title: PP6 clone 19.5 shRNA transduced, biological rep 3

city: Providence

first: Joan

last: Boylan

address: 593 Eddy Street

department: Pediatrics

institute: Rhode Island Hospital

description:
PP6KD 19.5-3
Gene expression data from untreated cell lines.
HepG2 cell line derivation/description: tissue: liver, hepatocellular carcinoma; morphology: epithelial; gender: male.

hyb_protocol: After fragmentation, 2.475ug cRNA was hybridized for 17 h at 45 C, 60rpm, on a GeneChip Human Gene 1.0 ST Array. Then, washing and staining (SAPE (streptavidin-conjugated Phycoerythrin)) were done according to manufacturer's instructions using the Fluidics recommended for the arrays and Affymetrix Wash/Stain/Hyb kit.

scan_protocol: The arrays were scanned with an Affymetrix 3000 7G scanner using manufacturer's instructions.

data_processing: Generation of RMA data and identification of differentially expressed genes were done in GenePattern (Broad Institute) (Reich M, et. Al. GenePattern 2.0 Nature Genetics 38 no. 5 (2006): pp500-501) using the Expression File Creator module.

source_name: HepG2 cells transduced, Mission TRCN0000379835 shRNA

label_protocol: Samples (100ng total RNA) were labeled with biotin using the Affymetrix WT labeling kit (Cat# 900670) according to manufacturer's instructions.

growth_protocol: HepG2 cells were obtained from the American Type Culture Collection. Low passage cells were maintained in minimal essential medium (MEM) with Earle’s salts, L-glutamine and non-essential amino acids (Invitrogen, Carlsbad, CA ) supplemented with 1 mM sodium pyruvate, 10% fetal bovine serum, 50 units/ml penicillin and 50 μg/ml streptomycin.

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

treatment_protocol:
To generate cell lines in which PP6-C was reduced in expression (PP6-C knock-down; PP6KD), HepG2 cells were seeded into 96-well plates and transduced with lentiviral particles (multiplicity of infection of 5) corresponding to different short hairpin RNA (shRNA) constructs targeted to the PP6-C gene (Mission shRNA; Sigma-Aldrich, St. Louis, MO). Procedures followed the manufacturer’s protocol. Cell lines were selected in 2 µg/ml puromycin and surviving colonies of cells were expanded as mass cultures in puromycin.
Cells were plated at 2x10^6 per 100mm plate in MEM with Earle's salts, L-glutamine and non-essential amino acids supplemented with 1mM sodium pyruvate, 10% fetal calf serum, 50 units/ml penicillin and 50ug/ml streptomycin, and 2ug/ml puromycin. Cells were extracted after 48hr in culture at 37oC and 5% CO2.

value: hepatocellular carcinoma cell line

tag: shRNA

value: Mission TRCN0000379835 targeted to the PP6-C gene

tag: clone

value: PP6-C knock-down

tag: treatment


title: PP6 clone 18.5 shRNA transduced, biological rep 1

status: Public on Jun 01 2015

type: RNA

middle: M

state: RI

country: USA

description:
PP6KD 18.5-1
Gene expression data from untreated cell lines.
HepG2 cell line derivation/description: tissue: liver, hepatocellular carcinoma; morphology: epithelial; gender: male.

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: HepG2 cells transduced, Mission TRCN0000297274 shRNA

tag: cell line

tag: cell type

value: Mission TRCN0000297274 targeted to the PP6-C gene

tag: genotype/variation


title: G001#5-2_A7133

city: Bethesda

first: Timothy

middle: G

last: Myers

state: MD

address: 50 South Drive, Room 5509

department: Research Technologies Branch

institute: National Institute of Allergy and Infectious Diseases

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Prior to normalization, raw data was filtered to include only probes detected in at least two arrays, using the detection_pvalue parameter output from Genome Studio software, with a cutoff value of 0.1; Each array normalized using quantile normalization of bead_average intensity, performed using JMP/Genomics software.

label: biotin

molecule: polyA RNA

organism: Mus musculus

source_name: spleen

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

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

tag: strain

tag: parasite strain

tag: experiment

tag: tissue

value: spleen


title: x273

city: Odense C

first: Martin

middle: Jakob

last: Larsen

address: Sdr. Boulevard 29

department: Dept. of Clinical Genetics

country: Denmark

institute: Odense University Hospital

hyb_protocol: Fragmentation, hybridization and washing for the spotted arrays were carried out using Agilent Gene Expression Hybridization Kit (Agilent Technologies ) and Gene Expression Wash Buffer Kit (Agilent Technologies) according to the manufacturer’s protocol in a low ozone environment.

scan_protocol: Scanned using a Agilent G2565CA Microarray scanner

data_processing: Scanned images were quantified by Gene Pix Pro 6.0 (Molecular Devices). Bad quality features flagged during feature extraction were removed and the remaining data were pre-processed. Data were background corrected (normexp, offset=50), then within-array normalized by loess normalization method and between-array normalizatized by the quantile method. The normalized values were used to calculate log2 transformed Cy5/Cy3 ratios. Replicate probes were collapsed by calculating the median. The 92 samples were processed together with 154 other breast tumor samples. ComBat method was used for adjustment of the batch effects across the different spotting batches [PMID: 16632515]. In cases of multiple probes per gene symbol only the probe with the maximum mean (Cy5) intensity was kept. Missing expression values were imputed by k-nearest neighbors averaging (k = 10).

source_name: Breast tumor tissue

label_protocol: RNA was amplified and labeled using the Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion) according to the manufacturer’s protocol.

extract_protocol: Total RNA was extracted from freshly frozen tumor tissue using Trizol Reagent (Invitrogen) and RNeasy Micro Kit (Qiagen).

tag: group

value: BRCAx

value: LumA

source_name: Universal Human Reference RNA (Stratagene)

tag: reference


title: Control 5_rep 2

city: Vero Beach

first: James

middle: C

last: Ryan

state: FL

institute: ProteoGenomics, LLC

hyb_protocol: Agilent One Color Gene Expression Hybridization manual

scan_protocol: Default for Agilent scanner B with extended dynamic range

data_processing: Agilent feature extraction

source_name: Whole blood

label_protocol: Agilent Low Input Quick Amplification kit

extract_protocol: Qiagen PAXgene Blood micro RNA Kit

treatment_protocol: Blood was drawn from subjects into PAXgene RNA collection tubes. Tubes were incubated at room temperature for 4-6 hours then frozen and stored at -80 till extraction. Total RNA was extracted according to manufacturers protocol.

tag: disease state

value: healthy

tag: gender

value: Male

tag: age


title: N67-1_A7183


title: G008#2-2_A7121


title: Control 6_rep 1


title: PP6 clone 18.5 shRNA transduced, biological rep 3

description:
PP6KD 18.5-3
Gene expression data from untreated cell lines.
HepG2 cell line derivation/description: tissue: liver, hepatocellular carcinoma; morphology: epithelial; gender: male.


title: Patient 2_rep 2

value: Ciguatera


title: Control 5_rep 1


title: PP6 clone 19.5 shRNA transduced, biological rep 2

description:
PP6KD 19.5-2
Gene expression data from untreated cell lines.
HepG2 cell line derivation/description: tissue: liver, hepatocellular carcinoma; morphology: epithelial; gender: male.


title: x298

value: Universal Human Reference RNA (Stratagene)


title: Control 6_rep 2


title: G004#2-2_A7136


title: x219


title: APC(Min/+), Dnmt3a(2lox/2lox), Fabpl(4x at -132)-Cre(-/-) rep2

city: Heidelberg

first: Heinz

last: Linhart

address: Im Neuenheimer Feld 581

department: Translational Oncology

country: Germany

institute: DKFZ

description:
Sample 2
animal 2

data_processing: The data were normalised using quantile normalisation in R-2.15

source_name: control colon mucosa cells

label_protocol: Biotinylated cRNA were prepared using the Illumina® Total Prep™ RNA Amplification Kit (Life Technologies)

extract_protocol: RNA was extracted using the QIAGEN RNeasy mini kit and DNaseI trated using the DNA-free RNA Kit (Zymo Research Inc.) in accordance with the prescribed protocol provided with the kits. Quality control was performed with Agilent Bioanalyser.

tag: strain background

value: APC(Min/+), Dnmt3a(2lox/2lox), Fabp-Cre- (control)

value: 5 months

value: colon mucosa


title: PP6 clone 18.5 shRNA transduced, biological rep 2

description:
PP6KD 18.5-2
Gene expression data from untreated cell lines.
HepG2 cell line derivation/description: tissue: liver, hepatocellular carcinoma; morphology: epithelial; gender: male.


title: Control shRNA transduced, biological rep 3

description:
Control-3
Gene expression data from untreated cell lines.
HepG2 cell line derivation/description: tissue: liver, hepatocellular carcinoma; morphology: epithelial; gender: male.

source_name: HepG2 cells transduced, Mission TRC2 nontarget shRNA

value: Mission TRC2 nontarget

value: control


title: x216


title: x100R

value: Basal


title: x247


title: Control 3_rep 2

value: Female


title: Control 4_rep 1


title: Control 1_rep 2


title: E982#1-2_A7154


title: Untreated 3

city: Stirling

first: Kevin

last: Petrie

state: Stirling

address: Stirling

department: Biological and Environmental Sciences

country: United Kingdom

institute: University of Stirling

hyb_protocol: The quality and quantity of labeled cRNA was checked and 750 ng of labeled cRNA were hybridized to a GeneChip Human Gene 1.0 ST Arrays using GeneChip Hybridization, Wash, and Stain Kit (Affymetrix).

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

data_processing: Raw data were processed with the Expression Console (Affymetrix) for background correction and normalization using RMA algorithm. Secondary analysis of the data was performed by Transcriptome analysis console (Affymetrix).

source_name: 231 breast cancer cell line

label_protocol: All samples were normalized to 200ng and processed according to standard Affymetrix protocols using GeneChip WT Terminal Labeling and Controls Kit (Affymetrix) and WT Expression Kit (Ambion).

growth_protocol: MDA-MB-231 cell lines were maintained in DMEM supplemented with 10% FBS, 1% GlutaMAX (Invitrogen), 10mM HEPES, 1mM sodium pyruvate, non-essential amino acids and 1% antibiotic-antimycotic solution.

extract_protocol: Total RNA was isolated using the ZR RNA MiniPrep Kit (Zymo Research). The concentration and quality of the total RNA was assessed on an Agilent 2100 BioAnalyzer (Agilent Technologies).

treatment_protocol: MDA-MB-231 cells were treated with vehicle or 1µM selamectin for 24h.

value: Breast cancer cell line


title: Selamectin 1uM 24hr 2


title: Control shRNA transduced, biological rep 1

description:
Control-1
Gene expression data from untreated cell lines.
HepG2 cell line derivation/description: tissue: liver, hepatocellular carcinoma; morphology: epithelial; gender: male.

value: hepatocellular carcinoma cell line


title: Control 4_rep 2


title: F996#1-2_A7160


title: F245#1-2_A7169


title: F996#5-2_A7172


title: Selamectin 1uM 24hr 3


title: x071R

value: LumB


title: x027R


title: Control 3_rep 1


title: Control 1_rep 1


title: x073


title: x164


title: G001#4-2_A7166

value: spleen


title: Control shRNA transduced, biological rep 2

description:
Control-2
Gene expression data from untreated cell lines.
HepG2 cell line derivation/description: tissue: liver, hepatocellular carcinoma; morphology: epithelial; gender: male.


title: Control 2_rep 2


title: Untreated 1


title: Control 2_rep 1


title: x024R

value: BRCAx


title: Untreated 2


title: x135

value: LumA


title: F115#5-2_A7130


title: E891#5-1_A7177


title: E890#3-1_A7108


title: F239#4-1_A7174


title: Selamectin 1uM 24hr 1


title: G013#3-1_A7162


title: PP6 clone 19.5 shRNA transduced, biological rep 1

description:
PP6KD 19.5-1
Gene expression data from untreated cell lines.
HepG2 cell line derivation/description: tissue: liver, hepatocellular carcinoma; morphology: epithelial; gender: male.

value: Mission TRCN0000379835 targeted to the PP6-C gene

value: PP6-C knock-down


title: F114#1-1_A7147


title: SiCHD8_EtOH, biological rep2

city: Sevilla

first: Jose

middle: C.

last: Reyes

address: Av. Américo Vespucio

department: Genome biology

country: Spain

institute: CABIMER

description: Gene expression data from T47D-MTVL transfected with siCHD8 and treated with EtOH for 6 h

hyb_protocol: Labelled ssDNA was hybridized to the GeneChip® human Gene 1.0 ST array oligonucleotide microarray using standard protocols of Affymetrix.

scan_protocol: The arrays were scanned using the GeneChip Scanner 3000 7G (Affymetrix), using standard parameters.

data_processing: Raw data were extracted from the scanned images and analyzed with the Affymetrix GeneChip Command Console Software (Affymetrix). The raw array data were preprocessed and normalized using the Robust Multichip Average (RMA) method. Data were further processed using oneChannelGUI.

label_protocol: RNA (100 ng) was used for production of end-labelled biotinylated ssDNA

growth_protocol: Cells were  grown in RPMI 1640 medium supplemented with 10% FBS, 2mM L-glutamine, 100 U/ml penicillin and 100 mg/ml streptomycin

extract_protocol: Total RNA was isolated in triplicate using RNeasy Mini Kit (Qiagen)

treatment_protocol: T47D-MTVL cells were transfected with control siRNA (siCt) or siRNA against CHD8 (siCHD8), subjected to serum deprivation during 48 h in RPMI medium without phenol red, and then stimulated with 10 nM R5020 (R5020) or vehicle (EtOH) for 6 h

tag: cell line characteristics

value: Cell line derived from T47D that contain one copy of MMTV promoter


title: x163

value: Universal Human Reference RNA (Stratagene)


title: SiCt_R5020, biological rep3

description: Gene expression data from T47D-MTVL transfected with siCt and treated with R5020 for 6 h


title: F117#2-1_A7141


title: SiCt_R5020, biological rep2

source_name: T47D-MTVL transfected with siCt and treated with R5020 for 6 h


title: x185


title: SiCHD8_R5020, biological rep2

description: Gene expression data from T47D-MTVL transfected with siCHD8 and treated with R5020 for 6 h


title: F120#5-1_A7138


title: x285


title: x148


title: SiCHD8_R5020, biological rep3

source_name: T47D-MTVL transfected with siCHD8 and treated with R5020 for 6 h


title: G055#3-1_A7144


title: SiCHD8_EtOH, biological rep3

source_name: T47D-MTVL transfected with siCHD8 and treated with EtOH for 6 h


title: F994#3-1_A7117


title: SiCHD8_EtOH, biological rep1


title: SiCHD8_R5020, biological rep1


title: x214


title: x089R


title: x290


title: x317


title: x217

value: Normal


title: E986#4-1_A7123


title: F995#4-1_A7114


title: x320


title: x116R


title: SiCt_R5020, biological rep1


title: E995#3-1_A7111


title: SiCt_EtOH, biological rep3

description: Gene expression data from T47D-MTVL transfected with siCt and treated with EtOH for 6 h


title: SiCt_EtOH, biological rep1

source_name: T47D-MTVL transfected with siCt and treated with EtOH for 6 h


title: x218


title: SiCt_EtOH, biological rep2


title: x322


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 germinal center B-cell sub-populations from tonsils F

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_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: Tonsil samples were first fine-minced in normal culture medium (RPMI1640, 10% FBS, Life Technologies, Paisley, UK) and passed through a cell strainer (BD) with a 70 µm grid to obtain single cell suspensions. Total B-cells were first enriched by using EasySep human B-cell enrichment kit, negative selection (Stem cell Technology, Vancouver, Canada) using RoboSep instrument (Stemcell Technology). Tonsil B-cells were first stained with the following antibodies: FITC-polyclonal anti-IgD (Dako, Glostrup, Denmark), APC anti-CD19 mAb (BD), PE-polyclonal anti-IgM (Dako), Pe-Cy5 (Beckman Coulter, Brea, CA, USA) or PE-CF594 (BD) anti-CD27 mAb, PE-Cy7 anti-CD38 mAb (BD). Gating CD19+ B-cells were further purified by FACS sorting based on the expression of IgD versus CD38. In particular, the following non abutting gates were drawn to separate naïve B-cells (N) (IgD bright CD38 - CD27 - ); marginal zone (MZ)-like B-cells (IgD low IgM bright  CD38 ? ); germinal center (GC) B cells (IgD - CD38 + ) and switched memory (SM) B cells (IgD - IgM - CD38 - )

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


title: F114#1-2_A7148


description: Gene expression data from Human germinal center B-cell sub-populations from tonsils C


title: x079R


title: x090R


description: Gene expression data from Human germinal center B-cell sub-populations from tonsils G


title: F118#4-2_A7157


title: x069R


title: x126


title: x308


title: E891#5-2_A7178


description: Gene expression data from Human germinal center B-cell sub-populations from tonsils B


description: Gene expression data from Human memory B-cell sub-populations from tonsils C


title: F239#4-2_A7175


title: F120#5-2_A7139


title: F122#2-1_A7126


title: 17XNL-1_A7180


description: Gene expression data from Human memory B-cell sub-populations from tonsils B


title: G013#3-2_A7163


title: x141


title: Naive-2_A7193

value: Naive


title: x193


description: Gene expression data from Human marginal zone B-cell sub-populations from tonsils E


title: F994#3-2_A7118


description: Gene expression data from Human memory B-cell sub-populations from tonsils A


description: Gene expression data from Human naive B-cell sub-populations from tonsils B


title: x209


description: Gene expression data from Human marginal zone B-cell sub-populations from tonsils D


title: E890#3-2_A7109


description: Gene expression data from Human naive B-cell sub-populations from tonsils C


title: G055#3-2_A7145


title: E986#4-2_A7124


title: x204


title: x293


title: x158


title: 194 na

city: College Station

first: Michelle

last: Dawes

state: TX

address: 213K Heldenfelds

department: Health and Kinesiology

institute: Texas A&M University

hyb_protocol: Dried samples resuspended in 17μl nuclease-free water and added 1μl 3rd dilution hyb spike in, add 4.5μl 10x blocking agent + 22.5μl 2x Hi-RPM hyb buffer to each sample. Incubate at 100°for 5 min, quench in ice water for 5 min. Loaded hybridization assembly according to manufactures directions. Hybridized for 20 hours at 55°C. Added Trition X to wash buffers; warmed buffer 2 overnight.   Scanned slides immediately after washing using Agilent Scanner B, AgilentG3_miRNA setting for the 8X60k format.  Resolution, 3 microns; extended range (using 16 bit TIFF setting); dye channel, green. Used GEML file 035430_D_F_20121221.

scan_protocol: Scanned slides immediately after washing using Agilent G2505C scanner, AgilentG3_miRNA  setting for the 8X60k format.  Resolution, 3 microns ; extended range (using 16 bit TIFF setting); dye channel, green.

data_processing: Used GEML file 035430_D_F_20121221 for feature extraction, along with miRNA_107_Sept09 protocol. Quality reports were viewed and heterogenous intensity and 5 arrays were discluded (blank sample names in metadata template). Agilent GeneSpring GX12.5 software was used to process arrays. For soleus and nucleus accumbens, probes with low values caused errors in statistical analysis (homogenous p-values and FC values for all 'significantly different' miRNAs). Throughcommunication with Agilent,  low intensity probes were removed from the raw files and entity list were manually imported into GeneSpring for further analysis. Separate 'experiments' were created in GeneSpring for each tissue, thus the only variable is strain. Percentile shift normalization was used (setting at defult of 90%) and threshold raw signals to 1.0, baseline to median. Additionally, filtered on expression of normalized data, by percent (20-100%), 75% of values in any 1 out of 2 conditions included. Filtered on flags, including 'detected' and 'not detected', again,  75% of values in any 1 out of 2 conditions included. Statistical analysis done by moderated t-test, p value < 0.05 and FC > 2, with Benjamini-Hochberg multiple testing correction.

source_name: low-active, nucleus accumbens

label_protocol: total RNA diluted to 50ng/μl; prepared 3 dilutions of labeling spike-in. Prepared CIP Master Mix (10.8μl 10X calf intestinal phosphatase buffer, 29.7μl labeling spike-in, 13.5μl calf intestinal phosphatase; total volume for 24 reactions). Mixed 2μl diluted RNA + 2μl Master Mix, incubate at 37°C in heat block for 30min. Stored in -80 until further use. Denature by adding 2.8μl DMSO and incubating at 100° for 5-10min; quench on ice. Warmed 10x T4 Ligate buffer at 37° and then cooled to RT. Prepared ligation master mix (27μl T4 ligase buffer, 81μl  Cy3, 13.5μl T4 RNA ligase; total volume for 24 reactions). 4.5μl ligation MM added to each sample; incubate at 16°° for 2 hours. Used micro bio-spin columns for labeled RNA purification. Concentrated samples using vacuum at 50°C for 1 hour.

growth_protocol: Eight week old mice were housed individually with 'locked' running wheel. Food / water provided ad libitum; 12h light/dark cycles; temperature and humidity maintained at 19-21°C and 40-50%, respectively.  After one week, the mice were anesthetized and subsequently euthanized, with 2-4% isofluorine.  Body composition was analyzed prior to sacrificing, using the Lunar Piximus DEXA.

extract_protocol: Total RNA was extracted from nucleus accumbens, soleus, and EDL using the Qiagen miRNeasy kit (Qiagen, Valencia, CA), with inclusion of the on-column DNA treatment.  RNA quantified using  Nanodrop 1000 spectrophotometer  and quality of RNA was determined using an Agilent 2100 Bioanalyzer.

treatment_protocol: No treatments were applied

value: nucleus accumbens


title: 225 na

source_name: high-active, nucleus accumbens


title: 195 na


description: Gene expression data from Human naive B-cell sub-populations from tonsils A


description: Gene expression data from Human chronic lymphocytic leukemia patient WB0269

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).

value: unmut


title: F122#2-2_A7127


title: F995#4-2_A7115


title: F117#2-2_A7142


title: E995#3-2_A7112


description: Gene expression data from Human chronic lymphocytic leukemia patient VS0140

value: mut


description: Gene expression data from Human chronic lymphocytic leukemia patient VG0442


title: 17XNL-2_A7181


title: 227 na


title: 197 na


title: x318

value: Basal


description: Gene expression data from Human chronic lymphocytic leukemia patient VP0089


description: Gene expression data from Human chronic lymphocytic leukemia patient VS0016


title: G007#3-1_A7150


description: Gene expression data from Human chronic lymphocytic leukemia patient VD0354


description: Gene expression data from Human chronic lymphocytic leukemia patient VD0026


title: G008#2-1_A7120


title: 224 na


title: 223 na


title: 227 edl

source_name: high-active, EDL

value: EDL


title: 195 edl

source_name: low-active, EDL


title: x048


description: Gene expression data from Human chronic lymphocytic leukemia patient VC0315


title: N67-2_A7184


title: 194 edl


title: G001#5-1_A7132


title: G004#2-1_A7135


title: 197 edl


title: F245#1-1_A7168


description: Gene expression data from Human chronic lymphocytic leukemia patient VC0142


description: Gene expression data from Human chronic lymphocytic leukemia patient UL0266


title: 196 edl


description: Gene expression data from Human chronic lymphocytic leukemia patient VB0013


title: 225 edl


title: liver_hom_rep4 [BH4 study]

city: Neuherberg

last: Irmler

state: Bayern

address: Ingolstaedter Landstrasse 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum München GmbH

description:
SAMPLE 16
replicate 4

scan_protocol: Standard Illumina scanning protocol using HiScan

data_processing: The data were normalized using cubic spline normalization with Illumina Genomestudio 2011.1

source_name: liver

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

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

value: homozygous

tag: allels

value: 17 weeks

tag: mouse id

value: male

value: liver


title: 225 sol

source_name: high-active, soleus tissue

value: soleus


description: Gene expression data from Human chronic lymphocytic leukemia patient TG0139


title: KO_clone2_12h_2

city: tsu

first: masao

last: yuda

state: mie

address: edobashi 2-174

country: Japan

institute: mie university

hyb_protocol: 1.65  ug Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 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 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 (G2565BA) using one color scan setting for 1x44k array slide.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters.

organism: Plasmodium berghei

source_name: cultured, 12hr, biologically independent

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1.0 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Ookinetes were obtained from asexual parasite-depleted infected mouse blood that had been cultured for 12 h in an ookinete culture medium.

extract_protocol: Total RNA was extracted using the RNeasy mini kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocols.

value: ANKA

tag: Stage

value: ookinete

tag: genotype

value: AP2-O KO clone 2

tag: host

value: mouse


description: Gene expression data from Human chronic lymphocytic leukemia patient SV0046


title: 227 sol

tag: strain


description: Gene expression data from Human chronic lymphocytic leukemia patient TL0397


title: 195 sol

source_name: low-active, soleus


title: liver_hom_rep3 [BH4 study]

description:
SAMPLE 15
replicate 3

tag: genotype/variation


title: KO_clone2_12h_1


title: KO_clone1_12h_5

value: AP2-O KO clone 1


description: Gene expression data from Human chronic lymphocytic leukemia patient TG0263


title: liver_hom_rep1 [BH4 study]

description:
SAMPLE 13
replicate 1


title: KO_clone1_12h_3


title: liver_wt_rep4 [BH4 study]

description:
SAMPLE 12
replicate 4

value: wild type


description: Gene expression data from Human chronic lymphocytic leukemia patient TM0259


title: KO_clone1_12h_4


title: liver_wt_rep2 [BH4 study]

description:
SAMPLE 10
replicate 2


title: KO_clone1_12h_2


title: liver_hom_rep2 [BH4 study]

description:
SAMPLE 14
replicate 2


title: liver_wt_rep3 [BH4 study]

description:
SAMPLE 11
replicate 3


title: 224 sol


title: liver_wt_rep1 [BH4 study]

description:
SAMPLE 9
replicate 1


title: 194 sol


description: Gene expression data from Human chronic lymphocytic leukemia patient SS0275


description: Gene expression data from Human chronic lymphocytic leukemia patient SL0083


title: WT_12h_5


description: Gene expression data from Human chronic lymphocytic leukemia patient SS0299


title: 223 sol


description: Gene expression data from Human chronic lymphocytic leukemia patient SG0168


description: Gene expression data from Human chronic lymphocytic leukemia patient SF0098


description: Gene expression data from Human chronic lymphocytic leukemia patient SG0114


title: KO_clone1_12h_1


description: Gene expression data from Human chronic lymphocytic leukemia patient SA0205


description: Gene expression data from Human chronic lymphocytic leukemia patient SA0093


title: WT_12h_1


title: WT_12h_2


description: Gene expression data from Human chronic lymphocytic leukemia patient SA0021


description: Gene expression data from Human chronic lymphocytic leukemia patient SA0219


title: WT_12h_4


title: brain_hom_rep3 [BH4 study]

description:
SAMPLE 7
replicate 3

source_name: brain

value: brain


title: brain_hom_rep4 [BH4 study]

description:
SAMPLE 8
replicate 4


title: brain_hom_rep2 [BH4 study]

description:
SAMPLE 6
replicate 2


title: brain_wt_rep2 [BH4 study]

description:
SAMPLE 2
replicate 2


title: Athal_PNM_7dpi_R1

city: Regensburg

first: Urs

last: Lahrmann

address: Am Biopark 9

department: Project Group Personalized Tumor Therapy

institute: Fraunhofer ITEM

description:
SAMPLE 16
A. thaliana plants were pre-grown for 14 days prior to mock treatment

hyb_protocol: Hybridization and washing was performed according to Agilent's One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling protocol (version 6.5).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 2um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing:
The scanned images were analyzed with Feature Extraction Software 10.5 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities (gProcessedSignal).
For the current manuscript, we analyzed (a) S. vermifera probes/genes responsive to A. thaliana colonization (using fungal probes from samples 4-15) and (b) A. thaliana probes/genes responsive to either S. vermifera or P. indics colonization (using plant probes from all samples except 13-15).
For the analysis of fungal genes, the plant probes in the dataset were set to null and vice versa as they would bias the normalization.
Furthermore all control probes (e.g. dark corner, spike ins, etc) were set to null as they are unimportant for the analysis.

organism: Arabidopsis thaliana

source_name: A. thaliana grown on 1/10 PNM, 7 days post mock treatment, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng total RNA according to Agilent's One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling protocol (version 6.5) followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop-1000 Spectrophotometer (Agilent)

growth_protocol: Piriformospora indica Sav. Verma, Aj. Varma, Rexer, G. Kost & P. Franken (DSM11827, Deutsche Sammlung von Mikroorganismen und Zellkulturen, DSMZ, Braunschweig, Germany) cultures were propagated at 28°C in liquid complete medium (CM) (Pham et al., 2004) supplemented with 2% glucose and 130 rpm shaking or on solid medium supplemented with 1.5% agar. S. vermifera cultures were propagated at 25°C in liquid MYP medium (0.7% w/v malt extract; 0.1% w/v peptone; 0.05% w/v yeast extract) and 120 rpm shaling or on solid medium supplemented with 1.5% agar. For microarray experiments P. indica and S. vermifera were cultivated on 1/10 PNM-agar plates (Basiewicz et al., 2011) for 3 days. Arabidopsis thaliana seeds (Ecotype Columbia-0) were incubated for 5 min in 70 % ethanol, surface sterilized for 5 min with 6 % sodium hypochlorite and washed 6 times for 5 min in sterile water. After stratification for 3 days at 4°C in the dark on 1/10 PNM medium, Arabidopsis seedlings were grown for 14 days under sterile conditions in a phytochamber (Vötsch, Balingen-Frommern, Germany) at long day conditions (day: 16 h, 23°C (350 µmol/m-2s-1); night: 8 h, 18°C; 60% humidity).

extract_protocol: Arabidopsis root material was harvested in liquid nitrogen 3, 7 and 14 dpi. For each time point roots from 45 to 60 plants were pooled. S. vermifera hyphae grown on plate were thoroughly scratched from the agar surface with a sterile scalpel 3 dpi and immediately frozen in liquid nitrogen. All experiments were performed in 3 independent biological replications. Total RNA from 200 mg grounded material was extracted with TRIzol (Invitrogen, Karlsruhe, Germany) following the manufacturer's instructions. Amount and quality of the extracted RNA was estimated by NanoDrop-1000 Spectrophotometer (Agilent) and by a 2100 Bioanalyzer (Agilent, Santa Clara, USA).

treatment_protocol: For inoculation of Arabidopsis roots with P. indica or S. vermifera, plants of roughly the same size were first transferred to square petri dishes containing 1/10 PNM. Arabidopsis roots were inoculated directly with either 500.000 P. indica spores per 20 seedlings or 2 plugs S. vermifera mycellium per plant root or mock treated with tween water (0.002% TWEEN20).

value: root

tag: growth protocol

value: grown on 1/10 PNM alone

tag: inoculant

value: mock treatment

tag: time (dpi)

value: 7 days

value: 21 days


title: brain_wt_rep4 [BH4 study]

description:
SAMPLE 4
replicate 4

tag: tissue


title: x314

source_name: Breast tumor tissue

tag: group

value: LumA

source_name: Universal Human Reference RNA (Stratagene)

tag: reference


description: Gene expression data from Human chronic lymphocytic leukemia patient RS0260

value: unmut


description: Gene expression data from Human chronic lymphocytic leukemia patient RS0325


title: WT_12h_3


title: brain_hom_rep1 [BH4 study]

description:
SAMPLE 5
replicate 1

value: homozygous

tag: age

value: 17 weeks

tag: gender

value: male


description: Gene expression data from Human chronic lymphocytic leukemia patient RM0400

value: mut


title: brain_wt_rep1 [BH4 study]

description:
SAMPLE 1
replicate 1


description: Gene expression data from Human chronic lymphocytic leukemia patient RG0077


title: 7 days, valproic acid 1 mM, nr6

city: Bilthoven

first: Jeroen

last: Pennings

address: A. van Leeuwenhoeklaan 9

country: Netherlands

institute: Natl. Inst. Public Health & Environment

hyb_protocol: The labeled cRNA was fragmented and hybridized to the Affymetrix HT HG-U133 + PM plates.

scan_protocol: Plates were scanned with Genechip HT array plate scanner and analysed with Affymetrix HT software suite.

data_processing: Quality control and normalization of Affymetrix CEL files were performed using the ArrayAnalysis website (http://www.arrayanalysis.org/) (Maastricht University, The Netherlands) , using the Robust Multichip Average (RMA) algorithm and MBNI custom CDF version 14.

source_name: human embryonic stem cells

label_protocol: Amplification, labeling and hybridization was performed according to Affymetrix protocols, using an automated Affymetrix Genechip console. For each individual sample 100 ng RNA was used for the biotin-labelling reaction.

growth_protocol: H9 hESC were routinely cultured on mytomycin mitotically inactivated mouse embryonic fibroblast at 37˚C in hESC medium, containing DMEM-F12, supplemented with 20% Knock Out Serum Replacement (KOSR), 1mM L-Glutamine, 0.5% 5000 IU/ ml Penicillin/5000 μg/ml Streptomycin, 1%  non-essential amino acids, 0.1mM β-Mercaptoethanol and 0.2µg/ml fibroblast growth factor-basic(bFGF). hESC were passaged 2-3 per week.   hESC cells were differentiated as described in (Schulpen et. al 2014) . Briefly, hESC were enzymatically dissociated after incubation with Collagenase IV and transferred to bacterial culture dishes containing hESC culture medium. Within 4 days the cells formed cell aggregates, which were transferred to Poly-D-Lysine (PDL)/ Laminin coated cell culture dishes containing DMEM-F12 supplemented 1% 5000 IU/ ml Penicillin/ 5000 μg/ml Streptomycin, 1.5 mM L-Glutamine and 10% insulin, transferrin and Selenium (ITS) premix. The cell aggregates attached to the bottom of the dishes and were cultured for 3 days. At day 7 the ITS medium was replaced by neurobasal medium supplemented with 1% 5000 IU/ ml Penicillin/ 5000 μg/ml Streptomycin, N-2- and B27 premix.

extract_protocol: Cells ready for RNA extraction, were stored at -20˚C in RNA protect (Qiagen). Before RNA extraction, the cells in RNA protect were thawed, centrifuged and the RNA protect was discarded. The RNA was extracted using the QiaCube and  RNeasy mini kit (Qiagen) including an DNase incubation step, following the manufactures manual. The extracted RNA was stored at -80˚C. The concentration of the RNA samples was measured using the Nanodrop (Thermo Scientific)

treatment_protocol: Differentiating cell cultures were exposed for either 1 or 7 days to either 0.1, 0.33 or 1mM VPA; or 0.033 , 0.1 or 0.33 mM CBZ . VPA and CBZ were dissolved in medium and 0.25% DMSO respectively. Control samples were collected at day 0, 1, 4, 7, and 9. At day 1 and 7 also samples cultured with 0.25% DMSO were collected serving as a control for CBZ.

tag: time

tag: exposure

value: valproic acid

tag: concentration

value: 1 mM


description: Gene expression data from Human chronic lymphocytic leukemia patient RG0443

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


description: Gene expression data from Human chronic lymphocytic leukemia patient RG0045


title: 7 days, valproic acid 1 mM, nr4


title: 7 days, valproic acid 1 mM, nr5


title: Athal_PNM_7dpi_R3

description:
SAMPLE 18
A. thaliana plants were pre-grown for 14 days prior to mock treatment

source_name: A. thaliana grown on 1/10 PNM, 7 days post mock treatment, replicate 3


title: 7 days, valproic acid 1 mM, nr2


title: 7 days, valproic acid 0.33 mM, nr6


title: 7 days, valproic acid 1 mM, nr3


description: Gene expression data from Human chronic lymphocytic leukemia patient RR0157


title: 7 days, valproic acid 1 mM, nr1


title: Seba_PNM_3dpi_R3

description: SAMPLE 15

organism: Serendipita vermifera

source_name: S. vermifera grown on 1/10 PNM, 3 days post inoculation, replicate 3

value: hyphae

value: 3 days


title: Seba_PNM_3dpi_R1

description: SAMPLE 13

source_name: S. vermifera grown on 1/10 PNM, 3 days post inoculation, replicate 1


title: Athal_PNM_7dpi_R2

description:
SAMPLE 17
A. thaliana plants were pre-grown for 14 days prior to mock treatment

source_name: A. thaliana grown on 1/10 PNM, 7 days post mock treatment, replicate 2


title: 7 days, valproic acid 0.33 mM, nr4


title: 7 days, valproic acid 0.33 mM, nr5


title: Seba_Athal_14dpi_R3

description:
SAMPLE 12
A. thaliana plants were pre-grown for 14 days prior to inoculation

source_name: A. thaliana root, S. vermifera inoculated, 14 days post inoculation, replicate 3

value: A. thaliana

tag: host tissue

value: S. vermifera

value: 14 days

value: 28 days


description: Gene expression data from Human chronic lymphocytic leukemia patient RA0211


title: Seba_PNM_3dpi_R2

description: SAMPLE 14

source_name: S. vermifera grown on 1/10 PNM, 3 days post inoculation, replicate 2

value: grown on 1/10 PNM alone

value: mock treatment


title: 1 days, valproic acid 1 mM, nr6

value: 1 days


title: 7 days, valproic acid 0.33 mM, nr3

value: 7 days


title: Seba_Athal_14dpi_R2

description:
SAMPLE 11
A. thaliana plants were pre-grown for 14 days prior to inoculation

source_name: A. thaliana root, S. vermifera inoculated, 14 days post inoculation, replicate 2

value: root


title: Seba_Athal_7dpi_R3

description:
SAMPLE 9
A. thaliana plants were pre-grown for 14 days prior to inoculation

source_name: A. thaliana root, S. vermifera inoculated, 7 days post inoculation, replicate 3

value: 21 days


description: Gene expression data from Human chronic lymphocytic leukemia patient RA0288


description: Gene expression data from Human chronic lymphocytic leukemia patient PZ0305

value: unmut


description: Gene expression data from Human chronic lymphocytic leukemia patient RB0087


title: 1 days, valproic acid 1 mM, nr5


title: 1 days, valproic acid 1 mM, nr4


title: 7 days, valproic acid 0.1 mM, nr2


description: Gene expression data from Human chronic lymphocytic leukemia patient RB0040


title: Seba_Athal_3dpi_R3

description:
SAMPLE 6
A. thaliana plants were pre-grown for 14 days prior to inoculation

source_name: A. thaliana root, S. vermifera inoculated, 3 days post inoculation, replicate 3

value: 17 days


description: Gene expression data from Human chronic lymphocytic leukemia patient RD0296


title: 7 days, valproic acid 0.33 mM, nr2


description: Gene expression data from Human chronic lymphocytic leukemia patient PV0322


description: Gene expression data from Human chronic lymphocytic leukemia patient RA0023


title: Seba_Athal_3dpi_R2

description:
SAMPLE 5
A. thaliana plants were pre-grown for 14 days prior to inoculation

source_name: A. thaliana root, S. vermifera inoculated, 3 days post inoculation, replicate 2


title: 7 days, valproic acid 0.1 mM, nr1


title: Seba_Athal_7dpi_R1

description:
SAMPLE 7
A. thaliana plants were pre-grown for 14 days prior to inoculation

source_name: A. thaliana root, S. vermifera inoculated, 7 days post inoculation, replicate 1


title: Seba_Athal_7dpi_R2

description:
SAMPLE 8
A. thaliana plants were pre-grown for 14 days prior to inoculation

source_name: A. thaliana root, S. vermifera inoculated, 7 days post inoculation, replicate 2


title: 7 days, valproic acid 0.33 mM, nr1


title: Wild Type EB

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

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.

source_name: Wild Type EB

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

growth_protocol: V6.5, PKM1 KI, 2TS22c and ZHBTc4 cells were cultured the medium containing LIF. EB were cultured the medium without LIF for 1 week in floating culture.

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

treatment_protocol: Total RNA were extracted using Trizol.

tag: cell line

value: differentiated from V6.5

tag: cell type

value: embryoid body


title: 1 days, valproic acid 1 mM, nr2

value: valproic acid

value: 1 mM


title: Seba_Athal_3dpi_R1

description:
SAMPLE 4
A. thaliana plants were pre-grown for 14 days prior to inoculation

source_name: A. thaliana root, S. vermifera inoculated, 3 days post inoculation, replicate 1

tag: host

value: 3 days


title: ZHBTc4

value: embryonic stem cells


title: Seba_Athal_14dpi_R1

description:
SAMPLE 10
A. thaliana plants were pre-grown for 14 days prior to inoculation

source_name: A. thaliana root, S. vermifera inoculated, 14 days post inoculation, replicate 1

value: A. thaliana

value: S. vermifera


description: Gene expression data from Human chronic lymphocytic leukemia patient PS0212

value: mut


title: 2TS22c


description: Gene expression data from Human chronic lymphocytic leukemia patient PV0286


title: brain_wt_rep3 [BH4 study]

description:
SAMPLE 3
replicate 3

source_name: brain

tag: strain

tag: genotype/variation

value: wild type

tag: allels

value: 17 weeks

tag: mouse id

value: male

value: brain


title: 1 days, valproic acid 1 mM, nr3

source_name: human embryonic stem cells

value: 1 days


title: Wild Type ES

source_name: V6.5 ES cell line


title: PKM1 KI ES

source_name: PKM1 KI ES

value: PKM1 KI


title: 1 days, valproic acid 0.33 mM, nr5


description: Gene expression data from Human chronic lymphocytic leukemia patient PS0044


description: Gene expression data from Human chronic lymphocytic leukemia patient PR0084


description: Gene expression data from Human chronic lymphocytic leukemia patient PP0195

value: unmut


description: Gene expression data from Human chronic lymphocytic leukemia patient PM0340


title: 1 days, valproic acid 0.33 mM, nr4


description: Gene expression data from Human chronic lymphocytic leukemia patient PM0117


title: 1 days, valproic acid 1 mM, nr1


title: 1 days, valproic acid 0.33 mM, nr3


title: 1 days, valproic acid 0.1 mM, nr2


title: 1 days, valproic acid 0.33 mM, nr6


description: Gene expression data from Human chronic lymphocytic leukemia patient PG0216

value: nd


description: Gene expression data from Human chronic lymphocytic leukemia patient PI0172


description: Gene expression data from Human chronic lymphocytic leukemia patient PG0276


title: 7 days, carbamazepine 0.33 mM, nr4

value: 7 days

value: carbamazepine


description: Gene expression data from Human chronic lymphocytic leukemia patient PF0177


title: 1 days, valproic acid 0.1 mM, nr1

value: valproic acid


title: 1 days, valproic acid 0.33 mM, nr2


description: Gene expression data from Human chronic lymphocytic leukemia patient PF0024


description: Gene expression data from Human chronic lymphocytic leukemia patient PD0164


description: Gene expression data from Human chronic lymphocytic leukemia patient PC0304


title: 7 days, carbamazepine 0.33 mM, nr6


title: 7 days, carbamazepine 0.1 mM, nr6


description: Gene expression data from Human chronic lymphocytic leukemia patient PA0351


description: Gene expression data from Human chronic lymphocytic leukemia patient PG0028


title: 7 days, carbamazepine 0.1 mM, nr5


title: 1 days, valproic acid 0.33 mM, nr1


title: 7 days, carbamazepine 0.1 mM, nr4


description: Gene expression data from Human chronic lymphocytic leukemia patient OV0127


description: Gene expression data from Human chronic lymphocytic leukemia patient PA0145


title: 7 days, carbamazepine 0.1 mM, nr3


description: Gene expression data from Human chronic lymphocytic leukemia patient PA0146


title: 7 days, carbamazepine 0.33 mM, nr1


title: 7 days, carbamazepine 0.1 mM, nr2


title: 7 days, carbamazepine 0.33 mM, nr2


title: patient 48 ALL 48

city: Petach Tikva

first: Smadar

last: Avigad

address: 14 Kaplan Street

department: Pediatric Hematology Oncology

country: Israel

institute: Schneider Children's Medical Center of Israel

hyb_protocol: The fluorescently labeled samples were hybridized overnight to miRXplore TM Microarrays using the a-HybTM Hybridization station.The miRXplore Universal Reference (UR), representing a pool of 979 synthetic miRNAs, was used as control for comparison of multiple samples.

scan_protocol: Fluorescent signals of the hybridized miRXploreTM microarray were detected using a laser scanner from Agilent (Agilent technologies).

data_processing: Mean signal and mean local background intensities were obtained for each spot of the microarray images using Imagene® software (Biodiscovery). Low quality spots were flagged and excluded from data analysis. Unflagged spots were analyzed with the PIQORTM Analyzer software. The PIQOR Analyzer allows automated data processing of the raw data text files derived from the ImaGene software. This includes background subtraction to obtain the net signal intensity, data normalization and calculation of the Hy5/Hy3 ratios. As an additional quality filtering step, only spots/genes that have a signal eaqual/higher than the 50 percentile of the background, are taken into account for the calculation of the Hy5/Hy3 ratio. Data was transformed to to Log2 ratios for data clustering (2D-clustering using Pearson correlation and average linkage. Data were permutated 1000 times and the false discovery rate (FDR) was set to a maximum of 5%.  Identification of differentially regulated miRNAs in various comparisons, based on clinical parameters, was performed using the rank product method (Breitling R et al., FEBS Lett 2004;573:83-92) for discrimination between two groups of samples.

source_name: Acute Lymphoblastic Leukemia

label_protocol: Sample labeling was prformed according to the undisclosed miRXplore TM  User manual. For samples with sufficient RNA yield 2 μg total of RNA were used for the labeling, for all other samples the available amount of total RNA was used. Experimental samples were labeled with Hy5 and control samples, provided by Miltenyi Biotec (Germany), were labeled with Hy3.

extract_protocol: Total RNA was extracted of 107 cells from 48 BM samples using miRNeasy mini kit (Qiagen, Hilden, Germany) according to protocol. RNA concentration was determined using NanoDrop (ThermoScientific, Wilmington, DE, USA). RNA quality was assessed by Agilent 2100 Bioanalyzer Platform (Agilent technologies) and visualized by means of agarose gel electrophoresis.

tag: disease

value: Acute Lymphoblastic Leukemia (ALL)

tag: tissue

value: Bone marrow

value: X>6 or X<1

value: Male

tag: type

value: B-cell

tag: wbc

tag: prednisone response at day 8

value: poor response

tag: relapse

value: No

tag: sample type

value: Reference


title: 7 days, carbamazepine 0.33 mM, nr3

tag: time

tag: exposure

tag: concentration


description: Gene expression data from Human chronic lymphocytic leukemia patient PA0234

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

value: mut


title: patient 46 ALL 46

tag: age

tag: gender

value: T-cell

source_name: miRXplore Universal Reference (UR), representing a pool of 979 synthetic miRNAs


title: patient 45 ALL 45

value: good response


title: 7 days, carbamazepine 0.1 mM, nr1


description: Gene expression data from Human chronic lymphocytic leukemia patient OM0201


description: Gene expression data from Human chronic lymphocytic leukemia patient PA0271


title: patient 44 ALL 44


title: patient 43 ALL 43


title: patient 47 ALL 47


title: 7 days, carbamazepine 0.033 mM, nr1


description: Gene expression data from Human chronic lymphocytic leukemia patient OI0282


title: 7 days, carbamazepine 0.033 mM, nr2


title: 1 days, carbamazepine 0.33 mM, nr6

value: 1 days


description: Gene expression data from Human chronic lymphocytic leukemia patient NG0068

value: unmut


title: 1 days, carbamazepine 0.33 mM, nr4


title: patient 42 ALL 42

value: Female


description: Gene expression data from Human chronic lymphocytic leukemia patient NS0060


description: Gene expression data from Human chronic lymphocytic leukemia patient NB0333


title: 1 days, carbamazepine 0.33 mM, nr5


title: 1 days, carbamazepine 0.33 mM, nr3


description: Gene expression data from Human chronic lymphocytic leukemia patient NM0156


title: patient 41 ALL 41


title: patient 40 ALL 40


title: recurrent implantation failure after IVF_9P

city: Amsterdam

first: Sander

middle: Roeland

last: van Hooff

address: Meibergdreef 9

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

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.

source_name: recurrent implantation failure after IVF_endometrium

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.

value: endometrium

tag: condition

tag: batch

value: cohort 1

tag: time of biopsy

value: 7 days after the putative luteinizing hormone surge

tag: medical center

value: UMCU

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

tag: bmi

tag: previous implantation

tag: embryo implantations

tag: embryos replaced

source_name: Universal Human Reference RNA catalog #740000, Stratagene

value: UHR


title: 1 days, carbamazepine 0.33 mM, nr2

value: carbamazepine


title: patient 39 ALL 39

tag: disease

value: Acute Lymphoblastic Leukemia (ALL)

tag: tissue

value: Bone marrow

tag: type

tag: wbc

tag: prednisone response at day 8

tag: relapse


title: 1 days, carbamazepine 0.1 mM, nr6

tag: time

tag: exposure

tag: concentration


description: Gene expression data from Human chronic lymphocytic leukemia patient MS0321

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


description: Gene expression data from Human chronic lymphocytic leukemia patient MV0334


title: recurrent implantation failure after IVF_8P

tag: condition

tag: batch

value: cohort 2, batch 1

tag: time of biopsy

value: 6 days after the putative luteinizing hormone surge

tag: age

tag: sample type


description: Gene expression data from Human chronic lymphocytic leukemia patient MS0357


description: Gene expression data from Human chronic lymphocytic leukemia patient MS0273


title: control_8C

value: control

tag: medical center

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

tag: bmi

tag: previous implantation

tag: embryo implantations


title: patient 38 ALL 38

tag: disease

tag: tissue

tag: gender

tag: type

value: B-cell

tag: wbc

value: No

value: Reference


title: 1 days, carbamazepine 0.1 mM, nr5

tag: time

value: 1 days

tag: exposure

tag: concentration


title: control_9C

tag: condition

tag: batch

value: 8 days after the putative luteinizing hormone surge

tag: embryos replaced


title: 1 days, carbamazepine 0.1 mM, nr4


title: 1 days, carbamazepine 0.1 mM, nr3


title: patient 36 ALL 36

tag: age

value: Female

tag: prednisone response at day 8

value: poor response

tag: relapse

tag: sample type


title: patient 37 ALL 37

value: X>6 or X<1

value: Male

value: T-cell


description: Gene expression data from Human chronic lymphocytic leukemia patient MP0137

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

value: unmut


title: control_7C

value: endometrium

value: cohort 1

tag: time of biopsy

value: 7 days after the putative luteinizing hormone surge

tag: medical center

value: UMCU

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

tag: bmi

tag: previous implantation

tag: embryo implantations

value: UHR


title: 1 days, carbamazepine 0.1 mM, nr2

tag: time

value: carbamazepine


title: patient 35 ALL 35

tag: disease

value: Acute Lymphoblastic Leukemia (ALL)

tag: tissue

value: Bone marrow

tag: gender

tag: type

value: B-cell

tag: wbc

value: good response


title: recurrent implantation failure after IVF_7P

tag: condition

tag: batch

value: cohort 2, batch 1

value: 6 days after the putative luteinizing hormone surge

tag: age

tag: embryos replaced


title: control_71C

value: control

tag: sample type


description: Gene expression data from Human chronic lymphocytic leukemia patient MS0189

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

value: mut


description: Gene expression data from Human chronic lymphocytic leukemia patient MS0115


title: 1 days, carbamazepine 0.033 mM, nr2

value: 1 days

tag: exposure

tag: concentration


title: patient 33 ALL 33

value: X>6 or X<1

value: Female

tag: prednisone response at day 8

tag: relapse

value: No

value: Reference


title: patient 34 ALL 34

value: Male


title: 1 days, carbamazepine 0.1 mM, nr1


title: control_73C

value: endometrium

tag: time of biopsy

value: 7 days after the putative luteinizing hormone surge

tag: medical center

value: UMCU

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

tag: bmi

tag: previous implantation

tag: embryo implantations


title: patient 32 ALL 32

tag: disease

value: Acute Lymphoblastic Leukemia (ALL)

tag: tissue

tag: gender

tag: type

tag: wbc


description: Gene expression data from Human chronic lymphocytic leukemia patient MO0174


title: patient 31 ALL 31

value: Bone marrow

tag: age

value: poor response

tag: sample type


description: Gene expression data from Human chronic lymphocytic leukemia patient MO0323

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


title: control_70C

tag: condition

tag: batch

tag: embryos replaced

value: UHR


description: Gene expression data from Human chronic lymphocytic leukemia patient MN0167


title: patient 30 ALL 30

value: B-cell

tag: prednisone response at day 8

tag: relapse


title: 1 days, carbamazepine 0.033 mM, nr1

tag: time

tag: exposure

value: carbamazepine

tag: concentration


title: recurrent implantation failure after IVF_6P

value: cohort 2, batch 1

tag: time of biopsy

tag: medical center

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

tag: bmi

tag: previous implantation

tag: embryo implantations


title: control_72C

tag: tissue

value: control

tag: age


title: control_69C

value: 5 days after the putative luteinizing hormone surge

tag: sample type


description: Gene expression data from Human chronic lymphocytic leukemia patient MM0097

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

value: unmut


title: control_68C

tag: condition

tag: batch


title: 7 days, DMSO, nr5

value: 7 days

value: DMSO


title: patient 29 ALL 29

tag: disease

value: X>6 or X<1

tag: gender

value: Female

tag: type

tag: wbc

tag: prednisone response at day 8

value: good response

value: No

value: Reference


title: control_6C

value: endometrium

tag: time of biopsy

value: 8 days after the putative luteinizing hormone surge

value: UMCU

tag: embryos replaced


description: Gene expression data from Human chronic lymphocytic leukemia patient MM0330

value: mut


description: Gene expression data from Human chronic lymphocytic leukemia patient ML0298


title: 7 days, DMSO, nr6

tag: time

tag: exposure

tag: concentration


title: patient 28 ALL 28

value: Acute Lymphoblastic Leukemia (ALL)

value: Bone marrow

value: Male

value: B-cell

tag: relapse


title: control_67C

tag: tissue

value: control

value: cohort 2, batch 1

tag: medical center

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

tag: bmi

tag: previous implantation

tag: embryo implantations

value: UHR


title: patient 27 ALL 27

tag: disease

tag: age

tag: sample type


title: 7 days, DMSO, nr2

value: 7 days

value: DMSO


title: patient 25 ALL 25

value: X>6 or X<1

tag: gender

tag: type

tag: wbc


title: 1 days, DMSO, nr6

value: 1 days


description: Gene expression data from Human chronic lymphocytic leukemia patient MG0110

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


title: patient 26 ALL 26

value: T-cell

tag: prednisone response at day 8

value: good response

value: No


title: 7 days, DMSO, nr4

tag: time

tag: exposure


description: Gene expression data from Human chronic lymphocytic leukemia patient MG0248


title: control_66C

value: endometrium

tag: condition

tag: batch

value: cohort 1

tag: time of biopsy

value: 6 days after the putative luteinizing hormone surge

tag: embryos replaced


description: Gene expression data from Human chronic lymphocytic leukemia patient MF0379

value: unmut


title: 7 days, DMSO, nr3

tag: concentration


title: 1 days, DMSO, nr5


title: control_65C

tag: tissue

value: 7 days after the putative luteinizing hormone surge

tag: medical center

value: UMCU

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

tag: bmi

tag: previous implantation


title: patient 24 ALL 24

tag: disease

value: Acute Lymphoblastic Leukemia (ALL)

value: Bone marrow

tag: age

tag: gender

value: Male

value: B-cell

tag: relapse

tag: sample type

value: Reference


title: 1 days, DMSO, nr4

tag: time

value: DMSO


title: control_62C

value: control

value: cohort 2, batch 1

tag: embryo implantations

value: UHR


description: Gene expression data from Human chronic lymphocytic leukemia patient MG0170

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


description: Gene expression data from Human chronic lymphocytic leukemia patient MF0274

value: mut


title: 1 days, DMSO, nr3

value: 1 days

tag: exposure


title: patient 22 ALL 22

value: X>6 or X<1

value: Female

tag: type

tag: wbc

tag: prednisone response at day 8

value: good response

value: No


title: control_64C

tag: tissue

value: endometrium

tag: condition

tag: batch

tag: time of biopsy

value: 7 days after the putative luteinizing hormone surge

tag: embryos replaced


description: Gene expression data from Human chronic lymphocytic leukemia patient MF0048


title: control_61C

value: cohort 1

value: 6 days after the putative luteinizing hormone surge

tag: medical center

value: UMCU

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

tag: bmi

tag: previous implantation


description: Gene expression data from Human chronic lymphocytic leukemia patient MC0134


title: 1 days, DMSO, nr2

tag: concentration


title: patient 21 ALL 21

tag: disease

value: Acute Lymphoblastic Leukemia (ALL)

value: Bone marrow

tag: age

tag: gender

value: Male

value: T-cell

tag: relapse

tag: sample type


title: patient 20 ALL 20

tag: type

value: B-cell

tag: wbc

value: Reference


description: Gene expression data from Human chronic lymphocytic leukemia patient MC0105

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

value: unmut


title: patient 23 ALL 23

tag: tissue

tag: prednisone response at day 8


title: 1 days, DMSO, nr1

tag: time

value: 1 days

tag: exposure

value: DMSO


title: recurrent implantation failure after IVF_5P

tag: condition

tag: batch

value: cohort 2, batch 1

tag: time of biopsy

tag: medical center

tag: embryo implantations

tag: embryos replaced

value: UHR


title: patient 19 ALL 19

tag: disease

tag: age

value: X>6 or X<1

value: good response

value: Yes


title: patient 18 ALL 18

tag: gender

value: Female

tag: relapse


description: Gene expression data from Human chronic lymphocytic leukemia patient MC0055


title: control_60C

value: endometrium

value: control

value: 7 days after the putative luteinizing hormone surge

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

tag: bmi

tag: previous implantation

tag: sample type


title: patient 17 ALL 17

value: Acute Lymphoblastic Leukemia (ALL)

tag: tissue

value: Bone marrow

tag: type

tag: wbc

tag: prednisone response at day 8


description: Gene expression data from Human chronic lymphocytic leukemia patient MB0065

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


title: control_5C

tag: condition

tag: batch

value: cohort 1

tag: time of biopsy

value: UMCU


description: Gene expression data from Human chronic lymphocytic leukemia patient MA0209


title: 11 days, unexposed, nr1

tag: time

value: 11 days

tag: exposure

value: unexposed

tag: concentration

value: 0 mM


description: Gene expression data from Human chronic lymphocytic leukemia patient MA0151

value: mut


title: control_63C

tag: medical center

tag: age

tag: embryo implantations

tag: embryos replaced


title: control_58C

value: cohort 2, batch 1

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

tag: bmi

tag: previous implantation


title: control_59C

tag: tissue

value: 5 days after the putative luteinizing hormone surge

tag: sample type

value: UHR


title: 11 days, unexposed, nr2


title: 11 days, unexposed, nr4


title: control_57C

value: 6 days after the putative luteinizing hormone surge


title: 11 days, unexposed, nr3


title: 9 days, unexposed, nr2

value: 9 days


description: Gene expression data from Human chronic lymphocytic leukemia patient MA0088


title: control_56C


title: patient 13 ALL 13

tag: disease

value: X>6 or X<1

tag: gender

value: Male

tag: type

value: B-cell

tag: wbc

tag: prednisone response at day 8

value: good response

tag: relapse

value: Yes

value: Reference


title: patient 16 ALL 16

value: Acute Lymphoblastic Leukemia (ALL)

value: Bone marrow

value: poor response


title: patient 15 ALL 15

value: Female


title: patient 14 ALL 14


title: 7 days, unexposed, nr6

tag: time

value: 7 days

tag: exposure

value: unexposed

value: 0 mM


title: patient 12 ALL 12


description: Gene expression data from Human chronic lymphocytic leukemia patient LP0364

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

value: unmut


title: 7 days, unexposed, nr5

tag: concentration


title: control_54C

value: endometrium

tag: condition

value: control

tag: batch

value: cohort 2, batch 1

tag: time of biopsy

value: 7 days after the putative luteinizing hormone surge

tag: medical center

value: UMCU

tag: age

tag: embryo implantations

value: UHR


description: Gene expression data from Human chronic lymphocytic leukemia patient LR0247

value: mut


title: patient 10 ALL 10

tag: tissue

value: Male

value: B-cell

value: good response

value: Yes

tag: sample type


description: Gene expression data from Human chronic lymphocytic leukemia patient LP0076


description: Gene expression data from Human chronic lymphocytic leukemia patient MG0449


description: Gene expression data from Human chronic lymphocytic leukemia patient LV0118


title: patient 9 ALL 9

tag: disease

value: Acute Lymphoblastic Leukemia (ALL)

value: Bone marrow

tag: gender

value: poor response

value: Reference


description: Gene expression data from Human chronic lymphocytic leukemia patient LM0150


title: 9 days, unexposed, nr1

value: 9 days

value: unexposed

value: 0 mM


title: 7 days, unexposed, nr2

value: 7 days


title: 7 days, unexposed, nr3


title: control_55C

value: endometrium

value: control

value: cohort 1

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

tag: bmi

tag: previous implantation

tag: embryos replaced


title: control_50C

value: 6 days after the putative luteinizing hormone surge

value: UMCU

value: UHR


title: control_52C

value: cohort 2, batch 1


title: 7 days, unexposed, nr4

tag: time

tag: exposure


title: control_53C

value: 5 days after the putative luteinizing hormone surge


title: recurrent implantation failure after IVF_4P

value: 7 days after the putative luteinizing hormone surge


title: patient 11 ALL 11

value: Acute Lymphoblastic Leukemia (ALL)

value: Male

tag: type

value: B-cell

tag: wbc

tag: prednisone response at day 8

value: good response

tag: relapse

value: Yes


title: 7 days, unexposed, nr1

value: unexposed

tag: concentration


description: Gene expression data from Human chronic lymphocytic leukemia patient LL0130

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

value: unmut


title: control_51C

tag: condition

tag: batch

value: cohort 2, batch 2

tag: time of biopsy

value: 8 days after the putative luteinizing hormone surge

tag: medical center

value: AMC

tag: age

tag: embryo implantations


title: control_4C

tag: tissue

value: endometrium

value: control

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

tag: bmi

tag: sample type


title: 4 days, unexposed, nr3

tag: time

value: 4 days

tag: exposure

value: 0 mM


title: patient 6 ALL 6

tag: disease

value: Bone marrow

value: X>6 or X<1

tag: gender

tag: type

value: T-cell

tag: wbc

value: Reference


title: 4 days, unexposed, nr4

tag: concentration


title: patient 7 ALL 7

value: Acute Lymphoblastic Leukemia (ALL)

value: Male

tag: prednisone response at day 8

value: poor response

tag: relapse


title: patient 8 ALL 8

value: B-cell

value: good response

value: Yes


title: control_49C

tag: condition

tag: batch

value: cohort 2, batch 1

tag: time of biopsy

value: 7 days after the putative luteinizing hormone surge

value: UMCU

tag: previous implantation

tag: embryos replaced

value: UHR


title: patient 5 ALL 5

tag: tissue

tag: age


description: Gene expression data from Human chronic lymphocytic leukemia patient LG0224

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

value: mut


description: Gene expression data from Human chronic lymphocytic leukemia patient LI0133


title: patient 4 ALL 4

value: Female

tag: sample type


title: patient 3 ALL 3


description: Gene expression data from Human chronic lymphocytic leukemia patient LG0038

value: unmut


description: Gene expression data from Human chronic lymphocytic leukemia patient LG0337


title: 4 days, unexposed, nr2

tag: time

value: 4 days

tag: exposure

value: unexposed

value: 0 mM


title: 1 days, unexposed, nr4

value: 1 days


description: Gene expression data from Human chronic lymphocytic leukemia patient LF0102


description: Gene expression data from Human chronic lymphocytic leukemia patient IA0025


title: control_46C

value: endometrium

value: control

tag: medical center

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

tag: bmi

tag: embryo implantations


title: 1 days, unexposed, nr5

tag: concentration


title: control_47C


title: patient 2 ALL 2

tag: disease

value: Acute Lymphoblastic Leukemia (ALL)

value: Bone marrow

value: X>6 or X<1

tag: gender

tag: type

value: T-cell

tag: wbc

tag: prednisone response at day 8

tag: relapse

value: Reference


title: control_44C

tag: tissue

tag: condition

tag: batch

value: cohort 2, batch 1

tag: time of biopsy

value: 8 days after the putative luteinizing hormone surge

value: AMC

tag: previous implantation

tag: embryos replaced


title: 4 days, unexposed, nr1

tag: time

tag: exposure


title: control_48C

value: 5 days after the putative luteinizing hormone surge

tag: medical center

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

tag: age

tag: bmi

tag: sample type

value: UHR


title: 1 days, unexposed, nr3

tag: concentration


title: control_45C

value: 7 days after the putative luteinizing hormone surge

value: UMCU

tag: embryo implantations


description: Gene expression data from Human chronic lymphocytic leukemia patient HG0135

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

value: unmut


title: patient 1 ALL 1

tag: disease

tag: gender

value: Male

tag: type

tag: wbc

tag: prednisone response at day 8

value: good response

tag: relapse

value: Yes


description: Gene expression data from Human chronic lymphocytic leukemia patient GR0169

value: mut


title: 7 days, DMSO, nr1

value: 7 days

value: DMSO


title: 0 days, unexposed, nr6

value: 0 days

value: unexposed

value: 0 mM


description: Gene expression data from Human chronic lymphocytic leukemia patient GR0092


title: 1 days, unexposed, nr1

value: 1 days


title: 1 days, unexposed, nr2


description: Gene expression data from Human chronic lymphocytic leukemia patient GS0343


title: 0 days, unexposed, nr5


title: recurrent implantation failure after IVF_42P

tag: tissue

value: endometrium

tag: condition

tag: batch

value: cohort 1

tag: time of biopsy

tag: previous implantation

tag: embryos replaced


title: recurrent implantation failure after IVF_43P

value: cohort 2, batch 1

value: 5 days after the putative luteinizing hormone surge

tag: medical center

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

tag: age

tag: bmi


title: Dominican_IM_123

city: Houston

first: Hiroyuki

last: Nagashima

state: Texas

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

department: Department of Medicine Gastroenterology and Hepatology

institute: Baylor College of Medicine

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

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.

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)

value: gastric epithelium

value: M

tag: country

value: Dominican Republic

tag: gastritis grade

value: IM


title: control_42C

value: control

value: UMCU

tag: embryo implantations

tag: sample type

value: UHR


description: Gene expression data from Human chronic lymphocytic leukemia patient GR0033

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

value: mut


title: 0 days, unexposed, nr4

tag: time

tag: exposure

tag: concentration


title: recurrent implantation failure after IVF_41P

tag: tissue

tag: condition

value: 7 days after the putative luteinizing hormone surge


title: Dominican_IM_138

source_name: gastric epithelium in DR Hp-positive IM gastritis epithelium

tag: gender


description: Gene expression data from Human chronic lymphocytic leukemia patient GP0329

value: unmut


description: Gene expression data from Human chronic lymphocytic leukemia patient GP0278


title: 0 days, unexposed, nr3

value: 0 days

value: unexposed


title: control_43C

tag: batch

tag: time of biopsy

value: 6 days after the putative luteinizing hormone surge

tag: previous implantation


title: 0 days, unexposed, nr2

value: 0 mM


title: Dominican_severe_142

description: Gene expression gastric epithelium in DR Hp-positive severe gastritis epithelium

value: F

value: severe


description: Gene expression data from Human chronic lymphocytic leukemia patient GP0348


title: Dominican_IM_116


title: Dominican_IM_109


title: recurrent implantation failure after IVF_40P

value: endometrium

value: cohort 1

tag: medical center

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

tag: embryos replaced


title: 0 days, unexposed, nr1


title: control_41C

value: cohort 2, batch 1

tag: age

tag: bmi


description: Gene expression data from Human chronic lymphocytic leukemia patient GN0095


description: Gene expression data from Human chronic lymphocytic leukemia patient GP0171


description: Gene expression data from Human chronic lymphocytic leukemia patient GM0252


description: Gene expression data from Human chronic lymphocytic leukemia patient GM0041


title: Dominican_severe_49

source_name: gastric epithelium in DR Hp-positive severe gastritis epithelium

value: gastric epithelium

value: M

tag: country

value: Dominican Republic

tag: gastritis grade


title: Dominican_mild_131

description: Gene expression gastric epithelium in DR Hp-positive mild gastritis epithelium

value: mild


title: Dominican_mild_135

source_name: gastric epithelium in DR Hp-positive mild gastritis epithelium


title: ConA+BW245C_24hr_rep5

city: Kyoto

first: Tomoko

last: Fujita

address: Yoshida Konoe-Cho

department: Medicine

institute: Kyoto University

description: Gene expression of liver 24hr after ConA and BW245C injection mouse #5

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.

source_name: liver, 24hr post ConA + BW245C injection

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: ConA + BW245C injection

tag: treatment time point

value: 24 hr

value: female

tag: strain


title: control_40C

value: control

value: cohort 2, batch 2

value: 7 days after the putative luteinizing hormone surge

value: UMCU

tag: embryo implantations

tag: sample type

value: UHR


title: ConA+BW245C_24hr_rep2

description: Gene expression of liver 24hr after ConA and BW245C injection mouse #2

tag: tissue


description: Gene expression data from Human chronic lymphocytic leukemia patient GG0301

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

value: mut


title: control_3C

value: endometrium

tag: condition

tag: batch


title: Dominican_normal_80

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

tag: gender

value: normal


title: ConA+BW245C_24hr_rep4

description: Gene expression of liver 24hr after ConA and BW245C injection mouse #4


title: Dominican_mild_148

value: F


title: Dominican_severe_132

value: gastric epithelium

value: severe


title: Dominican_severe_128

value: M

value: Dominican Republic


title: ConA+BW245C_24hr_rep1

description: Gene expression of liver 24hr after ConA and BW245C injection mouse #1

value: liver


title: ConA+BW245C_24hr_rep3

description: Gene expression of liver 24hr after ConA and BW245C injection mouse #3

value: ConA + BW245C injection


title: recurrent implantation failure after IVF_39P

tag: time of biopsy

value: 6 days after the putative luteinizing hormone surge

tag: medical center

value: AMC

tag: previous implantation


title: control_39C

value: control

value: cohort 2, batch 1

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

tag: age

tag: embryos replaced


title: Dominican_mild_73

tag: country

tag: gastritis grade

value: mild


title: recurrent implantation failure after IVF_38P

value: 7 days after the putative luteinizing hormone surge

value: UMCU

tag: bmi


title: ConA+vehicle_24hr_rep5

description: Gene expression of liver 24hr after ConA and vehicle injection mouse #5

source_name: liver, 24 hr post ConA + vehicle injection

tag: treatment

value: ConA + vehicle injection

tag: treatment time point

value: 24 hr

value: female

tag: strain


title: recurrent implantation failure after IVF_3P

tag: tissue

value: endometrium

value: cohort 1

tag: embryo implantations

tag: sample type

value: UHR


description: Gene expression data from Human chronic lymphocytic leukemia patient GG0027

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

value: unmut


description: Gene expression data from Human chronic lymphocytic leukemia patient GF0281


description: Gene expression data from Human chronic lymphocytic leukemia patient GE0125

value: mut


title: control_37C

tag: condition

tag: batch

value: cohort 2, batch 2


title: Dominican_normal_70

source_name: gastric epithelium in DR Hp-negative normal epithelium

value: gastric epithelium

tag: gender

value: F

value: Dominican Republic

value: normal


title: ConA+vehicle_24hr_rep3

description: Gene expression of liver 24hr after ConA and vehicle injection mouse #3

value: liver


description: Gene expression data from Human chronic lymphocytic leukemia patient IL0066


title: control_38C

value: control

value: cohort 2, batch 1

tag: time of biopsy

tag: medical center

value: AMC

tag: previous implantation


title: recurrent implantation failure after IVF_37P

value: 5 days after the putative luteinizing hormone surge

value: UMCU

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

tag: age

tag: embryos replaced


title: DR_normal_1

value: M

tag: country

tag: gastritis grade


title: Dominican_normal_68


title: recurrent implantation failure after IVF_36P

value: endometrium

value: 7 days after the putative luteinizing hormone surge

tag: bmi


description: Gene expression data from Human chronic lymphocytic leukemia patient GD0262


title: ConA+vehicle_24hr_rep4

description: Gene expression of liver 24hr after ConA and vehicle injection mouse #4

tag: treatment

value: ConA + vehicle injection

tag: treatment time point

value: 24 hr

value: female

tag: strain


description: Gene expression data from Human chronic lymphocytic leukemia patient GC0328

value: mut


title: ConA+BW245C_3hr_rep4

description: Gene expression of liver 3hr after ConA and BW245C injection mouse #4

source_name: liver, 3hr post ConA + BW245C injection

tag: tissue

value: ConA + BW245C

value: 3 hr


description: Gene expression data from Human chronic lymphocytic leukemia patient GD0158

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


title: control_36C

tag: condition

tag: embryo implantations

tag: sample type

value: UHR


title: recurrent implantation failure after IVF_35P

tag: batch

value: cohort 1

tag: time of biopsy


description: Gene expression data from Human chronic lymphocytic leukemia patient GD0051


title: control_35C

tag: medical center

tag: previous implantation


title: Bhutan_IM_181

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

value: gastric epithelium

tag: gender

value: F

tag: age

value: Bhutan

value: IM


title: recurrent implantation failure after IVF_34P

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

tag: embryos replaced


title: ConA+vehicle_24hr_rep1

description: Gene expression of liver 24hr after ConA and vehicle injection mouse #1

value: liver


title: ConA+vehicle_24hr_rep2

description: Gene expression of liver 24hr after ConA and vehicle injection mouse #2


title: ConA+BW245C_3hr_rep5

description: Gene expression of liver 3hr after ConA and BW245C injection mouse #5


title: Bhutan_IM_164

source_name: gastric epithelium in Bhutan Hp-positive IM gastritis epithelium

tag: country

tag: gastritis grade


description: Gene expression data from Human chronic lymphocytic leukemia patient GC0147

value: unmut


description: Gene expression data from Human chronic lymphocytic leukemia patient GL0368


title: ConA+BW245C_3hr_rep3

description: Gene expression of liver 3hr after ConA and BW245C injection mouse #3

tag: treatment

tag: treatment time point


title: Bhutan_IM_186

tag: tissue


title: ConA+BW245C_3hr_rep2

description: Gene expression of liver 3hr after ConA and BW245C injection mouse #2

tag: strain


title: Bhutan_severe_77

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

value: severe


description: Gene expression data from Human chronic lymphocytic leukemia patient GC0096

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


title: ConA+BW245C_3hr_rep1

description: Gene expression of liver 3hr after ConA and BW245C injection mouse #1


title: Bhutan_severe_36

source_name: gastric epithelium in Bhutan Hp-positive severe gastritis epithelium

value: M


description: Gene expression data from Human chronic lymphocytic leukemia patient GC0015


title: control_34C

value: endometrium

tag: condition

value: control

value: 7 days after the putative luteinizing hormone surge

value: UMCU

tag: bmi

tag: embryo implantations


description: Gene expression data from Human chronic lymphocytic leukemia patient GB0267

value: mut


description: Gene expression data from Human chronic lymphocytic leukemia patient GB0293


title: control_33C

tag: batch

value: cohort 2, batch 1

tag: time of biopsy

value: 6 days after the putative luteinizing hormone surge

tag: sample type


description: Gene expression data from Human chronic lymphocytic leukemia patient GA0141


description: Gene expression data from Human chronic lymphocytic leukemia patient GA0398


description: Gene expression data from Human chronic lymphocytic leukemia patient GA0091


title: ConA+vehicle_3hr_rep5

description: Gene expression of liver 3hr after ConA and vehicle injection mouse #5

source_name: liver, 3 hr post ConA + vehicle injection

value: ConA + vehicle

value: 3 hr

tag: gender

value: female


title: recurrent implantation failure after IVF_32P

tag: medical center

tag: age

tag: previous implantation

value: UHR


title: recurrent implantation failure after IVF_31P

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

tag: embryos replaced


title: Bhutan_mild_146

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

value: gastric epithelium

tag: country

value: Bhutan

tag: gastritis grade

value: mild


title: ConA+vehicle_3hr_rep3

description: Gene expression of liver 3hr after ConA and vehicle injection mouse #3

tag: tissue

value: liver

tag: treatment

tag: treatment time point


title: Bhutan_severe_74

value: F

value: severe


title: ConA+vehicle_3hr_rep4

description: Gene expression of liver 3hr after ConA and vehicle injection mouse #4

tag: strain


title: control_32C

value: endometrium

tag: condition

tag: bmi


title: control_31C

value: control

tag: batch

value: cohort 2, batch 2

tag: embryo implantations


title: non-treated liver_rep_5

description: Gene expression of non-treated liver mouse #5

source_name: liver, unstimulated

value: unstimulated


title: recurrent implantation failure after IVF_33P

value: cohort 1

tag: time of biopsy

value: UMCU

tag: sample type


title: Bhutan_mild_140

source_name: gastric epithelium in Bhutan Hp-positive mild gastritis epithelium

tag: gender

value: M


title: ConA+vehicle_3hr_rep2

description: Gene expression of liver 3hr after ConA and vehicle injection mouse #2

value: ConA + vehicle


title: ConA+vehicle_3hr_rep1

description: Gene expression of liver 3hr after ConA and vehicle injection mouse #1

value: 3 hr


title: Bhutan_severe_32

tag: age


title: Bhutan_mild_143


title: Bhutan_mild_108


title: recurrent implantation failure after IVF_30P

value: cohort 2, batch 1

value: 6 days after the putative luteinizing hormone surge

tag: medical center

value: AMC

tag: previous implantation


description: Gene expression data from Human chronic lymphocytic leukemia patient FR0283

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

value: unmut


description: Gene expression data from Human chronic lymphocytic leukemia patient FS0155


title: control_30C

value: 7 days after the putative luteinizing hormone surge

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

tag: embryos replaced

value: UHR


title: control_2C

tag: tissue


description: Gene expression data from Human chronic lymphocytic leukemia patient FO0291

value: mut


description: Gene expression data from Human chronic lymphocytic leukemia patient FP0153


title: non-treated liver_rep_4

description: Gene expression of non-treated liver mouse #4

value: liver

tag: treatment

value: female