title: Bhutan_normal_160

description: Gene expression gastric epithelium in Bhutan Hp-negative normal epithelium

value: gastric epithelium

value: F

tag: country

value: Bhutan

tag: gastritis grade

value: normal


title: control_29C

status: Public on Jun 01 2015

type: RNA

city: Amsterdam

first: Sander

middle: Roeland

last: van Hooff

address: Meibergdreef 9

department: Center for Experimental and Molecular Medicine (CEMM),

country: Netherlands

institute: AUMC

hyb_protocol: * 60 ul labeled sample is combined with 60 ul 2x-hybmix, containing 50% formamide, 10xSSC, 0.2% SDS, 200 ug/ml herring sperm DNA  * Hybridizations of spotted oligo-arrays (Codelink glass) are performed on a HS4800Pro Hybstation (Tecan)  * Priming: 5xSSC, 0.1%SDS  * Probe injection: pre-hyb, 5xSSC, 25% formamide, 0.1%SDS, 1%BSA, Volume 110ul  * Hybridization: 45 min at 42C.  * Wash 2x: milliQ  * Wash: 5xSSC, 0.1%SDS  * Probe injection: sample. Volume 110ul  * Hybridization: 16 uur bij 42C.  * Wash 2x: 1xSSC, 0.2%SDS at 23C  * Wash 2x: 0.1xSSC, 0.2%SDS at 23C  * Wash 2x: 0.1xSSC at 23C  * Drying: blow with nitrogen for 3min at 30C

scan_protocol: Scanner  of slides using the Agilent G2565B was carried out according to the manufacturer’s instructions. Features were extracted using Imagene software from Biodiscovery.

data_processing: Mean spot intensities were normalized using quantile normalization (Bolstad, 2003) and the two dye-swapped profiles per sample were merged by averaging the fold changes. Quality control checks using principal component analysis (PCA) revealed a correlation between gene expression variation and the time of biopsy relative to the LH surge as well as a batch effect. Both effects were modelled for each gene using linear models (limma package, Smyth, 2005) and the effect estimates used to correct the data. The time of biopsy taking varied from 5 to 8 days after the LH surge. We lacked the sample numbers (specifically in the “Cohort 2, Batch 2” group consisting of only six samples) to fit a single model including biopsy timing, batch and sample class. We therefore opted to estimate the biopsy timing effect using all control samples from the first batch of the second cohort (n=45). This selection avoids a confounding of the biopsy timing effect with a batch effect (by only including a single batch) or sample effect (by including only control samples). The effects estimates where used to correct the data using LH+7 as the reference. After the biopsy timing correction we turned our attention to the batch effects present. One batch consisted of the first cohort, whereas the second cohort separated into two batches which were expression profiled in separate experimental runs. The batch effects were estimated using only control samples (n=73). This selection avoids confounding the batch effect with the sample effect (by including only control samples). Again, we didn’t have enough samples to fit a single model including batch and sample class. After estimating the batch effect we corrected the data using the first batch of the second cohort as the reference batch.

molecule: total RNA

organism: Homo sapiens

label_protocol: All amplification and labeling procedures are performed in 96 wells plates (Abgene) on a customized Sciclone ALH 3000 Workstation (Caliper LifeSciences), supplemented with a PCR PTC-200 (Bio-Rad Laboratories), SpectraMax 190 spectrofotometer (Molecular Devices), and a magnetic bead-locator (Beckman).   mRNA amplification protocol description:  * all RNAs are diluted to 0.6 ug/ul and 5 ul is put in a 96-wells plate (Abgene). All subsequent steps are performed by the robot script.  * mix1 containing 100 ng T7 Mlu VN primer (custom mix) and EC-control RNA per 5 ul is added and mixed in each well.  * plate is incubated @ 70C for 10 mins, cooled to 48C.  * mix2 containing 4ul 5x 1st strand buffer, 2 ul 0.1M DTT (Invitrogen), 1ul RNAse Inhibitor (Boehringer), 1ul 20mM dNTPs (GE Healthcare), 1ul linear acrylamide, and 1ul SuperScriptIII (Invitrogen) per sample is prewarmed to 48C; 10 ul per sample is added and mixed in each well.  * plate is incubated @ 48C for 2 hours and cooled to room temperature.  * 106 ul water and subsequently mix3 containing 15ul second strand buffer, 3ul 20mM dNTPs (GE Healthcare), 1 ul T4 DNA ligase, 4 ul E.coli DNA polymerase I and 1 ul RNAseH (Promega) is added and mixed in each well.  * plate is incubated @ 16C for 2 hours, @65C for 10 mins. * ds cDNA product is purified and concentrated with RNAClean (Agencourt, GC biotech) according to manufacturers protocol, to an end volume of 25 ul .  * 8 ul cDNA is put in a 96 wells plate and mixed with 12 ul IVT mix containing 2 ul 10x rxn-buffer, 2 ul each ATP, CTP, GTP, 0.6 ul UTP, 2 ul T7 enzyme mix (MegaScript kit, Ambion, Applied Biosystems), and 2.1 ul 50 mM 5-(3-aminoallyl)-UTP (Ambion, Applied Biosystems).  * Plate is incubated @37C for 4 hours.  * cRNA product is purified with RNAClean (Agencourt, GC biotech) according to manufacturers protocol.  * Concentration is measured (SpectraMax 190) and adjusted to 600 ng/ul by the robot.  * Resulting cRNA plates are sampled for Bioanalyzer QC, snapfrozen and stored at -80C.   Labeling protocol description:  * NHS-ester Cy3 or Cy5 dye (Amersham PA 23001 and 25001): entire tube is resuspended in 100 ul DMSO (Merck 8.02912.10).  All subsequent steps are performed by the robot script :  * 8 ul of each cRNA (0.6 ug/ul) is put in a 96-wells plate (Abgene), the accompanying reference sample is put in the next column (final step combines cy3 and cy5 labeled material ).  * 3 ul 0.5 M NaBicarbonate buffer, pH 9 is added and mixed to all wells.  * 3 ul cy-dye solution is added and mixed to the appropriate wells, plate is incubated at 18C for 1 hour.  * 4.5 ul 5M hydroxylamine is added and mixed, incubated at 18o C for 15 minutes.  * Labeled cRNA product is purified with RNA Clean (Agencourt, GC biotech) according to manufacturers protocol.  * RNA concentration and labeling incorporation are measured (SpectraMax 190).  * 2.5 ug of each labeled sample and reference cRNA are pooled and subjected to fragmentation according to protocol (Ambion, Applied Biosystems), 15 min 70C.  * Samples are stored at -20C until hybridization.

extract_protocol: Trizol RNA isolation of tissue sections:  1. After sectioning, store sections in ice-cold RNAlater (~10 ml RNAlater per 20-mm section). Make sure that the sections do not thaw before they are in ice-cold RNAlater. 50 ml RNAlater. 2. Add X ml Trizol (10x volume of RNAlater) and mix by inverting the tube several times. 500 ml Trizol. 3. Incubate 5 min at room temperature. 4. Pre-incubate Proteinase K (10 mg/ml) at 37 C for at least 10 minutes. 5. Add 10 ml of the pre-heated Proteinase K solution to Trizol mixture. 10 ml Prot-K. 6. Incubate 30 min at 55 C.  7. Add X ml chloroform (20 ml per 100 ml Trizol), mix for 15 seconds by shaking vigorously. Incubate 2-3 min at room temperature. 100 ml chloroform. 8. Centrifuge 20 min at 14000 rpm without brake at 4 C. After centrifugation, transfer the water-phase to a new 1.5 ml micro centrifuge tube (~300 ml). 9. Continue with RNeasy columns (Qiagen) for clean-up of RNA. 10. Adjust each sample to a volume of 300 ml with sterile MilliQ water. Add 160 ml buffer RLT to the samples, and mix (= lysis buffer). 11. Add 240 ml ethanol (100% stored at -20 C) to the lysate, mix well by pipetting and immediately apply the sample to an RNeasy mini spin column sitting in a 2 ml collection tube (use a second P1000 pipette and work as quickly as possible). Next lysate, and so on. 12. Centrifuge at 8000 rpm for 15 seconds in an Eppendorf centrifuge. Discard flow-through and collection tube. 13. Transfer the RNeasy column into a new 2 ml collection tube. Add 500 ml buffer RPE, wait 1 minute, and centrifuge at 8000 rpm for 15 seconds. Discard flow-through and reuse the collection tube in step 5. 14. Pipette 500 ml buffer RPE onto the RNeasy column, wait 1 minute, and centrifuge at 8000 rpm for 15 seconds. Discard flow-through and reuse collection tube. 15. Centrifuge at 10,000 rpm for 2 minutes (to dry the RNeasy membrane). 16. Transfer the RNeasy column into a new 1.5 ml collection tube. Pipette 100 ml milliQ directly onto the RNeasy membrane and incubate for 4 minutes at room temperature. Centrifuge at 14,000 rpm for 1 minute to elute. 17. Pipette the eluate of step 7 again onto the RNeasy membrane and incubate for another 4 minutes at room temperature. Centrifuge at 14,000 rpm for 1 minute to elute.

treatment_protocol: [biopsy protocol] An endometrial biopsy was scheduled 6 or 7 days after the putative luteinizing hormone (LH) surge in a natural cycle in patients and controls, which is considered to be the representative day of the window of implantation. Urinary LH was monitored by a home LH ovulation predictor kit (Ovulady, Clindia Benelux, The Netherlands). Among patients, the biopsy was not scheduled in the first natural cycle occurring after an unsuccessful IVF or ICSI cycle. Biopsies were collected using an endometrial suction curette under sterile conditions. The sample was snap frozen in liquid nitrogen and stored at -80 Â°C until use.

tag: tissue

value: endometrium

tag: condition

value: control

tag: batch

value: cohort 2, batch 1

tag: time of biopsy

value: 8 days after the putative luteinizing hormone surge

tag: medical center

value: UMCU

tag: smoking (0=non-smoker, 1=smoker)

tag: age

tag: bmi

tag: previous implantation

tag: embryo implantations

tag: embryos replaced

source_name: Universal Human Reference RNA catalog #740000, Stratagene

tag: sample type

value: UHR


title: recurrent implantation failure after IVF_2P

source_name: recurrent implantation failure after IVF_endometrium

value: cohort 1

value: 7 days after the putative luteinizing hormone surge


title: Bhutan_normal_68

city: Houston

first: Hiroyuki

last: Nagashima

state: Texas

address: 2002 Holcombe Blvd. (3B-172)

department: Department of Medicine Gastroenterology and Hepatology

country: USA

institute: Baylor College of Medicine

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Human Gene Expression Microarray 8x60K v2; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities of two samples were log2-transformed and normalized by the quantile algorithm with the Bioconductor.

source_name: gastric epithelium in Bhutan Hp-negative normal epithelium

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

extract_protocol: Total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega)

tag: gender

value: M


city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

country: Italy

institute: IRCCS Istituto Nazionale dei Tumori

description: Gene expression data from Human chronic lymphocytic leukemia patient FD0404

hyb_protocol: The fragmented labeled single-stranded DNA target was hybridized for 16 hours and 30 minutes at 45°C on GeneChip® Gene 1.0 ST array according to the standard Affymetrix protocol.

scan_protocol: Washing and scanning were performed using GeneChip System of Affymetrix (GeneChip Hybridization Oven 640, GeneChip Fluidics Station 450 and GeneChip Scanner 7G).

data_processing: Log2-transformed expression values were extracted from CEL files and normalized using NetAffx Transcript Cluster Annotations, Release 31 and robust multi-array average (RMA) procedure in Expression Console software (Affymetrix Inc.). The expression values of transcript cluster ID specific for loci representing naturally occurring read-through transcriptions were summarized as median value for each sample.

label: biotin

label_protocol: 5.5 micrograms of single-stranded DNA target obtained from 100 ng of purified total RNA was fragmented and then labeled using the WT Terminal Labeling Kit according to the standard Affymetrix protocol (GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Manual).

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

treatment_protocol: Peripheral blood mononuclear cells from B-CLL patients were isolated by Ficoll-Hypaque (Seromed, Biochrom KG, Berlin, Germany) density-gradient centrifugation and the proportion of CD5/CD19/CD23 triple positive B cells in the suspension was determined by direct immunofluorescence performed using a FACS-sort flow cytometer (Becton Dickinson & Co, Sunnyvale, CA) with antibodies to: CD19 FITC/PE, CD23 PE and CD5 Cy-Chrome (Becton Dickinson). If B-CLL cells were less than 90%, T cells, NK cells and monocytes were removed by negative selection using CD3, CD56, CD16, and CD14 monoclonal antibody (mAb) treatment (Becton Dickinson) followed by magnetic beads (Goat Anti-Mouse IgG Dynabeads, Dynal Biotech ASA, Oslo, Norway).

tag: igvh mutational status (fais et al. j clin invest, 1998)

value: unmut


description: Gene expression data from Human chronic lymphocytic leukemia patient FI0152

value: mut


title: non-treated liver_rep_2

city: Kyoto

first: Tomoko

last: Fujita

address: Yoshida Konoe-Cho

department: Medicine

country: Japan

institute: Kyoto University

description: Gene expression of non-treated liver mouse #2

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 SurePrint G3 Mouse GE 8x60K Microarray for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (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) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Mus musculus

source_name: liver, unstimulated

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.

extract_protocol: Liver was homogenized using a tissue homogenizer. RNA was prepared using RNAeasy column purification (QIAGEN, Valencia, CA) following the manufacturer's recommendations. NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: C57BL/6 female mice were injected with 10 mg/kg concanavalin A. Fifteen minutes later, vehicle or 1 mg/kg BW245C was injected i.p. and liver was collected 3 hr or 24 hr later.

value: liver

tag: treatment

value: unstimulated

value: female

tag: strain


description: Gene expression data from Human chronic lymphocytic leukemia patient FM0309


title: recurrent implantation failure after IVF_29P


title: non-treated liver_rep_1

description: Gene expression of non-treated liver mouse #1


title: Bhutan_normal_116

value: gastric epithelium

tag: country

tag: gastritis grade


description: Gene expression data from Human chronic lymphocytic leukemia patient FB0332


title: non-treated liver_rep_3

description: Gene expression of non-treated liver mouse #3

tag: tissue


title: control_28C

tag: condition

tag: batch


description: Gene expression data from Human chronic lymphocytic leukemia patient FA0429


description: Gene expression data from Human chronic lymphocytic leukemia patient FC0075


description: Gene expression data from Human chronic lymphocytic leukemia patient FA0347


title: control_26C

tag: time of biopsy

tag: medical center


title: recurrent implantation failure after IVF_28P

value: 6 days after the putative luteinizing hormone surge

tag: smoking (0=non-smoker, 1=smoker)

tag: age


title: Bhutan_normal_97

value: F

value: Bhutan

value: normal


title: Bhutan_IM_55

description: Gene expression gastric epithelium in Bhutan Hp-positive IM gastritis epithelium

value: IM


title: recurrent implantation failure after IVF_26P

value: endometrium

tag: bmi

tag: previous implantation


description: Gene expression data from Human chronic lymphocytic leukemia patient FA0294


title: recurrent implantation failure after IVF_25P

value: cohort 2, batch 1

value: AMC

tag: embryo implantations

tag: embryos replaced


title: recurrent implantation failure after IVF_27P

value: 8 days after the putative luteinizing hormone surge

tag: sample type

value: UHR


title: control_25C

value: control

value: cohort 1

value: 7 days after the putative luteinizing hormone surge

value: UMCU


description: Gene expression data from Human chronic lymphocytic leukemia patient EB0042

tag: igvh mutational status (fais et al. j clin invest, 1998)

value: mut


title: recurrent implantation failure after IVF_24P


title: recurrent implantation failure after IVF_23P


description: Gene expression data from Human chronic lymphocytic leukemia patient ET0128

value: unmut


description: Gene expression data from Human chronic lymphocytic leukemia patient DT0300


title: control_24C


description: Gene expression data from Human chronic lymphocytic leukemia patient DN0063


description: Gene expression data from Human chronic lymphocytic leukemia patient EG0341


description: Gene expression data from Human chronic lymphocytic leukemia patient DG0186


description: Gene expression data from Human chronic lymphocytic leukemia patient DG0193


title: control_22C


description: Gene expression data from Human chronic lymphocytic leukemia patient DF0319


title: control_23C


title: recurrent implantation failure after IVF_22P


description: Gene expression data from Human chronic lymphocytic leukemia patient DE0279


title: recurrent implantation failure after IVF_21P


title: control_21C


description: Gene expression data from Human chronic lymphocytic leukemia patient DR0312


description: Gene expression data from Human chronic lymphocytic leukemia patient DE0085


title: recurrent implantation failure after IVF_20P


title: recurrent implantation failure after IVF_1P


title: control_1C


description: Gene expression data from Human chronic lymphocytic leukemia patient DD0280


title: recurrent implantation failure after IVF_19P


title: control_20C


description: Gene expression data from Human chronic lymphocytic leukemia patient DC0371


description: Gene expression data from Human chronic lymphocytic leukemia patient DA0094


description: Gene expression data from Human chronic lymphocytic leukemia patient CS0030


title: control_19C


description: Gene expression data from Human chronic lymphocytic leukemia patient CS0290


description: Gene expression data from Human chronic lymphocytic leukemia patient DA0029


title: recurrent implantation failure after IVF_18P


description: Gene expression data from Human chronic lymphocytic leukemia patient CR0203


title: recurrent implantation failure after IVF_17P


title: control_18C


description: Gene expression data from Human chronic lymphocytic leukemia patient CR0297


title: DCIS_sample55

type: genomic

city: Hanover

first: Kevin

middle: Crowley

last: Johnson

state: NH

address: 72 College Street

department: Epidemiology

institute: Geisel School of Medicine at Dartmouth College

hyb_protocol: bisulfite converted DNA was processed with the Illumina FFPE restoration kit, amplified, fragmented and hybridized to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: ChAMP, Morris et al Bioinformatics 2013

label: Cy5 and Cy3

molecule: genomic DNA

source_name: DCIS

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was isolated using the QIAamp DNA formalin-fixed paraffin embedded tissue kit

tag: gender

value: Female

value: DCIS

tag: future development of invasive breast cancer

value: IDC Diagnosis

tag: subject age


title: control_16C


title: Adjacent-Normal_sample52

source_name: Adjacent-Normal

value: Adjacent-Normal


title: control_17C


title: DCIS_sample54

value: No IDC Diagnosis


title: Adjacent-Normal_sample48


title: Adjacent-Normal_sample50


title: DCIS_sample53


title: DCIS_sample49


title: recurrent implantation failure after IVF_15P


title: DCIS_sample51


title: recurrent implantation failure after IVF_16P

value: 6 days after the putative luteinizing hormone surge


description: Gene expression data from Human chronic lymphocytic leukemia patient CM0289


title: DCIS_sample47


title: DCIS_sample41


description: Gene expression data from Human chronic lymphocytic leukemia patient CM0246


description: Gene expression data from Human chronic lymphocytic leukemia patient CR0159


description: Gene expression data from Human chronic lymphocytic leukemia patient CP0109


title: DCIS_sample42


title: DCIS_sample46


title: recurrent implantation failure after IVF_13P

value: endometrium


title: DCIS_sample45


title: Adjacent-Normal_sample40


title: recurrent implantation failure after IVF_14P


title: control_13C

value: cohort 2, batch 1


title: control_14C


description: Gene expression data from Human chronic lymphocytic leukemia patient CM0057


title: Adjacent-Normal_sample44


title: recurrent implantation failure after IVF_12P


description: Gene expression data from Human chronic lymphocytic leukemia patient CL0317


title: control_15C


description: Gene expression data from Human chronic lymphocytic leukemia patient CG0166


description: Gene expression data from Human chronic lymphocytic leukemia patient CG0204


title: DCIS_sample35


title: DCIS_sample36


description: Gene expression data from Human chronic lymphocytic leukemia patient CP0104


title: FM11

city: Kanagawa

first: Satoko

last: Takizawa

state: Kamakura

institute: Toray Industries, Inc.

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

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

data_processing:
The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals. Measurements of both duplicate spots with the signal intensities greater than 2 standard deviations (SD) of the background signal intensity were considered to be valid. A relative expression level of a given miRNA was calculated by comparing the signal intensities of the averaged valid spots with their mean value throughout the microarray experiments. Global normalization was applieds to all microarray data.
Global normalization was applied manually.

source_name: PBMC

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

growth_protocol: Human PBMCs were purified with Ficoll-Paque.

extract_protocol: RNA samples were extracted from cells using the mirVana miRNA isolation kit (LifeTechnologies, cat. AM1560)

treatment_protocol: not treated

value: Fibromyalgia

tag: cell type

value: PBMC


description: Gene expression data from Human chronic lymphocytic leukemia patient CE0399


title: FM10


title: FM9


title: FM8


description: Gene expression data from Human chronic lymphocytic leukemia patient CC0244


description: Gene expression data from Human chronic lymphocytic leukemia patient CI0005


title: Adjacent-Normal_sample38

tag: tissue


title: DCIS_sample37


description: Gene expression data from Human chronic lymphocytic leukemia patient FS0257


title: control_12C

tag: condition

value: UHR


title: recurrent implantation failure after IVF_10P

tag: batch


description: Gene expression data from Human chronic lymphocytic leukemia patient CA0345


title: recurrent implantation failure after IVF_11P

tag: time of biopsy


description: Gene expression data from Human chronic lymphocytic leukemia patient CC0311


description: Gene expression data from Human chronic lymphocytic leukemia patient CE0078


description: Gene expression data from Human chronic lymphocytic leukemia patient CD0310


title: Mouse mast cells exposed to MC38 colon adenocarcinoma-conditioned medium_IL3/KITL

city: Munich

first: Georgios

middle: T

last: Stathopoulos

state: Bayern

address: Max-Lebsche-Platz

department: Comprehensive Pneumology Center

country: Germany

institute: Helmholz Zentrum Munich

description: Mouse mast cells cultured with DMEM , 10% FBS, treated with il3 and kitl. Exposed to supernatants from MC38 cancer cell line

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: The data were processed and analyzed using GeneSpring 12.5 GX (Agilent) software.

source_name: IL-3/KITL-matured Mouse mast cells exposed to MC38 colon adenocarcinoma-conditioned medium

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

growth_protocol: To obtain cancer-conditioned media, cancer cells were cultured using Dulbecco's Modified Eagle's Medium (DMEM) from Sigma Lot D6429. To make the complete growth medium, we added fetal bovine serum to a final concentration of 10%. Cells incubated at 37°C with 5% CO2.

extract_protocol: Trizol followed by RNAeasy spin columns

treatment_protocol: Mouse mast cells were exposed to non-conditioned media (full DMEM as above) or conditioned cell-free supernatants from different cancer cell lines.

tag: maturation


title: Mouse mast cells exposed to LLC lung adenocarcinoma-conditioned medium_IL3/KITL

description: Mouse mast cells cultured with DMEM , 10% FBS, treated with il3 and kitl. Exposed to supernatants from LLC cancer cell line

source_name: IL-3/KITL-matured Mouse mast cells exposed to LLC lung adenocarcinoma-conditioned medium


title: control_10C

value: control

tag: medical center

tag: smoking (0=non-smoker, 1=smoker)


title: DCIS_sample39


title: control_11C

value: 5 days after the putative luteinizing hormone surge

tag: age

tag: bmi


title: FM7


title: DCIS_sample34


title: FM6


description: Gene expression data from Human chronic lymphocytic leukemia patient CA0101


title: FM5


description: Gene expression data from Human chronic lymphocytic leukemia patient CA0160


title: FM4


description: Gene expression data from Human chronic lymphocytic leukemia patient CA0058


title: Mouse mast cells exposed to MC38 colon adenocarcinoma-conditioned medium_IL3

description: Mouse mast cells cultured with DMEM , 10% FBS, treated with il3. Exposed to supernatants from MC38 cancer cell line

source_name: IL-3-matured Mouse mast cells exposed to MC38 colon adenocarcinoma-conditioned medium


title: FM3


description: Gene expression data from Human chronic lymphocytic leukemia patient BV0229


description: Gene expression data from Human chronic lymphocytic leukemia patient BV0176


description: Gene expression data from Human chronic lymphocytic leukemia patient BS0214


title: DCIS_sample43


title: MC38 wt

description: MC-38 wild type, mouse colon adenocarcinoma

source_name: MC38 wt

growth_protocol: Cancer cells were cultured using Dulbecco's Modified Eagle's Medium (DMEM) from Sigma Lot D6429. To make the complete growth medium, we added fetal bovine serum to a final concentration of 10%. Cells incubated at 37°C with 5% CO2.

tag: cell line

value: colon

tag: genotype

value: wildtype


title: PANO2 wt

description: PANO2 wild type, pancreatic carcinoma cells

source_name: PANO2 wt

value: pancreas


title: Adjacent-Normal_sample29


title: DCIS_sample28


title: C10

value: healthy participant


title: DCIS_sample31

value: Female


title: Adjacent-Normal_sample27


title: DCIS_sample32

value: DCIS


title: DCIS_sample26

value: IDC Diagnosis


title: B16F10 wt

description: B16F10 wild type, mouse melanoma cells

source_name: B16F10 wt

value: skin


title: Adjacent-Normal_sample33

value: Adjacent-Normal


title: C9


title: DCIS_sample24

value: No IDC Diagnosis


title: FM1


description: Gene expression data from Human chronic lymphocytic leukemia patient BG0236

value: unmut


title: Mouse mast cells exposed to LLC lung adenocarcinoma-conditioned medium_IL3

description: Mouse mast cells cultured with DMEM , 10% FBS, treated with il3. Exposed to supernatants from LLC cancer cell line

source_name: IL-3-matured Mouse mast cells exposed to LLC lung adenocarcinoma-conditioned medium


title: C8


title: DCIS_sample18


title: DCIS_sample21


title: C7


title: DCIS_sample22


description: Gene expression data from Human chronic lymphocytic leukemia patient BL0162

value: mut


title: FM2

value: Fibromyalgia


title: Adjacent-Normal_sample20


title: DCIS_sample25


title: C6

value: PBMC


title: DCIS_sample30


title: Adjacent-Normal_sample19


description: Gene expression data from Human chronic lymphocytic leukemia patient BF0316


description: Gene expression data from Human chronic lymphocytic leukemia patient BG0163


title: AE17 wt

description: AE17 wild type, mouse malignant mesothelioma

source_name: AE17 wt

value: lung


title: Ethanol inducible amiAG 4

city: Dublin

first: Pat

last: Ryan

address: College Green

country: Ireland

institute: TCD

description: Biological replicate 4

hyb_protocol: Fragmentation buffer and Hybridization Buffer HI-RPM (Agilent Gene Expression Hybridization Kit) were added and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers and hybridized for 16 hrs at 65°C. After hybridization, slides were washed sequentially according to the manufacturer's instruction.

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (v 10.5.1).

data_processing: Agilent Feature Extraction Software (v 10.5.1) was used for background subtraction and LOWESS normalization

organism: Arabidopsis thaliana

source_name: whole infloresence

label_protocol: 500ng of total RNA were primed with 0.6µl of T7 DNA primer at 65°C for 10 min, then reverse transcribed at 40°C  for 2 hrs in the presence of 300 U MMLV Reverse Transcriptase and 10mM dNTP mix, with Cy3-label and Cy5- label.

growth_protocol: Plants were grown on a soil:vermiculite:perlite (3:1:1) mixture at 20 degrees (16 degrees for plants used for temperature-sensitive perturbation experiments) under constant illumination with cool white fluorescent light

extract_protocol: Total RNA was isolated from tissue samples using the Plant Total RNA kit (Sigma-Aldrich), according to the manufacturer's instructions

treatment_protocol: For all experiments,  ~4 week-old plants were used. For experiments using the FIS (35S:AP1-GR ap1-1 cal-1 plants), flower development was induced using a solution containing 10 μM dexamethasone (Sigma-Aldrich), 0.01% (v/v) ethanol and 0.015% (v/v) Silwet L-77 (De Sangosse) – as described in  Wellmer F, et al. (2006) Genome-Wide Analysis of Gene Expression during Early Arabidopsis Flower Development. PLoS Genetics 2(7):e117.

tag: treatment

value: Mock

value: FIS (ap1 cal1 AP1-GR) Alc:amiAG

value: Ethanol


title: DCIS_sample17


title: C5


title: DCIS_sample16


title: DCIS_sample15


title: C4


description: Gene expression data from Human chronic lymphocytic leukemia patient BF0217

tag: igvh mutational status (fais et al. j clin invest, 1998)


title: C1


title: C2


title: Adjacent-Normal_sample23

tag: gender


description: Gene expression data from Human chronic lymphocytic leukemia patient BC0047


title: C3


description: Gene expression data from Human chronic lymphocytic leukemia patient BB0245


title: Ethanol inducible amiAG 2

description: Biological replicate 2


description: Gene expression data from Human chronic lymphocytic leukemia patient AS0407


description: Gene expression data from Human chronic lymphocytic leukemia patient BP0326


description: Gene expression data from Human chronic lymphocytic leukemia patient BE0192


title: Ethanol inducible amiAP3 9

description: Biological replicate 9

value: FIS (ap1 cal1 AP1-GR) Alc:amiAP3


title: Ethanol inducible amiAP3 8

description: Biological replicate 8


title: DCIS_sample14

tag: future development of invasive breast cancer


title: Ethanol inducible amiAG 1

description: Biological replicate 1


description: Gene expression data from Human chronic lymphocytic leukemia patient AS0012


title: DCIS_sample12

tag: subject age


description: Gene expression data from Human chronic lymphocytic leukemia patient AR0242


description: Gene expression data from Human chronic lymphocytic leukemia patient AM0270


title: Adjacent-Normal_sample13


title: Ethanol inducible amiAP3 6

description: Biological replicate 6


description: Gene expression data from Human chronic lymphocytic leukemia patient AR0131


title: Ethanol inducible amiAP3 10

description: Biological replicate 10


title: Ethanol inducible amiAG 3

description: Biological replicate 3


title: DCIS_sample10


title: DCIS_sample9


description: Gene expression data from Human chronic lymphocytic leukemia patient BR0218


title: Adjacent-Normal_sample11


title: DCIS_sample8


description: Gene expression data from Human chronic lymphocytic leukemia patient AM0106


title: DCIS_sample7


title: Ethanol inducible amiAP3 7

description: Biological replicate 7


title: Ethanol inducible amiAP3 4

description: Biological replicate 4


description: Gene expression data from Human chronic lymphocytic leukemia patient AM0220


title: Dexamethasone inducible amiAP3 7

description: Biological replicate 7

value: Dexamethazone

value: FIS (ap1 cal1 AP1-GR) LhG4-GR:amiAP3


title: Ethanol inducible amiAP3 2

description: Biological replicate 2


description: Gene expression data from Human chronic lymphocytic leukemia patient AM0067


description: Gene expression data from Human chronic lymphocytic leukemia patient AG0268


title: HS306 line after 15 enzymatic passages

city: Montpellier

first: Qiang

last: BAI

address: 371 Avenue du Doyen Gaston Giraud

country: France

institute: PhyMedExp INSERM U1046

description:
HS306_p25+EP15
Gene expression data from human embryonic cell line HS306 after 15 enzymatic passages + initial passages 25 mechanic passages

hyb_protocol: Labeled cRNA was fragmented in fragmentation buffer (5x buffer:200 mM Tris-acetate (pH 8.1)/500nM KOAc/150 mM MgOAc) before hybridization on the array. Fragmented cRNA was hybridized to the microarrays in 90ul hybridization solution.

scan_protocol: Human Genome U219 array plate was processed in Gene Atlas according to manufacturer's instructions.

data_processing: The data were analyzed with RMA method in Expression Console (Affymetrix).

source_name: hESC in enzymatic passaging condition

label_protocol: cRNA synthesis was made using 3`IVT Express kit (Affymetrix) following manufacterer's instructions and starting with 200ng of total RNA.

growth_protocol: These lines were maintained in culture media consisting of 80% KO-DMEM, 20% KOSR, 2 mM L-glutamine, 1% non-essential amino acids, 0.5 mM β-mercaptoethanol (all from Gibco Invitrogen, Cergy-Pontoise, France) and complemented with 10 ng/mL bFGF (Abcys, Paris, France). These cells were maintained in 35-mm dishes with pre-coated irradiated (40 Gy) human foreskin fibroblast (hFF) feeders and were either enzymatically or mechanically passaged every week.

extract_protocol: In mechanically passaged culture, the hESC colonies were exscinded carefully using a scalpel. In enzymatic-passaged culture, the singles cells were released as described above. As SSEA4 is one of most obstinate pluripotence markers (Ramirez et al., 2011), hESC cells were purified and enriched using the magnetic beads Dynabeads® SSEA-4 (Invitrogen) and the manufacture’s instructions were rigorously followed. The quality control of the purification showed high efficiency and no over-selection of SSEA4+ sub-population.   Total RNA was purified from cell culture using the RNeasy Mini Kit (Qiagen, Courtaboeuf, France) following manufacture’s instructions. We added an RNAse-Free DNase step in RNA extraction and an RNsae A treatment in DNA extraction to eliminate residual DNA or RNA.

treatment_protocol: Mechanical passaging was carried out under an inverted microscope under the hood using scalpels (Assou et al., 2009; Bai et al., 2011). For enzymatic single cell passaging, the cells were pre-treated with Y-27632 for 1h and dissociated with TrypLE™ Select (Invitrogen) for 10 mn at 37C. The reaction was stopped by hESC culture media and single hESC were released by pipetting and passed through a 20 µm strainer to eliminate hFF feeders, then counted and seeded on newly prepared feeder in density of 20 000 cells/cm2 at beginning and progressively to 3 000 cells/cm2 when cells were adaptated to enzymatic passaging. Both mechanic and enzymatic passaging were performed weekly. Experiments on HD291, HD129 and HS306 lines were initiated at p13, p16 and p25 respectively (termed initiating passages) and maintained independently using mechanic passaging (+MP) or enzyamatic passaging (+EP). All cell cultures were regularly checked for mycoplasma contamination and remained negative throughout the experiments.

tag: cell line source gender

value: female

tag: cell type

value: Human embryonic stem cells (hESCs)


title: Ethanol inducible amiAP3 1

description: Biological replicate 1


description: Gene expression data from Human chronic lymphocytic leukemia patient AG0318


title: HS306 line after 16 mechanic passages

description:
HS306_p25+MP16
Gene expression data from human embryonic cell line HS306 after 16 mechanic passages + initial passages 25 mechanic passages

source_name: hESC in mechanic passaging condition


title: Dexamethasone inducible amiAP3 4

description: Biological replicate 4


title: Ethanol inducible amiAP3 5

description: Biological replicate 5


title: HD291 line after 15 mechanic passages

description:
HD291_p13+MP15
Gene expression data from human embryonic cell line HD291 after 15 mechanic passages + initial passages 13 mechanic passages

value: male


description: Gene expression data from Human chronic lymphocytic leukemia patient AG0136


title: LLC wt

description: LLC wild type, Lewis lung carcinoma wild type, mouse lung cancer

source_name: LLC wt

value: LLC

tag: tissue

value: wildtype


description: Gene expression data from Human chronic lymphocytic leukemia patient AM0034


title: Dexamethasone inducible amiAP3 6

description: Biological replicate 6


description: Gene expression data from Human chronic lymphocytic leukemia patient AG0403


title: HD291 line after 30 mechanic passages

description:
HD291_p13+M30
Gene expression data from human embryonic cell line HD291 after 30 mechanic passages + initial passages 13 mechanic passages


title: Adjacent-Normal_sample6

value: Female

value: Adjacent-Normal


title: Ethanol inducible amiAP3 3

description: Biological replicate 3


description: Gene expression data from Human chronic lymphocytic leukemia patient AC0120

value: mut


title: Dexamethasone inducible amiAP3 5

description: Biological replicate 5


title: HD291 line after 31 enzymatic passages

description:
HD291_p13+EP31
Gene expression data from human embryonic cell line HD291 after 31 enzymatic passages + initial passages 13 mechanic passages


title: Dexamethasone inducible amiAP3 8

description: Biological replicate 8


description: Gene expression data from Human chronic lymphocytic leukemia patient AA0284


title: DCIS_sample4

value: DCIS

value: IDC Diagnosis


title: DCIS_sample5

value: No IDC Diagnosis


description: Gene expression data from Human chronic lymphocytic leukemia patient AB0350


title: DCIS_sample2


title: NX rats-alfacalcidol_1

status: Public on May 29 2015

city: Chicago

first: J. Ruth

last: Wu-Wong

state: IL

address: 2201 W. Campbell Park Dr., Suite 13

institute: Vidasym

description:
SAMPLE 10
Gene expression

hyb_protocol: 600ng of Cy3-labelled cRNA (specific activity > 6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human Gene Expression 8x60k Microarrays (V1) 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 using one color scan setting  (Scan Area 61 x 21.6 mm, Scan resolution 3 um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing:
Raw data were loaded into Partek genomics Suite 6.0. The raw data can be found on the series record in the file "Raw_Feature_Extraction_data.txt". This file contains the feature number, probe sequences and probe annotation as well as the gProcessed signal values.
Thresholds for selecting significant genes were set at ≥ 1.5-fold  or ≤  -1.5-fold and p ≤ 0.01. Genes that met both criteria simultaneously were considered as exhibiting significant changes.

organism: Rattus norvegicus

source_name: Aorta from NX-alfacalcidol

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200ng RNA using the Agilent Low-Input Quick Amp Labeling 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 NanoDrop8000 Spectrophotometer.

extract_protocol: RNA was prepared using a TriZol-based RNA Purification kit (Invitrogen) following the manufacturer's recommendations.  The RNAs were intact as judged by Agilent 2100 DNA Analyzer.

treatment_protocol: Five groups in this study: sham, NX-vehicle, NX-paricalcitol at 0.08 μg/kg, NX-alfacalcidol at 0.04 μg/kg, and NX-VS-105 at 0.01 μg/kg. To obtain enough RNA, two aortic RNA samples in the same treatment group  were randomly combined and three pooled samples per treatment group were randomly selected for the microarray analysis. Thus, representative samples at n=3 were achieved for each of the 5 treatment groups.

value: Aorta

tag: strain

value: Sprague Dawley


title: NX rats-paricalcitol_3

description:
SAMPLE 9
Gene expression

source_name: Aorta from NX-paricalcitol


title: NX rats-paricalcitol_1

description:
SAMPLE 7
Gene expression


title: NX rats-alfacalcidol_2

description:
SAMPLE 11
Gene expression


title: NX rats-alfacalcidol_3

description:
SAMPLE 12
Gene expression


title: RNAseq DE Sample 3: ERCC no2

status: Public on Mar 24 2015

type: SRA

city: Paris

first: Giovanni

last: Bussotti

address: 25-28 Rue du Dr Roux

institute: Institute Pasteur

description: PBMC RNAseq

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Before mapping FastQC was utilized to confirm sequence quality. Reads were trimmed with the Trim Galore Cutadapt11 wrapper using the –paired option.
For K562 and PBMC ERCC capture, sequenced reads (.fastq files) were aligned to the human genome using Tophat2 12 with the firststrand library type option selected. A human Bowtie213 index containing the ERCC controls was utilized for Tophat2 mapping, along with a transcriptome index.
For lncRNA capture from tissues and cell lines, sequenced reads (.fastq files) were aligned to the human genome using STAR 14. A reference annotation from GENCODE V19 was supplied during alignment. A splice junction library file was then derived from alignments and used for a second-round alignment solely using TopHat2 12.
To reduce memory requirements and improve runtimes the lncRNA cell line capture samples were preprocessed with trinity’s read normalization 17 release 2013-02-25 with parameter --max_cov 30. Reads from separated sequencing runs and lanes were mapped to the human genome (GRCh37, ENSEMBL 74) considering GENCODE version 19 reference annotations using STAR 14 version 2.3.1z with parameters --outFilterIntronMotifs RemoveNoncanonical --outFilterType BySJout. The resulting sam files were processed to remove the soft-clipping. Transcriptome assemblies were generated using cufflinks version 2.1.1 masking rRNA genes and providing the parameters -u --library-type fr-firststrand -b. The comprehensive transcriptome assembly (merged_transcript_assembly.gtf) was generated merging the individual assemblies with cuffmerge version 2.1.1, and selecting with bedtools intersect v2.19.1 the transcript overlapping the capture probes. The gene expression was estimated by merging for each tissue the individual mapping files with samtool version 0.1.19-44428cd. Then the gene counts for each tissue (norm.counts.tsv) were estimated by HTSeq (version 0.6.1) and normalized by DESeq2 (version 1.2.10)
Genome_build: hg19
Supplementary_files_format_and_content: Excel file with spike-in ERCC counts

growth_protocol: Human K562, MCF-7 and SK-N-SH cells were purchased from Cellbank. All cell lines were cultured at 37°C, 5% C02 with ten percent fetal bovine serum and penicillin/streptomycin. K562 and HeLa cells were cultured in RPMI and DMEM respectively, MCF-7 and SK-N-SH cells were cultured in MEM. Briefly, RNA was extracted by TRIzol, DNase treated with Turbo™ DNase (Life Technologies), confirmed DNA-free4 and its integrity confirm by Agilent 2100 Bioanalyzer (Agilent Technologies). 5 μg quantities of RNA were ribodepleted with Ribo-Zero™ (Epicentre). The Ambion® FirstChoice® Human Total RNA Survey Panel (Life technologies) was utilized to examine 20 human tissues. 5 μg quantities of RNA were ribodepleted with Ribo-Zero™ (Epicentre) and successful rRNA removal validated with Agilent 2100 Bioanalyzer (Agilent Technologies). Collection and RNA extraction from peripheral blood mononuclear cells (PBMCs) Whole blood was collected from individuals (Princess Alexandra Hospital REC approval 2005/221). PMBCs were purified by a ficoll gradient and RNA extracted by TRIzol. Purified RNA was prepared for Capture as per cell line RNA.

extract_protocol: Capture sequencing was performed by combining and modifying the NimbleGen SeqCap EZ Library SR User’s Guide V3.0 and the NimbleGen Arrays User’s Guide: Sequence Capture Array Delivery v3.2. RNA sequencing libraries of ribodepleted total RNA from three K562 biological replicates were created using the TruSeq® Stranded mRNA Sample Preparation Kit (Illumina). Different index adaptors (4,6,12) were added to each K562 biological replicate. Library input consisted of ribodepleted RNA from 5 μg original total RNA after quality checking. ERCC RNA Spike-In Control mix 1 (Invitrogen) was added to ribodepleted RNA to give a final ERCC concentration of 1% (replicate 1 and 2) and 1.08% (replicate 3). Library preparation was begun at the fragmentation step by the addition of 9 μl EPH buffer and the standard protocol followed until “Enrich DNA Fragments”. The 20 μl obtained at the end of the “Ligate Adaptors” step was increased to 21 μl with resuspension buffer and mixed well. One microliter of this solution was added to 19 μl resuspension buffer in a new 0.3ml PCR plate and mixed. This new plate was utilised for the “Enrich DNA Fragments” step to create amplified test libraries to guide PreCapture LMPCR with the remaining 20 μl. Precapture LMPCR and QIAquick PCR Purification Kit (Qiagen) were performed as described by the NimbleGen SeqCap EZ Library SR User’s Guide V3.0. To test LMPCR yields K562 biological replicate 3 libraries were amplified for 8, 9 or 10 cycles, quantified on the bioanalyzer and then pooled. K562 biological replicate 1 and 2 libraries were thus amplified for 9 cycles and the yield quantified by bioanalyzer. Capture hybridization was modified from the NimbleGen Arrays User’s Guide: Sequence Capture Array Delivery V3.2. The NimbleGen Hybridization System was set to 42°C and allowed 3 h to equilibrate. Equal nanograms of library from each K562 biological replicate were pooled, some of pooled library was allocated for pre-capture sequencing and 1ug of the pooled library utilized for capture. The library for capture was mixed with 300 µg human Cot-1 DNA (Invitrogen) and 3.34 µl 100 μm TS-INV-HE (hybridisation enhancing) Index Oligos (IDT) to each index adaptor plus 1 µl 1000 μm TS-HE Universal Oligo 1 (IDT) in a 1.5 ml tube. Lid of tube was pierced with an 18 gauge needle and the sample dried at 60 °C in a vacuum concentrator. Once dry the tube was given a new lid to prevent contamination through the needle hole. Library/Cot/Oligo mix was resuspended in 11.2 µl of nuclease and nucleic acid free water, vortexed for 10 s and centrifuged at max speed for 10 s. Sample was solubilised at 70 °C for 10 m before repeating vortexing and centrifugation. Nimblegen 2 x SC Hybridization Buffer (18.5 µl) and SC Hybridization Component A (7.3 µl) were added and vortexing and centrifugation repeated. Sample was denatured at 95°C for 10 m. During this time the “Prepare Mixers” procedure from the NimbleGen Arrays User’s Guide was performed with the omission of the compressed gas step. After denaturation samples was vortexed for 10 s, centrifuged at max speed for 10 s and incubated at 42°C until ready to load onto the NimbleGen Hybridization system. The ‘Load and Hybridize Samples’ procedure from the NimbleGen Arrays User’s Guide was performed to begin array hybridization. Hybridization was conducted for ~3 days. The NimbleGen Arrays User’s Guide protocol was followed to prepare the elution chamber, disassemble, wash and elute the captured DNA from the microarray, with the following modifications. Gasket and elution chamber was setup in a DNA-free laminar flowhood. All washes were conducted with 50 ml buffer in 50 ml falcon tubes. Minelute purification (Qiagen) was conducted using a microfuge. Captured DNA was recovered with two 30 µl elutions from a Minelute column and the final volume adjusted to 60 µl. Post-capture LMPCR and cleanup was performed similar to the NimbleGen SeqCap EZ Library SR User’s Guide V3.0, with the following modifications. LMPCR was run using 5x Phusion buffer for 17 cycles. Each PCR contained 70 µl of master mix and 30 µl of captured DNA. Quantity and quality of amplified captured DNA was determined by bioanalyzer. Enrichment of captured transcripts was measured by qPCR using SYBR Green PCR Master Mix and real time cyclers (Applied Biosystems). Enrichment was determined by the ratio of transcript abundance between the pre and post capture samples using equal nanograms of each. Enrichment was determined for three Nimblegen capture controls and 3 sequences captured specifically by the branchpoint array. Two transcripts not targeted by the capture array were also tested to examine the specificity of capture. Concentrations and volumes were as per the NimbleGen SeqCap EZ Library SR User’s Guide V3.0. Precapture and post capture samples (3 K562 biological replicates) were each sequenced on a single lane of an Illumina® HiSeq.

value: PBMC


title: NX rats-VS-105_3

description:
SAMPLE 15
Gene expression

source_name: Aorta from NX-VS-105


title: HD291 line after 15 enzymatic passages

description:
HD291_p13+EP15
Gene expression data from human embryonic cell line HD291 after 15 enzymatic passages + initial passages 13 mechanic passages


title: NX rats-paricalcitol_2

description:
SAMPLE 8
Gene expression


title: NX rats-vehicle_2

description:
SAMPLE 5
Gene expression

source_name: Aorta from NX-vehicle


title: NX rats-VS-105_1

description:
SAMPLE 13
Gene expression


title: Dexamethasone inducible amiAP3 3

description: Biological replicate 3

value: Mock


title: Sham (normal rats)_2

description:
SAMPLE 2
Gene expression

source_name: Aorta from Sham


title: DCIS_sample1

source_name: DCIS


title: Dexamethasone inducible amiAP3 1

description: Biological replicate 1

value: Dexamethazone


title: NX rats-VS-105_2

description:
SAMPLE 14
Gene expression


title: HD129 line after 10 mechanic passages

description:
HD129_P16+MP10
Gene expression data from human embryonic cell line HD129 after 10 mechanic passages + initial passages 16 mechanic passages


title: Sham (normal rats)_1

description:
SAMPLE 1
Gene expression


title: Dexamethasone inducible amiAP3 2

description: Biological replicate 2

value: FIS (ap1 cal1 AP1-GR) LhG4-GR:amiAP3


title: DCIS_sample3


title: Sham (normal rats)_3

description:
SAMPLE 3
Gene expression


title: M4_adh_1

status: Public on Mar 17 2015

city: Seattle

first: Anne

last: Grosse-Wilde

state: WA

address: 401 Terry Ave N

institute: Institute for Systems Biology

hyb_protocol: 1.65 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 55ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 55ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-014850 Whole Human Genome Microarray 4x44K (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by compressed air.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using the AgilentHD-GX-1-color scan setting for 4x44k arrays.

data_processing:
The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 014850_D_F_20100115).
Normalized signal intensity: The normalization of the gene expression arrays was generated using the program 'GeneData', and was first a Central Tendency normalization, followed by relative normalization towards the average expression of adherent E and M clones.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50 to 100 ng total RNA using Agilent’s Low Input Quick Amp One-Color Labeling Kit according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: _adh cells were grown in normal tissue culture plates in a mixture of 1:1 DMEM:MEGM medium, and lysed directly in the dish by adding Trizol; _sus cells were grown in ultra-low adhesion plates for 21 days in DMEM:MEGM with 1% methylcellulose and B27, and lyzed by gentle dissociation with trypsin, followed by Trizol lysis.

extract_protocol: RNA was extracted using Trizol (Life Technologies) using the manufacturer's instructions. Ethanol-precipitated RNA was additionally purified using the RNeasy micro kit (Qiagen).

treatment_protocol: Cells were either grown in adhesion (_adh) or grown in suspension (_sus) as mammospheres.

tag: source cell line

value: HMLER

tag: condition

value: adhesion culture

tag: clonality

value: single cell-derived clone


title: M4_sus_2

value: mammosphere suspension culture


title: HD129 line after 11 enzymatic passages

description:
HD129_P16+EP11
Gene expression data from human embryonic cell line HD129 after 11 enzymatic passages + initial passages 16 mechanic passages

value: male

value: Human embryonic stem cells (hESCs)


title: NX rats-vehicle_3

description:
SAMPLE 6
Gene expression


title: M3_adh_1


title: M1_adh_2


title: M4_sus_1


title: HP_adh_3

source_name: HP

value: parental cell line


title: M3_adh_3


title: HP_sus_1


title: HP_adh_2


title: M4_adh_2


title: E4_adh_2


title: E5_adh_2


title: E4_adh_1


title: M1_adh_1


title: E3_adh_1


title: M3_adh_2


title: HP_adh_4


title: E3_adh_2


title: HP_adh_1


title: HP_sus_2


title: E3_adh_3


title: E5_adh_1


title: Pth-3

status: Public on Mar 03 2015

city: San Antonio

first: stephen

middle: e

last: harris

state: TX

address: 7703 Floyd Curl Drive

department: Periodontics

institute: U. of Texas Health Sci Center at San Antonio

description: pth replicate 3

hyb_protocol: Standard illumina hybridization protocol

scan_protocol: Standard illumina scanning protocol

data_processing: The data were analyzed using Genome Studio-GeneExpression module with and without quantile normalization with background model on for the normalized data.

source_name: mouse cortical bone, cultured with PTH at 250nM for 24hr

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

growth_protocol: The bones from 3 month old mice, after removing the muscle while in aMEM plus penicillin-streptomycin-gentimycin 10ug/ml media, the epiphysis are removed just below the growth plate, the marrow flushed out, and then treated with 0.2% Type I collagenase (Sigma C) 130 107K1218 and 0.05% trypsin (Sigma 026J7770) in aMEM plus antibiotics, for 30min with rotation at 150 rpm 37 degrees.  The marrow region from each bone, tibia and femurs, is again flushed with large volume of media, until completely white in appearance.  The bone tubes are then treated  20min each, 3 time with the collagenase-trypsin mixture as above. Usually, about 5ml per 10 bones tubes is used.  By histology, these bone tube  with osteocyte in their natural environment, are free of osteoblasts and cells on  the periosteal and endosteal surface and contain no growth plate material. The osteocyte bone tubes are put in culture with aMEM plus antibiotics plus 10% fetal calf serum (FCS) overnight with rotation at 50 rpms, The next day, the bone osteocyte tubes are transferred to a new plate with fresh media. The ex vivo osteocyte bone tubes can be treated with any factor or concentration, or osteocyte bone tubes can be made from various mutant mice. In these experiments, the bone osteocyte tubes were treated with Pth 1-34 for 24hrs.

extract_protocol: Frozen tibia and femur bone tubes (osteocytes in the bone matrix) from 4-5 mice per experiment, were place in a bone 'gun in liq N2 and pluverized with 3-5 strokes with a hammer.  To the frozen bone powder, fbp, about 10 bone per preparation, 5ml of Trizol is added and allowed to come to room temperature (about 1 hr). The mixture is place in a glass-teflon homogenizer and given 10 strokes.  The RNA is then extracted following the standard proceducre.

treatment_protocol: Cultures are then treated with Pth 1-34 at 250nM  (Pth) or not treated (Ctr) for 24hrs and bone tubes frozen-80 degrees until extracted for RNA

value: 3 months

value: femur and tibia osteocyte in cortical bone


title: Pth-1

description: pth replicate 1


title: BA Luminal A, TUM083

status: Public on Jan 23 2015

city: PARIS

first: Thierry

last: Dubois

address: 26 rue d’Ulm

department: Recherche Center

institute: Institut Curie

description: Breast tumor sample from IHC defined Luminal A subgroup

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Data were analyzed using standard AffyCDF or Brainarray HGU133Plus2_Hs_ENTREZG version 13 custom chipset definition file. Data were normalized using GC-RMA. Batch and hybridization effects were corrected using a linear model in which they were treated as fixed effects. Samples with technical replicates were subsequently averaged.

label_protocol: Following RNA quality and quantity control, 2 µg of total RNA were amplified and labeled according to the Affymetrix one cycle synthesis target preparation protocol to hybridize Affymetrix U133 plus 2.0 chips, as described by the company.

growth_protocol: Tumor samples were obtained from patients treated at the hospital of Institut Curie (Biological Resource Center, Paris, France). Healthy samples were obtained from mammary plastic surgery. Cell lines were grown from the American Type Culture Collection (ATCC),

extract_protocol: Total RNA was extracted and purified from frozen tumor samples using the RNeasy Mini Kit (Qiagen) followed by the RNA clean up kit (Macherey Nagel), according to manufacturers’ instructions.

value: Luminal A

tag: hybridation batch


title: BA Luminal A, TUM078

source_name: Breast tumor sample from IHC defined Luminal A subgroup


title: BA Luminal A, TUM084


title: Ctr-3

description: control replicate 3

source_name: mouse cortical bone, untreated

tag: age


title: NX rats-vehicle_1

description:
SAMPLE 4
Gene expression


title: BA Luminal A, TUM079


title: Pth-2

description: pth replicate 2


title: BA Luminal A, TUM075


title: BA Luminal A, TUM077


title: Ctr-2

description: control replicate 2


title: Ctr-1

description: control replicate 1


title: BA Luminal A, TUM080


title: BA Luminal A, TUM076


title: BA Luminal A, TUM081


title: BA Her2, TUM055

description: Breast tumor sample from IHC defined Er- Her2+ subgroup


title: BA TNBC, TUM048_repA

description: Breast tumor sample from IHC defined Triple Negative subgroup

value: TNBC


title: BA TNBC, TUM064_repA

source_name: Breast tumor sample from IHC defined Triple Negative subgroup


title: BA TNBC, TUM051_repA


title: BA Her2, TUM057

source_name: Breast tumor sample from IHC defined Er- Her2+ subgroup


title: BA TNBC, TUM056


title: BA TNBC, TUM051_repB


title: BA TNBC, TUM045_repB


title: BA Luminal A, TUM072


title: BA Luminal A, TUM074


title: BA TNBC, TUM045_repA


title: RNAseq DE Sample 2: ERCC no2

description: PBMC RNAseq

source_name: PBMC


title: BA TNBC, TUM067_repA


title: BA TNBC, TUM043_repA


title: BA Her2, TUM035_repB


title: BA TNBC, TUM032_repB


title: BA Her2, TUM035_repA


title: BA TNBC, TUM032_repA


title: BA TNBC, TUM017_repA


title: BA TNBC, TUM028_repA


title: BA TNBC, TUM030


title: BA TNBC, TUM018_repA


title: BA TNBC, TUM024


title: BA TNBC, TUM028_repB


title: BA Her2, TUM015_repA


title: BA Her2, TUM009


title: BA TNBC, TUM013_repA


title: BA TNBC, TUM006_repA


title: BA TNBC, TUM013_repB


title: BA TNBC, TUM006_repB


title: BA TNBC, TUM001_repA


title: BA Luminal B, TUM130

description: Breast tumor sample from IHC defined Luminal B subgroup

value: Luminal B


title: BA Her2, TUM015_repB


title: BA Her2, TUM020_repA


title: BA Her2, TUM026_repA


title: BA TNBC, TUM005


title: BA Luminal B, TUM124

source_name: Breast tumor sample from IHC defined Luminal B subgroup


title: BA Luminal B, TUM128


title: BA Luminal B, TUM129


title: BA Her2, TUM002_repA


title: BA TNBC, TUM010_repA


title: BA Luminal B, TUM121


title: BA Luminal B, TUM123


title: BA Luminal B, TUM118


title: BA Luminal B, TUM116


title: BA Luminal B, TUM120


title: BA Luminal B, TUM127


title: BA Her2, TUM016_repA


title: BA Luminal B, TUM113


title: BA Luminal B, TUM114


title: BA Luminal B, TUM119


title: BA Luminal B, TUM106


title: BA Luminal B, TUM110


title: BA Her2, TUM059


title: BA Luminal B, TUM101


title: BA Luminal B, TUM104


title: BA Luminal B, TUM105


title: BA Luminal A, TUM100


title: BA Luminal B, TUM103


title: BA Luminal A, TUM099


title: BA Luminal A, TUM098


title: BA Luminal A, TUM096


title: BA Luminal A, TUM097


title: BA Luminal A, TUM095


title: BA Luminal A, TUM085


title: H3K4me3_stomach

status: Public on Jan 20 2015

city: Bethesda

first: Ian

last: Fingerman

state: MD

address: 45 Center Dr.

department: NCBI Epigenomics

institute: National Institutes of Health

description:
H3K4me3, in gastric tissue (average of 4 experiments)
Sequencing performed on multiple instruments: Illumina Genome Analyzer II, Illumina HiSeq 2000

library_source: genomic

data_processing:
For each tissue type, input tracks were selected based on the following criteria. Experiments from the Roadmap Epigenomics datasets were pooled, based on body site, tissue or cell type.  Donor age was weighed and sample data from adults was segregated from those of fetal or neonatal.  Donor sex was not taken into account, so some cases the track average is generated from pooled male and female tissues. Each input track was normalized by scaling all values to achieve a constant genome-wide summed signal. In the final track, the value in each 20 bp window is the arithmetic mean of the scaled input values.
Genome_build: GRCh37
Supplementary_files_format_and_content: WIG files generated by track averaging

source_name: stomach

extract_protocol:
Refer to extraction protocols described in the individual sample inputs for each average track
Refer to library contruction protocols described in the individual sample inputs for each average track

tag: body site

value: stomach

tag: developmental stage

value: adult


title: BA Luminal A, TUM091


title: BA Luminal A, TUM090


title: H3K4me3_chondrocyte

description: H3K4me3, in chondrocytes (average of 5 experiments)

source_name: heart

value: chondrocyte


title: H3K4me3_skeletal_muscle

description: H3K4me3, in skeletal muscle tissue (average of 3 experiments)

source_name: skeletal muscle

tag: tissue type

value: skeletal muscle


title: H3K4me3_rectal

description: H3K4me3, in rectal tissue (average of 3 experiments)

source_name: rectum

value: rectum

tag: Sex

value: female


title: H3K4me3_pancreas

description:
H3K4me3, in adult pancreas (average of 2 experiments)
Sequencing performed on multiple instruments: Illumina Genome Analyzer II, Illumina HiSeq 2000

source_name: pancreas

value: pancreas


title: H3K4me3_kidney

description:
H3K4me3, in adult kidney (average of 2 experiments)
Sequencing performed on multiple instruments: Illumina Genome Analyzer II, Illumina HiSeq 2000

source_name: kidney

value: kidney


title: H3K4me3_brain

description:
H3K4me3, brain primary tissue (average of 15 experiments)
Sequencing performed on multiple instruments: Illumina Genome Analyzer IIx, Illumina HiSeq 2000

source_name: brain

value: brain


title: H3K4me3_fetal_lung

description: H3K4me3, in fetal lung primary tissue(average of 2 experiments)

source_name: fetal lung

value: lung

value: fetus


title: H3K4me3_T_lymphocyte

description:
H3K4me3, in various T-cell types (average of 18 experiments)
Sequencing performed on multiple instruments: Illumina Genome Analyzer II, Illumina Genome Analyzer IIx, Illumina HiSeq 2000

source_name: T lymphocyte

value: T lymphocyte


title: H3K4me3_colon

description:
H3K4me3, in adult colon (average of 4 experiments)
Sequencing performed on multiple instruments: Illumina Genome Analyzer II, Illumina HiSeq 2000

source_name: colon

value: colon


title: H3K4me3_liver

description: H3K4me3, in adult liver (average of 3 experiments)

source_name: liver

value: liver


title: H3K4me3_fetal_brain

description:
H3K4me3, in fetal brain primary tissue (average of 6 experiments)
Sequencing performed on multiple instruments: Illumina Genome Analyzer II, Illumina HiSeq 2000

source_name: fetal brain


title: H3K4me3_foreskin

description:
H3K4me3, in foreskin cells (average of 9 experiments)
Sequencing performed on multiple instruments: Illumina Genome Analyzer II, Illumina HiSeq 2000

source_name: foreskin

value: foreskin

value: male

value: neonate


title: H3K4me3_bonemarrow_mesechymal

description:
H3K4me3, bone marrow derived mesechymal stem cells (average of 4 experiments)
Sequencing performed on multiple instruments: Illumina Genome Analyzer II, Illumina Genome Analyzer IIx

source_name: bone marrow derived mesenchymal stem cells

value: iliac crest

value: bone marrow

value: mesenchymal stem cell


title: H3K4me3_hematopoietic

description:
H3K4me3, in various hematopoietic cell types (average of 11 experiments)
Sequencing performed on multiple instruments: Illumina Genome Analyzer II, Illumina Genome Analyzer IIx

source_name: hematopoietic progenitor cells

value: hematopoietic progenitor cell


title: H3K4me3_duodenum

description:
H3K4me3, in adult duodenum (average of 4 experiments)
Sequencing performed on multiple instruments: Illumina Genome Analyzer II, Illumina HiSeq 2000

source_name: duodenum

value: duodenum

value: adult


title: H3K4me3_adipose_mesenchymal

description:
H3K4me3, adipose-derived mesenchymal stem cells (average of 5 experiments)
Sequencing performed on multiple instruments: Illumina Genome Analyzer II, Illumina Genome Analyzer IIx

source_name: adipose derived mesenchymal stem cells

value: adipose

value: female


title: H3K4me3_adipose

description:
H3K4me3, adipose (average of 5 experiments)
Sequencing performed on multiple instruments: Illumina Genome Analyzer II, Illumina Genome Analyzer IIx

source_name: adipose


title: normal miRNA in colon mucosa 330

status: Public on Jan 01 2015

first: R.

middle: Alan

last: Harris

address: 1 Baylor Plaza

department: Molecular and Human Genetics

description: Normal colon mucosa sample

hyb_protocol: Fluidics Protocol FS450-0003

scan_protocol: Affymetrix Genechip Scanner 7G

data_processing: The Affymetrix Expression Console was used to generate RMA-DABG normalized miRNA expression levels.

source_name: colon mucosa 330

label_protocol: Genisphere FlashTag HSR

extract_protocol: Qiangen/Qiazol - miRNA Isolation Kit

treatment_protocol: Flash freezing of biopsy samples on dry ice

value: Female

value: Colon mucosa

tag: disease state

value: normal


title: H3K4me3_breast

description: H3K4me3, in various breast cell types (average of 2 experiments)

source_name: breast

value: breast


title: Pooled normal endometrium.MRE

status: Public on Oct 12 2014

city: SAINT LOUIS

first: Daofeng

last: Li

state: MO

address: 4515 McKinley Avenue

department: Genetics

institute: Washington University in St. Louis

data_processing:
Sequencing reads were aligned to the hg19 (GRCh37) genome build with Bowtie.
For MeDIP-seq, redundant reads were discarded.
For MRE-seq, reads were filtered by MRE recognization site in genome.
Bed files were transformed to bigWig format.
Genome_build: GRCh37
Supplementary_files_format_and_content: bigWig

source_name: Pooled normal endometrium cell

extract_protocol:
For MRE, DNA was isolated using the DNeasy Tissue kit (Qiagen, Valencia, CA). Three parallel digests were performed (HpaII, AciI and Hin6I; Fermentas), each with 1μg of DNA. Five units of enzyme per microgram DNA were added and incubated at 37 °C in Fermentas Tango buffer for 3 h. Digested DNA was precipitated with sodium acetate and ethanol, and 500 ng of each digest were combined into one tube. Combined DNA was size-selected by electrophoresis on a 1% agarose TBE gel. A 100-300 bp gel slice was excised using a sterile scalpel and gel-purified using Qiagen QIAquick columns, eluting in 30 µl of Qiagen EB buffer.
Library construction was performed using the Illumina Genomic DNA Sample Kit (Illumina) with single-end adapters, following the manufacturer's instructions with the following changes. For the end repair reaction, T4 DNA polymerase and T4 polynucleotide kinase were excluded and the Klenow DNA polymerase was diluted 1:5 in water and 1 ul used per reaction. For single-end oligo adaptor ligation, adapters were diluted 1:10 in water and 1 ul used per reaction. Fifteen cycles of PCR were performed using the single-end Illumina PCR primers. The resulting reactions were purified with Qiagen MinElute columns, after which a final size selection (220-520bp) was performed by electrophoresis in DNA was eluted in 36 ul EB buffer using Qiagen QIAquick columns. After cleanup with Qiagen MinElute columns, each library was examined by spectrophotometry (Nanodrop, Thermo Scientific) and Agilent DNA Bioanalyzer (Agilent).2% agarose. Libraries were quality controlled by spectrophotometry and Agilent DNA Bioanalyzer analysis.

value: normal endometrium


title: CTRL NB4 untreated vs. NB4 treated, replicate 3

status: Public on Dec 22 2014

city: Naples

first: carmela

last: dell'aversana

address: Pietro Castellino 111

institute: IGB - Institute of Genetics and Biophysics - CNR

description: Biological replicate 3 of 3.

hyb_protocol: LC Sciences service procedure.

scan_protocol: Axon GenePix 4000B Microarray Scanner.

data_processing:
LC Sciences service procedure.
Background Subtraction: Background is determined using a regression-based background mapping method. The regression is performed on 5% to 25% of the lowest intensity data points excluding blank spots. Raw data matrix is then subtracted by the background matrix.

Normalization: Normalization is carried out using a LOWESS (Locally-weighted Regression) method on the background-subtracted data. The normalization is to remove system-related variations, such as sample amount variations, different labeling dyes, and signal gain differences of scanners so that biological variations can be faithfully revealed.

Detectivity Determination: A transcript to be listed as detectable must meet at least two conditions: signal intensity higher than 3×(background standard deviation) and spot CV < 0.5. CV is calculated by (standard deviation)/(signal intensity). When repeating probes are present on an array, a transcript is listed as detectable only if the signals from at least 50% of the repeating probes are above detection level.

source_name: NB4 human acute promyelocytic leukemia (APL) cell line, untreated

label_protocol: LC Sciences service procedure.

growth_protocol: The NB4 promyelocytic cell line was cultured in RPMI 1640 containing 10% decomplemented FBS.

extract_protocol: Total RNA, including miRNA, was extracted using Trizol.

tag: cell line

tag: treatment

source_name: NB4 human acute promyelocytic leukemia (APL) cell line, treated with 5µM SAHA for 6 hours

treatment_protocol: SAHA treatment at 5 µM concentration for 6 hours.

value: suberoylanilide hydroxamic acid (SAHA)


title: CTRL NB4 untreated vs. NB4 treated, replicate 1

description: Biological replicate 1 of 3.


title: CTRL NB4 untreated vs. NB4 treated, replicate 2

description: Biological replicate 2 of 3.


title: H3K4me3_B_lymphocyte

description: H3K4me3, in various B-cell types (average of 5 experiments)

source_name: B lymphocyte

value: B lymphocyte


title: normal miRNA in colon mucosa 296

description: Normal colon mucosa sample

source_name: colon mucosa 296

tag: gender


title: Pooled normal endometrium.MeDIP

extract_protocol:
For MeDIP, 5-15 μg DNA isolated using the DNeasy Tissue kit (Qiagen, Valencia, CA) was sonicated to ~100-500 bp with a Bioruptor sonicator (Diagenode). Sonicated DNA was end-repaired, A-tailed, and ligated to single-end adapters following the standard Illumina protocol. After agarose size-selection to remove unligated adapters, 2-5 μg of adaptor-ligated DNA was used for each immunoprecipitation using a mouse monoclonal anti-methylcytidine antibody (1 mg ml-1, Eurogentec, catalog no. BI-MECY-0100). For this, DNA was heat-denatured at 95 °C for 10 min, rapidly cooled on ice, and immunoprecipitated with 1 μl primary antibody per microgram of DNA overnight at 4 °C with rocking agitation in 500 μl immunoprecipitation buffer (10 mM sodium phosphate buffer, pH 7.0, 140 mM NaCl, 0.05% Triton X-100). To recover the immunoabsorbed DNA fragments, 4 μl of rabbit anti-mouse IgG secondary antibody (2.5 mg ml-1, Jackson Immunoresearch, catalog no. 315-005-008) and 100 μl Protein A/G beads (Pierce Biotechnology, catalog no. PI20421) were added and incubated for an additional 2 h at 4 °C with agitation. After immunoprecipitation, a total of six immunoprecipitation washes were performed with ice-cold immunoprecipitation buffer. Washed beads were resuspended in TE buffer with 0.25% SDS and 0.25 mg ml-1proteinase K for 2 h at 55 °C and then allowed to cool to room temperature. MeDIP and supernatant DNA were purified using Qiagen MinElute columns and eluted in 16 μl EB (Qiagen).
Fifteen cycles of PCR were performed on 5 ul of the immunoprecipitated DNA using the single-end Illumina PCR primers. The resulting reactions were purified with Qiagen MinElute columns, after which a final size selection (220-520bp) was performed by electrophoresis in DNA was eluted in 36 ul EB buffer using Qiagen QIAquick columns. After cleanup with Qiagen MinElute columns, each library was examined by spectrophotometry (Nanodrop, Thermo Scientific) and Agilent DNA Bioanalyzer (Agilent).2% agarose. Libraries were quality controlled by spectrophotometry and Agilent DNA Bioanalyzer analysis.


title: SNU484 Normoxia

status: Public on Jan 07 2015

city: Daegu

first: You Mie

last: Lee

address: 80, Daehak-ro

country: South Korea

institute: Kyungpook National University

description: Gene expression from SNU484 cells expressing GFP vector under normoxic condition.

hyb_protocol: Complementary RNA was hybridized using the Agilent's Gene Expression Hybridization Kit.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for array slides.

data_processing: The scanned images were analyzed Agilent's GeneSpring Software.

source_name: Gastric cancer cell line, normoxia

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.

extract_protocol: RNA was prepared using the Trizol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: microenvironment

value: Normoxia


title: group2, Phenobarbital wild-type 2018

status: Public on Aug 24 2014

city: Basel

first: Jonathan

last: Moggs

address: Fabrikstrasse 2

country: Switzerland

institute: Novartis

description:
group2, Phenobarbital wild-type
NUID-0000-0136-1407

hyb_protocol: Processing of miRNA 2.0 experiments was conducted as recommended by the manufacturer of the GeneChip system (Affymetrix, Santa Clara, CA).

scan_protocol: Processing of mi RNA 2.0 experiments was conducted as recommended by the manufacturer of the GeneChip system (Affymetrix, Santa Clara, CA).

data_processing: Affymetrix mi-croRNA chips were preprocessed and normalized according to the Affymetrix miRNA QCTool manual. Briefly, the back- ground control probes of the chips were grouped into bins of same dinucleotide Guanine-Cytosine (GC) content. The median signal of the background bin that matches with the GC con- tent of the probe was then subtracted from the probe signal. The background corrected probes (for all probes on the chip in- cluding those of other species) were quantile normalized across chips, log2 transformed and summarized into probe sets with the median polish method as in standard RMA (Bolstad et al., 2003). We floored all normalized signal values to 1.0.

source_name: mouse liver

growth_protocol: C57BL/6 male wild-type, knock-out CARKO -PXRKO and humanized CARh - PXRh mice were obtained from TaconicArtemis (Germany). For the 13-week time course study, 9–11 week-old mice (age selected to avoid the confounding effect of liver maturation observed in younger animals) were allowed to acclimatize for 5 days prior to being randomly divided into two treatment groups (n = 5 per time point).

extract_protocol: Frozen liver samples were homogenized in TRIzol reagent (Invitrogen, Carlsbad, CA) and subsequently purified on a silica-gel-based-membrane (RNeasy, Qiagen, Venlo, Netherlands) according to the manufacturer’s instructions. RNA quality was assessed by measuring the RIN (RNA Integrity Number) using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA). RNA was stored at −80◦C. miRNA was quantified using the Rediplate Ribogreen RNA quantitation kit (Life Technologies).

treatment_protocol: Phenobarbital (PB; free acid, >99.0%, Sigma, St Louis, MO, no. 04710, 0.05% (wt/vol) in drinking water) was administered to one group through ad libitum access to drinking water, as previously reported (see methods in PMID: 24690595). Mice were reated with PB starting at 8 weeks of age. PB was adminis- tered via the drinking water (PB solution prepared freshly every fourth day) at concentrations of 0.005, 0.01, 0.02, and 0.05% (wt/vol). Mice were kept on a 12 h dark/light cycle and had ac- cessed to food and water ad libitum. All animals were sacrificed between 9 and 11 a.m. to avoid circadian influences.checked daily for activity and behavior and sacrificed on the indicated dates. Liver (incl. left, caudal and median parts) were sampled. To ensure sample homo- geneity for different molecular profiling methods, frozen liver samples were reduced to powder with CovarisCryoprep (Co- varis Inc., Woburn, MA) system and aliquoted on dry ice. For the 4-week dose response study, mice (n = 4 per group) were treated with PB starting at 8 weeks of age. PB was adminis- tered via the drinking water (PB solution prepared freshly every fourth day) at concentrations of 0.005, 0.01, 0.02, and 0.05% (wt/vol). Mice were kept on a 12 h dark/light cycle and had ac- cessed to food and water ad libitum. All animals were sacrificed between 9 and 11 a.m. to avoid circadian influences.

value: liver

tag: genotype

value: wild type

value: 9 to 11 weeks

value: Phenobarbital

tag: time point

value: 28 days

tag: donorid


title: SNU484 G9a

description: Gene expression from SNU484 cells expressing GFP-G9a vector under normoxic condition

source_name: Gastric cancer cell line, G9a overexpression

value: G9a overexpression


title: group2, Phenobarbital wild-type 2021

description:
group2, Phenobarbital wild-type
NUID-0000-0137-8870

label_protocol: Processing of miRNA 2.0 experiments was conducted as recommended by the manufacturer of the GeneChip system (Affymetrix, Santa Clara, CA).

tag: tissue

value: 91 days


title: group2, Phenobarbital wild-type 2015

description:
group2, Phenobarbital wild-type
NUID-0000-0136-1404

value: 14 days


title: group2, Phenobarbital wild-type 2017

description:
group2, Phenobarbital wild-type
NUID-0000-0136-1406


title: group2, Phenobarbital wild-type 2027

description:
group2, Phenobarbital wild-type
NUID-0000-0136-1403

value: 119 days


title: group2, Phenobarbital wild-type 2019

description:
group2, Phenobarbital wild-type
NUID-0000-0136-1408


title: group2, Phenobarbital wild-type 2016

description:
group2, Phenobarbital wild-type
NUID-0000-0136-1405


title: group2, Phenobarbital wild-type 2010

description:
group2, Phenobarbital wild-type
NUID-0000-0136-1397

value: 7 days


title: group2, Phenobarbital wild-type 2009

description:
group2, Phenobarbital wild-type
NUID-0000-0136-1396


title: group2, Phenobarbital wild-type 2012

description:
group2, Phenobarbital wild-type
NUID-0000-0136-1399


title: SNU484 Hypoxia

description: Gene expression from SNU484 cells expressing GFP vector under hypoxic condition

source_name: Gastric cancer cell line, hypoxia

value: Hypoxia


title: group2, Phenobarbital wild-type 2020

description:
group2, Phenobarbital wild-type
NUID-0000-0136-1409


title: group2, Phenobarbital wild-type 2026

description:
group2, Phenobarbital wild-type
NUID-0000-0136-1402


title: group2, Phenobarbital wild-type 2014

description:
group2, Phenobarbital wild-type
NUID-0000-0136-1401


title: group2, Phenobarbital wild-type 2013

description:
group2, Phenobarbital wild-type
NUID-0000-0136-1400


title: group2, Phenobarbital wild-type 2011

description:
group2, Phenobarbital wild-type
NUID-0000-0136-1398


title: group2, Phenobarbital wild-type 2003

description:
group2, Phenobarbital wild-type
NUID-0000-0136-1390

value: 1 days


title: group2, Phenobarbital wild-type 2005

description:
group2, Phenobarbital wild-type
NUID-0000-0136-1392


title: group2, Phenobarbital wild-type 2002

description:
group2, Phenobarbital wild-type
NUID-0000-0136-1389


title: Expression in colon mucosa 330

city: Houston

institute: Baylor College of Medicine

description: Normal colon mucosa sample

hyb_protocol: Fluidics Protocol FS450_0002

data_processing: The R Bioconductor affy package rma function was used to compute expression. The rma function performs probe specific correction of the PM probes using a model based on observed intensity being the sum of signal and noise, normalization of corrected PM probes using quantile normalization, and calculation of expression measure using median polish.

label_protocol: Nugen Ovation Pico WTA System V2 /Encore Biotin Module

extract_protocol: Qiangen QIAzol

value: Female

tag: sample type

value: Colon mucosa

value: normal


title: Expression in colon mucosa 296

description: Normal colon mucosa sample


title: group2, Phenobarbital wild-type 2004

description:
group2, Phenobarbital wild-type
NUID-0000-0136-1391


title: group2, Phenobarbital wild-type 2006

description:
group2, Phenobarbital wild-type
NUID-0000-0136-1393


title: group2, Phenobarbital wild-type 2007

description:
group2, Phenobarbital wild-type
NUID-0000-0136-1394


title: group1, control wild-type 1029

description:
group1, control wild-type
NUID-0000-0136-1386

value: control


title: group2, Phenobarbital wild-type 2008

description:
group2, Phenobarbital wild-type
NUID-0000-0136-1395


title: group1, control wild-type 1028

description:
group1, control wild-type
NUID-0000-0136-1385


title: group1, control wild-type 1030

description:
group1, control wild-type
NUID-0000-0136-1387


title: group1, control wild-type 1024

description:
group1, control wild-type
NUID-0000-0136-1383


title: group1, control wild-type 1025

description:
group1, control wild-type
NUID-0000-0136-1384


title: group1, control wild-type 1023

description:
group1, control wild-type
NUID-0000-0136-1382


title: Methylation in colon mucosa 296

description: Normal colon mucosa sample

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to the Illumina Infinium HumanMethylation450 BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner settings

data_processing:
GenomeStudio software version 2010.3.0.30128
Average beta values were normalized to internal array controls as implemented in GenomeStudio

label_protocol: Standard Illumina protocol

extract_protocol: Genomic DNA was extracted and purified from colon mucosa samples using QIAamp DNA Mini Kit (Qiagen, Valencia, CA) starting at step 5 of the Tissue Protocol following bead beating and Qiagen TissueLyser treatment. All samples were quality tested with PicoGreen prior to proceeding with the microarrays.


title: group1, control wild-type 1016

description:
group1, control wild-type
NUID-0000-0136-1375


title: group1, control wild-type 1015

description:
group1, control wild-type
NUID-0000-0136-1374


title: group2, Phenobarbital wild-type 2001

description:
group2, Phenobarbital wild-type
NUID-0000-0136-1388


title: group1, control wild-type 1021

description:
group1, control wild-type
NUID-0000-0136-1380


title: group1, control wild-type 1017

description:
group1, control wild-type
NUID-0000-0136-1376


title: group1, control wild-type 1027

description:
group1, control wild-type
NUID-0000-0136-1373


title: group1, control wild-type 1022

description:
group1, control wild-type
NUID-0000-0136-1381


title: group1, control wild-type 1018

description:
group1, control wild-type
NUID-0000-0136-1377


title: group1, control wild-type 1014

description:
group1, control wild-type
NUID-0000-0136-1371


title: group1, control wild-type 1020

description:
group1, control wild-type
NUID-0000-0136-1379


title: group1, control wild-type 1019

description:
group1, control wild-type
NUID-0000-0136-1378


title: group1, control wild-type 1011

description:
group1, control wild-type
NUID-0000-0136-1368


title: group1, control wild-type 1013

description:
group1, control wild-type
NUID-0000-0136-1370


title: group1, control wild-type 1012

description:
group1, control wild-type
NUID-0000-0136-1369


title: group1, control wild-type 1005

description:
group1, control wild-type
NUID-0000-0136-1362


title: group1, control wild-type 1002

description:
group1, control wild-type
NUID-0000-0136-1359


title: Methylation in colon mucosa 326

description: Normal colon mucosa sample

source_name: colon mucosa 326

value: Male


title: group1, control wild-type 1010

description:
group1, control wild-type
NUID-0000-0136-1367

value: liver


title: Methylation in colon mucosa 330

description: Normal colon mucosa sample


title: group1, control wild-type 1009

description:
group1, control wild-type
NUID-0000-0136-1366

value: wild type


title: group1, control wild-type 1006

description:
group1, control wild-type
NUID-0000-0136-1363

value: 9 to 11 weeks


title: group1, control wild-type 1003

description:
group1, control wild-type
NUID-0000-0136-1360


title: group1, control wild-type 1004

description:
group1, control wild-type
NUID-0000-0136-1361


title: group5, control CAR/PXR  h 5007

description:
group5, control CAR/PXR  h
NUID-0000-0136-1354

value: human CAR/PXR


title: group1, control wild-type 1001

description:
group1, control wild-type
NUID-0000-0136-1358


title: group5, control CAR/PXR  h 5006

description:
group5, control CAR/PXR  h
NUID-0000-0136-1353


title: group5, control CAR/PXR  h 5008

description:
group5, control CAR/PXR  h
NUID-0000-0136-1355


title: group5, control CAR/PXR  h 5009

description:
group5, control CAR/PXR  h
NUID-0000-0136-1356


title: group1, control wild-type 1026

description:
group1, control wild-type
NUID-0000-0136-1372


title: group5, control CAR/PXR  h 5028

description:
group5, control CAR/PXR  h
NUID-0000-0136-1346


title: group1, control wild-type 1007

description:
group1, control wild-type
NUID-0000-0136-1364


title: group1, control wild-type 1008

description:
group1, control wild-type
NUID-0000-0136-1365


title: group5, control CAR/PXR  h 5004

description:
group5, control CAR/PXR  h
NUID-0000-0136-1351


title: group5, control CAR/PXR  h 5024

description:
group5, control CAR/PXR  h
NUID-0000-0136-1342


title: group5, control CAR/PXR  h 5002

description:
group5, control CAR/PXR  h
NUID-0000-0136-1349


title: group5, control CAR/PXR  h 5017

description:
group5, control CAR/PXR  h
NUID-0000-0136-1336

value: 28 days


title: group5, control CAR/PXR  h 5010

description:
group5, control CAR/PXR  h
NUID-0000-0136-1357


title: group5, control CAR/PXR  h 5003

description:
group5, control CAR/PXR  h
NUID-0000-0136-1350


title: group5, control CAR/PXR  h 5026

description:
group5, control CAR/PXR  h
NUID-0000-0136-1344


title: group5, control CAR/PXR  h 5030

description:
group5, control CAR/PXR  h
NUID-0000-0136-1348


title: group5, control CAR/PXR  h 5029

description:
group5, control CAR/PXR  h
NUID-0000-0136-1347


title: group5, control CAR/PXR  h 5018

description:
group5, control CAR/PXR  h
NUID-0000-0136-1337


title: group5, control CAR/PXR  h 5005

description:
group5, control CAR/PXR  h
NUID-0000-0136-1352


title: group5, control CAR/PXR  h 5019

description:
group5, control CAR/PXR  h
NUID-0000-0136-1338


title: group5, control CAR/PXR  h 5027

description:
group5, control CAR/PXR  h
NUID-0000-0136-1345


title: group5, control CAR/PXR  h 5021

description:
group5, control CAR/PXR  h
NUID-0000-0136-1339


title: group5, control CAR/PXR  h 5012

description:
group5, control CAR/PXR  h
NUID-0000-0136-1331


title: group5, control CAR/PXR  h 5001

description:
group5, control CAR/PXR  h
NUID-0000-0136-1329


title: group6, Phenobarbital CAR/PXR h 6023

description:
group6, Phenobarbital CAR/PXR h
NUID-0000-0136-1321

value: Phenobarbital


title: group5, control CAR/PXR  h 5011

description:
group5, control CAR/PXR  h
NUID-0000-0136-1330


title: group6, Phenobarbital CAR/PXR h 6029

description:
group6, Phenobarbital CAR/PXR h
NUID-0000-0136-1327


title: group5, control CAR/PXR  h 5016

description:
group5, control CAR/PXR  h
NUID-0000-0136-1335


title: group5, control CAR/PXR  h 5025

description:
group5, control CAR/PXR  h
NUID-0000-0136-1343

value: 91 days


title: group6, Phenobarbital CAR/PXR h 6028

description:
group6, Phenobarbital CAR/PXR h
NUID-0000-0136-1326


title: group5, control CAR/PXR  h 5015

description:
group5, control CAR/PXR  h
NUID-0000-0136-1334

value: 14 days


title: group6, Phenobarbital CAR/PXR h 6025

description:
group6, Phenobarbital CAR/PXR h
NUID-0000-0136-1323


title: group6, Phenobarbital CAR/PXR h 6024

description:
group6, Phenobarbital CAR/PXR h
NUID-0000-0136-1322


title: group6, Phenobarbital CAR/PXR h 6026

description:
group6, Phenobarbital CAR/PXR h
NUID-0000-0136-1324

value: 119 days


title: group6, Phenobarbital CAR/PXR h 6030

description:
group6, Phenobarbital CAR/PXR h
NUID-0000-0136-1328


title: group5, control CAR/PXR  h 5023

description:
group5, control CAR/PXR  h
NUID-0000-0136-1341


title: group6, Phenobarbital CAR/PXR h 6020

description:
group6, Phenobarbital CAR/PXR h
NUID-0000-0136-1318


title: group5, control CAR/PXR  h 5013

description:
group5, control CAR/PXR  h
NUID-0000-0136-1332


title: group6, Phenobarbital CAR/PXR h 6022

description:
group6, Phenobarbital CAR/PXR h
NUID-0000-0136-1320


title: group5, control CAR/PXR  h 5022

description:
group5, control CAR/PXR  h
NUID-0000-0136-1340


title: group6, Phenobarbital CAR/PXR h 6015

description:
group6, Phenobarbital CAR/PXR h
NUID-0000-0136-1313


title: group5, control CAR/PXR  h 5014

description:
group5, control CAR/PXR  h
NUID-0000-0136-1333


title: group6, Phenobarbital CAR/PXR h 6014

description:
group6, Phenobarbital CAR/PXR h
NUID-0000-0136-1312


title: group6, Phenobarbital CAR/PXR h 6021

description:
group6, Phenobarbital CAR/PXR h
NUID-0000-0136-1319


title: group6, Phenobarbital CAR/PXR h 6016

description:
group6, Phenobarbital CAR/PXR h
NUID-0000-0136-1314


title: group6, Phenobarbital CAR/PXR h 6019

description:
group6, Phenobarbital CAR/PXR h
NUID-0000-0136-1317


title: group6, Phenobarbital CAR/PXR h 6027

description:
group6, Phenobarbital CAR/PXR h
NUID-0000-0136-1325


title: group6, Phenobarbital CAR/PXR h 6017

description:
group6, Phenobarbital CAR/PXR h
NUID-0000-0136-1315


title: group6, Phenobarbital CAR/PXR h 6012

description:
group6, Phenobarbital CAR/PXR h
NUID-0000-0136-1310


title: group6, Phenobarbital CAR/PXR h 6018

description:
group6, Phenobarbital CAR/PXR h
NUID-0000-0136-1316


title: group6, Phenobarbital CAR/PXR h 6013

description:
group6, Phenobarbital CAR/PXR h
NUID-0000-0136-1311


title: group6, Phenobarbital CAR/PXR h 6007

description:
group6, Phenobarbital CAR/PXR h
NUID-0000-0136-1305

value: 7 days


title: group6, Phenobarbital CAR/PXR h 6006

description:
group6, Phenobarbital CAR/PXR h
NUID-0000-0136-1304


title: group6, Phenobarbital CAR/PXR h 6009

description:
group6, Phenobarbital CAR/PXR h
NUID-0000-0136-1307


title: group6, Phenobarbital CAR/PXR h 6001

description:
group6, Phenobarbital CAR/PXR h
NUID-0000-0136-1299


title: group6, Phenobarbital CAR/PXR h 6008

description:
group6, Phenobarbital CAR/PXR h
NUID-0000-0136-1306


title: group6, Phenobarbital CAR/PXR h 6003

description:
group6, Phenobarbital CAR/PXR h
NUID-0000-0136-1301


title: group4, Phenobarbital CAR/PXR KO 4030

description:
group4, Phenobarbital CAR/PXR KO
NUID-0000-0136-1298

value: CAR/PXR knock-out


title: group6, Phenobarbital CAR/PXR h 6011

description:
group6, Phenobarbital CAR/PXR h
NUID-0000-0136-1309


title: group6, Phenobarbital CAR/PXR h 6010

description:
group6, Phenobarbital CAR/PXR h
NUID-0000-0136-1308


title: group6, Phenobarbital CAR/PXR h 6005

description:
group6, Phenobarbital CAR/PXR h
NUID-0000-0136-1303

value: 1 days


title: group4, Phenobarbital CAR/PXR KO 4024

description:
group4, Phenobarbital CAR/PXR KO
NUID-0000-0136-1295


title: group4, Phenobarbital CAR/PXR KO 4022

description:
group4, Phenobarbital CAR/PXR KO
NUID-0000-0136-1293


title: group6, Phenobarbital CAR/PXR h 6004

description:
group6, Phenobarbital CAR/PXR h
NUID-0000-0136-1302


title: group4, Phenobarbital CAR/PXR KO 4023

description:
group4, Phenobarbital CAR/PXR KO
NUID-0000-0136-1294


title: group4, Phenobarbital CAR/PXR KO 4020

description:
group4, Phenobarbital CAR/PXR KO
NUID-0000-0136-1291


title: group6, Phenobarbital CAR/PXR h 6002

description:
group6, Phenobarbital CAR/PXR h
NUID-0000-0136-1300


title: group4, Phenobarbital CAR/PXR KO 4021

description:
group4, Phenobarbital CAR/PXR KO
NUID-0000-0136-1292


title: group4, Phenobarbital CAR/PXR KO 4025

description:
group4, Phenobarbital CAR/PXR KO
NUID-0000-0136-1296


title: group4, Phenobarbital CAR/PXR KO 4027

description:
group4, Phenobarbital CAR/PXR KO
NUID-0000-0136-1285


title: group4, Phenobarbital CAR/PXR KO 4015

description:
group4, Phenobarbital CAR/PXR KO
NUID-0000-0136-1286


title: group4, Phenobarbital CAR/PXR KO 4028

description:
group4, Phenobarbital CAR/PXR KO
NUID-0000-0136-1297


title: group4, Phenobarbital CAR/PXR KO 4026

description:
group4, Phenobarbital CAR/PXR KO
NUID-0000-0136-1284


title: group4, Phenobarbital CAR/PXR KO 4019

description:
group4, Phenobarbital CAR/PXR KO
NUID-0000-0136-1290


title: group4, Phenobarbital CAR/PXR KO 4018

description:
group4, Phenobarbital CAR/PXR KO
NUID-0000-0136-1289


title: group4, Phenobarbital CAR/PXR KO 4017

description:
group4, Phenobarbital CAR/PXR KO
NUID-0000-0136-1288


title: group4, Phenobarbital CAR/PXR KO 4012

description:
group4, Phenobarbital CAR/PXR KO
NUID-0000-0136-1281


title: group4, Phenobarbital CAR/PXR KO 4011

description:
group4, Phenobarbital CAR/PXR KO
NUID-0000-0136-1280