title: WT mouse liver, ZT 16, replicate 3 [SIRT1]

description:
WT SIRT1 16.3
Gene expression data from mouse liver at indicated ZT.


title: WT mouse liver, ZT 16, replicate 1 [SIRT1]

status: Public on Aug 05 2014

type: RNA

city: Irvine

first: Paolo

last: Sassone-Corsi

state: CALIFORNIA

address: Sprague Hall

country: USA

institute: University of California, Irvine

description:
WT SIRT1 16.1
Gene expression data from mouse liver at indicated ZT.

hyb_protocol: 3.3ug of the labeled, fragmented single-stranded cDNA was hybridized at 45oC with rotation for 17 hours (Affymetrix GeneChip Hybridization Oven 640) to probe sets present on an Affymetrix GeneChip 2.0 ST array.

scan_protocol: Arrays were scanned using GeneChip Scanner 3000 7G and Command Console Software v. 3.2.3 to produce .CEL intensity files.

data_processing:
The probe cell intensity files (*.CEL) were analyzed in Affymetrix Expression Console software v1.1.1 using the PLIER algorithm to generate probe level summarization files (*.CHP).
The settings used were algorithm-PLIER v2.0; quantification scale-Linear; quantification type-signal and detection p-value; background-PM-GCBG; normalization method-sketch-quantile.

label: Biotin

molecule: total RNA

organism: Mus musculus

source_name: liver, WT, ZT 16

label_protocol: Labeling using a recombinant terminal deoxynucleotidyl transferase (TdT) and an Affymetrix proprietary DNA labeling reagent was done to covalently link to biotin.

growth_protocol: Animals were housed in 12 hour Light/Dark conditions and harvested over the circadian cycle.

extract_protocol: Total RNA was prepared by Trizol extraction, and RNA was cleaned-up prior to array analysis with Qiagen RNeasy clean-up kit.

treatment_protocol: WT and SIRT6 liver-specific knockout mice, and WT and SIRT1 liver-specific knockout mice, were harvested every 4 hours over the circadian cycle and livers were flash frozen in liquid nitrogen after sacrifice.

tag: strain/background

tag: genotype/variation

value: WT

tag: tissue

value: liver

tag: circadian cycle time point

value: ZT 16


title: WT mouse liver, ZT 12, replicate 1 [SIRT1]

description:
WT SIRT1 12.1
Gene expression data from mouse liver at indicated ZT.

source_name: liver, WT, ZT 12

value: ZT 12


title: WT mouse liver, ZT 8, replicate 2 [SIRT1]

description:
WT SIRT1 8.2
Gene expression data from mouse liver at indicated ZT.

source_name: liver, WT, ZT 8

value: ZT 8


title: WT mouse liver, ZT 12, replicate 2 [SIRT1]

description:
WT SIRT1 12.2
Gene expression data from mouse liver at indicated ZT.


title: WT mouse liver, ZT 4, replicate 1 [SIRT1]

description:
WT SIRT1 4.1
Gene expression data from mouse liver at indicated ZT.

source_name: liver, WT, ZT 4

value: ZT 4


title: WT mouse liver, ZT 4, replicate 2 [SIRT1]

description:
WT SIRT1 4.2
Gene expression data from mouse liver at indicated ZT.


title: SIRT6 KO mouse liver, ZT 20, replicate 3

description:
SIRT6 KO 20.8
Gene expression data from mouse liver at indicated ZT.

source_name: liver, SIRT6 KO, ZT 20

value: 129 mixed

value: SIRT6 KO

value: ZT 20


title: WT mouse liver, ZT 8, replicate 3 [SIRT1]

description:
WT SIRT1 8.3
Gene expression data from mouse liver at indicated ZT.


title: SIRT6 KO mouse liver, ZT 16, replicate 2

description:
SIRT6 KO 16.7
Gene expression data from mouse liver at indicated ZT.

source_name: liver, SIRT6 KO, ZT 16


title: SIRT6 KO mouse liver, ZT 16, replicate 3

description:
SIRT6 KO 16.8
Gene expression data from mouse liver at indicated ZT.


title: WT mouse liver, ZT 0, replicate 1 [SIRT1]

description:
WT SIRT1 0.1
Gene expression data from mouse liver at indicated ZT.

source_name: liver, WT, ZT 0

value: ZT 0


title: SIRT6 KO mouse liver, ZT 20, replicate 2

description:
SIRT6 KO 20.7
Gene expression data from mouse liver at indicated ZT.


title: SIRT6 KO mouse liver, ZT 4, replicate 2

description:
SIRT6 KO 4.7
Gene expression data from mouse liver at indicated ZT.

source_name: liver, SIRT6 KO, ZT 4


title: WT mouse liver, ZT 0, replicate 2 [SIRT1]

description:
WT SIRT1 0.2
Gene expression data from mouse liver at indicated ZT.


title: WT mouse liver, ZT 8, replicate 1 [SIRT1]

description:
WT SIRT1 8.1
Gene expression data from mouse liver at indicated ZT.


title: WT mouse liver, ZT 0, replicate 3 [SIRT1]

description:
WT SIRT1 0.3
Gene expression data from mouse liver at indicated ZT.


title: SIRT6 KO mouse liver, ZT 12, replicate 1

description:
SIRT6 KO 12.6
Gene expression data from mouse liver at indicated ZT.

source_name: liver, SIRT6 KO, ZT 12


title: WT mouse liver, ZT 4, replicate 3 [SIRT1]

description:
WT SIRT1 4.3
Gene expression data from mouse liver at indicated ZT.


title: SIRT6 KO mouse liver, ZT 4, replicate 3

description:
SIRT6 KO 4.8
Gene expression data from mouse liver at indicated ZT.


title: SIRT6 KO mouse liver, ZT 16, replicate 1

description:
SIRT6 KO 16.6
Gene expression data from mouse liver at indicated ZT.


title: SIRT6 KO mouse liver, ZT 0, replicate 2

description:
SIRT6 KO 0.7
Gene expression data from mouse liver at indicated ZT.

source_name: liver, SIRT6 KO, ZT 0


title: SIRT6 KO mouse liver, ZT 12, replicate 2

description:
SIRT6 KO 12.7
Gene expression data from mouse liver at indicated ZT.


title: SIRT6 KO mouse liver, ZT 20, replicate 1

description:
SIRT6 KO 20.6
Gene expression data from mouse liver at indicated ZT.


title: SIRT6 KO mouse liver, ZT 0, replicate 3

description:
SIRT6 KO 0.8
Gene expression data from mouse liver at indicated ZT.


title: SIRT6 KO mouse liver, ZT 0, replicate 1

description:
SIRT6 KO 0.6
Gene expression data from mouse liver at indicated ZT.


title: SIRT6 KO mouse liver, ZT 12, replicate 3

description:
SIRT6 KO 12.8
Gene expression data from mouse liver at indicated ZT.


title: WT mouse liver, ZT 20, replicate 1 [SIRT6]

description:
WT SIRT6 20.1
Gene expression data from mouse liver at indicated ZT.

source_name: liver, WT, ZT 20


title: SIRT6 KO mouse liver, ZT 8, replicate 1

description:
SIRT6 KO 8.6
Gene expression data from mouse liver at indicated ZT.

source_name: liver, SIRT6 KO, ZT 8


title: WT mouse liver, ZT 20, replicate 2 [SIRT6]

description:
WT SIRT6 20.2
Gene expression data from mouse liver at indicated ZT.


title: WT mouse liver, ZT 16, replicate 1 [SIRT6]

description:
WT SIRT6 16.1
Gene expression data from mouse liver at indicated ZT.


title: WT mouse liver, ZT 8, replicate 3 [SIRT6]

description:
WT SIRT6 8.3
Gene expression data from mouse liver at indicated ZT.


title: SIRT6 KO mouse liver, ZT 8, replicate 2

description:
SIRT6 KO 8.7
Gene expression data from mouse liver at indicated ZT.


title: WT mouse liver, ZT 12, replicate 3 [SIRT6]

description:
WT SIRT6 12.3
Gene expression data from mouse liver at indicated ZT.


title: WT mouse liver, ZT 8, replicate 2 [SIRT6]

description:
WT SIRT6 8.2
Gene expression data from mouse liver at indicated ZT.


title: WT mouse liver, ZT 16, replicate 3 [SIRT6]

description:
WT SIRT6 16.3
Gene expression data from mouse liver at indicated ZT.


title: SIRT6 KO mouse liver, ZT 4, replicate 1

description:
SIRT6 KO 4.6
Gene expression data from mouse liver at indicated ZT.


title: WT mouse liver, ZT 4, replicate 3 [SIRT6]

description:
WT SIRT6 4.3
Gene expression data from mouse liver at indicated ZT.


title: WT mouse liver, ZT 4, replicate 1 [SIRT6]

description:
WT SIRT6 4.1
Gene expression data from mouse liver at indicated ZT.


title: WT mouse liver, ZT 16, replicate 2 [SIRT6]

description:
WT SIRT6 16.2
Gene expression data from mouse liver at indicated ZT.


title: WT mouse liver, ZT 4, replicate 2 [SIRT6]

description:
WT SIRT6 4.2
Gene expression data from mouse liver at indicated ZT.


title: WT mouse liver, ZT 12, replicate 2 [SIRT6]

description:
WT SIRT6 12.2
Gene expression data from mouse liver at indicated ZT.


title: Kidney_miR-155-/-_72hr_rep4

city: Jefferson

first: Tao

last: Han

state: Arkansas

address: 3900 NCTR Road

department: Division of Systems Biology

institute: National Center for Toxicological Research

description: whole ground tissue homogenized

hyb_protocol: Hybridizations were conducted accourding to manufacturer's protocol (65 degrees for 17 hours).

scan_protocol: Arrays were scanned using the Agilent High Resolution C Scanner according to manufacturer's protocols.

data_processing: Array data was normalized using 75th percentile normalization (TargetValue=1000) within USFDA's ArrayTrack.

source_name: miR-155 -/-, kidney, 72hr, rep4

label_protocol: Single color (Cy3) Agilent Whole Mouse Genome 4x44k microarrays (v2) and reagents were used according to manufacturer’s protocols using 500 nanograms of total RNA. An Agilent one-color spike-in kit was used as a positive control.

growth_protocol: All mice were maintained under standard housing conditions in accordance with NIH guidelines for the care and use of laboratory animals

extract_protocol: Total RNA was isolated from homogenized kidney tissue of independent animals using the Qiagen miRNeasy Mini Kit according to manufacturer’s protocol.  The yield of the extracted RNA was determined spectrophotometrically by measuring the optical density at 260 nm (Nanodrop-1000, Thermo Scientific, Wilmington, DE). The purity and quality of extracted RNA were evaluated using the RNA 6000 LabChip and Agilent 2100 Bioanalyzer. RNA samples with RNA integrity numbers (RINs) greater than 8.0 were used for microarray experiments with an average RIN of 8.5 for all samples.

treatment_protocol: miR-155-/- mice (B6.Cg-Mir155tm1.1Rsky/J originally purchased from The Jackson Laboratory) and age- and weight-matched C57BL/6 (wild type) mice (Charles River Laboratories) were used in this study. Mice were injected with one single 20mg/kg dose of cisplatin. Kidney tissues were collected at 0, 24, 48, and 72 hours i.p. with saline-injected mice as control. Total RNA extracted from the kidney tissues were used for gene expression analysis with Agilent Mouse whole genome 4x44k v2 array.

tag: strain

tag: Sex

value: male

tag: age


title: WT mouse liver, ZT 8, replicate 1 [SIRT6]

description:
WT SIRT6 8.1
Gene expression data from mouse liver at indicated ZT.


title: WT mouse liver, ZT 0, replicate 1 [SIRT6]

description:
WT SIRT6 0.1
Gene expression data from mouse liver at indicated ZT.


title: WT mouse liver, ZT 0, replicate 3 [SIRT6]

description:
WT SIRT6 0.3
Gene expression data from mouse liver at indicated ZT.


title: WT mouse liver, ZT 12, replicate 1 [SIRT6]

description:
WT SIRT6 12.1
Gene expression data from mouse liver at indicated ZT.


title: SIRT6 KO mouse liver, ZT 8, replicate 3

description:
SIRT6 KO 8.8
Gene expression data from mouse liver at indicated ZT.


title: Kidney_miR-155-/-_72hr_rep1

description: whole ground tissue homogenized

source_name: miR-155 -/-, kidney, 72hr, rep1


title: Kidney_C57BL/6_72hr_rep4

description: whole ground tissue homogenized

source_name: wild type, kidney, 72hr, rep4


title: Kidney_miR-155-/-_72hr_rep2

description: whole ground tissue homogenized

source_name: miR-155 -/-, kidney, 72hr, rep2


title: rxLeptin injection juvenile frog 6

city: Ann Arbor

first: Robert

middle: J

last: Denver

state: Michigan

address: 1105 North University Ave

department: MCDB

institute: University of Michigan

description: Gene expression data from frogs given i.c.v. rxLeptin injection

hyb_protocol: Following fragmentation, 16 ug of aRNA were hybridized for 16 hr at 45C on Xenopus Genome 2.0 GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Data was analyzed using the limma and affy Bioconductor packages implemented in the R-statistical environment. RMA was used to normalize the data and fit log2 transformed expression values.

label: biotin

organism: Xenopus laevis

source_name: Juvenile X. laevis frogs

label_protocol: Biotinylated aRNA were prepared according to the Ambion Premier kit protocol from 250 ng total RNA (MessageAmp Premier RNA Amplification Kit Instruction Manual, 2008, Ambion)

extract_protocol: RNA extraction with Trizol followed by Qiagen total RNA extraction columns

tag: Stage

value: juvenile

value: preoptic area/hypothalamus/pituitary

tag: avg body weight

tag: treatment

value: rxLeptin injection


title: Vehicle injection juvenile frog 3

description: Gene expression data from frogs given i.c.v. saline injection

value: saline injection


title: rxLeptin injection juvenile frog 5


title: Vehicle injection juvenile frog 1


title: rxLeptin injection juvenile frog 4


title: Kidney_miR-155-/-_48hr_rep3

description: whole ground tissue homogenized

source_name: miR-155 -/-, kidney, 48hr, rep3


title: Kidney_C57BL/6_72hr_rep2

description: whole ground tissue homogenized

source_name: wild type, kidney, 72hr, rep2


title: Kidney_C57BL/6_48hr_rep4

description: whole ground tissue homogenized

source_name: wild type, kidney, 48hr, rep4


title: Kidney_miR-155-/-_72hr_rep3

description: whole ground tissue homogenized

source_name: miR-155 -/-, kidney, 72hr, rep3


title: Kidney_miR-155-/-_48hr_rep2

description: whole ground tissue homogenized

source_name: miR-155 -/-, kidney, 48hr, rep2


title: Kidney_miR-155-/-_48hr_rep1

description: whole ground tissue homogenized

source_name: miR-155 -/-, kidney, 48hr, rep1


title: Kidney_miR-155-/-_48hr_rep4

description: whole ground tissue homogenized

source_name: miR-155 -/-, kidney, 48hr, rep4


title: Vehicle injection juvenile frog 2


title: Kidney_C57BL/6_72hr_rep1

description: whole ground tissue homogenized

source_name: wild type, kidney, 72hr, rep1


title: Kidney_C57BL/6_48hr_rep3

description: whole ground tissue homogenized

source_name: wild type, kidney, 48hr, rep3


title: Kidney_C57BL/6_48hr_rep1

description: whole ground tissue homogenized

source_name: wild type, kidney, 48hr, rep1


title: Kidney_C57BL/6_72hr_rep3

description: whole ground tissue homogenized

source_name: wild type, kidney, 72hr, rep3


title: Kidney_C57BL/6_48hr_rep2

description: whole ground tissue homogenized

source_name: wild type, kidney, 48hr, rep2


title: SIRT1 KO mouse liver, ZT 8, replicate 3

description:
SIRT1 KO 8.6
Gene expression data from mouse liver at indicated ZT.

source_name: liver, SIRT1 KO, ZT 8

value: SIRT1 KO


title: Kidney_miR-155-/-_24hr_rep4

description: whole ground tissue homogenized

source_name: miR-155 -/-, kidney, 24hr, rep4


title: WT mouse liver, ZT 0, replicate 2 [SIRT6]

description:
WT SIRT6 0.2
Gene expression data from mouse liver at indicated ZT.

source_name: liver, WT, ZT 0


title: Kidney_miR-155-/-_24hr_rep3

description: whole ground tissue homogenized

source_name: miR-155 -/-, kidney, 24hr, rep3


title: Kidney_miR-155-/-_24hr_rep1

description: whole ground tissue homogenized

source_name: miR-155 -/-, kidney, 24hr, rep1


title: Kidney_miR-155-/-_24hr_rep2

description: whole ground tissue homogenized

source_name: miR-155 -/-, kidney, 24hr, rep2


title: Kidney_C57BL/6_24hr_rep3

description: whole ground tissue homogenized

source_name: wild type, kidney, 24hr, rep3


title: Kidney_C57BL/6_24hr_rep4

description: whole ground tissue homogenized

source_name: wild type, kidney, 24hr, rep4


title: C65: DNA_Sry-negative XX sex reversal dog_7

type: genomic

city: Pavia

first: Elena

last: Rossi

state: Pavia

address: forlanini 14

department: Molecular Medicine

country: Italy

institute: University of Pavia

hyb_protocol: After sample denaturation and pre-annealing with 5µl of Human Cot-1 DNA (Invitrogen, Carlsbad, CA), hybridization was performed at 65°C with shaking for 24 hours. After two washing steps, the array was analyzed through the Agilent scanner and the Feature Extraction software (v10.7.3.1).

scan_protocol: Scanned on an Agilent G2539A scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.Graphical overview was obtained using the DNA Analytics (v7.0.4.0). All the array experiments were analysed using the ADM-2 algorithm at threshold 5. Text aberration summaries were analyzed to calculate the average log2 ratios of each Copy Number Variation and we considered at least 5 adjacent oligonucleotides needed for a reliable call. The positions of oligomeres refer to the Canis lupus familiaris Genome May 2005 assembly (canFam2).

molecule: genomic DNA

organism: Canis lupus familiaris

source_name: genomic DNA extracted from lymphocytes of a Sry-negative XX sex reversal dog

label_protocol: 500ng of test DNA and control DNA  were double-digested with RsaI and AluI (Promega) for 1 hour at 37°C. After digestion, samples were incubated at 65°C for 20 minutes to inactivate the enzymes, then labeled by random priming (Agilent Technologies) for 2 hours using Cy5-dUTP for the test DNA and Cy3-dUTP (Agilent Technologies) for the control DNA. Labeled DNAs were incubated at 65°C for 10 minutes and then purified with Microcon YM-30 filter units (Millipore, Billerica, USA). Every purified sample was brought to a total volume of 21µl in 1XTE (pH 8.0, Promega), and yield and specific activity were determined for each sample using a NanoDrop ND-1000 UV-VIS Spectrophotometer (Labtech International LTD). The appropriate cyanine 5- and cyanine 3-labeled samples were combined in a total volume of 39μl.

extract_protocol: Genomic DNA extracted using QIAamp DNA mini kit  following manufacturer's instructions

tag: breed

value: pug

tag: cfa9 cnv code

source_name: genomic DNA extracted from lymphocytes of the reference female control subject

value: boxer


title: 7.036_Vac_LN

city: Baltimore

first: Lei

last: Zheng

state: MD

address: 1650 Orleans Street, CRB1 Rm 488

institute: Johns Hopkins University School of Medicine

hyb_protocol: In NuGEN's modification of Affymetrix's protocol, the samples were combined with hybridization cocktail and denatured at 99ºC for 2 minutes. After 5 minutes of pre-hybridization at 45ºC, samples were spun and loaded onto their arrays.  The arrays were hybridized for 18 hours at 45ºC, 60 rpm. The cocktail was removed and the arrays were stained and washed on the Affymetrix GeneChip Fluidics Station 450 using NuGEN fluidics scripts.

scan_protocol: Fluorescence was detected using the Affymetrix G3000 GeneArray Scanner and image analysis of each GeneChip was perfomed through the Affymetrix GeneChip Command Console version 3.4 (AGCC v3.4) Affymetrix software.

data_processing: Data were extracted from the CEL files, RMA normalized and converted to Log2 notation with Partek Genomics Suite (Partek, Missouri, USA).  The samples were annotated as to experimental characteristics and the groups compared with a standard 1-way ANOVA, Student's t-test.

organism: Homo sapiens

source_name: Formalin-Fixed Paraffin-Embedded (FFPE) tissue

label_protocol: The NuGEN Ovation Encore Biotin Module V2 (Part No. 4200) was used according to manufacturer's protocol.

growth_protocol: Not applicable, surgically resected tissue.

extract_protocol: The microdissected FFPE tissue was stored in RNALater  solution (Ambion) until RNA was purified using the RecoverAll™ Total Nucleic Acid Isolation Kit for FFPE (Ambion) and amplified by the WT-Ovation™ FFPE System (NuGEN Technologies) according to the manufacturers' protocols.

treatment_protocol: Approximately 20 3-μm thick sections of  FFPE tissue blocks from each subject were stained by H&E immediately before the lymphoid aggregates were microdissected  using a dissection microscope.

tag: vaccination status

value: Vaccinated patient

tag: tissue type

value: Lymph nodes


title: C61: DNA_Sry-negative XX sex reversal dog_5

value: pinscher


title: H524_siPRL_C4

city: La Tronche

first: Sophie

last: Rousseaux

address: Bd de la Chantourne

department: IAB

country: France

institute: INSERM-UGA

hyb_protocol: Hybridization, staining and detection of cRNAs on Illumina Human HT12 v4 Expression BeadChips were performed according to the manufacturer’s protocol.

scan_protocol: The Illumina I-Scan system was used to scan Expression BeadChips, according to Illumina recommendations.

data_processing: The data were normalised using quantile normalisation.

source_name: Cell line PRL-

label_protocol: The starting amount of total RNA used for the reactions was 200 nanograms per sample. The Illumina Total Prep RNA Amplification Kit (Applied Biosystems / Ambion, Austin, USA) was used to generate biotinylated, amplified cRNA according to the manufacturer recommendations.

growth_protocol: H524 cells were cultured in Roswell Park Memorial Institute medium (RPMI 1640, Gibco) supplemented with 10% fetal bovine serum (PAA), 2 mM L-glutamine (Gibco) and 1% penicillin-streptomycin (Gibco). For H146 cells, complete RPMI medium was supplemented with 10 mM HEPES (Gibco), 1 mM sodium pyruvate (Gibco), 4.5 g/L glucose (Gibco) and 1.5 g/L sodium bicarbonate (Gibco). Cells were maintained in 75 cm2-flasks at 37°C in a humidified 5% CO2. incubator.

extract_protocol: SCLC cells growing in suspension were harvested by pipetting two days after seeding (and transfection of siRNA). The extraction of total RNA was performed with the NucleoSpin RNA II (Macherey-Nagel) kit according to the supplier's recommendations. Briefly, the cell pellet was lysed in lysis buffer containing β-mercaptoethanol. After filtration of the lysate, precipitated RNA was bound onto the column. Following a desalting step, DNA was digested directly on the membrane. After washings, RNA was eluted in a volume of 40 µL. RNA content and purity were assessed using NanoDrop 1000 (Thermo Scientific).

treatment_protocol: siRNAs targeting human prolactin and nonspecific control siRNAs were designed and synthesized by Eurogentec. PRL siRNAs sequences are 5’-CCGAAUCAUCCACAACAAUU-3’ (forward, couple 1), 5'-UUGUUGUGGAUGAUUCGGCUU-3’ (reverse, couple 1), 5’-GUUCAGCGAAUUCGAUAAAUU-3’ (forward, couple 2) and 5’-UUUAUCGAAUUCGCUGAACUU-3’ (reverse, couple 2) and scrambled siRNA sequence is 5’-AGGUAGUGUAAUCGCCUUGTT-3’. Transfection was carried out in 6-well plates with 1.5 µL siRNA duplex (20 µM), 5 µL LipofectAmine RNAiMAX Reagent (Invitrogen), 500 µL Opti-MEM medium (Gibco) and 250,000 cells in antibiotic-free culture medium.

tag: cell line

value: si PRL


title: C64: DNA_Sry-negative XX sex reversal dog_6


title: H524_siPRL_E4


title: C2: DNA_Sry-negative XX sex reversal dog_1

value: mixed breed


title: P330_Unvac_PLA

value: Unvaccinated patient

value: peritumoral lymphoid aggregates


title: Kidney_C57BL/6_24hr_rep2

description: whole ground tissue homogenized

source_name: wild type, kidney, 24hr, rep2


title: C44: DNA_Sry-negative XX sex reversal dog_4

value: pit bull


title: leaf, biological rep 1

city: Oeiras

first: Jorg

middle: D

last: Becker

address: Rua da Quinta Grande No 6

country: Portugal

institute: Instituto Gulbenkian de Ciencia

description: rosette leaves collected after bolting

hyb_protocol: 15 µg of fragmented cRNA was used in a 300-µl hybridization containing added hybridization controls. 200 µl of mixture was hybridized on arrays for 16 h at 45°C. Standard post hybridization wash and double-stain protocols (EukGE-WS2v5_450) were used on an Affymetrix GeneChip Fluidics Station 450.

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

data_processing: Scanned arrays were analyzed first with GCOS 1.4 software to obtain Absent/Present calls (MAS5 detection algorithm). Subsequently the 16 arrays used in this study were analyzed with dChip 2006 (http://www.dchip.org, Wong Lab, Harvard) . The following conditions were applied to ensure reliability of the analyses: First, each GeneChip experiment was performed with biological replicates. Second, we used a samplewise normalization to the median median probe cell intensity (CEL) of all arrays: For each sample, the median CEL intensity of one of the replicates was scaled to the median median CEL intensity of all arrays. Then the remaining replicates were normalized to this array (baseline) applying an Invariant Set Normalization  Method (Li and Wong, 2001). Third, normalized CEL intensities of the 16 arrays were used to obtain model-based gene expression indices based on a Perfect Match-only model (Li and Hung Wong, 2001). Potential array outliers that were detected in all replicates of one tissue/cell type were not called array outliers because we assumed that these genes might be expressed in a tissue-specific manner and therefore are not true array outliers. Replicate data for the same sample were weighted genewise by using inverse-squared SE as weights. Finally, all genes compared were considered to be differentially expressed if they were called present in at least one of the arrays and if the 90% lower confidence bound of the fold change between experiment and baseline was above 1.2.

organism: Arabidopsis thaliana

source_name: Arabidopsis leaves

label_protocol: Root hair total RNA was processed for use on Affymetrix (Santa Clara, CA, USA) Arabidopsis ATH1 genome arrays, according to the manufacturer’s Two-Cycle Target Labeling Assay. Briefly, 100 ng of total RNA containing spiked in Poly-A RNA controls (GeneChip Expression GeneChip Eukaryotic Poly-A RNA Control Kit; Affymetrix) was used in a reverse transcription reaction (Two-Cycle DNA synthesis kit; Affymetrix) to generate first-strand cDNA. After second-strand synthesis, double-stranded cDNA was used in an in vitro transcription (IVT) reaction to generate cRNA (MEGAscript T7 kit; Ambion, Austin, TX). 600 ng of the cRNA obtained was used for a second round of cDNA and cRNA synthesis, resulting in biotinylated cRNA (GeneChip Expression 3’-Amplification Reagents for IVT-Labeling; Affymetrix). Size distribution of the cRNA and fragmented cRNA, respectively, was assessed using an Agilent 2100 Bioanalyzer with a RNA 6000 Nano Assay.

growth_protocol: Seeds for root hair isolation were sterilized in 5% sodium hypochlorite, washed by water and sown on half strength Murashige and Skoog (Duchefa, Haarlem, The Netherlands) medium (pH 5.8) containing 1% sucrose and 0.8% phytagel. For all other samples see Pina et al. (Plant Physiology 138: 744-56, 2005) and Boavida et al. (Plant Physiology 155: 2066-80, 2011), respectively.

extract_protocol: Arabidopsis Col-0 plants were grown on cellophane disc for 4 or 5 days. The cellophane discs on which plants grew were transferred on the top of a metal tower placed in liquid nitrogen, left for 1-2 seconds, and plants except for root hairs were removed by brush. Root hairs attached on the cellophane disc were released in RNA extraction buffer. Other tissues such as root tips in the buffer were removed carefully with forceps under a stereomicroscope.

tag: ecotype

value: Columbia

value: leaf


title: C10: DNA_Sry-negative XX sex reversal dog_3


title: H524_siPRL_D4


title: C9: DNA_Sry-negative XX sex reversal dog_2

value: cocker spaniel


title: Kidney_miR-155-/-_0hr_rep4

description: whole ground tissue homogenized

source_name: miR-155 -/-, kidney, 0hr, saline-injected, rep4

value: male


title: WT mouse liver, ZT 20, replicate 3 [SIRT6]

description:
WT SIRT6 20.3
Gene expression data from mouse liver at indicated ZT.

source_name: liver, WT, ZT 20

value: 129 mixed

value: WT

value: liver

value: ZT 20


title: Kidney_C57BL/6_24hr_rep1

description: whole ground tissue homogenized

source_name: wild type, kidney, 24hr, rep1


title: Kidney_miR-155-/-_0hr_rep2

description: whole ground tissue homogenized

source_name: miR-155 -/-, kidney, 0hr, saline-injected, rep2


title: Kidney_miR-155-/-_0hr_rep3

description: whole ground tissue homogenized

source_name: miR-155 -/-, kidney, 0hr, saline-injected, rep3


title: Kidney_miR-155-/-_0hr_rep1

description: whole ground tissue homogenized

source_name: miR-155 -/-, kidney, 0hr, saline-injected, rep1


title: unpollinated_pistil, biological rep 1

description: unpollinated pistils

source_name: Arabidopsis unpollinated pistils

value: pistil


title: leaf, biological rep 2

description: rosette leaves collected after bolting


title: P840_Unvac_PLA2


title: H524_siPRL_A4


title: unpollinated_pistil, biological rep 2

description: unpollinated pistils


title: H524_siCtrl_D3

source_name: Cell line PRL+

value: si ctrl


title: H524_siCtrl_C3


title: seedling, biological rep 1

description: seedlings grown on plate for 7 days

source_name: Arabidopsis seedlings

value: seedling


title: 7.005_Vac_TLA

value: Vaccinated patient

value: Intratumoral lymphoid aggregates


title: 7.012_Vac_LN

value: Lymph nodes


title: H524_siCtrl_B3


title: 7.036_Vac_TLA


title: P840_Unvac_PLA

value: Unvaccinated patient


title: ovule, biological rep 1

description: ovules dissected from unpollinated pistils

source_name: Arabidopsis ovules

value: ovule


title: Kidney_C57BL/6_0hr_rep4

description: whole ground tissue homogenized

source_name: wild type, kidney, 0hr, saline-injected, rep4


title: ovule, biological rep 2


title: seedling, biological rep 2

description: seedlings grown on plate for 7 days


title: 7.012_Vac_TLA


title: 7.004_Vac_TLA


title: H524_siCtrl_E3


title: H524_siCtrl_A3


title: silique, biological rep 2

description: siliques collected two weeks after bolting

source_name: Arabidopsis siliques

value: silique


title: Kidney_C57BL/6_0hr_rep3

description: whole ground tissue homogenized

source_name: wild type, kidney, 0hr, saline-injected, rep3


title: silique, biological rep 1

value: Columbia


title: flower, biological rep 2

description: open flowers

source_name: Arabidopsis flowers

value: flower


title: Kidney_C57BL/6_0hr_rep2

description: whole ground tissue homogenized

source_name: wild type, kidney, 0hr, saline-injected, rep2


title: 7.006_Vac_TLA

source_name: Formalin-Fixed Paraffin-Embedded (FFPE) tissue


title: pollen, biological rep 1

description: mature pollen grains isolated by FACS

source_name: Arabidopsis pollen

value: pollen grain


title: 7.009_Vac_TLA


title: Mmp19_WT_rep2

city: Mexico

first: Annie

last: Pardo

state: Mexico DF

address: 200n lothrop st

department: Facultad de Ciencias

country: Mexico

institute: Universidad Nacional Autónoma de México

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 DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k 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 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Mouse lung fibroblast

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS 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.

growth_protocol: 0.08 u of bleomycin was administrated intratracheally into mouse lungs, at 21st day the mice was sacrificed and isolated the lung fibroblasts and culturing in FBM medium from Lonza.

extract_protocol: RNA was prepared using miRNA mini kit (Qiagen) following the manufacturer's instructions.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: The cultures were incubated for 72 hours at 37 ºC in a humidified incubator with 5% CO2.

tag: gender

value: female

value: 11 weeks

value: Lung

tag: cell type

value: fibroblast

value: wild type


title: Mmp19_WT_rep3

tag: genotype/variation


title: H146_siPRL_E2

source_name: Cell line PRL-

value: si PRL


title: 7.008_Vac_TLA


title: H146_siPRL_D2


title: Mmp19_KO_rep3

tag: tissue

value: Mmp19 knockout


title: H524_siPRL_B4


title: pollen, biological rep 2

description: mature pollen grains isolated by FACS


title: H146_siPRL_B2


title: root_hair, biological rep 1

description: root hairs isolated from seedlings

source_name: Arabidopsis root hairs

value: root hairs


title: H146_siPRL_A2


title: H146_siPRL_C2


title: root_hair, biological rep 2

description: root hairs isolated from seedlings


title: 7.036_Vac_ITS

value: Vaccinated patient

value: Intratumoral stroma


title: H146_siCtrl_E1

value: si ctrl


title: P330_Unvac_ITS

value: Unvaccinated patient


title: Kidney_C57BL/6_0hr_rep1

description: whole ground tissue homogenized

source_name: wild type, kidney, 0hr, saline-injected, rep1

value: male


title: 7.001_Vac_TLA

value: Intratumoral lymphoid aggregates


title: 7.002_Vac_TLA


title: P819_Unvac_ITS


title: Mmp19_KO_rep2


title: 7.009_Vac_ITS


title: flower, biological rep 1

description: open flowers

value: Columbia


title: Mmp19_WT_rep1


title: H146_siCtrl_D1


title: H146_siCtrl_C1


title: 7.002_Vac_ITS


title: Mmp19_KO_rep1


title: H146_siCtrl_A1


title: 786-O cells, 6 hrs pentamidine, Replicate 1b

city: Boston

first: Manoj

last: Bhasin

state: MA

address: 330 Brookline Avenue  RN 380E

institute: Beth Israel Deaconess Medical Center

description: Gene expression data from 786-O cells treated with pentamidine

hyb_protocol: The hybridization and subsequent washing and staining were performed on the Affymetrix GeneChip® Array Station (GCAS) automation platform.

scan_protocol: The arrays were scanned on the GeneChip® HT Array Plate Scanner (Affymetrix 00-0332).

data_processing:
affymetrix-algorithm-name = ExpressionStat
affymetrix-algorithm-version = 5.0
affymetrix-progid = GeneChip.CallGEBaseCall.1
program-name = Expression Console

source_name: 786-O cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA.1 µg of total RNA was used to prepare complementary RNA (cRNA) target with the Genechip® HT One-Cycle cDNA synthesis Kit (Affymetrix 900687) and the GeneChip® HT IVT Labeling Kit (Affymetrix 900688).

growth_protocol: 786-O cells were grown in RPMI-1640 medium (BioWhitaker, Walkersville, MD, USA).The medium was supplemented with 10% fetal bovine serum (FBS), 50 units/ml penicillin, and 50 µg/ml streptomycin (all from Life Technologies, Inc.). Cells were maintained in a 5% CO2-humidified incubator at 37°C.

extract_protocol: Total RNA was isolated from 786-O cells using Qiagen Rneasy.

treatment_protocol: 786-O cells were treated with 25 μM pentamidine or vehicle control (DMSO) for 6 hours. Biological duplicates were used for this analysis.

value: 6 hrs with 25 μM pentamidine

value: 786-O cells


title: subcutaneous progenitor cell, patient 5

city: Ulm

first: Daniel

last: Tews

address: Eythstrasse 24

department: Department of Pediatric Endocrinology and Diabetes

country: Germany

institute: University Medical Center Ulm

description: Gene expression data from progenitor cells isolated from subcutaneous adipose tissue

hyb_protocol: Labeled ssDNA (5.5 µg) was hybridized to Human Gene 1.0 ST Affymetrix GeneChip arrays (Affymetrix, Santa Clara, CA). Array were washed using the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: The chips were scanned with a Affymetrix GeneChip Scanner 3000 and subsequent images analyzed using Affymetrix® Expression Console™ Software (Affymetrix).

data_processing: A transcriptome analysis was performed using BRB-ArrayTools developed by Dr. Richard Simon and BRB-ArrayTools Development Team (http://linus.nci.nih.gov/BRB-ArrayTools.html). Raw feature data were normalized and log2 intensity expression summary values for each probe set were calculated using robust multiarray average (RMA)

source_name: subcutaneous adipose tissue progenitor cells

label_protocol: Microarray analyses were performed using 200 ng total RNA as starting material and 5.5 µg ssDNA per hybridization (GeneChip Fluidics Station 450; Affymetrix, Santa Clara, CA). The total RNAs were amplified and labeled following the Whole Transcript (WT) Sense Target Labeling Assay (http://www.affymetrix.com).

growth_protocol: Progenitor cells were isolated by collagense digestion and seeded into cell culture flasks. After rinsing with PBS, cells were cultured in growth ,edium until reaching subconfluency

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

treatment_protocol: Cells were rinsed with PBS and lyzed by Qiazol solution (Qiagen).

value: female


title: H146_siCtrl_B1


title: P840_Unvac_ITS


title: subcutaneous progenitor cell, patient 6


title: 786-O cells, 6 hrs DMSO, Replicate 2b

description: Gene expression data from 786-O cells treated with DMSO

value: 6 hrs with DMSO


title: 786-O cells, 6 hrs pentamidine, Replicate 2b


title: deep neck progenitor cells, patient 6

description: Gene expression data from progenitor cells isolated from supraclavicular adipose tissue

source_name: deep neck adipose tissue progenitor cells


title: 786-O cells, 6 hrs pentamidine, Replicate 1


title: deep neck progenitor cells, patient 5


title: 786-O cells, 6 hrs DMSO, Replicate 1b


title: subcutaneous progenitor cell, patient 3


title: 786-O cells, 6 hrs pentamidine, Replicate 2


title: control maxilla -1

city: Calgary

first: Benedikt

last: Hallgrimsson

state: AB

address: 3330 Hospital Dr NW

department: Cell Bio and Anatomy

country: Canada

institute: University of Calgary

description: gene expression from pooled aflox control  E10.5 mouse maxillary promience facial tissues

hyb_protocol: Next, the cRNA was hybridized to Affymetrix GeneChipH Mouse430 2.0 microarrays, which contain probes corresponding to 39,000 mouse transcripts, at 45uC for 16 hr in a GeneChipH Hybridiza- tion Oven 640 (Affymetrix, Santa Clara, CA.). The microarrays were washed and stained using an Affymetrix Fluidics Station 450 according to the manufacturer’s standard protocol and scanned using the Affymetrix GeneChip Scanner 3000 (Affymetrix).

scan_protocol: Raw image data from array scans was processed in the GeneChipH Operating Software (Affymetrix) using the option in which a scaling factor was applied to bring the average intensity for all probes on the array to the same target intensity value (TGT) of 500

data_processing: All data from our analysis are MIAME compliant MA

source_name: E10.5 Maxillary Prominence control

label_protocol: Microarray analyses were carried out by the UCD Gene Expression Core Facility. Total RNA (2–5 mg) was converted to double-stranded cDNA (ds-cDNA) using the Superscript Choice System (Life Technologies, Inc.) and an oligo-dT primer containing a T7 RNA polymerase promoter (Genset Corp.). Subsequently, the reaction mixture was extracted with phenol: chloroform:isoamyl alcohol and the ds-cDNA was recovered by ethanol precipitation. In vitro transcription (IVT) was performed to generate biotin-labeled cRNA using an RNA Transcript Labeling Kit (Enzo. Inc.) and 3.3 mL ds-cDNA template in the presence of a mixture of biotin-labeled ribonucleotides. Biotin-labeled cRNA was then purified using an RNeasy affinity column (Qiagen) and the cRNA was fragmented to ensure optimal hybridization to the oligonucleotide array. Fragments between 35–200 bp in length were generated by incubating the cRNA at 94uC for 35 min in a fragmentation buffer. The quality of total RNA, labeled cRNA and fragmented cRNA were assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA). Only samples that passed all tests of quantity and quality were used for hybridization to microarrays. The sample was then added to 200 ml of hybridization solution containing 100 mM MES, 1 M NaCl, and 20 mM EDTA in the presence of 0.01% Tween 20 to give a 0.05 mg/mL final concentration of fragmented cRNA.

growth_protocol: Embryos were dissected at E10.5 and the maxillary and nasal process were microdissected and pooled to generate 3 independent biological repilcates of 1ug total RNA

extract_protocol: Tissue pools were dissolved in 1 ml Trizol (Invitrogen) and total RNA was extracted according to the manufacturer’s instructions and resuspended in a final volume of 100 ml DEPC-treated water. Subsequently, the sample was further purified using the RNeasy Mini Kit (Qiagen, Inc.). The concentration of each total RNA sample was determined from absorbance at 260 nm (A260) and the quality of each sample was determined based on the ratio of A260 to A280. Samples with a ratio between 1.9–2.1 were considered adequately pure for cDNA synthesis.

treatment_protocol: NeoNull and aflox/wt (contol) embryos were used

value: Maxilla

tag: genotype

value: control (aflox/wt)


title: control nasal -3

description: gene expression from pooled aflox control E10.5 mouse frontal nasal promience facial tissues

source_name: E10.5 Frontal Nasal Prominence control

value: Frontal Nasal


title: control maxilla -3


title: control maxilla -2


title: control nasal -2


title: subcutaneous progenitor cell, patient 4


title: deep neck progenitor cells, patient 3


title: WT25-_rep1

first: Laurence

last: Turka

institute: Harvard Medical School and Massachusetts General Hospital

hyb_protocol: Ambion WT Expression Kit

scan_protocol: Affymetrix GeneChip Scanner

data_processing: The datasets was pre-filtered to keep only those probesets for which a gene symbol could be found in the Affymetrix annotation. CEL files were normalized using Affymetrix Power Tools on the predefined probeset ID list mentioned above, and using the standard RMA workflow (background adjustment, quantile normalization, median polish probeset summarization). Output on 2^ scale.

source_name: Spleen & Lymph Node

label_protocol: Affymetrix GeneChip WT Terminal Labeling and Controls Kit

extract_protocol: TriZol

value: 7 weeks old

tag: strain

tag: phenotype markers

value: CD4+ Foxp3+ CD25-

tag: separation method

value: FACSAria

value: Female


title: subcutaneous progenitor cell, patient 2

tag: age


title: control nasal -1


title: WT25-_rep3

tag: Sex


title: NeoNull maxilla -3

description: gene expression from pooled NeoNull  E10.5 mouse maxillary promience facial tissues

source_name: E10.5 Maxillary Prominence NeoNull

value: NeoNull (aflox/null)


title: 786-O cells, 6 hrs DMSO, Replicate 1

tag: treatment


title: deep neck progenitor cells, patient 2


title: subcutaneous progenitor cell, patient 1


title: NeoNull nasal -1

description: gene expression from pooled NeoNull  E10.5 mouse frontal nasal promience facial tissues

source_name: E10.5 Frontal Nasal Prominence NeoNull


title: 786-O cells, 6 hrs DMSO, Replicate 2


title: WT25-_rep2


title: NeoNull nasal -3


title: WT25+_rep1

value: CD4+ Foxp3+ CD25+


title: NeoNull maxilla -1


title: PTEN25-_rep1


title: PTEN25-_rep3


title: CCR6- regulatory T cell

city: Zunyi

first: Lin

last: Xu

state: Guizhou

address: 201 Dalian Road

department: Immunology

country: China

institute: Zunyi Medical College

hyb_protocol: Samples were hybridized, for 16 hours at 45°C. All washing steps were performed by a GeneChip Fluidics Station 450

scan_protocol: Axon GenePix 4000B microarray scanner

data_processing:
a) The intensity of green signal is calculated after background subtraction and four Replicated spots of each probe on the same slide have been averaged.  b) We use Median Normalization Method to obtain “Normalized Data”, Normalized Data= (Foreground-Background)¬/¬median, the median is 50 percent quantile of microRNA intensity which is larger than 30 in all samples after background correction.  c) After normalization, the statistical significance of differentially expressed miRNA was analyzed by T-test.  d) Unsupervised hierarchical clustering and Correlation analysis was performed on miRNA data.
Replicated miRNAs were averaged and miRNAs that intensities>=30 in all samples were chosen for calculating Median normalization factor. Expressed miRNA data were normalized using the Median normalization and chosen for differentially expressed miRNAs screening. miRBase 19.0.

source_name: lymphocytes

label_protocol: According to the protocol of miRCURYTM Array Power Labeling kit (Cat #208032-A, Exiqon)

extract_protocol: Total RNA was extracted from CCR6+regulatory T cells and CCR6- regulatory T cells. Then RNA was first converted to cDNA, followed by in vitro transcription to make cRNA. 5 ug of single stranded cDNA was synthesized; end labeled

treatment_protocol: The splenoytes were havested and stained by anti-CD4-PerCP, anti-CD25-APC and anti-CCR6-FITC. Then, cells were washed three times with PBS and sorted by FACS.

value: CCR6- regulatory T cell


title: NeoNull nasal -2


title: PTEN25+_rep3


title: deep neck progenitor cells, patient 1

value: male


title: Ducuts arteriosis, biological replicate 1

city: Nashville

first: John

middle: Jeffrey

last: Reese

state: TN

address: 2200 Children's Way

department: Division of Neonatology

institute: Vanderbilt

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix mouse Gene 1.0 ST arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using an Affymetrix high resolution GenePix 4000B scanner

data_processing: The data were analyzed with Partek Genomics Suite 6.6 software using gene expression analysis default analysis settings and RMA (Robust Multi-chip Average) as the normalization method.

source_name: Ducuts arteriosis

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Primary tissues were obtained from CD88 wild type mice

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

treatment_protocol: No treatment

value: Ducuts arteriosis


title: WT25+_rep3


title: PTEN25+_rep2


title: Ducuts arteriosis, biological replicate 4


title: deep neck progenitor cells, patient 4


title: Ducuts arteriosis, biological replicate 2


title: Plasma, chronic hiv, rep9

status: Public on Aug 04 2014

city: Vienna

first: Matthias

last: Hackl

state: Austria

address: Leberstrasse 20

country: Austria

institute: TAmiRNA GmbH

description: HIV, chronic infected

data_processing:
Annotation: miRBase version 19 microRNA ID
Matrix non-normalized contains raw Ct-values, derived from second derivative maximum method
Matrix normalized contains delta Ct values: Normalization was performed based on the average of miRNAs detected in all samples (25). In the present study, this included 96 miRNAs. It has been shown that the stability of the average of the 96 miRNAs is higher than any single miRNA in the data set as measured by the normfinder software (26). Normalized Cp values (dCp) were calculating using the follow formula:  Normalized Cp = average Cp (n=96 assays) – assay Cp (sample)  Where a higher value indicates that a determined miRNA is more abundant in the analyzed sample.
For the fold change data, delta Ct values were averaged for each of three groups, healthy controls, chronic HIV, elite HIV controllers. Delta-delta Ct values (log2 fold change) were calculated: i) chronic - healthy, ii) chronic - elite, iii) elite - healthy
Matrix normalized: delta Ct-values
Fold Change: delta-delta Ct-values (log2 fold change)

label: SYBR Green

source_name: EDTA-Plasma

label_protocol: miRNA expression profiling was performed by Exiqon Inc., Denmark using an LNA qPCR Array platform and the commercially available serum/plasma miRNA focus panel in 384-well format.  In order to evaluate the reverse transcription efficiency, prior to the reverse transcription step synthetic RNA oligonucleotides (RNA spike-in, UniSp6) were added to all samples (Supplemental figure 1b). Then, 15 µl RNA were reverse transcribed in 75 µl volume reactions using the miRCURY LNA™ Universal RT miRNA PCR, Polyadenylation and cDNA synthesis kit (Exiqon). At this step, a synthetic DNA spike-in (UniSp3) was added to all the cDNA samples (Supplemental figure 1b). Subsequently, cDNA was diluted and assayed in 10 µl PCR reactions according to the protocol for miRCURY LNA™ Universal RT miRNA PCR Human serum/plasma focus panel. Negative controls excluding template from the reverse transcription reaction were performed and profiled similar to the samples. qPCR amplifications were performed in 384-well plates, in a LightCycler® 480 Real-Time PCR System (Roche). The determination of Crossing point (Cp) and melting curve analysis were done using the Roche LC software and the 2nd derivative method.

extract_protocol: EDTA-blood samples were obtained by venipuncture and plasma was separated by one centrifugation step at 2000xg for 10 minutes at room temperature (RT). All plasma samples were RNA spiked in with 3.5 μL of synthetic Caenorhabditis elegans miR-39 (cel-miR-39, 10nM) to validate the efficiency of RNA extraction. Then, RNA was extracted using QIAzol Lysis Reagent (Qiagen) in combination with miRNeasy mini kit (Qiagen). One mL QIAZOL was added to 200 μL of plasma and homogenized by vigorous mixing on a vortex (15 seconds) and then incubated at RT for 5 minutes. Next, 200 μL Chloroform were added and mixed on a vortex for 10 seconds followed by incubation at RT for 2 minutes. Samples were then centrifuged at 12000xg and 4°C for 15 minutes. The upper (aqueous) phase was transferred to a new RNase-free tube and 20 μL Glycogen (Ambion) plus 1.5 vol. ethanol were added. After that, the protocol was performed using the miRNeasy mini kit (Qiagen) and according to the manufacturer's instructions. Briefly, 750 μL of the samples were transfered to a RNeasy Mini Spin Column, centrifuged at 13000xg for 30 seconds at RT and the flow through was discarded. This step was repeated with the remaining sample and then the column was washed once with 700 µl RWT buffer and next 3 times with RPE buffer.   Finally, RNA was eluted by adding 30 µl of DNase/RNase-free water to the column and centrifuged at 13000xg for 1 minute at RT. Eluted RNA samples were stored at -80°C until use. Quantitation of cel-miR-39 by qRT-PCR was performed in quadruplicate using human TaqMan MicroRNA Assay Kits (Applied Biosystems) on a Corbett Rotorgene rotorcycler (Qiagen, Germany)

tag: disease status

value: chronic HIV

value: plasma


title: Plasma, chronic hiv, rep8

description: HIV, chronic infected


title: Ducuts arteriosis, biological replicate 3


title: Plasma, chronic hiv, rep6

description: HIV, chronic infected


title: Plasma, chronic hiv, rep5

description: HIV, chronic infected


title: Plasma, chronic hiv, rep1

description: HIV, chronic infected


title: Plasma, chronic hiv, rep7

description: HIV, chronic infected


title: Plasma, chronic hiv, rep2

description: HIV, chronic infected


title: Aortic tissue, biological replicate 1

source_name: Aortic tissue

value: Aortic tissue


title: NeoNull maxilla -2


title: Plasma, elite hiv control, rep9

description: HIV Elite control

value: elite HIV


title: Aortic tissue, biological replicate 4


title: Plasma, chronic hiv, rep4

description: HIV, chronic infected


title: Aortic tissue, biological replicate 3


title: PTEN25+_rep1


title: Plasma, chronic hiv, rep3

description: HIV, chronic infected


title: Plasma, elite hiv control, rep8

description: HIV Elite control


title: Plasma, elite hiv control, rep5

description: HIV Elite control


title: Plasma, elite hiv control, rep4

description: HIV Elite control


title: Plasma, elite hiv control, rep3

description: HIV Elite control


title: Plasma, elite hiv control, rep6

description: HIV Elite control


title: Aortic tissue, biological replicate 2


title: Plasma, healthy, rep6

description: control

value: healthy


title: Plasma, healthy, rep5

description: control


title: Plasma, elite hiv control, rep7

description: HIV Elite control


title: Plasma, elite hiv control, rep1

description: HIV Elite control


title: Plasma, healthy, rep3

description: control


title: Plasma, healthy, rep4

description: control


title: Plasma, elite hiv control, rep2

description: HIV Elite control


title: Plasma, healthy, rep2

description: control


title: Lung4Wk5Con

city: Bethesda

first: WeiPing

last: Chen

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

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

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

data_processing: RMA by software Partek 6.5

source_name: Control

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Manual, 2001, Affymetrix).

growth_protocol: All animal studies were approved by the NICHD/NIH Animal Care and Use Committee.

treatment_protocol: Mice were maintained in a pathogen-free facility, with 4–5 animals  per cage in a temperature-controlled room with a 12-h light/dark cycle and access to food  and water ad libitum. Age and sex matched littermate cohorts were used for all the  experiments to account for potential strain differences.

value: Lung


title: Nucleosome positions (before NME2 induced A549)

city: Delhi

first: Vinod

middle: Kumar

last: Yadav

state: Delhi

address: Mall Road

department: Bioinformatics

country: India

institute: IGIB

description: rep 1 & 2

hyb_protocol: Purified product was fragmented and labeled as per Affymetrix Chromatin Immunoprecipitation Assay protocol before hybridization to Gene ChipHuman Promoter Tiling array 1.0R (Affymetrix) as per manufacturer’s protocol

scan_protocol: Arrays were scanned on an Affymetrix Scanner 3000 7G

data_processing: DTT files obtained were processed by GCOS to generate CEL files which upon processing by TAS gave signal and P-values for each array. The signal intensities obtained were averaged across replicates and log2ratio between treated versus control was calculated. The log2ratio was used for nucleosome position generation using iChip (Bioconductor package) at *P* value cutoff=0.05.

source_name: mononucleosomal DNA

label_protocol: The uracil glycosilase treatment, streptavidin/phycoerythrin labeling, hybridization and microarray scanning were performed as per Affymetrix Chromatin Immunoprecipitation Assay Protocol (http://www.affymetrix.com/products/arrays/specific/human_promoter.affx)

growth_protocol: A549 cells were procured from ATCC and cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) (Sigma, USA) supplemented with 10% FBS and 5% CO2 at 37°C.

extract_protocol: A549 cells (NME2-induced or -depleted, along with respective control cells) were grown in T-75 flasks till 80% confluency in DMEM, trypsinized, pelleted and washed with ice cold 1X PBS. Five times the packed pellet volume of 1X hypotonic buffer was added, cells homogenized, IGEPAL was added to final concentration of 0.6% lysate, vortexed and centrifuged at 12000 rpm. Pellet (nuclei) was resuspended in MNase digestion buffer and incubated on ice. OD was measured and 1 unit of MNase/OD was added to the suspension. Following incubation at 37 ºC for 30 min the reaction was stopped using stop-buffer, treated with proteinase K (1 mg/ml) overnight at 37 ºC before phenol chloroform purification and ethanol precipitation to pellet down the mononucleosomal DNA.

treatment_protocol: MNase digestion

value: lung carcinoma

value: not induced

source_name: Empty vector  (Control for induction Study)

tag: sample type

value: empty vector


title: Lung4Wk4K4


title: Nucleosome positions (after NME2 induced A549)

description: rep 1 & 2

value: induced


title: Lung4Wk4K27


title: Lung4Wk3K4


title: Lung4Wk5K4


title: Lung4Wk3Con


title: Nucleosome positions (NME2 depleted A549)

description: rep 1 & 2

value: depleted

source_name: scrambled siRNA  (control for depletion study)

value: scrambled siRNA


title: Lung4Wk1K4


title: Plasma, healthy, rep1

description: control


title: Lung4Wk1K27


title: Lung4Wk3K27


title: Lung1Wk5K4


title: Lung1Wk5K27


title: Lung4Wk2K27


title: Lung1Wk4K4


title: Lung1Wk5Con


title: Lung1Wk4Con


title: Lung1Wk4K27


title: Lung1Wk1K27


title: Lung1Wk2K27


title: Lung1Wk3K4


title: Lung1Wk1K4


title: Lung1Wk1Con


title: Kid_K4_4wk4

value: Kidney


title: Lung1Wk3Con


title: Lung4Wk4Con


title: Kid_K4_4wk2


title: Kid_K4_4wk3


title: Kid_K4_4wk1


title: Kid_K4_1wk3


title: Kid_K4_1wk4


title: Kid_K4_1wk2


title: Kid_K27_4wk4


title: Kid_K27_4wk3


title: Kid_K4_1wk1


title: Lung4Wk1Con


title: Kid_K27_4wk2


title: Kid_K27_4wk1


title: Kid_K27_1wk2


title: Kid_K27_1wk3


title: Kid_K27_1wk4


title: Kid Control 4Wk4


title: Kid_K27_1wk1


title: Kid Control 4Wk2


title: Kid Control 4Wk1


title: Kid Control 1wk4


title: Kid Control 1Wk3


title: Kid Control 1Wk2


title: CCR6+ regulatory T cell

value: CCR6+ regulatory T cell


title: CHO empty vector R2

hyb_protocol: The arrays were hybridized for 16 h at 56°C followed by automated washing and drying with nitrogen using a Tecan HS 400 hybridization station (Tecan, Switzerland).

scan_protocol: Slides were then scanned at 10 µm resolution and auto-gain settings using a Roche Nimblegen MS200 scanner (Roche, Germany).

data_processing: Feature extraction was conducted using the GenePix software (Molecular Devices, Sunnyvale, CA, USA). The LIMMA package of R/Bioconductor (Smyth 2004) was applied for background correction, normalization and statistical analysis as previously described (Hackl et al. 2010). Normexp background correction and Global Loess normalization were performed and log2-fold changes of miRNA expression for each sample were calculated against the common reference.

organism: Cricetulus griseus

source_name: Chinese hamster ovary cell lines, steady-state

label_protocol: End-labeling of 800 ng of total RNA was conducted using the Exiqon Power Labeling Kit (Exiqon, Denmark) together with synthetic spike-in controls according to the manufacturer’s instructions.

growth_protocol: Steady-state cultivations were conducted in 800 mL cell culture bioreactors (DS0700TPSS, DASGIP, Germany). The inocula were expanded in spinner flasks starting from the working cell bank. Exponentially growing cells from passage six were used for inoculation. The initial cell concentration was 2.5E5 cells/mL. The cultures were maintained at 37°C, pH 7.0, 30% dissolved oxygen and an agitation speed of 80 rpm. The medium was composed of DMEM without glucose and Ham’s F12 (1:1) supplemented with 4 mM L-glutamine, 0.25% soy peptone (Quest International, The Netherlands), 0.1% Pluronic F68 and a protein free supplement (Polymun Scientific, Austria). After 3 days of batch cultivation, the process was switched to continuous operation for 11 days. Fresh medium was supplied at a constant flow rate to maintain a dilution rate D of 0.5 1/d. The working volume was kept constant at 400 mL using a DASGIP level sensor. Total RNA for microarray analysis was extracted at the end of the process (steady-state).

extract_protocol: Total RNA samples were isolated from 5E6 cells using the Ambion TRI Reagent (Life Technologies, CA, USA) according to the manufacturer’s instructions using chloroform for extraction. Yield and purity were determined using the NanoDrop 1000 sprectrophotometer (Thermo Fisher Scientific, MA, USA). Only total RNA samples with an A260/A280 ratio between 1.8 and 2.0 and an A260/A230 ratio >2.0 were used in this study. The integrity of the RNA samples was analyzed using the Agilent 2100 Bioanalyser together with the RNA 6000 Nano LabChip kit (Agilent, CA, USA). The RNA integrity number (RIN) was ≥9.9 for all samples which indicates a very high sample quality.

treatment_protocol: No treatments were performed

tag: cho cell line

value: DUKXB-11 recombinant

value: CHO

tag: recombinant protein

tag: productivity

value: not applicable

source_name: Chinese hamster ovary cell pool

tag: growth rate


title: CHO empty vector R1

tag: cell line


title: CHO empty vector R3


title: CHO HSA high R3

value: HSA

value: high


title: Kid Control 4wk3


title: CHO HSA high R1


title: CHO HSA high R2


title: CHO HSA low R3

value: low


title: CHO HSA low R2


title: CHO HSA low R1


title: Kid Control 1Wk1


title: CHO 3D6scFv-Fc high R3


title: CHO 3D6scFv-Fc high R2


title: CHO 3D6scFv-Fc high R1


title: CHO 3D6scFv-Fc low R3


title: CHO 3D6scFv-Fc low R1


title: CHO 3D6scFv-Fc low R2


title: leukemiaRNA_CLL99

city: Brno

first: Marek

last: Mraz

address: Kamenice 5

country: Czech Republic

institute: Masaryk University and University Hospital Brno

hyb_protocol: Samples were hybridized with GeneChip HG-U133 Plus 2.0 Arrays (Affymetrix) and scanned at the UCSD GeneChip Core Facility.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Raw data were processed with dChip software (dChip_2010_01) for background correction and normalization.

source_name: leukemiaRNA_high 1/3

label_protocol: First-strand cDNA was synthesized from 5 μg total RNA using a T7-(dT)24 primer (Genset Corp., San Diego, CA) and reverse transcribed with the SuperScript Double-Stranded cDNA Synthesis kit (Life Technologies Bethesda Research Laboratories). After synthesis of the second strand of cDNA, the product was used an in vitro transcription reaction (Bioarray kit, Enzo Diagnostics, Farmingdale, NY) to generate biotinylated complementary RNA and subsequently fragmented.

extract_protocol: Total RNA was extracted from leukemia cells using TRIzol® reagent (Life Technologies,Carlsbad, CA) according to the manufacturer’s protocol followed by Turbo DNase treatment (Life Technologies, Carlsbad, CA) to remove trace amounts of genomic DNA.

tag: subject status

value: CLL patient

tag: cell type

value: isolated leukemia cells

tag: mir-150 level


title: leukemiaRNA_CLL100


title: leukemiaRNA_CLL94


title: leukemiaRNA_CLL96


title: leukemiaRNA_CLL97


title: leukemiaRNA_CLL93


title: leukemiaRNA_CLL98


title: leukemiaRNA_CLL91


title: leukemiaRNA_CLL89


title: leukemiaRNA_CLL92


title: leukemiaRNA_CLL85


title: leukemiaRNA_CLL87


title: leukemiaRNA_CLL90


title: leukemiaRNA_CLL86


title: leukemiaRNA_CLL95


title: leukemiaRNA_CLL83


title: leukemiaRNA_CLL81


title: leukemiaRNA_CLL88


title: leukemiaRNA_CLL80


title: with.3 biological rep3

city: Tokyo

first: Keiko

last: Midorikawa

address: 1-1-1, Yayoi, Bunkyo-ku

country: Japan

institute: The University of Tokyo

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

scan_protocol: GeneChips were scanned using the Affymetrix Gene Chip Scanner 3000.

data_processing: The data were analyzed with the statistical language R and Bioconductor software. The files were normalized using the Distribution Free Weighted method (DFW) algorithm.

organism: Oryza sativa Japonica Group

source_name: with additional fertilization, 15DAF

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

growth_protocol: Rice are grown at 28C/22C (12-h-day/12-h-night cycle) in a plant incubator (FLI2000A/TOKYORIKAKIKAI Co. Ltd.) which allows continuous illumination at an intensity of 5 lm·s.

extract_protocol: About 100mg seedlings were pooled and immediately transferred into liquid nitrogen. Samples were then ground to a fine powder and extracted with the RNeasy Plant Mini Kit (Qiagen, Hilden, Germany), according to the manufacturer's instructions.

treatment_protocol: With the time of heading and bloom, a pack is rearranged on two trays so that a bloom situation may become comparable, ground surface spraying of 400 mg per container the ammonium chloride was carried out at the additional fertilization division tray.

tag: tissue

value: developing seed

value: additional fertilization


title: leukemiaRNA_CLL82


title: leukemiaRNA_CLL84


title: KO_0.00_3

city: Seattle

first: James

middle: William

last: MacDonald

state: WA

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

institute: University of Washington

hyb_protocol: The standard hybridization protocol was used as recommended by Affymetrix

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner 3000 through the University of Washington Functional Genomics Laboratory in the Center for Ecogenetics and Environmental Health (http://depts.washington.edu/ceeh/ServiceCores/FC1/FC1.html).

data_processing: RMA normalization log2 at the transcript level using the oligo package of Bioconductor (R-2.15.1/BioC-2.11); The sessionInfo() is provided in the readme.txt.

label: Cy3 fluorescent label

label_protocol: For microarray hybridization, RNA was processed for hybridization to Affymetrix Mouse Gene 1.0 ST Array through a core facility in the Functional Genomics Laboratory in the Center for Ecogenetics and Environmental Health at the University of Washington according to the manufacturer's instructions.

extract_protocol: Fetal brains were incubated in RNAlater for at least 12 h at 4oC, then stored at -80oC. Total RNA was isolated using TRIZOL Reagent and the QIAamp Tissue Kit from QIAGEN Inc., according to the manufacturer’s established protocols. The quality of the total RNA was evaluated using an Agilent 2100 Bioanalyzer.

tag: strain background

tag: genotype/variation

value: PON1-knockout (KO)

tag: exposed to

value: CPO 0 mg/kg/d for 12 days (gestational days 6-17)

value: murine fetal brains


title: KO_0.50_1

value: CPO 0.5 mg/kg/d for 12 days (gestational days 6-17)


title: leukemiaRNA_CLL79


title: with.1 biological rep1


title: KO_0.00_2


title: KO_0.00_4


title: KO_0.00_5


title: without.3 biological rep3

source_name: control

value: control


title: without.2 biological rep2


title: with.2 biological rep2


title: without.1 biological rep1


title: leukemiaRNA_CLL78


title: WT_0.85_4

value: wild type (WT)

value: CPO 0.85 mg/kg/d for 12 days (gestational days 6-17)


title: leukemiaRNA_CLL77


title: leukemiaRNA_CLL76


title: leukemiaRNA_CLL75


title: WT_0.75_5

value: CPO 0.75 mg/kg/d for 12 days (gestational days 6-17)


title: leukemiaRNA_CLL71


title: WT_0.85_5


title: WT_0.85_2


title: R-tg_0.85_4

value: tgHuPON1R192 (R-tg)


title: R-tg_0.75_4


title: leukemiaRNA_CLL74


title: KO_0.75_1


title: leukemiaRNA_CLL66

source_name: leukemiaRNA_middle 1/3

value: middle


title: KO_0.00_1


title: Q-tg_0.75_2

value: tgHuPON1Q192 (Q-tg)


title: R-tg_0.75_1


title: leukemiaRNA_CLL69

value: high


title: R-tg_0.75_2


title: leukemiaRNA_CLL67


title: leukemiaRNA_CLL72


title: R-tg_0.00_3


title: leukemiaRNA_CLL70


title: leukemiaRNA_CLL64


title: leukemiaRNA_CLL65


title: R-tg_0.75_3


title: R-tg_0.00_5


title: leukemiaRNA_CLL62


title: leukemiaRNA_CLL63


title: leukemiaRNA_CLL68


title: R-tg_0.00_2


title: R-tg_0.00_1


title: leukemiaRNA_CLL73


title: leukemiaRNA_CLL61


title: leukemiaRNA_CLL58


title: leukemiaRNA_CLL59


title: Q-tg_0.85_5


title: Q-tg_0.85_3


title: leukemiaRNA_CLL60


title: leukemiaRNA_CLL57


title: Q-tg_0.85_2


title: R-tg_0.00_4


title: WT_0.85_3


title: leukemiaRNA_CLL54


title: leukemiaRNA_CLL53


title: Q-tg_0.85_4


title: leukemiaRNA_CLL52


title: leukemiaRNA_CLL56


title: WT_0.75_4


title: leukemiaRNA_CLL51


title: Q-tg_0.85_1


title: leukemiaRNA_CLL50


title: leukemiaRNA_CLL55


title: leukemiaRNA_CLL49


title: WT_0.75_3


title: Q-tg_0.75_5


title: WT_0.85_1


title: WT_0.75_2


title: leukemiaRNA_CLL47


title: leukemiaRNA_CLL46


title: WT_0.00_4


title: WT_0.00_3


title: leukemiaRNA_CLL48


title: leukemiaRNA_CLL45


title: leukemiaRNA_CLL44


title: WT_0.00_1


title: R-tg_0.85_5


title: leukemiaRNA_CLL42


title: leukemiaRNA_CLL41


title: WT_0.75_1


title: WT_0.00_2


title: WT_0.00_5


title: leukemiaRNA_CLL39


title: R-tg_0.75_5

value: CPO 0.75 for 12 days (gestational days 6-17)


title: R-tg_0.85_3


title: leukemiaRNA_CLL40

value: CLL patient


title: R-tg_0.85_2


title: Q-tg_0.75_1


title: Q-tg_0.75_3


title: leukemiaRNA_CLL37

value: isolated leukemia cells


title: Q-tg_0.75_4


title: leukemiaRNA_CLL35


title: leukemiaRNA_CLL43


title: leukemiaRNA_CLL38


title: Q-tg_0.00_5


title: leukemiaRNA_CLL36


title: R-tg_0.85_1


title: leukemiaRNA_CLL34


title: Q-tg_0.00_2


title: Q-tg_0.00_3


title: Q-tg_0.00_1


title: leukemiaRNA_CLL30

source_name: leukemiaRNA_low 1/3

value: low


title: leukemiaRNA_CLL33


title: leukemiaRNA_CLL32


title: leukemiaRNA_CLL29


title: leukemiaRNA_CLL28


title: KO_0.75_4


title: KO_0.75_5


title: KO_0.50_5


title: KO_0.50_4


title: leukemiaRNA_CLL26


title: leukemiaRNA_CLL31


title: Q-tg_0.00_4


title: KO_0.50_3


title: leukemiaRNA_CLL21


title: leukemiaRNA_CLL23


title: leukemiaRNA_CLL22


title: leukemiaRNA_CLL27


title: leukemiaRNA_CLL24


title: pifQ over WT replicate 3

city: Daejeon

first: Jinkil

last: Jeong

address: 291 Daehak-ro

department: Biological sciences

country: South Korea

institute: KAIST

description: Biological replicate 3 of 3

hyb_protocol: Fragmented target was used for hybridization of Agilent oligo microarray. Fragmented target was added into 2X hybridization buffer from In situ Hybridization kit of Agilent. Hybridization solution was applied onto Agilent oligo microarray, and then microarray was hybridized for 16hr at 60°C. Microarray was washed with wash solution I (6X SSC, 0.00005% Triton-X 102) for 10min at room temperature, and then microarray was washed with wash solution II (0.1X SSC, 0.00005% Triton-X 102) for 10min at 4°C.

scan_protocol: The arrays were scanned using the Agilent DNA Microarray Scanner (G2565CA) and image files were processed using the Agilent Feature Extraction Software (v 10.7).

data_processing: Background correction was performed using the normexp method in LIMMA and intensity data were normalized using LOWESS method.

source_name: pifQ

label_protocol: 2ug of total RNA were primed with T7 oligo dT primer at 70°C for 10 min, then reversed transcribed at 42°C for 2 h in the presence of SuperscriptTM II RNase H– reverse transcriptase (200 U/µl) 400 U SuperScript II RTase (Invitrogen). To synthesize second-strand cDNA, 10ul of 10X second-strand buffer, 63ul of nuclease free water, 4ul of 5mM dNTP mix, 2ul of DNA polymerase mix (20U/ul) and 1ul of RNase H (2U/ul) were added into the mixture of 20ul. The reaction mixture was incubated for 2hr at 16°C. The dsDNA was purified and then we adjusted the volume of dsDNA solution using drying the solution or adding the nuclease free water to make a final volume of 14ul. 4ul of 10X reaction buffer, 12ul of ATP, CTP, GTP mix (25mM), 3ul of UTP (50mM), 3ul of amino allyl UTP and 4ul of T7 enzyme mix were added into 14ul of dsDNA solution for the IVT (in vitro transcription). The reaction mix was incubated for 14hr at 37°C and then cRNA was purified. cRNA yield was quantified by measuring the UV absorbance at 260nm, and 3ug of cRNA for each sample was coupled with Cy-dye (Amersham Pharmacia, Uppsala, Sweden). Cy-dye labeled cRNA (target) was fragmented for hybridization. Fragmentation resulted typically in a fragmented target with a size range between 100 and 200 bases.

growth_protocol: Surface sterilized seeds were plated on 1/2 MS agarose medium and imbibed for 3 days at 4°C in the dark. Plates were transferred to continuous white light (100 μmol·m^-2·s^-1) for 7 days at 22°C and kept in the dark for 2 days.

extract_protocol: Total RNA was extracted from the seedlings using SpectrumTM Plant Total RNA Kit(Sigma, www.sigma-aldrich.com), according to the manufacturer’s instructions.

treatment_protocol: The plants were grown in continuous white light (100 μmol·m^-2·s^-1) for 7 days and trasferred to the dark for 2 days.

tag: genotype

value: pifQ mutant

value: whole seedlings

source_name: wild type

value: wild type (Col-0)


title: pifQ over WT replicate 1

description: Biological replicate 1 of 3


title: KO_0.50_2

value: PON1-knockout (KO)

value: murine fetal brains


title: KO_0.75_3


title: pifQ over WT replicate 2

description: Biological replicate 2 of 3


title: KO_0.75_2


title: leukemiaRNA_CLL20


title: leukemiaRNA_CLL15


title: leukemiaRNA_CLL16


title: leukemiaRNA_CLL19


title: leukemiaRNA_CLL13


title: leukemiaRNA_CLL11


title: leukemiaRNA_CLL17


title: leukemiaRNA_CLL12


title: leukemiaRNA_CLL10


title: leukemiaRNA_CLL25


title: leukemiaRNA_CLL14


title: leukemiaRNA_CLL9


title: leukemiaRNA_CLL7


title: leukemiaRNA_CLL6


title: leukemiaRNA_CLL5


title: leukemiaRNA_CLL2


title: leukemiaRNA_CLL8


title: NME2 induced A549 cell Replicate3

description: SAMPLE 6

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with BeadStudio

source_name: NME2 induced A549 cell

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

growth_protocol: A549 cells were procured from ATCC. Cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) (Sigma, USA) supplemented with 10% FBS and 5% CO2 at 37°C

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

treatment_protocol: A549 cells were transfected with pcDNA-NME2-MYC or pcDNA-MYC (control).

value: lung adenocarcinoma

tag: transfection


title: leukemiaRNA_CLL4


title: Control A549 cell Replicate3

description: SAMPLE 3

source_name: Control A549 cell

value: pcDNA-MYC (control)


title: NME2 induced A549 cell Replicate1

description: SAMPLE 4


title: leukemiaRNA_CLL3


title: Sig5_NTHi(-)

city: Taipei

first: Takashi

last: Angata

address: 128, Section 2, Academia Road, Nangang District

department: Institute of Biological Chemistry

country: Taiwan

institute: Academia Sinica

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45 degC on Human Genome U133 Plus 2.0 (Affymetrix). GeneChips were washed and stained with GeneChip Hybridization, Wash, and Stain Kit (Affymetrix) in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with GeneChip Operating Software (GCOS; Affymetrix) using default analysis settings and global scaling as normalization method.

source_name: Siglec-5/THP-1, without NTHi stimulation

label_protocol: Biotinylated cRNA were prepared from 250 ng total RNA, using GeneChip 3’IVT Express Kit (Affymetrix).

extract_protocol: Total RNA was extracted with Rneasy Mini (Qiagen), according to the manufacturer's instructions.

treatment_protocol: Siglec-14/THP-1 and Siglec-5/THP-1, two cell lines representing monocytes from homozygous wild-type and homozygous SIGLEC14-null people, respectively, were incubated for 6 hours with or without heat-killed non-typeable Haemophilus influenzae (NTHi), strain 2019 (MOI = 100), in Macrophage serum-free media (LifeTechnologies).

value: THP-1 (monoblastoid), expressing Siglec-5


title: Control A549 cell Replicate1

description: SAMPLE 1


title: PrS_ESC1

city: Kyoto

first: Kazutoshi

last: Takahashi

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

department: Center for iPS Cell Research and Application

institute: Kyoto University

description: Primitive streak differentiated from human embryonic stem cells 1

hyb_protocol: Agilent standard protocol

scan_protocol: Agilent standard protocol

data_processing: The data were analyzed using the Gene Spring GX 11.5.1 software program (Agilent Technologies).The data processing was performed as follows; (i) Threshold raw signals were set to 1.0, (ii) Log base 2 transformation was performed, (iii) 75th percentile normalization was chosen as the normalized algorithm.

label_protocol: Agilent standard protocol

extract_protocol: Total RNA was isolated by Trizol reagent (Life Technologies) according to the manufacturer's instruction.


title: PrS_iPSC_BR2

description: Primitive streak differentiated from human induced pluripotent stem cells 2


title: PrS_iPSC

description: Primitive streak differentiated from human induced pluripotent stem cells 1


title: leukemiaRNA_CLL18


title: Sig5_NTHi(+)

source_name: Siglec-5/THP-1, with NTHi stimulation


title: NME2 induced A549 cell Replicate2

description: SAMPLE 5


title: Control A549 cell Replicate2

description: SAMPLE 2


title: leukemiaRNA_CLL1


title: Sig14_NTHi(-)

source_name: Siglec-14/THP-1, without NTHi stimulation

value: THP-1 (monoblastoid), expressing Siglec-14


title: NE_ESC

description: Neuroectodermal cells differentiated from human embryonic stem cells


title: NE_iPSC2

description: Neuroectodermal cells differentiated from human induced pluripotent stem cells 2


title: PrS_ESC2

description: Primitive streak differentiated from human embryonic stem cells 2


title: NE_iPSC1

description: Neuroectodermal cells differentiated from human induced pluripotent stem cells 1


title: primary colorectal carcinoma S99-Frozen-rep1

city: Paris

first: Nabila

last: Elarouci

address: 14 rue Corvisart

department: Recherche

institute: Ligue Nationale contre le Cancer

hyb_protocol: Following fragmentation, 10 μg of cRNAs were hybridized for 16 hours at 45°C, 60 rpm on Human GeneChip HG-U133 Plus 2.0 arrays (Affymetrix).  The chips were washed and stained in the GeneChip Fluidics Station 450 (Affymetrix) using the EukGE-WS2v5_450.

scan_protocol: Scanner GeneChip 3000 7G ; Wavelenght : 570 nm, size pixel: 1.56 µm ; each chip is scanned once; Http://www.affymetrix.com/support/technical/manual/expression_manual.affx

data_processing: RMA signal intensity generated using Bioconductor R affy package

source_name: Frozen tissue of primary colorectal carcinoma

label_protocol: Biotinylated cRNA targets were prepared from 3.0 mg of total RNA, according to the GeneChip Expression Analysis Technical Manual : One-Cycle Target Labeling Assay (P/N 701021 Rev.5, Affymetrix, Santa Clara, USA).

growth_protocol: samples stored at -80 C

extract_protocol: total RNA was extracted using Trizol (Invitrogen, Carlsbad, CA)

treatment_protocol: total RNA was performed according to the manufacturer's instructions.

tag: gender

value: F

tag: lastnews or death.date

tag: death

value: tumor

tag: relapse

value: right colon

tag: tnm

tag: msi.status [mismatch repair status]

value: High

value: M

value: WT

tag: group

tag: histology

value: primary colorectal carcinoma

tag: organism part

value: colorectal


title: EN_iPSC1

description: Endodermal cells differentiated from human induced pluripotent stem cells 1

tag: cell type


title: EN_ESC

description: Endodermal cells differentiated from human embryonic stem cells


title: primary colorectal carcinoma S95-Frozen-rep1

value: No


title: primary colorectal carcinoma S94-Frozen-rep1

value: left colon


title: TGF-beta

city: Dallas

first: Qiuyue

state: TX

address: 5323 Harry Hines Blvd.

department: Molecular Genetics

institute: UT Southwestern Medical Center

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on the GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: Genechips were scaned on the GeneArray® Scanner or the GeneChip® Scanner 3000

data_processing: MAS 5.0

source_name: A549 cells treated with 1ng/ml TGF-β for 12h

label_protocol: First and second strand cDNA was prepared using Superscirpt Choice System (invitrogen). Biotinylated cRNA were prepared using RNA Transcript Labeling Kit (T7) (Enzo)  according to the manufacturer's protocol.

extract_protocol: RNeasy Mini Kit  (Qiagen) was used to extract RNA according to the manufacturer's protocol

treatment_protocol: Cells were treated with or without 1ng/ml TGF-β for 12h.

tag: cell line

tag: treatment

value: TGF-beta


title: H9

description: human embryonic stem cell line H9

source_name: human embryonic stem cell line H9

value: human embryonic stem cell line H9


title: primary colorectal carcinoma S98-Frozen-rep1


title: KhES3

description: human embryonic stem cell line khES3

source_name: human embryonic stem cell line khES3

value: human embryonic stem cell line khES3


title: 253G1-KLF4 dox1 T60

description: KLF4-overexpressed human induced pluripotent stem cell line 253G1

source_name: KLF4-overexpressed TRA-1-60 (+) human induced pluripotent stem cell line 253G1


title: Sig14_NTHi(+)

source_name: Siglec-14/THP-1, with NTHi stimulation


title: primary colorectal carcinoma S96-Frozen-rep1


title: 253G1-KLF4 dox0 T60

source_name: TRA-1-60 (+) human induced pluripotent stem cell line 253G1


title: EN_iPSC2

description: Endodermal cells differentiated from human induced pluripotent stem cells 2


title: primary colorectal carcinoma S92-Frozen-rep1


title: primary colorectal carcinoma S88-Frozen-rep1


title: ME_iPSC2

description: Mesendodermal cells differentiated from human induced pluripotent stem cells 2


title: ME_ESC

description: Mesendodermal cells differentiated from human embryonic stem cells


title: KhES1

description: human embryonic stem cell line khES1

source_name: human embryonic stem cell line khES1

value: human embryonic stem cell line khES1


title: H1

description: human embryonic stem cell line H1

source_name: human embryonic stem cell line H1

value: human embryonic stem cell line H1


title: ME_iPSC1

description: Mesendodermal cells differentiated from human induced pluripotent stem cells 1


title: primary colorectal carcinoma S91-Frozen-rep1


title: primary colorectal carcinoma S97-Frozen-rep1


title: primary colorectal carcinoma S90-Frozen-rep1


title: primary colorectal carcinoma S93-Frozen-rep1


title: primary colorectal carcinoma S87-Frozen-rep1


title: control

source_name: A549 cells

value: control


title: arm-GFP 1st instar rep4

city: San Francisco

first: Charlie

last: Kim

state: CA

address: 1001 Potrero Ave

department: Medicine

institute: University of California, San Francisco

hyb_protocol: 825 ng of each aRNA hybridized to custom Agilent 4x44k microarrays as per manufacturer's instructions

scan_protocol: Molecular Devices Genepix 4000B scanner at 5 um resolution

data_processing: Ratio normalized, filters: 'B532' <= 350 AND 'B635' <= 350) AND 'F532 % Sat.' <= 60 AND 'F635 % Sat.' <= 60 AND 'F532 CV' <= 80 AND 'F635 CV' <= 80 AND 'Flags' >= 0 AND 'Dia.' >= 50 AND 'Dia.' <= 80 AND ('% > B532+2SD' >= 70 OR '% > B635+2SD' >= 70) AND 'Substance Name' begins with 'f' AND 'Circularity' >= 60

organism: Drosophila melanogaster

source_name: pooled reference amplified RNA from whole animals and sorted populations

label_protocol: 1.5 ug of aRNA coupled to Cy5 (or Cy3 for common pooled reference aRNA) as per standard protocols

growth_protocol: Timed larvae collections on grape juice agar plates

extract_protocol: Dissociated cells isolated by FACS.  Up to 10k cells sorted into Ambion RNAqueous Micro kit lysis buffer.  RNA isolated as per manufacturer's instructions with DNase treatment.  RNA amplified in two rounds with Ambion Aminoallyl MessageAmp II kit.

tag: sample type

value: pooled reference

source_name: Amplified RNA from 1st instar epithelial cells from wild type larvae

value: Epithelial cells

tag: marker

value: arm

tag: age (instar)

value: 1st instar


title: arm-GFP 1st instar rep3


title: OSKM_d49_2

description: TRA-1-60 (+) cells on day 49

source_name: TRA-1-60 (+) cells on day 49

value: TRA-1-60 (+) cells on day 49


title: primary colorectal carcinoma S86-Frozen-rep1

value: M

value: right colon


title: primary colorectal carcinoma S84-Frozen-rep1

value: tumor

value: WT

value: primary colorectal carcinoma


title: OSKM_d49_3

description: TRA-1-60 (+) cells on day 49


title: primary colorectal carcinoma S85-Frozen-rep1

value: F

value: No

value: colorectal


title: OSKM_d49_1

description: TRA-1-60 (+) cells on day 49


title: OSKM_d42_3

description: TRA-1-60 (+) cells on day 42

source_name: TRA-1-60 (+) cells on day 42

value: TRA-1-60 (+) cells on day 42


title: OSKM_d42_1

description: TRA-1-60 (+) cells on day 42


title: OSKM_d28_1

description: TRA-1-60 (+) cells on day 28

source_name: TRA-1-60 (+) cells on day 28

value: TRA-1-60 (+) cells on day 28


title: OSKM_d28_4

description: TRA-1-60 (+) cells on day 28


title: OSKM_d35_3

description: TRA-1-60 (+) cells on day 35

source_name: TRA-1-60 (+) cells on day 35

value: TRA-1-60 (+) cells on day 35


title: OSKM_d28_3

description: TRA-1-60 (+) cells on day 28


title: ban arm-GFP 3rd instar rep2

source_name: Amplified RNA from 3rd instar epithelial cells from ban mutants

value: 3rd instar


title: arm-GFP 3rd instar rep4

value: pooled reference

source_name: Amplified RNA from 3rd instar epithelial cells from wild type larvae


title: OSKM_d35_1

description: TRA-1-60 (+) cells on day 35


title: primary colorectal carcinoma S80-Frozen-rep1

source_name: Frozen tissue of primary colorectal carcinoma

value: left colon


title: OSKM_d20_3

description: TRA-1-60 (+) cells on day 20

source_name: TRA-1-60 (+) cells on day 20

value: TRA-1-60 (+) cells on day 20


title: OSKM_d28_2

description: TRA-1-60 (+) cells on day 28


title: OSKM_d20_4

description: TRA-1-60 (+) cells on day 20


title: primary colorectal carcinoma S83-Frozen-rep1


title: ban arm-GFP 3rd instar rep1

value: Epithelial cells

value: arm


title: arm-GFP 3rd instar rep5


title: OSKM_d35_2

description: TRA-1-60 (+) cells on day 35


title: primary colorectal carcinoma S82-Frozen-rep1

value: M


title: arm-GFP 1st instar rep2

value: 1st instar


title: OSKM_d42_2

description: TRA-1-60 (+) cells on day 42


title: arm-GFP 1st instar rep1


title: primary colorectal carcinoma S81-Frozen-rep1


title: primary colorectal carcinoma S79-Frozen-rep1

value: tumor

value: low rectum


title: OSKM_d20_2

description: TRA-1-60 (+) cells on day 20


title: arm-GFP 3rd instar rep3


title: arm-GFP 3rd instar rep2


title: primary colorectal carcinoma S78-Frozen-rep1

value: right colon

value: WT

value: primary colorectal carcinoma


title: primary colorectal carcinoma S77-Frozen-rep1

value: No

value: colorectal


title: OSKM_d15_2

description: TRA-1-60 (+) cells on day 15

source_name: TRA-1-60 (+) cells on day 15

value: TRA-1-60 (+) cells on day 15


title: OSKM_d15_3

description: TRA-1-60 (+) cells on day 15


title: OSKM_d20_1

description: TRA-1-60 (+) cells on day 20


title: arm-GFP 3rd instar rep1


title: OSKM_d15_1

description: TRA-1-60 (+) cells on day 15


title: OSKM_d11_3

description: TRA-1-60 (+) cells on day 11

source_name: TRA-1-60 (+) cells on day 11

value: TRA-1-60 (+) cells on day 11


title: OSKM_d7_2

description: TRA-1-60 (+) cells on day 7

source_name: TRA-1-60 (+) cells on day 7

value: TRA-1-60 (+) cells on day 7


title: OSKM_d11_1

description: TRA-1-60 (+) cells on day 11


title: OSKM_d11_2

description: TRA-1-60 (+) cells on day 11


title: OSKM_d7_1

description: TRA-1-60 (+) cells on day 7


title: OSKM_d7_3

description: TRA-1-60 (+) cells on day 7


title: OSKM_d3_3

description: human dermal fibroblast transduced OSKM on day 3


title: OSKM_d3_2

source_name: human dermal fibroblast transduced OSKM on day 3


title: primary colorectal carcinoma S74-Frozen-rep1

value: F


title: primary colorectal carcinoma S76-Frozen-rep1


title: TH cells from LC, Mecp2 null, young time point, biological replicate 3

city: Ashburn

first: Ken

last: Sugino

state: VA

address: 19700 Helix Dr

institute: Janelia Research Campus

description:
Gene expression data from TH GFP labeled neurons from the locus coeruleus (LC), Mecp2 null
TH_LCY_KO_3

hyb_protocol: Following fragmentation, 15 or 20 ug of cRNA were hybridized for 18 hr at 45C on GeneChip Mouse Genome 430 v2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned with the Affymetrix GeneArray Scanner G3000.

data_processing: The data were processed with fRMA (McCall MN, Bolstad BM, Irizarry RA (2010) Frozen robust multiarray analysis (fRMA). Biostatistics 11:242-253) algorithm in the Bioconductor with default settings.

source_name: brain, locus coeruleus neurons, Mecp2 null

label_protocol: Biotinylated cRNA were prepared using two rounds of T7 in vitro transcription based aRNA amplification (Affymetrix Small Sample Target Labeling Assay Version II) from about 0.3 to 1 ng of total RNA.

growth_protocol: Mecp2 heterozygous null female mice were mated to male mice.  Either male or female carried one of the fluorescent alleles (G42, YFPH or TH). Male offsprings which are hemizygous to Mecp2 null allele and hemizygous to one of the fluorescent alleles were used for experiments. Littermates which are wild type for X chromosome and hemyzygous to one of the fluorescent alleles were used for controls. Mice were weaned around P30. Normal 12 hour-12 hour light dark cycle were used. Normally only up to 4 mice were put in a cage.

extract_protocol: PicoPure RNA Isolation Kit (Arcturus) was used to extract total RNA according to the manufacturer's instructions.

treatment_protocol: Mice at postnatal day 22-25 were sacrificed, the brain extracted and sliced on a vibratome (Leica). Slices were incubated in ACSF with pronase E (1mg/mL; Sigma) for 1 hour and desired regions were microdissected. Three Pasteur pipettes with decreasing tip size were used for tritration in a 1.5 ml Eppendorf tube. Tritrated samples were diluted 20 times with ACSF with FBS (1%) and plated on a 10cm petri dish with Sylgard substriatum. Glass pipette of tip size around 50 um was used to aspirate fluorescent cells under a fluorescent stereomicroscope (Leica). Aspirated cells were transferred to a new dish with fresh ACSF and aspirated again to purify the sample. This wash was repeated twice more (total of 3 washes). After the last wash, the sample was transfered to a 200 ul PCR tube with 50 ul of XB (extraction and lysis buffer from PicoPure RNA Isolation Kit; Arcturus).

tag: strain

tag: pooled

tag: amplification batch

tag: # cells

tag: Sex

value: male

tag: region

value: LC (locus coeruleus)

tag: age

tag: genotype

tag: tissue

value: brain

value: tyrosine hydroxylase (TH)-positive locus coeruleus (LC) neurons


title: primary colorectal carcinoma S72-Frozen-rep1

tag: gender

value: M

tag: lastnews or death.date

tag: death

tag: relapse

tag: tnm

tag: msi.status [mismatch repair status]

tag: group

tag: histology


title: TH cells from LC, Mecp2 null, young time point, biological replicate 1

description:
Gene expression data from TH GFP labeled neurons from the locus coeruleus (LC), Mecp2 null
TH_LCY_KO_1

tag: strain

tag: cell type


title: primary colorectal carcinoma S71-Frozen-rep1

value: left colon

tag: organism part


title: HDFa

description: human dermal fibroblast

source_name: human dermal fibroblast

value: human dermal fibroblast


title: primary colorectal carcinoma S73-Frozen-rep1

value: low rectum


title: HDF-1388

description: human dermal fibroblast


title: primary colorectal carcinoma S70-Frozen-rep1


title: TH cells from LC, wild type control, young time point, biological replicate 3

description:
Gene expression data from TH GFP labeled neurons from the locus coeruleus (LC), wild type control
TH_LCY_WT_3

source_name: brain, locus coeruleus neurons, wild type

tag: pooled

tag: amplification batch

tag: # cells

value: Y/X;TH/-


title: OSKM_d3_1

value: human dermal fibroblast transduced OSKM on day 3


title: HDF1

description: human dermal fibroblast


title: HDF3

description: human dermal fibroblast


title: TH cells from LC, wild type control, young time point, biological replicate 2

description:
Gene expression data from TH GFP labeled neurons from the locus coeruleus (LC), wild type control
TH_LCY_WT_2

tag: Sex

tag: region

tag: age


title: TH cells from LC, Mecp2 null, young time point, biological replicate 2

description:
Gene expression data from TH GFP labeled neurons from the locus coeruleus (LC), Mecp2 null
TH_LCY_KO_2

tag: genotype

tag: tissue


title: primary colorectal carcinoma S66-Frozen-rep1

tag: gender

tag: lastnews or death.date

tag: death

value: right colon

value: WT

value: primary colorectal carcinoma


title: TH cells from LC, wild type control, young time point, biological replicate 1

description:
Gene expression data from TH GFP labeled neurons from the locus coeruleus (LC), wild type control
TH_LCY_WT_1

value: No


title: TKCBV5-6s11

description: human induced pluripotent stem cell line TKCBV5-6 subclone


title: TKCBV5-6s8

source_name: human induced pluripotent stem cell line TKCBV5-6 subclone


title: TKCBV5-6s14

value: human induced pluripotent stem cell line TKCBV5-6 subclone


title: TKCBV5-6s9


title: primary colorectal carcinoma S65-Frozen-rep1

value: tumor

tag: relapse

tag: tnm

tag: msi.status [mismatch repair status]

value: colorectal


title: primary colorectal carcinoma S63-Frozen-rep1

value: F

tag: group

tag: histology


title: primary colorectal carcinoma S68-Frozen-rep1

tag: organism part


title: TKCBV5-6s13

tag: cell type


title: primary colorectal carcinoma S69-Frozen-rep1

value: Low


title: TKCBV5-6s10


title: TKCBV5-6s7


title: TKCBV5-6s4


title: TKCBV5-6s6


title: primary colorectal carcinoma S61-Frozen-rep1


title: TKCBV5-6s3


title: TKCBV5-6s5


title: Untreated Animal #26, Tumor

city: Northbrook

first: Michael

last: Falduto

state: IL

address: 1808 Janke, Unit M

institute: GenUs BioSystems, Inc.

hyb_protocol: 1 µg of purified cRNA was fragmented to uniform size and applied to Agilent Whole Human Genome microarrays (Agilent Technologies, Santa Clara, CA) in hybridization buffer. Arrays were hybridized at 65° C for 17 hrs. in a rotating incubator, and washed at 37° C for 1 min.

scan_protocol: Rinsed and dried arrays were scanned with an Agilent G2565 Microarray Scanner (Agilent Technologies, Santa Clara, CA) at 5 µm resolution.

data_processing: Agilent Feature Extraction software was used to process the scanned images from arrays (gridding and feature intensity extraction) and the data generated for each probe on the array was analyzed with GeneSpring GX software (Agilent Technologies, Santa Clara, CA).

organism: Rattus norvegicus

source_name: 4-NQO induced tongue lesion

label_protocol: First and second strand cDNA was prepared from the total RNA samples. Labeled cRNA target was prepared from the DNA template and verified on the Bioanalyzer.  cRNA was fragmented to uniform size and verified on the Bioanalyzer.

growth_protocol: Male F344 rats were received at six to seven weeks of age from virus-free barrier colonies that are maintained under contract to the National Cancer Institute, Frederick, MD. Rats were held in quarantine for a minimum of one week prior to study initiation; prior to randomization into a study, each rat underwent a hand-held physical examination to ensure its suitability for use as a test subject.  Animals were housed on hardwood bedding in polycarbonate shoebox cages (two to three per cage) in a windowless room that was illuminated for 12 hours each day and maintained at 22 ± 1°C and within the range of 30% to 70% relative humidity. Throughout all studies, rats were permitted free access to Purina 5001 Laboratory Diet (PMI Feeds, Brentwood, MO) and City of Chicago drinking water (provided in water bottles). All food cups and water bottles were replaced a minimum of twice weekly.

extract_protocol: Paired sets of normal and neoplastic oral tissues were harvested from rats at 23 to 26 weeks after their first exposure to 4-NQO.  At necropsy, gross lesions were collected from the tongue of 4-NQO-treated rats and bisected longitudinally. Half of each lesion was flash-frozen in liquid nitrogen for analysis of gene expression/promoter methylation. The other half of each lesion was fixed in formalin, processed using routine histologic methods, stained with H&E, and evaluated microscopically to confirm malignancy. Phenotypically normal tissue was collected from adjacent areas of the tongue of the same 4-NQO-treated rats, and was flash-frozen or fixed in a manner identical to that used for tumor tissues.  Total RNA was isolated from histologically confirmed squamous cell carcinomas and adjacent phenotypically normal tissues using Qiagen’s RNeasy Mini kit by following the manufacturer’s instructions.  Total RNA was used for microarray or RT-PCR analysis.

treatment_protocol: NQO was purchased from Sigma-Aldrich, St. Louis, MO, and was stored in the dark at −20°C until used. NQO was administered in the drinking water at 20 ppm for a period of 10 weeks. After dose preparation, all formulations of NQO were stored in the dark at 4°C until used. Bottles containing NQO-supplemented drinking water were wrapped with foil to preclude possible photodegradation of the carcinogen, and were changed at two- to three-day intervals throughout the study. Rats received their first exposure to NQO at seven to nine weeks of age.

value: 4-NQO induced tongue lesion

tag: strain

value: F344 Rat

value: Male

value: Squamous cell carcinoma

value: approximately 33 weeks

tag: treatment

value: 4-NQO at 20ppm in drinking water for 10 weeks.


title: TKCBV5-6s2


title: TKCBV5-6s1


title: primary colorectal carcinoma S60-Frozen-rep1

value: M


title: primary colorectal carcinoma S62-Frozen-rep1


title: TKCBV5-6s12


title: TIG118-4F1s10

description: human induced pluripotent stem cell line TIG118-4F1 subclone


title: primary colorectal carcinoma S58-Frozen-rep1

value: High


title: Untreated Animal #25, Tumor


title: TIG118-4F1s8

source_name: human induced pluripotent stem cell line TIG118-4F1 subclone


title: TIG118-4F1s11

value: human induced pluripotent stem cell line TIG118-4F1 subclone


title: TIG118-4F1s7


title: primary colorectal carcinoma S57-Frozen-rep1

value: right colon

value: WT


title: primary colorectal carcinoma S56-Frozen-rep1

value: primary colorectal carcinoma