega normal DNA as reference


title: DLBCL_DS-66_Specimen USC78

description: DLBCL_DS-66_Specimen USC78 as test DNA and Promega normal DNA as reference


title: DLBCL_DS-66_Specimen USC76

description: DLBCL_DS-66_Specimen USC76 as test DNA and Promega normal DNA as reference


title: A14856C

source_name: DCIS FFPE tissue

tag: file name

tag: grade

value: High

tag: er status

value: Positive

tag: recurrence status

tag: her2 copy number status


title: ex vivo Temra replicate1

description: ex vivo Temra 1

tag: subject status

tag: tissue

value: peripheral blood

value: CCR7-CD45RA+ CD8+ T cells; TEMRA


title: YCC3_CTNNB1 siRNA, Biological Replicate 3

description: Gene expression data of YCC3 gastric cancer cell line treated with CTNNB1 siRNA - Replicate 3

source_name: CTNNB1 siRNA treated YCC3 gastric cancer cells - Replicate 3

tag: cell line


title: YCC3_NTC siRNA, Biological Replicate 1

description: Gene expression data of YCC3 gastric cancer cell line treated with non-targeting control siRNA - Replicate 1

source_name: Non-targeting control siRNA treated YCC3 gastric cancer cells - Replicate 1


title: DLBCL_DS-66_Specimen USC80

description: DLBCL_DS-66_Specimen USC80 as test DNA and Promega normal DNA as reference

tag: disease state

source_name: Reference human genome DNA equimixture of normal male and normal female (Promega).


title: DLBCL_DS-66_Specimen USC82

description: DLBCL_DS-66_Specimen USC82 as test DNA and Promega normal DNA as reference

tag: treatment


title: first visit [6522]

tag: Sex

value: female

tag: age

tag: comorbid ptsd and depression status

tag: rin

value: V


title: DLBCL_DS-66_Specimen USC81

description: DLBCL_DS-66_Specimen USC81 as test DNA and Promega normal DNA as reference

tag: sample type


title: first visit [6519]

value: male

tag: hybridization batch

value: X

tag: principal component 1

tag: principal component 2

tag: principal component 3

tag: principal component 4


title: DLBCL_DS-66_Specimen USC77

description: DLBCL_DS-66_Specimen USC77 as test DNA and Promega normal DNA as reference


title: first visit [6497]

tag: principal component 5


title: first visit [6492]


title: A18003_2

tag: file name

value: DCIS

tag: grade

value: Low

tag: er status

tag: recurrence status

tag: her2 copy number status

value: Negative

value: Equivocal

tag: size (mm)

tag: age at initial diagnosis


title: first visit [6486]

tag: Sex

tag: age

tag: tissue

value: whole peripheral blood


title: DLBCL_DS-66_Specimen USC86

description: DLBCL_DS-66_Specimen USC86 as test DNA and Promega normal DNA as reference

tag: disease state

tag: treatment

tag: sample type


title: first visit [6496]

tag: comorbid ptsd and depression status

tag: rin

tag: hybridization batch

tag: principal component 1

tag: principal component 2


title: A11025K

tag: file name

tag: grade

value: Non-recurrence


title: DLBCL_DS-66_Specimen USC74

description: DLBCL_DS-66_Specimen USC74 as test DNA and Promega normal DNA as reference

value: diffuse large B-cell lymphoma


title: patient 64 IDC [validation]

city: New Lambton Heights

first: Kelly

last: Kiejda

state: NSW

address: HMRI

institute: University of Newcastle

description: 307 IDC

hyb_protocol: 100ng total RNA of all fresh frozen samples was amplified (Ovation FFPE WTA kit) and biotinylated (Encore Biotin module) according to the manufacturers’ instructions (Nugen, San Carlos, California, United States). The samples were hybridised to HuGene 2.0 arrays (Affymetrix, Santa Clara, California, United States) and 17 hours later washed and stained.

scan_protocol: The arrays were scanned on a GeneChip Scanner 3000 7G (Affymetrix).

data_processing: The data was imported to Genomic Suite 6.6 (Partek) and a robust multi-array analysis (RMA) was performed, which included log2 transformation, background correction, quantile normalisation and summarisation of the probe features resulting in a set of expression signal intensities.

source_name: fresh frozen tissue specimen

extract_protocol: Total RNA was extracted from fresh frozen tissue samples, using  Rneasy kit (Qiagen, Doncaster, VIC, Australia).

tag: tnbc type

value: No

tag: tissue type

value: invasive ductal carcinomas (IDC)


title: A17427E

value: High

tag: er status

tag: recurrence status

tag: her2 copy number status

tag: size (mm)


title: first visit [6462]

tag: Sex

tag: age

value: T

tag: principal component 3

tag: principal component 4

tag: principal component 5

tag: tissue


title: A21390D

value: Intermediate

value: Positive

tag: age at initial diagnosis


title: patient 63 IDC [validation]

description: 301 IDC


title: A16164B


title: DLBCL_DS-66_Specimen USC73

description: DLBCL_DS-66_Specimen USC73 as test DNA and Promega normal DNA as reference

tag: disease state

tag: treatment

value: R-CHOP or R-CHOP like immuno-chemo therapy

tag: sample type

value: reference


title: A17948A

tag: file name

tag: grade

value: Primary with recurrence


title: patient 61 IDC [validation]

description: 287 IDC

tag: tnbc type

value: Yes

tag: tissue type


title: A18779B

value: DCIS

tag: er status

tag: recurrence status


title: DLBCL_DS-66_Specimen USC71

description: DLBCL_DS-66_Specimen USC71 as test DNA and Promega normal DNA as reference


title: patient 59 IDC [validation]

description: 281 IDC


title: DLBCL_DS-66_Specimen USC70

description: DLBCL_DS-66_Specimen USC70 as test DNA and Promega normal DNA as reference


title: DLBCL_DS-66_Specimen USC72

description: DLBCL_DS-66_Specimen USC72 as test DNA and Promega normal DNA as reference


title: first visit [6436]

value: female

tag: comorbid ptsd and depression status

tag: rin

tag: hybridization batch

tag: principal component 1

tag: principal component 2


title: A15652B

tag: her2 copy number status

value: Negative

value: Low

tag: size (mm)


title: DLBCL_DS-66_Specimen USC69

description: DLBCL_DS-66_Specimen USC69 as test DNA and Promega normal DNA as reference


title: patient 60 IDC [validation]

description: 283 IDC


title: DLBCL_DS-66_Specimen USC68

description: DLBCL_DS-66_Specimen USC68 as test DNA and Promega normal DNA as reference


title: patient 57 IDC [validation]

description: 267 IDC


title: first visit [6394]

tag: Sex

tag: age

value: U

tag: principal component 3

tag: principal component 4

tag: principal component 5

tag: tissue

value: whole peripheral blood


title: patient 55 IDC [validation]

description: 247 IDC

tag: tnbc type


title: DLBCL_DS-66_Specimen USC67

description: DLBCL_DS-66_Specimen USC67 as test DNA and Promega normal DNA as reference

tag: disease state

value: diffuse large B-cell lymphoma

tag: treatment

tag: sample type


title: DLBCL_DS-66_Specimen USC66

description: DLBCL_DS-66_Specimen USC66 as test DNA and Promega normal DNA as reference


title: A10762C

tag: file name

tag: grade

tag: er status

tag: recurrence status

value: Non-recurrence

tag: age at initial diagnosis


title: first visit [6331]

tag: comorbid ptsd and depression status

tag: rin

tag: hybridization batch

tag: principal component 1

tag: principal component 2


title: patient 58 IDC [validation]

description: 269 IDC

value: No

tag: tissue type

value: invasive ductal carcinomas (IDC)


title: DLBCL_DS-66_Specimen USC65

description: DLBCL_DS-66_Specimen USC65 as test DNA and Promega normal DNA as reference


title: first visit [6334]

tag: Sex

value: male

tag: age

value: T

tag: principal component 3

tag: principal component 4

tag: principal component 5


title: patient 56 IDC [validation]

description: 259 IDC

tag: tnbc type


title: P11206I

description: recurrence of P14570

tag: file name

tag: tissue

value: High

value: Positive

value: Recurrence

tag: her2 copy number status

value: Equivocal

tag: size (mm)

value: nk


title: patient 62 IDC [validation]

description: 297 IDC


title: first visit [6446]


title: P14570A

value: DCIS

tag: grade

tag: er status

tag: recurrence status

value: Primary with recurrence

value: NK

tag: age at initial diagnosis


title: A16461A


title: patient 27 IDC [validation]

description: 241 IDC


title: first visit [6324]

value: female

tag: comorbid ptsd and depression status

tag: rin

tag: hybridization batch

tag: principal component 1


title: patient 53 IDC [validation]

description: 239 IDC

value: Yes

tag: tissue type


title: A016980J

value: Negative


title: first visit [6297]

tag: Sex

tag: age

value: U

tag: principal component 2

tag: principal component 3

value: whole peripheral blood


title: DLBCL_DS-66_Specimen USC62 2

description: DLBCL_DS-66_Specimen USC62 as test DNA and Promega normal DNA as reference

tag: disease state

value: diffuse large B-cell lymphoma

tag: treatment

value: R-CHOP or R-CHOP like immuno-chemo therapy

tag: sample type

value: reference


title: patient 52 IDC [validation]

description: 227 IDC

tag: tnbc type

value: No

value: invasive ductal carcinomas (IDC)


title: first visit [6302]

value: X

tag: principal component 4

tag: principal component 5

tag: tissue


title: P18585A_2

description: recurrence of P12589

tag: file name

tag: grade

value: Intermediate

tag: er status

value: Positive

tag: recurrence status

value: Recurrence

tag: her2 copy number status

value: Low

tag: size (mm)

tag: age at initial diagnosis


title: DLBCL_DS-66_Specimen USC64

description: DLBCL_DS-66_Specimen USC64 as test DNA and Promega normal DNA as reference


title: first visit [6283]

tag: Sex

tag: age

tag: comorbid ptsd and depression status

tag: rin

tag: hybridization batch

value: T

tag: principal component 1


title: first visit [6285]

value: male

tag: principal component 2

tag: principal component 3


title: DLBCL_DS-66_Specimen USC62 1

tag: disease state

tag: treatment

tag: sample type


title: P12589C_2

tag: file name

tag: tissue

value: DCIS

tag: grade

value: Primary with recurrence

value: NK


title: patient 50 IDC [validation]

description: 219 IDC

tag: tnbc type

tag: tissue type


title: first visit [6279]

value: female

tag: principal component 4

tag: principal component 5


title: DLBCL_DS-66_Specimen USC57

description: DLBCL_DS-66_Specimen USC57 as test DNA and Promega normal DNA as reference


title: P2831E

value: DCIS _set1

value: High

tag: er status

value: Negative

tag: recurrence status

tag: her2 copy number status

tag: size (mm)

tag: age at initial diagnosis


title: patient 51 IDC [validation]

description: 225 IDC

value: Yes


title: DLBCL_DS-66_Specimen USC59

description: DLBCL_DS-66_Specimen USC59 as test DNA and Promega normal DNA as reference

value: diffuse large B-cell lymphoma

value: R-CHOP or R-CHOP like immuno-chemo therapy

value: reference


title: patient 49 IDC [validation]

description: 209 IDC

value: No

value: invasive ductal carcinomas (IDC)


title: T825801B

description: recurrence of P7526

source_name: DCIS/IDC FFPE tissue

value: DCIS/IDC

value: Positive

value: Recurrence


title: patient 54 IDC [validation]

description: 245 IDC


title: T82580E

description: recurrence of P7526


title: patient 48 IDC [validation]

description: 201 IDC


title: DLBCL_DS-66_Specimen USC56

description: DLBCL_DS-66_Specimen USC56 as test DNA and Promega normal DNA as reference


title: T38458E

description: recurrence of T12664

value: Equivocal


title: patient 47 IDC [validation]

description: 197 IDC


title: DLBCL_DS-66_Specimen USC55

description: DLBCL_DS-66_Specimen USC55 as test DNA and Promega normal DNA as reference


title: first visit [6263]

tag: Sex

value: male

tag: age

tag: comorbid ptsd and depression status

tag: rin

tag: hybridization batch

value: T

tag: principal component 1

tag: principal component 2

value: whole peripheral blood


title: first visit [6233]

tag: principal component 3

tag: tissue


title: patient 46 IDC [validation]

description: 191 IDC

tag: tnbc type

tag: tissue type


title: P2123B

description: recurrence of P636

tag: file name

value: DCIS

tag: grade


title: patient 45 IDC [validation]

description: 189 IDC


title: patient 44 IDC [validation]

description: 183 IDC


title: first visit [6216]

value: female

tag: principal component 4

tag: principal component 5


title: DLBCL_DS-66_Specimen USC53

description: DLBCL_DS-66_Specimen USC53 as test DNA and Promega normal DNA as reference

tag: disease state

tag: treatment

tag: sample type


title: DLBCL_DS-66_Specimen USC54

description: DLBCL_DS-66_Specimen USC54 as test DNA and Promega normal DNA as reference


title: first visit [6402]

tag: Sex

tag: age

value: V


title: A18103

value: DCIS _set1

value: Low

tag: er status

tag: recurrence status

value: Non-Recurrence

tag: her2 copy number status

value: Negative

tag: size (mm)

tag: age at initial diagnosis


title: first visit [6228]

tag: comorbid ptsd and depression status

tag: rin

tag: hybridization batch

value: U

tag: principal component 1

tag: principal component 2

tag: principal component 3

tag: tissue


title: first visit [6204]

tag: principal component 4

tag: principal component 5


title: DLBCL_DS-66_Specimen USC51

description: DLBCL_DS-66_Specimen USC51 as test DNA and Promega normal DNA as reference

tag: disease state

value: diffuse large B-cell lymphoma

tag: treatment

value: R-CHOP or R-CHOP like immuno-chemo therapy

tag: sample type

value: reference


title: P8759

tag: file name

tag: grade

value: High

tag: er status

value: Primary with recurrence

value: Positive


title: A20166

tag: recurrence status

tag: her2 copy number status

value: Equivocal

tag: size (mm)


title: first visit [6181]

tag: Sex

tag: age

tag: comorbid ptsd and depression status

tag: rin


title: patient 26 IDC [validation]

description: 163 IDC

tag: tnbc type

value: No

tag: tissue type

value: invasive ductal carcinomas (IDC)


title: DLBCL_DS-66_Specimen USC50

description: DLBCL_DS-66_Specimen USC50 as test DNA and Promega normal DNA as reference


title: patient 43 IDC [validation]

description: 175 IDC


title: first visit [6163]

value: male

tag: hybridization batch

value: T

tag: principal component 1

tag: principal component 2

tag: principal component 3

tag: principal component 4

tag: tissue

value: whole peripheral blood


title: P636

tag: file name

value: DCIS _set1

value: DCIS

tag: grade

tag: age at initial diagnosis


title: T12664

tag: er status

tag: recurrence status

value: Primary but nonclonal recurrence

tag: her2 copy number status

value: Low


title: patient 25 IDC [validation]

description: 109 IDC


title: patient 41 IDC [validation]

description: 117 IDC


title: first visit [6220]

tag: Sex

tag: age

value: U

tag: principal component 5


title: A14635B

value: Intermediate

value: Non-recurrence

value: Negative

tag: size (mm)


title: first visit [6114]

value: female

tag: comorbid ptsd and depression status

tag: rin


title: A12108

value: High

value: Non-Recurrence


title: patient 42 IDC [validation]

description: 121 IDC

tag: tnbc type

tag: tissue type


title: first visit [6153]

tag: hybridization batch

tag: principal component 1

tag: principal component 2

tag: principal component 3


title: P13345

tag: file name

tag: tissue

tag: grade

value: Primary with recurrence


title: first visit [6100]

tag: principal component 4


title: DLBCL_DS-66_Specimen USC44

description: DLBCL_DS-66_Specimen USC44 as test DNA and Promega normal DNA as reference

tag: disease state

value: diffuse large B-cell lymphoma

tag: treatment

value: R-CHOP or R-CHOP like immuno-chemo therapy

tag: sample type

value: reference


title: first visit [6099]

tag: Sex

tag: age

value: T

tag: principal component 5


title: DLBCL_DS-66_Specimen USC45

description: DLBCL_DS-66_Specimen USC45 as test DNA and Promega normal DNA as reference


title: DLBCL_DS-66_Specimen USC43

description: DLBCL_DS-66_Specimen USC43 as test DNA and Promega normal DNA as reference


title: DLBCL_DS-66_Specimen USC41

description: DLBCL_DS-66_Specimen USC41 as test DNA and Promega normal DNA as reference


title: DLBCL_DS-66_Specimen USC48

description: DLBCL_DS-66_Specimen USC48 as test DNA and Promega normal DNA as reference


title: patient 39 IDC [validation]

description: 103 IDC

value: No

value: invasive ductal carcinomas (IDC)


title: first visit [6110]

value: male

tag: comorbid ptsd and depression status

tag: rin

value: whole peripheral blood


title: first visit [6361]


title: DLBCL_DS-66_Specimen USC46

description: DLBCL_DS-66_Specimen USC46 as test DNA and Promega normal DNA as reference


title: DLBCL_DS-66_Specimen USC38

description: DLBCL_DS-66_Specimen USC38 as test DNA and Promega normal DNA as reference


title: patient 37 IDC [validation]

description: 97 IDC

tag: tnbc type

tag: tissue type


title: T12334

value: DCIS _set1

value: DCIS

tag: er status

value: Positive

tag: recurrence status

tag: her2 copy number status

value: Equivocal

tag: size (mm)

tag: age at initial diagnosis


title: DLBCL_DS-66_Specimen USC37

description: DLBCL_DS-66_Specimen USC37 as test DNA and Promega normal DNA as reference


title: first visit [6096]

tag: hybridization batch

value: U

tag: principal component 1

tag: principal component 2

tag: principal component 3

tag: tissue


title: patient 36 IDC [validation]

description: 95 IDC


title: patient 40 IDC [validation]

description: 105 IDC


title: patient 38 IDC [validation]

description: 99 IDC

value: Yes


title: patient 35 IDC [validation]

description: 91 IDC


title: A10966

tag: file name

tag: grade

value: High

value: Negative


title: P4604

value: Primary with recurrence


title: first visit [6098]

tag: Sex

tag: age

tag: principal component 4

tag: principal component 5


title: patient 32 IDC [validation]

description: 35 IDC

tag: tnbc type

tag: tissue type


title: DLBCL_DS-66_Specimen USC36

description: DLBCL_DS-66_Specimen USC36 as test DNA and Promega normal DNA as reference

tag: disease state

value: diffuse large B-cell lymphoma

tag: treatment

tag: sample type


title: first visit [6053]

value: female

tag: comorbid ptsd and depression status

tag: rin


title: patient 30 IDC [validation]

description: 31 IDC


title: DLBCL_DS-66_Specimen USC32

description: DLBCL_DS-66_Specimen USC32 as test DNA and Promega normal DNA as reference

value: R-CHOP or R-CHOP like immuno-chemo therapy

value: reference


title: patient 31 IDC [validation]

description: 33 IDC


title: patient 34 IDC [validation]

description: 59 IDC

value: No


title: first visit [6023]

tag: hybridization batch

value: V

tag: principal component 1


title: DLBCL_DS-66_Specimen USC30

description: DLBCL_DS-66_Specimen USC30 as test DNA and Promega normal DNA as reference


title: DLBCL_DS-66_Specimen USC31

description: DLBCL_DS-66_Specimen USC31 as test DNA and Promega normal DNA as reference


title: DLBCL_DS-66_Specimen USC35

description: DLBCL_DS-66_Specimen USC35 as test DNA and Promega normal DNA as reference


title: patient 33 IDC [validation]

description: 45 IDC

value: invasive ductal carcinomas (IDC)


title: first visit [6070]

value: male

tag: principal component 2

tag: principal component 3

value: whole peripheral blood


title: DLBCL_DS-66_Specimen USC33

description: DLBCL_DS-66_Specimen USC33 as test DNA and Promega normal DNA as reference


title: DLBCL_DS-66_Specimen USC28

description: DLBCL_DS-66_Specimen USC28 as test DNA and Promega normal DNA as reference


title: first visit [6077]

value: T

tag: tissue


title: first visit [5988]


title: first visit [6094]


title: patient 29 IDC [validation]

description: 23 IDC


title: patient 28 IDC [validation]

description: 13 IDC


title: DLBCL_DS-66_Specimen USC34

description: DLBCL_DS-66_Specimen USC34 as test DNA and Promega normal DNA as reference


title: first visit [5994]


title: DLBCL_DS-66_Specimen USC29

description: DLBCL_DS-66_Specimen USC29 as test DNA and Promega normal DNA as reference


title: first visit [6078]


title: patient 26 NAT [validation]

description: 05-08-038 NAT

value: Normal

value: matched normal adjacent tissues from the tumour specimen (NAT)


title: DLBCL_DS-66_Specimen USC61

description: DLBCL_DS-66_Specimen USC61 as test DNA and Promega normal DNA as reference


title: patient 27 NAT [validation]

description: 05-10-030 NAT


title: first visit [5965]

value: U


title: HB3 - Epoxomicin

city: Notre Dame

first: Michael

middle: T

last: Ferdig

state: IN

address: 100 Galvin Life Sciences Center

department: Biological Sciences

institute: University of Notre Dame

description: 2012-12-07_D100813_522105_H7_HB3_Epoxomicin

hyb_protocol: Hybridizations were performed for 22 hrs followed by washing of the arrays as described according to standard protocols (Roche NimbleGen Inc., Madison, WI).

scan_protocol: The microarray image was obtained using a 2uM scanner and probe intensity values extracted using NimbleScan software (Roche NimbleGen Inc., Madison, WI).

data_processing: Probe intensities were normalized using robust multichip average (RMA) method (Irizarry, Hobbs et al. Biostatistics. 2003; 4(2):249-264). This normalization was performed across all samples hybridized on a single chip. Transcript level for each gene was obtained by averaging the processed signal intensity of all the probes across its exons as follows. Exon signal intensity for each gene was obtained by averaging the intensities of all probes within each exon. To determine a significance threshold for exon expression levels, a background distribution of signal intensities from a set of 10,000 negative control probes with no sequence matches to the P. falciparum genome was generated.  A threshold corresponding to the 95th percentile (5% FDR) of the signal distribution of the negative control probes was then applied (Clark, Schweitzer et al. Genome Biol. 2007; 8(4):R64).  To determine gene expression levels, exons that passed the 5% significance threshold were subjected to an additional threshold derived from intensities of 1000 simulated exons each consisting of 20 randomly sampled negative control probes. Intensities of exons that passed a 5% FDR threshold based on this background distribution were averaged to obtain an average transcript level for each gene.

organism: Plasmodium falciparum

source_name: Plasmodium falciparum blood stage parasites at 24 hpi perturbed with Epoxomicin

label_protocol: 1µg of cDNA was labeled with Cy3 dye using 65% AT rich pre-labeled random hexamers as primers for cDNA synthesis by Klenow fragment of DNA polymerase I.

growth_protocol: Parasite clones Dd2 and HB3 were cultured using standard methods in human red blood cells (Indiana Regional Blood Center, Indianapolis, Indiana) suspended in complete medium (CM) containing RPMI 1640 with L-glutamine (Invitrogen Corp.), 50 mg/L hypoxanthine (Sigma-Aldrich), 25 mM HEPES (Cal Biochem), 0.5% Albumax II (Invitrogen Corp.), 10 mg/L gentamicin (Invitrogen Corp.) and 0.225% NaHCO3 (Biosource) at 5% hematocrit. Cultures were grown separately in sealed flasks at 37˚C under an atmosphere of 5% CO2, 5% O2, and 90% N2.

extract_protocol: Total RNA was extracted from 20mls of culture using TriZol reagent (Invitrogen, Carlsbad, CA) as described previously (Bozdech, Llinas et al. PLoS Biol, 2003; 1(1):E5).

treatment_protocol: Sorbitol double-synchronized cultures of HB3 and Dd2 were exposed briefly for 2 hrs to each compound at a single developmental stage (24 hr trophozoites) at a concentration (IC50) obtained from literature sources or determined by our laboratory.

tag: strain

tag: small molecule

value: Epoxomicin


title: HB3 - PPMP

source_name: Plasmodium falciparum blood stage parasites at 24 hpi perturbed with PPMP

value: PPMP


title: first visit [5881]

tag: Sex

tag: age


title: DLBCL_DS-66_Specimen USC27

description: DLBCL_DS-66_Specimen USC27 as test DNA and Promega normal DNA as reference

extract_protocol: Extraction of genomic DNA was performed using Qiagen DNeasy Blood and Tissue kit according to the manufacturer's instructions.


title: HB3 - Z-Val-Asp

description: 2012-12-07_D100813_522105_H11_HB3_Z-Val-Asp

source_name: Plasmodium falciparum blood stage parasites at 24 hpi perturbed with Z-Val-Asp

value: Z-Val-Asp


title: Dd2 - Dideoxyadenosine

description: 2012-12-07_D100813_522105_D8_Dd2_Dideoxyadenosine

source_name: Plasmodium falciparum blood stage parasites at 24 hpi perturbed with Dideoxyadenosine

value: Dideoxyadenosine


title: DLBCL_DS-66_Specimen USC24

description: DLBCL_DS-66_Specimen USC24 as test DNA and Promega normal DNA as reference

value: diffuse large B-cell lymphoma


title: patient 25 NAT [validation]

description: 05-07-130 NAT


title: Dd2 - Cerulenin

description: 2012-12-07_D100813_522105_D6_Dd2_Cerulenin

source_name: Plasmodium falciparum blood stage parasites at 24 hpi perturbed with Cerulenin

value: Cerulenin


title: Dd2 - Olomucine

description: 2012-12-07_D100813_522105_D2_Dd2_Olomucine

source_name: Plasmodium falciparum blood stage parasites at 24 hpi perturbed with Olomucine

value: Olomucine


title: patient 21 IDC [validation]

description: 04-08-116 IDC


title: DLBCL_DS-66_Specimen USC22

description: DLBCL_DS-66_Specimen USC22 as test DNA and Promega normal DNA as reference

value: R-CHOP or R-CHOP like immuno-chemo therapy

value: reference


title: HB3 - Vincristine

description: 2012-12-07_D100813_522105_H3_HB3_Vincristine

source_name: Plasmodium falciparum blood stage parasites at 24 hpi perturbed with Vincristine

value: Vincristine


title: Dd2 - Fenofibrate

description: 2012-12-07_D100813_522105_D12_Dd2_Fenofibrate

source_name: Plasmodium falciparum blood stage parasites at 24 hpi perturbed with Fenofibrate

value: Fenofibrate


title: DLBCL_DS-66_Specimen USC21

description: DLBCL_DS-66_Specimen USC21 as test DNA and Promega normal DNA as reference

source_name: Human DLBCL specimen


title: GHS1, biological rep 1

city: Wuhan

first: Yuchao

last: LU

state: Hubei

address: 1095# Jiefang Avenue

department: Urology

institute: Tongji Hospital of Tongji medical college, Huazhong University of Science &Technology

description: Male GHS rats with a body weight of 250-280g, and fed with 13 g/d of a normal calcium diet (1.2% calcium, 0.65% phosphorus, 0.43% chloride, 0.4% sodium, and 0.24% magnesium per 1 g of food)

hyb_protocol: Hybridization cocktail for a single probe array contained 2.5 ?g of fragmented cRNA, 50 pM Control Oligonucleotide B2 (Affymetrix), 20X Eukaryotic Hybridization Controls (1.5 pM bioB, 5 pM bioC, 25 pM bioD, 100 pM cre) (Affymetrix), 7% DMSO, and 1X Hybridization Buffer. GeneChip Rat Gene 1.0 ST Array– Affymetrix was hybridized at 45?C for 18 hours in the GeneChip Hybridization Oven 640 (Affymetrix)

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

data_processing: The data were analyzed with GeneSpring version 7.3 using RMA normalization, then normalized to median of all samples.

source_name: mRNA profiling data from the kidney of GHS rat fed with 13 g/d of a normal calcium diet.

label_protocol: The Affymetrix Whole Transcript Sense Target Labeling Assay (Affymetrix) is used to create biotin – labeled sense -strand cDNA targets for hybridization to the Gene 1.0 ST Arrays.

growth_protocol: all rats were acclimated at 23℃ on a 12 h light/dark and fed with 13 g/d of a normal calcium diet in the SPF level animal house.

extract_protocol: RNA was extracted using RNeasy Fibrous Tissue kit (Qiagen) according to the manufacturer’s instructions.

treatment_protocol: The colony of GHS rats were created by the selective breeding of male and female SD rats with the highest 24 hour urine excretions (doi: 10.3390/ijms160716313). By the 28th generation, GHS rats stably excreted significantly higher levels of urine calcium than wild-type normal SD rats.

value: Sprague-Dawley

tag: gender

value: male

value: GHS

tag: diet

value: normal calcium diet

value: kidney


title: DLBCL_DS-66_Specimen USC26

city: Rutherford

first: Jane

last: Houldsworth

address: 201 Route 17 North

institute: Cancer Genetics, Inc.

description: DLBCL_DS-66_Specimen USC26 as test DNA and Promega normal DNA as reference

data_processing: Data extraction was performed using Feature Extraction Version 10.7.3.1 (Agilent Technologies).

label_protocol: Genomic DNA samples were labeled using the Agilent Genomic DNA Enzymatic Labeling Kit, according to the manufacturer's protocol, except that 1μg of DNA was used per 25μl labeling reaction mix.


title: GHS2, biological rep 2


title: patient 22 IDC [validation]

description: 04-09-157 IDC

tag: tnbc type

value: Yes

tag: tissue type

value: invasive ductal carcinomas (IDC)


title: patient 24 IDC [validation]

description: 05-07-008 IDC


title: GHS3, biological rep 3

tag: disease state


title: patient 20 IDC [validation]

description: 04-08-095 IDC

value: No


title: patient 23 IDC [validation]

description: 04-11-240 IDC


title: NOR2, biological rep 2

description: Male SD rats with a body weight of 250-280g, and fed with 13 g/d of a normal calcium diet (1.2% calcium, 0.65% phosphorus, 0.43% chloride, 0.4% sodium, and 0.24% magnesium per 1 g of food)

source_name: mRNA profiling data from the kidney of SD rat fed with 13 g/d of a normal calcium diet.

value: control


title: DLBCL_DS-66_Specimen USC20

description: DLBCL_DS-66_Specimen USC20 as test DNA and Promega normal DNA as reference

tag: treatment

tag: sample type


title: NOR3, biological rep 3


title: DLBCL_DS-66_Specimen USC19

description: DLBCL_DS-66_Specimen USC19 as test DNA and Promega normal DNA as reference


title: Dd2 - E64

source_name: Plasmodium falciparum blood stage parasites at 24 hpi perturbed with E64


title: patient 19 IDC [validation]

description: 04-07-053 IDC


title: Dd2 - Chloroquine (2)

description: 2012-12-07_D100813_522105_D_Dd2_Chloroquine

source_name: Plasmodium falciparum blood stage parasites at 24 hpi perturbed with Chloroquine

value: Chloroquine


title: LY-1 cell line

city: Kamakura

first: Satoshi

last: Kondo

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

description:
derivative of Pam212
LY-1-1

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: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: epidermal keratinocyte cell line

label_protocol: Extracted total RNA was labeled with Hy5 using the miRCURY LNA Array miR labeling kit (Exiqon, Vedbaek, Denmark)

growth_protocol: Pam212 and LY-1 cells were grown to cofluency in DMEM containing 10% FCS.

extract_protocol: RNA samples were extracted from cells using miRNesy mini kit (Quiagen).

treatment_protocol: No treatment was carried out.

value: Balb/c

tag: cell line

value: LY-1, metastatic derivative of Pam212


title: NOR1, biological rep 1


title: Pam212 cell line

description:
spontaneously transformed
pam212-2

value: Pam212, non-metastatic keratinocyte cell line


title: patient 18 IDC [validation]

description: 04-07-026 IDC


title: Dd2 - 5-Fluorouracil (2)

description: 2012-12-07_D100813_522105_D_Dd2_5-Fluorouracil

source_name: Plasmodium falciparum blood stage parasites at 24 hpi perturbed with 5-Fluorouracil


title: HB3 - Rapamycin (2)

description: 2012-11-02_D100813_522472_H1B_HB3_Rapamycin

source_name: Plasmodium falciparum blood stage parasites at 24 hpi perturbed with Rapamycin

value: Rapamycin


title: DLBCL_DS-66_Specimen USC17

description: DLBCL_DS-66_Specimen USC17 as test DNA and Promega normal DNA as reference

hyb_protocol: Oligoarray hybridization buffer, block (both from Agilent In Situ Hybridization Kit Plus), and Cot-1 DNA (Life Technologies) were added to each sample prior to application to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization for 24 hours, slides were washed sequentially as described by the manufacturer.

scan_protocol: Scanned on an Agilent Technologies Scanner G2505B.

value: diffuse large B-cell lymphoma

value: R-CHOP or R-CHOP like immuno-chemo therapy

source_name: Reference human genome DNA equimixture of normal male and normal female (Promega).

value: reference


title: patient 16 IDC [validation]

description: 02-09-037 IDC

source_name: fresh frozen tissue specimen


title: HB3 - Fenofibrate

description: 2012-11-02_D100813_522472_H12_HB3_Fenofibrate

value: Fenofibrate


title: patient 17 IDC [validation]

description: 02-09-082 IDC


title: patient 15 IDC [validation]

description: 01-10-133 IDC


title: DLBCL_DS-66_Specimen USC15

description: DLBCL_DS-66_Specimen USC15 as test DNA and Promega normal DNA as reference


title: DLBCL_DS-66_Specimen USC16

description: DLBCL_DS-66_Specimen USC16 as test DNA and Promega normal DNA as reference


title: DLBCL_DS-66_Specimen USC11

description: DLBCL_DS-66_Specimen USC11 as test DNA and Promega normal DNA as reference


title: KLF15_KO_quadriceps_Dex_rep4

first: Saptarsi

last: Haldar

address: 1650 Owens St

institute: Gladstone Institute of Cardiovascular Disease

hyb_protocol: 2µg of Cy3 labeled target were hybridized to Agilent whole mouse genome 4x44K Ink-jet arrays for 14 hrs, according to the manufacturer's protocol.

scan_protocol: Arrays were scanned using the Agilent microarray scanner and raw signal intensities were extracted with Feature Extraction v10.6 software.

data_processing: The dataset was normalized using the quantile normalization method (Bolstad, et al., 2003 Bioinformatics 19:185).  No background subtraction was performed and the median feature pixel intensity was used as the raw signal before normalization.

source_name: KLF15 KO quadriceps

label_protocol: Cy3-CTP labeling was performed using NimbleGen one-color labeling kits (Roche-NimbleGen Inc, Madison, WI)

extract_protocol: Samples were collected directly into lysis buffer and amplified cDNA was made using the WT-Ovation one-direct amplification system kits following the manufacturer's protocol (NuGen Technologies, Inc., San Carlos, CA)

treatment_protocol: Animals were injected with 2 mg/kg IP of dex or the equivalent volume of vehicle in 1 dose and assessed at 0 and 8hrs

tag: genotype

value: KLF15 KO

value: Dexamethasone 8hrs

value: quadriceps


title: HB3 - Fosmidomycin

description: 2012-12-07_D100813_522105_H5_HB3_Fosmidomycin

source_name: Plasmodium falciparum blood stage parasites at 24 hpi perturbed with Fosmidomycin

value: Fosmidomycin


title: Dd2 - PPMP

source_name: Plasmodium falciparum blood stage parasites at 24 hpi perturbed with PPMP

value: PPMP


title: DLBCL_DS-66_Specimen USC12

description: DLBCL_DS-66_Specimen USC12 as test DNA and Promega normal DNA as reference


title: KLF15_KO_quadriceps_Dex_rep1


title: patient 14 IDC [validation]

description: 01-10-115 IDC

value: invasive ductal carcinomas (IDC)


title: DLBCL_DS-66_Specimen USC05

description: DLBCL_DS-66_Specimen USC05 as test DNA and Promega normal DNA as reference


title: HB3 - E64


title: KLF15_KO_quadriceps_Dex_rep3


title: KLF15_KO_quadriceps_Dex_rep2


title: patient 13 IDC [validation]

description: 01-10-062 IDC

value: No


title: DLBCL_DS-66_Specimen USC09

description: DLBCL_DS-66_Specimen USC09 as test DNA and Promega normal DNA as reference


title: zyg.7

city: Basel

first: Antoine

last: Peters

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research (FMI)

data_processing:
The raw Ct were first subtracted from the global threshold value (30-Ct) and then normalized by subtracting the average signal for Ssu72, Hnrnpr and Ube2e1.
Excluded genes:
Gene-by-gene QC was performed by Fluidigm's qPCR Analysis software. In the Matrix normalized worksheet, the column Gene_QC indicates which whether a gene passed or failed QC.

source_name: zygote, rep12

label_protocol: CellsDirect (Invitrogen), Fluidigm qPCR

growth_protocol: Preimplantation embryos were cultured in KSOMaa medium under low oxygen conditions.

extract_protocol: single cells, obtained from preimplantation embryos, were directly transferred in RT-qPCR reaction mix.

tag: developmental stage

value: zygote (1-cell)


title: zyg.9

source_name: zygote, rep14


title: zyg.8

source_name: zygote, rep13


title: Dd2 - Epoxomicin (2)

description: 2012-11-02_D100813_522472_D7B_Dd2_Epoxomicin

source_name: Plasmodium falciparum blood stage parasites at 24 hpi perturbed with Epoxomicin

value: Epoxomicin


title: Dd2 - Curcumin

description: 2012-11-02_D100813_522472_D13_Dd2_Curcumin

source_name: Plasmodium falciparum blood stage parasites at 24 hpi perturbed with Curcumin

value: Curcumin


title: Dd2 - Vincristine

description: 2012-11-02_D100813_522472_D3_Dd2_Vincristine

source_name: Plasmodium falciparum blood stage parasites at 24 hpi perturbed with Vincristine

value: Vincristine


title: Dd2 - DMSO (Control) (3)

source_name: Plasmodium falciparum blood stage parasites at 24 hpi perturbed with DMSO (Control)

value: DMSO (Control)


title: Dd2 - Z-Val-Asp

description: 2012-11-02_D100813_522472_D11_Dd2_Z-val-Asp

source_name: Plasmodium falciparum blood stage parasites at 24 hpi perturbed with Z-Val-Asp

value: Z-Val-Asp


title: DLBCL_DS-66_Specimen USC02

description: DLBCL_DS-66_Specimen USC02 as test DNA and Promega normal DNA as reference

source_name: Human DLBCL specimen

value: diffuse large B-cell lymphoma


title: WT_quadriceps_Dex_rep2

source_name: WT quadriceps

value: WT


title: Dd2 - Fosmidomycin

description: 2012-11-02_D100813_522472_D5_Dd2_Fosmidomycin


title: patient 11 IDC [validation]

description: 01-09-077 IDC

value: Yes


title: zyg.6

source_name: zygote, rep11


title: KLF15_KO_quadriceps_vehicle_rep4

value: vehicle 8hrs


title: WT_quadriceps_Dex_rep1


title: patient 8 IDC [validation]

description: 01-07-053 IDC


title: patient 9 NAT [validation]

description: 01-08-002 NAT

value: Normal

value: matched normal adjacent tissues from the tumour specimen (NAT)


title: DLBCL_DS-66_Specimen USC04

description: DLBCL_DS-66_Specimen USC04 as test DNA and Promega normal DNA as reference

value: R-CHOP or R-CHOP like immuno-chemo therapy

value: reference


title: KLF15_KO_quadriceps_vehicle_rep3

value: KLF15 KO

value: quadriceps


title: KLF15_KO_quadriceps_vehicle_rep2


title: patient 7 IDC [validation]

description: 01-07-018 IDC

value: No

value: invasive ductal carcinomas (IDC)


title: patient 10 IDC [validation]

description: 01-08-034 IDC


title: patient 6 IDC [validation]

description: 01-07-016 IDC


title: patient 12 IDC [validation]

description: 01-10-019 IDC


title: patient 9 IDC [validation]

description: 01-08-002 IDC


title: WT_quadriceps_Dex_rep4

value: Dexamethasone 8hrs


title: DLBCL_DS-66_Specimen USC03

description: DLBCL_DS-66_Specimen USC03 as test DNA and Promega normal DNA as reference


title: Dd2 - Water control (3)

description: 2012-11-02_D100813_522472_D4_Dd2_Control

source_name: Plasmodium falciparum blood stage parasites at 24 hpi perturbed with Water control

value: Water control


title: zyg.5

source_name: zygote, rep10

value: zygote (1-cell)


title: zyg.4

source_name: zygote, rep9


title: zyg.3

source_name: zygote, rep8


title: zyg.2

source_name: zygote, rep7


title: zyg.14

source_name: zygote, rep6


title: zyg.13

source_name: zygote, rep5


title: HB3 - Water control (3)

description: 2012-11-02_D100813_522430_H4_HB3_Control


title: Dd2 - Rapamycin

description: 2012-11-02_D100813_522472_D1_Dd2_Rapamycin

source_name: Plasmodium falciparum blood stage parasites at 24 hpi perturbed with Rapamycin

value: Rapamycin


title: HB3 - Cerulenin

description: 2012-11-02_D100813_522430_H6_HB3_Cerulenin

source_name: Plasmodium falciparum blood stage parasites at 24 hpi perturbed with Cerulenin

value: Cerulenin


title: HB3 - Dideoxyadenosine

description: 2012-11-02_D100813_522430_H8_HB3_DideoxyAdenosine

source_name: Plasmodium falciparum blood stage parasites at 24 hpi perturbed with Dideoxyadenosine

value: Dideoxyadenosine


title: patient 5 IDC [validation]

description: 01-06-102 IDC

source_name: fresh frozen tissue specimen


title: WT_quadriceps_vehicle_rep4

value: WT


title: zyg.12

source_name: zygote, rep4


title: HB3 - Rapamycin

description: 2012-11-02_D100813_522430_H1_HB3_Rapamycin


title: Dd2 - Epoxomicin

description: 2012-11-02_D100813_522430_D7_Dd2_Epoxomicin

source_name: Plasmodium falciparum blood stage parasites at 24 hpi perturbed with Epoxomicin

value: Epoxomicin


title: HB3 - SJ77572

source_name: Plasmodium falciparum blood stage parasites at 24 hpi perturbed with SJ77572


title: WT_quadriceps_vehicle_rep3

value: vehicle 8hrs


title: patient 4 IDC [validation]

description: 01-06-074 IDC


title: WT_quadriceps_vehicle_rep1


title: HB3 - Olomucine

description: 2012-11-02_D100813_522430_H2_HB3_Olomucine

source_name: Plasmodium falciparum blood stage parasites at 24 hpi perturbed with Olomucine

value: Olomucine


title: WT_quadriceps_vehicle_rep2

source_name: WT quadriceps


title: KLF15_KO_quadriceps_vehicle_rep1

source_name: KLF15 KO quadriceps


title: patient 1 IDC [validation]

description: 01-06-010 IDC


title: IP_XY_replicate 2

city: Mishima

first: Yuzuru

last: Kato

state: Shizuoka

address: 1111 Yata

department: Division of Mammalian Development

institute: National Institute of Genetics

hyb_protocol: 0.2 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 50 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 50 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (G4122F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters (protocol GE1-v5_95 and Grid:014868_D_20070207) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: E14.5_XY gonads_IP

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50 ng (inputs) and 1 ng (preciptated) RNA using the One-Color Low RNA Input Linear Amplification kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Input and precipitated RNAs were dissolved in TRIzol reagent (Invitrogen) and were isolated according to the manufacture’s procedure.

treatment_protocol: Fifty gonads harvested from E14.5 embryos were homogenized in IP buffer (20 mM HEPES/KOH, pH7.5, 150 mM NaCl, 2.5 mM MgCl2, 0.1% NP-40, 1 mM DTT, 1x protease inhibitor cocktail, 100 units/ml RNase inhibitor). After removing debris by centrifuging lysates at 10,000xg at 4℃, supernatants were incubated with magnetic beads conjugated with protein G (Invitrogen, 10003D), which were pre-incubated with anti-Dazl (1:200, Abcam, ab34139) antibodies for 2 hours, for 6 hours at 4℃ with rotation. Beads-antibody complexes were washed 3 times with IP buffer and were transferred to new 1.5 ml tubes. After removing IP buffer, precipitated RNAs were eluted by incubating beads-antibody complexes with elution buffer (IP buffer containing 0.5% SDS) for 5 min at 37℃. Inputs (5% of start materials) were taken out from the centrifuged supernatants.

tag: strain background

value: MCH

value: male

value: Embryonic gonad

tag: antibody

value: anti-Dazl

tag: antibody vendor

value: Abcam

tag: antibody cat. #

tag: molecule subtype

value: preciptated RNA


title: zyg.11

source_name: zygote, rep3


title: IP_XY_replicate 1

tag: tissue


title: patient 3 IDC [validation]

description: 01-06-063 IDC

value: No

value: invasive ductal carcinomas (IDC)


title: AGS_Silenced-3, Biological Replicate 3

description: Gene expression data of AGS gastric cancer cell line treated with CTNNB1 siRNA - Replicate 3.

data_processing: Gene-level normalized expression signals were calculated from Affymetrix CEL files by RMA, in Affymetrix Expression Console version 1.1.

source_name: CTNNB1 siRNA treated AGS gastric cancer cells

growth_protocol: AGS gastric cancer cell line were seeded in 6 well culture plates and maintained in DMEM-F12 media with 10% FBS in a humidified incubator at 37˚C and 5% CO2.

treatment_protocol: Upon reaching 70-80% confluency, the cells were transfected with CTNNB1 siRNA or with Control siRNA (Dharmacon).

value: AGS

tag: cell type

value: gastric adenocarcinoma cell line

tag: sirna


title: HB3 - SJ194935 (2)

description: 2012-08-17_D100813_522475_HB3_SJ194935(2)

source_name: Plasmodium falciparum blood stage parasites at 24 hpi perturbed with SJ194935

tag: strain

tag: small molecule


title: zyg.10

source_name: zygote, rep2

value: zygote (1-cell)


title: zyg.1

source_name: zygote, rep1


title: patient 2 IDC [validation]

description: 01-06-033 IDC

tag: tnbc type

tag: tissue type


title: AGS_Silenced-2, Biological Replicate 2

description: Gene expression data of AGS gastric cancer cell line treated with CTNNB1 siRNA - Replicate 2.


title: HB3 - DMSO (Control) (2)

source_name: Plasmodium falciparum blood stage parasites at 24 hpi perturbed with DMSO (Control)

value: DMSO (Control)


title: HB3 - Nelfinavir

description: 2012-08-17_D100813_522475_HB3_Nelfinavir

source_name: Plasmodium falciparum blood stage parasites at 24 hpi perturbed with Nelfinavir

value: Nelfinavir


title: mor.5_b8

source_name: morual blastocyst, rep25

value: morula (16-cell)


title: HB3 - Geldanamycin

description: 2012-08-17_D100813_522475_HB3_Geldanamycin

source_name: Plasmodium falciparum blood stage parasites at 24 hpi perturbed with Geldanamycin

value: Geldanamycin


title: HB3 - Water control (2)

source_name: Plasmodium falciparum blood stage parasites at 24 hpi perturbed with Water control

value: Water control


title: mor.5_b7

source_name: morual blastocyst, rep24


title: WT_quadriceps_Dex_rep3

city: San Francisco

value: WT

tag: treatment

value: Dexamethasone 8hrs

value: quadriceps


title: mor.5_b9

source_name: morual blastocyst, rep26


title: Input_XY_replicate 1

source_name: E14.5_XY gonads_input

value: MCH

tag: gender

value: male

value: Embryonic gonad

value: total RNA (input)


title: AGS_Control-3, Biological Replicate 3

description: Gene expression data of AGS gastric cancer cell line treated with Control siRNA - Replicate 3.

source_name: Control siRNA treated AGS gastric cancer cells

tag: cell line

value: control


title: mor.5_b6

source_name: morual blastocyst, rep23


title: mor.5_b5

source_name: morual blastocyst, rep22


title: AGS_Silenced-1, Biological Replicate 1

description: Gene expression data of AGS gastric cancer cell line treated with CTNNB1 siRNA - Replicate 1.


title: AGS_Control-2, Biological Replicate 2

description: Gene expression data of AGS gastric cancer cell line treated with Control siRNA - Replicate 2.


title: HB3 - Apicidn

source_name: Plasmodium falciparum blood stage parasites at 24 hpi perturbed with Apicidn

value: Apicidn


title: AGS_Control-1, Biological Replicate 1

description: Gene expression data of AGS gastric cancer cell line treated with Control siRNA - Replicate 1.

value: AGS


title: Input_XY_replicate 2


title: IP_XX_replicate 1

source_name: E14.5_XX gonads_IP

value: female

value: anti-Dazl

value: Abcam

value: preciptated RNA


title: IP_XX_replicate 2


title: Input_XX_replicate 2

source_name: E14.5_XX gonads_input


title: Dd2 - SJ194935 (2)

description: 2012-08-17_D100813_522475_Dd2_SJ194935(2)

source_name: Plasmodium falciparum blood stage parasites at 24 hpi perturbed with SJ194935


title: Input_XX_replicate 1


title: mor.5_b4

source_name: morual blastocyst, rep21

value: morula (16-cell)


title: Dd2 - SJ119930

source_name: Plasmodium falciparum blood stage parasites at 24 hpi perturbed with SJ119930


title: mor.5_b17-19

source_name: morual blastocyst, rep20


title: mor.5_b15-16

source_name: morual blastocyst, rep19


title: OCI-AML3 GNF-7 (+) biological rep3

city: Boston

first: Atsushi

last: Nonami

state: MA

address: 450 Brookline Ave

institute: DFCI

description: Gene expression data of OCI-AML3 with 8hr treatment with GNF-7

hyb_protocol: Following fragmentation,  cRNA were hybridized  onto Affymetrix Human Gene 1.0ST arrays.The arrays were washed and stained on Fluidics Stations 450 using the Affymetrix Hybe/Wash/Stain

scan_protocol: The arrays were scanned on GeneChip Scanner 3000 7G

data_processing: Fluorescence intensities were normalized according to the RMA algorithm using the affymetrix Bioconductor package

source_name: OCI-AML3 with 8hr treatment with GNF-7

label_protocol: Biotinylated cRNA were prepared with Ambion WT Expression Kit followed by labeling with Affymetrix GeneChip WT Terminal Labeling and Hybridization

growth_protocol: cultured in RPMI1640 media with 10% of FBS

extract_protocol: used RNeasy kit of Qiagen

treatment_protocol: treat cells with GNF-7 for 8 hours

value: AML

tag: genotype

value: NRAS Q61L

tag: age


title: Dd2 - Geldanamycin

description: 2012-08-17_D100813_522475_Dd2_Geldanamycin

source_name: Plasmodium falciparum blood stage parasites at 24 hpi perturbed with Geldanamycin

value: Geldanamycin


title: OCI-AML3 GNF-7 (+) biological rep2


title: OCI-AML3 GNF-7 (+) biological rep1


title: Dd2 - Apicidin (2)

description: 2012-08-17_D100813_522475_Dd2_Apicidin(2)

source_name: Plasmodium falciparum blood stage parasites at 24 hpi perturbed with Apicidin

value: Apicidin


title: Dd2 - Water control (2)

source_name: Plasmodium falciparum blood stage parasites at 24 hpi perturbed with Water control

value: Water control


title: mor.5_b12

source_name: morual blastocyst, rep17

tag: developmental stage


title: GHS1, biological rep 1

description: Male GHS rats with a body weight of 250-280g, and fed with 13 g/d of a normal calcium diet (1.2% calcium, 0.65% phosphorus, 0.43% chloride, 0.4% sodium, and 0.24% magnesium per 1 g of food)

hyb_protocol: The labled RNA were hybridized for 16 hr at 60 rpm at 48C on Affymetrix miRNA4.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

data_processing: Raw data files were analyzed by using Affymetrix Expression Console with the default miRNA array settings. Raw data were processed and normalized on basis of organism rat using RMA-DABG algorithm.

source_name: Non-coding RNA profiling data from the kidney of GHS rat fed with 13 g/d of a normal calcium diet.

label_protocol: About 1ug total RNA were polyA tailed and labled with FlashTag™ Biotin HSR Labeling Kit(Affymetrix, Santa Clara, CA, USA).

value: Sprague-Dawley

tag: disease state

value: GHS

tag: diet

value: normal calcium diet

value: kidney


title: 3FlagNanos2_Oct4CreERT2_replicate 2

description: Gene expression after 24h tamoxifen administrattion

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 50 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 50 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (G4122F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

source_name: 3FlagNanos2_Oct4CreERT2_E11.5_XX gonads

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 µg RNA using the One-Color Low RNA Input Linear Amplification kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted with RNeasy mini kit  (QIAGEN, Valencia, CA) according to the manufacture's protocol.

treatment_protocol: Embryonic gonads were disected in ice-cold PBS and were immeadiately frozen in RNAlater (Ambion). Frozen tissues were stored at -80 degree until total RNA extraction.

tag: strain background

value: MCH

tag: genotype/variation

value: Embryonic gonad

tag: time point

value: 24h after tamoxifen administration


title: GHS3, biological rep 3

value: male

tag: tissue


title: 3FlagNanos2_Oct4CreERT2_replicate 1

value: female


title: GHS2, biological rep 2


title: mor.5_b11

source_name: morual blastocyst, rep16


title: NOR3, biological rep 3

description: Male SD rats with a body weight of 250-280g, and fed with 13 g/d of a normal calcium diet (1.2% calcium, 0.65% phosphorus, 0.43% chloride, 0.4% sodium, and 0.24% magnesium per 1 g of food)

source_name: Non-coding RNA profiling data from the kidney of SD rat fed with 13 g/d of a normal calcium diet.

value: control


title: HB3 - SJ292024

source_name: Plasmodium falciparum blood stage parasites at 24 hpi perturbed with SJ292024


title: 3FlagNanos2_replicate 1

source_name: 3FlagNanos2_E11.5_XX gonads


title: HB3 - SJ194935


title: OCI-AML3 GNF-7 (-) biological rep3

description: Gene expression data of OCI-AML3 without treatment with GNF-7

source_name: OCI-AML3 without treatment with GNF-7


title: 3FlagNanos2_replicate 2


title: OCI-AML3 GNF-7 (-) biological rep2


title: NOR2, biological rep 2


title: KO52 GNF-7 (+) biological rep3

description: Gene expression data of KO52 with 8hr treatment with GNF-7

source_name: KO52 with 8hr treatment with GNF-7

value: NRAS G13R


title: mor.5_b13-14

source_name: morual blastocyst, rep18

value: morula (16-cell)


title: mor.5_b10

source_name: morual blastocyst, rep15


title: OCI-AML3 GNF-7 (-) biological rep1

value: AML


title: HB3 - SJ119930

source_name: Plasmodium falciparum blood stage parasites at 24 hpi perturbed with SJ119930


title: KO52 GNF-7 (+) biological rep1


title: KO52 GNF-7 (-) biological rep3

description: Gene expression data of KO52 without treatment with GNF-7

source_name: KO52 without treatment with GNF-7


title: KO52 GNF-7 (+) biological rep2


title: KO52 GNF-7 (-) biological rep2