title: Fur_no_iron_2

city: La Jolla

first: Mallory

last: Embree

address: PFBH/EBU3a, 9500 Gilman Drive Rm. 414

department: Bioengineering

institute: University of California, San Diego

hyb_protocol: Hybridization was performed by the UCSD GeneChip Core, following the Nimblegen standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed with an Axon GenePix 4000B scanner by the UCSD GeneChip Core, following the Nimblegen standard operating protocol. See www.nimblegen.com.

data_processing:
IP/mock-IP ratios were computed and enriched regions (data in the 6th column of .gff file) were identified with NimbleScan software version 2.4.27 (Roche, Nimblegen) by using default parameters.
Peaks have to have at least 2-fold enrichment and have to be identified in 2/3 replicates. Peaks were subject to manual curation afterwards.

organism: Geobacter sulfurreducens PCA

source_name: G. sulfurreducens ChIP DNA (IP'd with Fur antibody)

label_protocol: Labeling was performed following the Nimblegen standard operating protocol. See www.nimblegen.com.

growth_protocol: G. sulfurreducens cells were cultured on Fresh Water Acetate Fumarate medium with no trace iron, and harvested during mid-log phase.

extract_protocol: Cells at appropriate cell density were cross-linked by 1% formaldehyde at room temperature for 25 min. Following quenching of the unused formaldehyde with a final concentration of 125 mM glycine at room temperature for 5 min., the cross-linked cells were harvested and washed three times with 50 mL of ice-cold TBS (Tris Buffered Saline). The washed cells were re-suspended in 0.5 mL lysis buffer composed of 50 mM Tris-HCl (pH 7.5), 100 mM NaCl, 1 mM EDTA, 1 ug/mL RNaseA, protease inhibitor cocktail (Sigma) and 1 kU Ready-LyseTM lysozyme (Epicentre). The cells were incubated at room temperature for 30 min and then treated with 0.5 mL of 2XIP buffer with the protease inhibitor cocktail. The lysate was then sonicated four times for 20 sec each in an ice bath to fragment the chromatin complexes using Misonix sonicator 3000 (output level = 2.5). The range of the DNA size resulting from the sonication procedure was 300 – 1000 bp. Specific antibody against the target protein was used to immunoprecipitate the chromatin protein complex and DNA. For the control (mock-IP), normal mouse IgG (Millipore) was added into the cell extract. IP DNAs were purified with QIAquick PCR Purification Kit (Qiagen) and then amplified by PCR.

tag: genotype/variation

value: Wild Type

tag: chip antibody

value: Fur

source_name: G. sulfurreducens ChIP DNA (IP'd without Fur antibody)

value: mouse IgG


title: Fur_no_iron_3

status: Public on Mar 10 2014

type: genomic

state: CA

country: USA

molecule: genomic DNA


title: Patient 2 (Vehicle Control)

type: RNA

city: Adelaide

first: Kathleen

middle: Irene

last: Pishas

address: Sarcoma Research group

country: Australia

institute: University of Adelaide

hyb_protocol: Standard Affymetrix procedure

scan_protocol: Standard Affymetrix procedure, Affymetrix GeneChip Scanner 3000 7G (software used was AGCC)

data_processing: Data processed using Partek Genomics Suite 6.5 (method is RMA, using quantile normalisation and mean probeset summarisation).  Data is in log2 format.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Patient 2 (SE41-Ewing Sarcoma)

label_protocol: Approximately 10ug of total RNA was processed to produce biotynylated cRNA targets

growth_protocol: Sarcoma tissues was collected from patients immediately following surgical resection, dissected into small pieces and explanted onto gelatinous sponges containing growth media. Explants were collected after 48 hours of incubation (37 degrees Celsius, 5% CO2)

extract_protocol: Total RNA was extracted using RNeasy mini Kit (Qiagen), using on-column RNAase-free Dnase digestion according to the manufacturer's instructions

treatment_protocol: Samples treated with vehicle control or Nutlin-3a (50uM) for 48 hours)

tag: pathology

value: De-differentiated Liposarcoma


title: M145-36 h

city: Shanghai

first: Yinhua

last: Lu

address: 300 Fenglin Road

department: Institute of Plant physiology and ecology

country: China

institute: Shanghai Institutes for Biological Sciences

description: 252091210002 1-3

hyb_protocol: Array hybridization was performed at 65°C for 17 h with constant rotation rate of 10 rpm.

scan_protocol: The arrays were scanned using Agilent DNA Microarray scanner (Agilent Technologies, Palo Alto, CA) with the resolution of 3 μm.

data_processing:
The obtained data were normalized in the Agilent’s Feature Extraction software (Agilent Technologies) using total array signals and LOWESS algorithm options.
The relative expression ratio (n-fold change: ∆draR-K vs. WT) was calculated from the normalized signal intensities.

organism: Streptomyces coelicolor

source_name: M145 after growth on MM supplemented with 75 mM Gln for 36 h

label_protocol: Purified RNA samples were reverse transcribed to cDNA using MMLV reverse transcriptase (Invitrogen), followed by transcription with T7 RNA polymerase (New England Biolabs, Beverly, MA), generating the aaUTP (Ambion, Austin, TX)-labeled cRNA. The cRNA was purified with RNeasy mini kit (QIAGEN) and then labeled with Cy3 (for both the original strain M145 and the ∆draR-K mutant).

growth_protocol: Cultures of S. coelicolor M145 and the ∆draR-K mutant grown on 75 mM glutamine-based MM plates covered with sterile plastic cellophane were harvested at three time points (36, 48 and 60 h).

extract_protocol: Total RNA preparation was conducted using TrizolTM (Invitrogen, Carlsbad, CA) following the procedures provided by the manufacturer. Subsequently, RNA samples were treated with DNase I (Takara) and then purified using RNAeasy mini kit (QIAGEN, Valencia, CA) to remove the contaminated chromosomal DNA.

treatment_protocol: Collected samples were frozen quickly in liquid nitrogen, and then ground into powder.

tag: genotype

value: wild-type M145

tag: culture time


title: Patient 2 (Nutlin 50uM)

source_name: Patient 2 (SE41-Ewing sarcoma)

value: Radiation Induced Sarcoma


title: Patient 1 (Nutlin 50uM)

source_name: Patient 1 (SE35-Myxoid liposarcoma)

value: Ewing's Sarcoma


title: M145-48 h

description: 252091210002 1-4

source_name: M145 after growth on MM supplemented with 75 mM Gln for 48 h


title: ΔdraR-K mutant-36 h

description: 252091210002 2-2

source_name: ΔdraR-K mutant after growth on MM supplemented with 75 mM Gln for 36 h

value: ΔdraR-K mutant


title: ΔdraR-K mutant-60 h

description: 252091210002 2-4

source_name: ΔdraR-K mutant after growth on MM supplemented with 75 mM Gln for 60 h


title: M145-60 h

description: 252091210002 2-1

source_name: M145 after growth on MM supplemented with 75 mM Gln for 60 h


title: Patient 9 (Vehicle Control)

source_name: Patient 9 (SE39-DDLPS)

value: Myxoid Liposarcoma


title: Patient 2 (Nutlin 10uM)


title: Fur_knock_out

growth_protocol: G. sulfurreducens cells were cultured on Fresh Water Acetate Fumarate medium, and harvested during mid-log phase.

value: Fur mutant


title: Patient 1 (Nutlin 10uM)


title: Fur_no_iron_1


title: Fur_3


title: Patient 9 (Nutlin 10uM)


title: ΔdraR-K mutant-48 h

description: 252091210002 2-3

source_name: ΔdraR-K mutant after growth on MM supplemented with 75 mM Gln for 48 h


title: Patient 22 (Nutlin 10uM)

source_name: Patient 22 (SE10 DDLPS)


title: Patient 11 (Nutlin 10uM)

source_name: Patient 11 (SE13 Myxofibrosarcoma)


title: Patient 14 (Nutlin 50uM)

source_name: Patient 14 (SE27-Radiation Induced)


title: Patient 9 (Nutlin 50uM)


title: Patient 1 (Vehicle Control)


title: gsexp_iron_excess_2

description: Gene expression of wild type G. sulfurreducens cultured in iron excess conditions

data_processing:
Probe level data was normalized with the Robust multi-array analysis (RMA) algorithm without background correction (data in the 6th column of .gff file), as implemented in NimbleScan 2.4 software
Fold changes, log2 difference values, and p-values were calculated. A gene was considered differentially expressed if the log2 difference was >1 and highly differentially expressed if the log2 difference was > 3 with a p-value < 0.05.

growth_protocol: Biological triplicates of wild type G. sulfurreducens were harvested during mid-log phase from the three following conditions: fresh water acetate fumarate media (iron sufficient condition), fresh water acetate fumarate media with NO trace iron (iron deficient condition), or ferric citrate acetate media (iron excess condition)

extract_protocol: Total RNA was extracted with TRIzol reagent (Invitrogen). Residual DNA was removed by digestion with DNAse I (Qiagen) followed by purification using the RNeasy Mini kit (Qiagen).


title: gsexp_iron_excess_3


title: Fur_2


title: Fur_1


title: Patient 11 (Vehicle Control)


title: gsexp_iron_excess_1


title: gsexp_iron_deficient_2

description: Gene expression of wild type G. sulfurreducens cultured in iron deficient conditions


title: gsexp_iron_deficient_1


title: Patient 14 (Nutlin 10uM)


title: gsexp_iron_sufficient_3

description: Gene expression of wild type G. sulfurreducens cultured in iron sufficient conditions


title: gsexp_iron_sufficient_2


title: MCF-7aro mouse xenograft treated with exemestane + LBH589, replicate 3

city: Duarte

first: Shiuan

last: Chen

address: 1500 E Duarte Rd

department: Surgical Research

institute: City of Hope

description: Gene expression data, continuous culture as indicated in 'characteristics'.

hyb_protocol: The chips were hybridized by Affymetrix Hybridization Oven 640 and washed by Affymetrix Fluidics Station 450 according to manufacturer's protocols.

scan_protocol: The chips were scanned by Affymetrix scanner 3000 7G using manufacturer's default settings.

data_processing: Raw Affymetrix intensity measurements of all probe sets were background-corrected, normalized, and summarized into gene level expression measurements using RMA method implemented in Partek Genomic Suite V6.5.

label: Biotin

source_name: MCF-7aro mouse xenograft, treated with EXE + LBH

label_protocol: WT Target Labeling Assay was performed using 100ng of total RNA according to Affymetrix's 100 ng Total RNA Labeling Protocol.

growth_protocol: MCF-7aro xenograft, EXE treatment at tumor volume of 400 cubic mm, random LBH589 or LBH589 + exe treatment at tumor volume of 700 cubic mm.

extract_protocol: RNeasy Mini Kit (QIAGEN) was used for RNA isolation from cell lines, according to manufacturer's protocol.

treatment_protocol: RNA was harvested from xenograft tumors growing in above-mentioned conditions.

tag: cell type

value: MCF-7aro mouse xenograft

tag: treatment

value: exemestane (EXE) + LBH589


title: gsexp_iron_deficient_3


title: gsexp_iron_sufficient_1


title: MCF-7aro mouse xenograft treated with exemestane + LBH589, replicate 2


title: Patient 14 (Vehicle Control)


title: MCF-7aro mouse xenograft treated with exemestane + LBH589, replicate 1


title: MCF-7aro mouse xenograft treated with exemestane, replicate 2

source_name: MCF-7aro mouse xenograft, treated with EXE

value: exemestane (EXE)


title: Patient 22 (Vehicle Control)


title: siGRAMD1B.4

city: Houston

first: Sangbae

last: Kim

state: TX

address: 1 Baylor plaza

department: HGSC

institute: Baylor Colleage of Medicine

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

hyb_protocol: Labeled, amplified material (750 ng per array) was hybridized to the Illumina HumanHT-12 V3.0 expression beadchip according to the Manufacturer's instructions (Illumina, Inc., San Diego, CA).

scan_protocol: Arrays were scanned with an Illumina Bead array Reader confocal scanner (BeadStation 500GXDW; Illumina, Inc., San Diego, CA) according to the Manufacturer's instructions

data_processing: Array data processing were performed on Illumina BeadStudio software. We normalized gene expression data using Quantile normalization and log2 transformatoin. To export to a data matrix, Sample Gene Profile option of this software was used.

source_name: Ovarian cancer cells

label_protocol: Biotin-labeled cRNA samples for hybridization were prepared according to Illumina's recommended sample labeling procedure: 500 ng of total RNA was used for cDNA synthesis, followed by an amplification/labeling step (in vitro transcription) to synthesize biotin-labeled cRNA using the Illumina. TotalPrep RNA Amplification kit (Ambion Inc., Austin, TX). cRNA concentrations using spectrophotometer (Nanodrop, ND-1000)

extract_protocol: Total RNA was isolated from tissues with mirVana RNA Isolation labeling kit (Ambion Inc) according to the manufacturer protocol. RNA quality and integrity were confirmed by ExperionTM Automated Electrophoresis System (BIO-RAD)

value: siRNA GRAMD1B

tag: cell line


title: MCF-7aro mouse xenograft treated with exemestane, replicate 1


title: siGRAMD1B.2


title: Control.4

value: siRNA Control


title: Control.2


title: MCF-7aro mouse xenograft treated with exemestane, replicate 3


title: siGRAMD1B.3


title: CF Female 2

city: Dublin

first: Paul

middle: Joseph

last: McKiernan

address: Beaumont Hospital - ERC

department: Medicine

country: Ireland

institute: RCSI

description: lncRNA and mRNA expression

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × blocking agent and 1 μl of 25 × fragmentation buffer, heated to 60 °C for 30 min, and diluted with  25 μl 2 × GE hybridization buffer. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the Human LncRNA Array v3.0 slide (8 x 60K, Arraystar). The slides were incubated for 17 hours at 65°C in an Agilent hybridization oven then washed, fixed and scanned.

scan_protocol: The slides were scanned using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: The scanned were images were analysed using the Agilent Feature Extraction software version 11.0.1.1. Data normalization was carried out using Agilent GeneSpring GX. After quantile normalization of the raw data, LncRNAs and mRNAs that at least 1 out of 6 samples have flags in Present or Marginal were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs between two groups were identified through Volcano Plot filtering.

source_name: endobronchial brushing

label_protocol: Each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method. The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: The bronchial brush was immediately placed in 5 ml MEM+Glutamax supplemented with 10% FCS and 1% penicillin-streptomycin (Life Technologies, Carlsbad, CA). Brushes were gently agitated to dislodge cells into the media, which was centrifuged at 300 × g for 5 minutes, and cell pellets were resuspended in 0.5 ml Tri Reagent (Sigma-Aldrich) before RNA extraction as per manufacturer’s protocol.  The quality and the concentration of the RNA samples were monitored at absorbance ratios of A260/A280 and A260/A230 using a NanoDrop 8000 spectrophotometer.

tag: tissue

value: bronchial epithelium

tag: gender

value: female

tag: phenotype

value: cystic fibrosis


title: NonCF Female 2

description: lncRNA and mRNA expression

value: healthy


title: NonCF Male

description: lncRNA and mRNA expression

value: male


title: Wt+PSY1_replication3

status: Public on Mar 08 2014

city: Slagelse

first: Khalid

last: Mahmood

address: Forsøgsvej 1

department: Agro-ecology

country: Denmark

institute: Aarhus University

hyb_protocol: Hybridizations were carried out in Agilent's SuperHyb Hybridization Chambers (Agilent Technologies) containing 5 μg of cyanine 3-labeled linearly amplified cRNA. The hybridization reaction was performed at 65 °C for 17 hours using the Agilent DNA microarray hybridization oven (Agilent Technologies), following procedures described in the Agilent One-Color Microarray-Based Gene Expression Analysis protocol.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides

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

organism: Arabidopsis thaliana

source_name: Whole seedlings

label_protocol: 200 ng of total RNA containing RNA spike in Mix was reverse transcribed in to cDNA that was then in vitro transcribed into cRNA, labelled with cyanine 3-CTP using Agilent Low RNA Input Linear Amp Kit (Agilent Technologies)

growth_protocol: Twenty five milligram (mg) of seeds of two plant lines (Wild type and psy1r knock out) were surface sterilized in micro-centrifuge tube by treating them with ethanol and then dipped in Klorin containing 0.2% tween for 10 min and washed again with ethanol for 10 min. Seeds were rinsed with sterile water twice and stored in wet conditions at 4 °C for three days for stratification. After stratification, seeds of two plant lines were grown hydroponically. The stratified seeds of two plant lines were grown in flask containing 250 ml MS. Flask were placed in growth chamber on shaker at 180 rpm under continuous light and fully sterilized conditions.

extract_protocol: Total RNA was extracted using the RNeasy Plant mini kit (Qiagen).RNA integrity was assessed using an Agilent 2100 Bioanalyser with RNA 6000 Nano Assay (Agilent Technologies) and was processed for use on Arabidopsis (V4) Gene Expression Microarray (Agilent Technologies).

treatment_protocol: After one week, plants were treated with PSY1 peptide at 10 nm concentration for 4 hrs and then plants were transferred into liquid nitrogen to be stored at -80 °C until RNA extraction.

value: wild type

value: treated with 10 nM PSY1 for 4 hr


title: psy1r_replication3

value: psy1r knockout

value: control


title: Control.1


title: CF Female 1

description: lncRNA and mRNA expression


title: psy1+PSY1_replication3


title: psy1+PSY1_replication1


title: Wt_replication3


title: psy1r_replication1


title: CF Male

description: lncRNA and mRNA expression


title: NonCF Female 1

description: lncRNA and mRNA expression


title: Wt+PSY1_replication1


title: psy1r_replication2


title: Wt_replication1


title: Wt_replication2


title: Wt+PSY1_replication2


title: HEECs incubated with P-treated HX conditioned HESC-derived CMS (HX + E + P-3)

city: Columbus

first: S.

last: Huang

state: Ohio

department: Ob/Gyn

institute: The Ohio State University

hyb_protocol: Total RNA samples were normalized to 500ng using Thermoscientific Nanodrop concentration readings. Samples were then amplified using Ambion's Illumina TotalPrep RNA Amplification Kit (P/N AMIL1791) following Ambion's protocol. Amplified RNA samples were measured for their concentration using the Thermoscientific Nanodrop and normalized to 750ng. Amplified RNA was hybridized to HumanHT-12 v4 Expression BeadChip using Illumina's Whole-Genome Gene Expression Direct Hybridization Assay Guide.

scan_protocol: Hybridized samples were washed using same Hybridization Assay Guide and stained with Amersham Cy3-Streptavidin (GE Healthcare PA43001).    BeadChips were scanned using the Illumina HiScan System.

data_processing: The data were normalised 75th percentile shift and transforming the baseline to the median of all samples with GX 12.6.1 software

source_name: Endometrium

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

growth_protocol: HESCs were grown to confluence in basal medium (BM), DMEM/F12 (Gibco, Grand Island, NY) supplemented with 10% charcoal-stripped calf serum. Confluent HESCs were incubated in parallel in BM with 10-8 M estradiol (E2; Sigma-Aldrich, St-Louis, MO) used as the control, or E2 + 10-7 M progesterone (P4; Sigma-Aldrich), or E2 + 10-7 M etonogestrel (ETO; Organon, Roseland, NJ) or E2 + 10-7 M medroxyprogesterone acetate (MPA ; Sigma-Aldrich ) for 7 days. then switched to serum-free defined media (DM) consisting of BM plus ITS+ (Collaborative Research, Waltham, MA), 5 uM of FeSO4, 50 uM of ZnSO4, 1 nM of CuSO4, 20 nM of Na2SeO3, trace elements (Gibco), 50 ug/ml of ascorbic acid (Sigma-Aldrich, St. Louis, MO) and 50 ng/ml of recombinant  EGF (Becton-Dickinson, Bedford, MA) containing corresponding vehicle control or steroids for 24h. The cultures were washed twice with PBS to remove the residual steroids and DM was added then incubated for 24h under NX (20% O2) or HX (0.5% O2). After collection and centrifugation, conditioned media supernatants (CMS) were stored in -70 C at the end of experimental test periods for future use in endothelial cell assays. HEECs were grown in EGM-2 MV Singlequot Medium (Cambrex Bio Science, Inc., Walkersville, MD) with 5% stripped fetal calf serum.

extract_protocol: Total RNA was isolated using Qiagen miRNeasy Mini Kit (Qiagen, Valencia, CA) and RNeasy MinElute Cleanup Kit (Qiagen, Valencia, CA) according to the manufacturer’s instructions.

treatment_protocol: Cultured HEECs were incubated 6h with vehicle control- or P4- or ETO- or MPA- treated HX or NX conditioned HESC-derived CMS. Then HEECs were washed with PBS and processed for total RNA extraction

tag: age

value: pre-menopausal

value: Female

value: HEEC

tag: cells incubated with cms

value: CMS derived from P-treated, HX conditioned HESCs


title: HEECs incubated with P-treated HX conditioned HESC-derived CMS (HX + E + P-2)


title: HEECs incubated with M-treated HX conditioned HESC-derived CMS (HX + E + M-3)

value: CMS derived from M-treated, HX conditioned HESCs


title: null stromal rep 1

city: Boston

first: Charlotte

last: Kuperwasser

address: 75 Kneeland St

institute: Tufts University

hyb_protocol: not provided

scan_protocol: not provided

data_processing: The data were normalised using quantile normalization

organism: Mus musculus

source_name: null stromal

label_protocol: not provided

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: tissue type

value: mammary gland

tag: cell population

value: Stromal

value: SNAI2 null


title: null basal rep 2

source_name: null basal

value: Basal


title: HEECs incubated with P-treated NX conditioned HESC-derived CMS (NX + E + P-1)

value: CMS derived from P-treated, NX conditioned HESCs


title: null unsort rep 2

source_name: null unsort

value: Unsorted


title: null stromal rep 3


title: null luminal rep 3

source_name: null luminal

value: Luminal


title: HEECs incubated with P-treated HX conditioned HESC-derived CMS (HX + E + P-1)


title: null stromal rep 2


title: HEECs incubated with ETO-treated HX conditioned HESC-derived CMS (HX + E + ETO-3)

value: CMS derived from ETO-treated, HX conditioned HESCs


title: WT basal rep 3

source_name: WT basal


title: HEECs incubated with M-treated NX conditioned HESC-derived CMS (NX + E + M-2)

value: CMS derived from M-treated, NX conditioned HESCs


title: HEECs incubated with ETO-treated HX conditioned HESC-derived CMS (HX + E + ETO-2)


title: null basal rep 3


title: null luminal rep 2


title: HEECs incubated with M-treated NX conditioned HESC-derived CMS (NX + E + M-3)


title: HEECs incubated with M-treated HX conditioned HESC-derived CMS (HX + E + M-1)


title: null unsort rep 3


title: mouse embryonic stem cell

city: Belmont

first: Kwang-Soo

state: MA

address: 115 Mill St.

institute: McLean Hospital/Harvard Medical School

hyb_protocol: protocol performed at Harvard Partners Center for Genomics and Genetics

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: mouse embryonic stem cell

growth_protocol: Primary mouse hepatocytes (mH) were isolated from 13.5-day-pregnant C57/BL6J mice and cultured in Dulbecco’smodified Minimal Essential Medium (DMEM, Invitrogen, Carlsbad, CA), supplemented with 10ng/ml of epidermal growth factor (EGF) (Pepprotech), 15% fetal bovine serum (FBS, Hyclone, Thermo Scientific, Logan UT), 100 U/ml penicillin and 100 μg/ml streptomycin (Invitrogen, Grand island, NY).  Reprogramming was initiated with proteins or viruses when cultures reached 10-20% confluence. Cultures were maintainedat 37°C and 5% CO2, and media changed everyother day. mESCs derived from murine strain C57/BL6J were purchased from Millipore (Cat No. SF-CMT1-2) and maintained in mouse ES medium (DMEM supplemented with 2mM L-glutamine (Invitrogen), 1mM β-mercaptoethanol, 1x non-essential amino acids (NEAA; Invitrogen, Carlsbad, CA), 15% fetal bovine serum (FBS, Hyclone, Thermo Scientific, Logan UT), 100 U/ml penicillin, 100 μg/ml streptomycin (Invitrogen), 1500U/ml (Millipore)). miPSCs were generated and maintained in mouse ES media. miPSCs were maintained on MEF feeder cells treated with mitomycin C (10μg/ml media, Sigma-Aldrich, St. Lake, MO) and passaged by washing twice with PBS, followed by dissociation with 1X trypsin-EDTA solution (Invitrogen; 10 mins).  Cells were suspended in an appropriate volume of medium and transferred onto MEF feeder cells in a new dish.

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

treatment_protocol: Cells were harvested by treating trypsin/EDTA.

value: embryonic stem cell

tag: strain


title: null luminal rep 1


title: mouse hepatocyte primary culture

scan_protocol: protocol performed at Harvard Partners Center for Genomics and Genetics

source_name: mouse hepatocyte primary culture

value: hepatocyte primary culture


title: null basal rep 1


title: HEECs incubated with P-treated NX conditioned HESC-derived CMS (NX + E + P-2)


title: WT stromal rep 3

source_name: WT stromal


title: HEECs incubated with ETO-treated HX conditioned HESC-derived CMS (HX + E + ETO-1)


title: HEECs incubated with P-treated NX conditioned HESC-derived CMS (NX + E + P-3)


title: HEECs incubated with M-treated HX conditioned HESC-derived CMS (HX + E + M-2)


title: protein based mouse iPS line 4

source_name: protein based mouse iPS line 4

label_protocol: protocol performed at Harvard Partners Center for Genomics and Genetics

value: protein based iPS line


title: HEECs incubated with M-treated NX conditioned HESC-derived CMS (NX + E + M-1)

value: pre-menopausal


title: WT luminal rep 3

source_name: WT luminal

value: Female


title: HEECs incubated with ETO-treated NX conditioned HESC-derived CMS (NX + E + ETO-2)

value: HEEC

value: CMS derived from ETO-treated, NX conditioned HESCs


title: 2-3 Cry1Ab protoxin diet-6hr-rep3

city: College Station

first: jianxiu

last: yao

state: Texas

address: 422 Minne heep center

department: Entomology

institute: Texas A&M university

description: gene expression after 6-hrs feeding

hyb_protocol: Cyanine-3 labeled cRNAs (600 ng) of each sample was hybridized to the microarray chip (six samples, including 3 from the control diet and 3 from the protoxin diet, and were hybridized on six individual microarray chips) and incubated at 65˚С for 17 h

scan_protocol: Slides were scanned using an Axon GenePix 4000B (Molecular Devices Inc. Sunnyvale, CA) with default value based on Aglient's recommendation microarray scanner at a 532 nm wavelength

data_processing:
The signal intensity of each hybridized spot was qualified and quantified with Agilent Feature Extraction Ver. 9.5 software (Agilent). Six raw data files with 12,972 customer designed probes and control probes extracted by Agilent Feature Extraction software were imported to GeneSpring GX11 and were applied ‘75% percentile shift’ normalization algorithm. Six samples were grouped into two groups (three controls and three treatments).
The quality control was assessed by examining principal components analysis (PCA) plots and correlation analysis of sample replicates. The correlation coefficients within Cry1Ab treatment or control group were larger than 97% indicating the high quality control (Fig. 3).  Analysis of variance (one-way ANOVA, p<0.05) was performed to test the variation between two groups. The Benjamini-Hochberg multiple testing correction (q<0.05) was also employed after ANOVA to identify the transcripts that were differentially expressed when the cutoff of the fold change was set at ≥2.0. The expression differences with p <0.05 and with expression ratios ≥2.0 were considered significantly different. A total of 758 probes were identified to be differentially expressed at the significant level as specified. These probes represented 174 unique transcripts found in the larval gut. Finally, gene ontologies of 174 transcripts were analyzed by using Blast2go (http://www.blast2go.org) at level 2.

organism: Ostrinia nubilalis

source_name: hemogenized whole gut tissue

label_protocol: Cyanine-3 labeled cRNAs were synthesized from Agilent single-color microarray-based gene expression kit. Dye-incorporation ratio was determined using NanoDrop 2000 spectrophotometry. The cRNA samples with the ratio cyanine-3 labeled cRNA ≥10 pmol/µg were used for hybridization

growth_protocol: The Bt-susceptible strain (Lee) of O. nubilalis was obtained from French Agricultural Research, Inc. (Minnesota, USA). Larvae were reared at 26ºC using artificial diet (Bio-Service Inc. NJ), and adults were reared in a metal cage under long-day conditions (L: D =16: 8) and 70% humidity, and routinely fed 2% sucrose water to provide supplementary reproductive nutrition.

extract_protocol: Total RNA was prepared independently for each replicate (a group of five larvae) using TRIzol reagent (Invitrogen Inc. Frederick, MD). The quantity and quality of the total RNA were determined by NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific Inc. Waltham, MA) and Agilent 2100 bioanalyzer (Agilent Technologies Inc. Santa Clara, CA).

treatment_protocol: this experiment 30 third-instar larvae were first starved for 24 h to ensure that they would feed immediately when placed on experimental diets. The larvae were divided into two groups (control and treated) and each group consisted of three replicates (5 individuals in each replicate). The larvae in the treated group were fed artificial diet containing the concentration of 0.25 μg of Cry1Ab protoxin per ml of diet. Cry1Ab protoxin was first dissolved in 50 mM sodium carbonate buffer, pH 10.0

value: whole gut

tag: developmental stage

value: 3rd instar larvae


title: WT stromal rep 2

value: mammary gland

value: Stromal

tag: genotype/variation


title: 2-2 control diet-6gr-rep3

description: gene expression after 6-hrs feeding


title: WT unsort rep 3

source_name: WT unsort


title: protein based mouse iPS line 2

source_name: protein based mouse iPS line 2


title: HEECs incubated with ETO-treated NX conditioned HESC-derived CMS (NX + E + ETO-1)


title: HEECs incubated with ETO-treated NX conditioned HESC-derived CMS (NX + E + ETO-3)


title: protein based mouse iPS line 3

source_name: protein based mouse iPS line 3


title: null unsort rep 1

value: SNAI2 null


title: HEECs incubated with control-treated HX conditioned HESC-derived CMS (HX + E-3)

value: CMS derived from control-treated, HX conditioned HESCs


title: HEECs incubated with control-treated NX conditioned HESC-derived CMS (NX + E-3)

value: CMS derived from control-treated, NX conditioned HESCs


title: WT basal rep 2

value: Basal


title: WT luminal rep 2

value: Luminal


title: HEECs incubated with control-treated HX conditioned HESC-derived CMS (HX + E-1)


title: 1-3 control diet-6gr-rep2

description: gene expression after 6-hrs feeding


title: WT stromal rep 1


title: 1-2 Cry1Ab protoxin diet-6hr-rep1

description: gene expression after 6-hrs feeding


title: HEECs incubated with control-treated NX conditioned HESC-derived CMS (NX + E-2)


title: protein based mouse iPS line 1

source_name: protein based mouse iPS line 1


title: HEECs incubated with control-treated HX conditioned HESC-derived CMS (HX + E-2)


title: Crossy clone alone

city: Stockholm

first: Tatiana

last: Pavlova

address: Nobelsvag 16

department: MTC

country: Sweden

institute: Karolinska Institutet

hyb_protocol: Array hybridization, washing and scanning were performed on a GeneTitan Instrument according to the manufacturer’s recommendations.

scan_protocol: Arrays were scanned using an Affymetrix GeneTitan scanner.

data_processing: Preprocessing was performed in Affymetrix Expression Console (v. 1.3.1) using the RMA method.

source_name: Immortalized human foreskin fibroblast cells

label_protocol: 150ng total RNA was used to generate sense strand cDNA using Ambion WT Expression kit that was fragmented and biotinylated using Affymetrix Gene Chip WT Terminal Labeling Kit.

growth_protocol: Both Whirly and Crossy cells were plated (0.5 X 106) in 10 cm dishes coated with collagen (Rat tail) (Corning) in IMDM medium for 5 days.

extract_protocol: Total RNA was prepared from 5-day-old monolayers of Whirly and Crossy fibroblasts using Ambion's RNAqueous-4PCR kit (Invitrogen).

treatment_protocol: Cells were trypsinized in trypsin-EDTA solution and then washed once with complete medium and once with PBS.

tag: clone type

value: crossy

value: BJhTERT


title: WT basal rep 1


title: WT unsort rep 1

value: Unsorted


title: 2-1 Cry1Ab protoxin diet-6hr-rep2

description: gene expression after 6-hrs feeding


title: WT unsort rep 2


title: WT luminal rep 1


title: 1-1 control diet-6hr-rep1

description: gene expression after 6-hrs feeding


title: HEECs incubated with control-treated NX conditioned HESC-derived CMS (NX + E-1)

source_name: Endometrium


title: 10_HR_SN

status: Public on Mar 07 2014

city: Xuzhou

first: Hui

last: Wang

state: Jiangsu

address: 209 Tongshan Rd

institute: Xuzhou Medical University

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a total volume of 25ul following the manufacturer's instructions. On completion of the fragmentation reaction, 25ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4851A) 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 using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent). Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. 24 samples were analyzed using the GPL16083 Platform, and 8 were analyzed using the GPL16705 Platform. Probes not detectable on either the GPL16083 or GPL16705 Platform were excluded. In addition, only probes common to both Platforms are presented. The raw data was extracted using GeneSpring GX software and was quantile normalized using the limma package in the R program. Batch effects were normalized using ComBat.

source_name: High responder, stimulated plus natalizumab treatment

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 15ng total RNA using a Low Input Quick Amp Labeling Kit (Agilent Technologies, Palo Alto, Calif, USA) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total CD4+ T cells were enriched by MACS negative sorting (Miltneyi Biotec, Auburn, CA, USA). Total RNA was extracted using TRIreagent (Cincinnati, OH, USA).

treatment_protocol: PBMCs were collected from 8 high responders (HR) and 8 low responders (LR) to natalizumab treatment and were stimulated with anti-CD3/-CD28 antibodies (0.1µg/mL, R&D Systems, Minneapolis, MN, USA), with or without addition of natalizumab (50µg/mL) and cultured for 48h.

tag: subject

tag: disease status

value: multiple sclerosis (MS)

value: male

tag: natalizumab responder type

value: high

value: whole blood

value: CD4+ T cells

value: natalizumab


title: 18_LR_S

source_name: Low responder, stimulated

value: low

tag: cell type


title: 33_HR_SN

tag: treatment


title: 35_LR_SN

source_name: Low responder, stimulated plus natalizumab treatment


title: 33_HR_S

source_name: High responder, stimulated


title: 18_LR_SN


title: 10_HR_S


title: 97_HR_SN

value: female


title: 97_HR_S


title: 35_LR_S


title: 30_LR_SN


title: Whirly clone alone

value: whirly

tag: cell line


title: 19_LR_SN

tag: tissue


title: 30_LR_S

tag: gender


title: 11_HR_SN


title: 12_HR_SN


title: 12_HR_S


title: 37_LR_SN


title: 37_LR_S


title: 11_HR_S


title: 26_HR_SN


title: 15_LR_S


title: normal tissue from patient 106

city: Beijing

first: Jiagen

last: Li

address: 17 Panjiayuannanli Chaoyang District

institute: Cancer Institute, CAMS

description: normal tissue from patient 106

hyb_protocol: The labeled RNA was purified and hybridized to microarrays according to the Agilent manufacturer's instructions.

scan_protocol: Images were scanned with the Agilent microarray scanner (Agilent), gridded, and analyzed using Agilent feature extraction software version 10.10.

data_processing: The lncRNA+mRNA array data were analyzed for data summarization, quantile normalization and quality control by using the GeneSpring software V11.5 (Agilent).

source_name: normal tissue from patient 106

label_protocol: cDNA labeled with a fluorescent dye (Cy5 and Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction.

extract_protocol: Total RNA was extracted from the specimens using Trizol reagent (Invitrogen) and purified with mirVana miRNA Isolation Kit (Ambion, Austin, TX, USA). RNA purity and concentration were determined from OD260/280 readings using spectrophotometer (NanoDrop ND-1000) and RNA integrity was determined by 1% formaldehyde denaturing gel electrophoresis.

tag: patient id

tag: Sex

tag: tobacco use

value: yes

tag: alcohol use

tag: tumor loation

value: lower

tag: tumor grade

value: well

tag: t stage

tag: n stage

tag: tnm stage

value: I

tag: arrhythmia

value: no

tag: pneumonia

tag: anastomotic leak

tag: adjuvant therapy

tag: death at fu

tag: survival time(months)

tag: disease state

value: esophageal squamous cell carcinoma

value: normal tissue from patient 106


title: 19_LR_S

tag: subject

tag: disease status

tag: gender

tag: age

tag: natalizumab responder type

tag: tissue

tag: cell type

tag: treatment


title: LR_P7_T

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent). Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. The raw data was extracted using GeneSpring GX software and was quantile normalized using the limma package in the R program.

source_name: Low responder, P7, allergen plus treatment

extract_protocol: Total CD4+ T cells were enriched by MACS negative sorting. Total RNA was extracted using a miRNeasy Mini Kit (Qiagen, Valencia, CA, USA).

treatment_protocol: PBMCs were collected from 8 high responders (HR) and 8 low responders (LR) to GC treatment and were challenged with diluent, grass pollen extract (ALK-Abelló A/S; 100 μg/mL) as well as grass pollen extract plus glucocorticoids (100ug/mL) for one week.

tag: patient

value: seasonal allergic rhinitis (SAR)

tag: gc responder type

value: allergen plus treatment


title: cancer tissue from patient 106

description: cancer tissue from patient 106

source_name: cancer tissue from patient 106

tag: patient id

tag: Sex

value: male

tag: tobacco use

tag: alcohol use

tag: tumor loation

tag: tumor grade

tag: t stage

tag: n stage

tag: tnm stage

tag: arrhythmia

value: cancer tissue from patient 106


title: normal tissue from patient 7

description: normal tissue from patient 7

source_name: normal tissue from patient 7

tag: age

value: middle

value: moderately

value: III

tag: pneumonia

tag: anastomotic leak

tag: adjuvant therapy

tag: death at fu

tag: survival time(months)

tag: disease state

value: normal tissue from patient 7


title: cancer tissue from patient 4

description: cancer tissue from patient 4

source_name: cancer tissue from patient 4

tag: patient id

value: upper

value: II

tag: tissue

value: cancer tissue from patient 4


title: normal tissue from patient 4

description: normal tissue from patient 4

source_name: normal tissue from patient 4

tag: Sex

tag: tobacco use

value: yes

value: normal tissue from patient 4


title: normal tissue from patient 97

description: normal tissue from patient 97

source_name: normal tissue from patient 97

value: female

tag: alcohol use

tag: tumor loation

value: unknown

value: normal tissue from patient 97


title: LR_P4_A

source_name: Low responder, P4, allergen

tag: patient

tag: disease status

tag: gc responder type

value: low

value: whole blood

tag: cell type

value: CD4+ T cells

tag: treatment

value: allergen


title: normal tissue from patient 94

description: normal tissue from patient 94

source_name: normal tissue from patient 94

tag: age

value: male

value: no

tag: tumor grade

tag: t stage

tag: n stage

tag: tnm stage

tag: arrhythmia

tag: pneumonia

value: esophageal squamous cell carcinoma

value: normal tissue from patient 94


title: 15_LR_SN

tag: subject

value: multiple sclerosis (MS)

tag: gender

tag: natalizumab responder type

tag: tissue

value: natalizumab


title: normal tissue from patient 6

description: normal tissue from patient 6

source_name: normal tissue from patient 6

tag: patient id

tag: Sex

tag: tobacco use

tag: alcohol use

tag: tumor loation

value: lower

value: poorly

value: III

tag: anastomotic leak

tag: adjuvant therapy

tag: death at fu

tag: survival time(months)

tag: disease state

value: normal tissue from patient 6


title: cancer tissue from patient 96

description: cancer tissue from patient 96

source_name: cancer tissue from patient 96

tag: age

value: yes

value: middle

tag: tumor grade

value: moderately

tag: t stage

tag: n stage

tag: tnm stage

value: cancer tissue from patient 96


title: cancer tissue from patient 94

description: cancer tissue from patient 94

source_name: cancer tissue from patient 94

value: II

tag: arrhythmia

tag: pneumonia

value: unknown

value: cancer tissue from patient 94


title: 26_HR_S

tag: subject

tag: disease status

tag: gender

value: male

tag: natalizumab responder type

value: high

tag: tissue

value: whole blood

tag: cell type

value: CD4+ T cells

tag: treatment


title: cancer tissue from patient 7

description: cancer tissue from patient 7

source_name: cancer tissue from patient 7

tag: patient id

tag: Sex

tag: tobacco use

value: no

tag: alcohol use

tag: tumor loation

tag: anastomotic leak

tag: adjuvant therapy

tag: death at fu

value: esophageal squamous cell carcinoma

value: cancer tissue from patient 7


title: cancer tissue from patient 97

description: cancer tissue from patient 97

source_name: cancer tissue from patient 97

tag: age

value: female

tag: tumor grade

tag: t stage

tag: n stage

tag: tnm stage

tag: arrhythmia

tag: survival time(months)

tag: disease state

value: cancer tissue from patient 97


title: cancer tissue from patient 101

description: cancer tissue from patient 101

source_name: cancer tissue from patient 101

value: lower

value: well

value: III

tag: pneumonia

tag: tissue

value: cancer tissue from patient 101


title: LR_P2_T

source_name: Low responder, P2, allergen plus treatment

tag: patient

tag: disease status

value: seasonal allergic rhinitis (SAR)

tag: gc responder type

value: low

tag: cell type

tag: treatment

value: allergen plus treatment


title: cancer tissue from patient 6

description: cancer tissue from patient 6

source_name: cancer tissue from patient 6

tag: patient id

tag: Sex

tag: tobacco use

value: yes

tag: alcohol use

tag: tumor loation

value: poorly

tag: anastomotic leak

tag: adjuvant therapy

value: unknown

value: cancer tissue from patient 6


title: normal tissue from patient 96

description: normal tissue from patient 96

source_name: normal tissue from patient 96

tag: age

value: male

value: middle

tag: tumor grade

value: moderately

tag: t stage

tag: n stage

tag: tnm stage

tag: arrhythmia

tag: death at fu

value: normal tissue from patient 96


title: LR_P8_T

source_name: Low responder, P8, allergen plus treatment

tag: patient

tag: disease status

tag: gc responder type

tag: tissue

value: whole blood

value: CD4+ T cells


title: cancer tissue from patient 92

description: cancer tissue from patient 92

source_name: cancer tissue from patient 92

tag: patient id

tag: Sex

value: no

value: II

tag: pneumonia

tag: survival time(months)

tag: disease state

value: esophageal squamous cell carcinoma

value: cancer tissue from patient 92


title: normal tissue from patient 101

description: normal tissue from patient 101

source_name: normal tissue from patient 101

tag: tobacco use

tag: alcohol use

tag: tumor loation

value: lower

value: well

value: III

tag: anastomotic leak

tag: adjuvant therapy

value: normal tissue from patient 101


title: LR_P3_A

source_name: Low responder, P3, allergen

value: seasonal allergic rhinitis (SAR)

value: low

tag: cell type

tag: treatment

value: allergen


title: LR_P7_D

source_name: Low responder, P7, diluent

value: diluent


title: cancer tissue from patient 91

description: cancer tissue from patient 91

source_name: cancer tissue from patient 91

tag: age

value: male

value: yes

value: middle

tag: tumor grade

tag: t stage

tag: n stage

tag: tnm stage

tag: arrhythmia

tag: death at fu

value: cancer tissue from patient 91


title: normal tissue from patient 92

description: normal tissue from patient 92

source_name: normal tissue from patient 92

tag: patient id

tag: Sex

value: poorly

tag: pneumonia

tag: tissue

value: normal tissue from patient 92


title: normal tissue from patient 91

description: normal tissue from patient 91

source_name: normal tissue from patient 91

tag: tobacco use

value: no

tag: alcohol use

value: moderately

value: II

tag: survival time(months)

tag: disease state

value: normal tissue from patient 91


title: normal tissue from patient 87

description: normal tissue from patient 87

source_name: normal tissue from patient 87

tag: tumor loation

value: well

tag: anastomotic leak

tag: adjuvant therapy

value: unknown

value: esophageal squamous cell carcinoma

value: normal tissue from patient 87


title: LR_P1_T

source_name: Low responder, P1, allergen plus treatment

tag: patient

tag: disease status

value: seasonal allergic rhinitis (SAR)

tag: gc responder type

value: low

value: whole blood

tag: cell type

value: CD4+ T cells

tag: treatment

value: allergen plus treatment


title: LR_P8_D

source_name: Low responder, P8, diluent

value: diluent


title: cancer tissue from patient 79

description: cancer tissue from patient 79

source_name: cancer tissue from patient 79

tag: age

value: male

value: middle

tag: tumor grade

tag: t stage

tag: n stage

tag: tnm stage

tag: arrhythmia

value: yes

tag: death at fu

value: cancer tissue from patient 79


title: normal tissue from patient 79

description: normal tissue from patient 79

source_name: normal tissue from patient 79

tag: patient id

tag: Sex

tag: tobacco use

value: no

tag: alcohol use

value: poorly

tag: pneumonia

tag: survival time(months)

tag: tissue

value: normal tissue from patient 79


title: cancer tissue from patient 73

description: cancer tissue from patient 73

source_name: cancer tissue from patient 73

tag: tumor loation

value: lower

value: III

tag: anastomotic leak

tag: adjuvant therapy

tag: disease state

value: cancer tissue from patient 73


title: cancer tissue from patient 76

description: cancer tissue from patient 76

source_name: cancer tissue from patient 76

tag: age

tag: tumor grade

value: moderately

value: unknown

value: esophageal squamous cell carcinoma

value: cancer tissue from patient 76


title: HR_P6_D

source_name: High responder, P6, diluent

tag: patient

tag: disease status

value: seasonal allergic rhinitis (SAR)

tag: gc responder type

value: high

value: whole blood

tag: cell type

value: CD4+ T cells

tag: treatment


title: HR_P5_A

source_name: High responder, P5, allergen

value: allergen


title: normal tissue from patient 74

description: normal tissue from patient 74

source_name: normal tissue from patient 74

tag: patient id

tag: Sex

value: male

value: yes

tag: t stage

tag: n stage

tag: tnm stage

tag: arrhythmia

tag: death at fu

value: normal tissue from patient 74


title: normal tissue from patient 77

description: normal tissue from patient 77

source_name: normal tissue from patient 77

tag: tobacco use

tag: alcohol use

tag: tumor loation

value: middle

value: no

tag: pneumonia

tag: anastomotic leak

tag: survival time(months)

tag: tissue

value: normal tissue from patient 77


title: normal tissue from patient 73

description: normal tissue from patient 73

source_name: normal tissue from patient 73

tag: age

value: lower

tag: tumor grade

value: poorly

value: III

tag: adjuvant therapy

tag: disease state

value: normal tissue from patient 73


title: cancer tissue from patient 77

description: cancer tissue from patient 77

source_name: cancer tissue from patient 77

tag: patient id

tag: Sex

value: moderately

value: esophageal squamous cell carcinoma

value: cancer tissue from patient 77


title: normal tissue from patient 76

description: normal tissue from patient 76

source_name: normal tissue from patient 76

tag: t stage

tag: n stage

value: unknown

value: normal tissue from patient 76


title: LR_P7_A

source_name: Low responder, P7, allergen

tag: patient

tag: disease status

value: seasonal allergic rhinitis (SAR)

tag: gc responder type

value: low

value: whole blood

tag: cell type

value: CD4+ T cells

tag: treatment


title: normal tissue from patient 71

description: normal tissue from patient 71

source_name: normal tissue from patient 71

value: male

tag: tobacco use

value: yes

tag: alcohol use

tag: tumor loation

value: upper

tag: tnm stage

value: II

tag: arrhythmia

tag: pneumonia

tag: death at fu

value: normal tissue from patient 71


title: cancer tissue from patient 74

description: cancer tissue from patient 74

source_name: cancer tissue from patient 74

tag: age

value: no

value: lower

tag: tumor grade

tag: anastomotic leak

tag: adjuvant therapy

tag: survival time(months)

tag: disease state

tag: tissue

value: cancer tissue from patient 74


title: HR_P5_T

source_name: High responder, P5, allergen plus treatment

tag: patient

tag: disease status

tag: gc responder type

value: high

value: allergen plus treatment


title: LR_P8_A

source_name: Low responder, P8, allergen

tag: cell type

tag: treatment

value: allergen


title: HR_P6_T

source_name: High responder, P6, allergen plus treatment


title: cancer tissue from patient 71

description: cancer tissue from patient 71

source_name: cancer tissue from patient 71

tag: patient id

tag: Sex

tag: tobacco use

tag: alcohol use

tag: tumor loation

value: moderately

tag: t stage

tag: n stage

value: unknown

value: esophageal squamous cell carcinoma

value: cancer tissue from patient 71


title: cancer tissue from patient 61

description: cancer tissue from patient 61

source_name: cancer tissue from patient 61

tag: age

value: female

tag: tumor grade

tag: tnm stage

value: III

tag: arrhythmia

tag: pneumonia

tag: anastomotic leak

tag: death at fu

value: cancer tissue from patient 61


title: HR_P6_A

source_name: High responder, P6, allergen

tag: patient

tag: disease status

value: seasonal allergic rhinitis (SAR)

tag: gc responder type

tag: tissue

value: whole blood

value: CD4+ T cells


title: HR_P5_D

source_name: High responder, P5, diluent

tag: cell type

tag: treatment

value: diluent


title: cancer tissue from patient 60

description: cancer tissue from patient 60

source_name: cancer tissue from patient 60

tag: patient id

tag: Sex

value: male

tag: tobacco use

value: yes

tag: alcohol use

value: middle

value: poorly

value: II

value: no

tag: adjuvant therapy

tag: survival time(months)

tag: disease state

value: cancer tissue from patient 60


title: normal tissue from patient 60

description: normal tissue from patient 60

source_name: normal tissue from patient 60

tag: age

tag: tumor loation

tag: tumor grade

tag: t stage

tag: n stage

tag: tnm stage

tag: arrhythmia

value: unknown

value: normal tissue from patient 60


title: normal tissue from patient 52

description: normal tissue from patient 52

source_name: normal tissue from patient 52

value: lower

value: well

value: I

tag: pneumonia

tag: anastomotic leak

tag: death at fu

value: esophageal squamous cell carcinoma

tag: tissue

value: normal tissue from patient 52


title: LR_P4_T

source_name: Low responder, P4, allergen plus treatment

tag: patient

tag: disease status

value: seasonal allergic rhinitis (SAR)

tag: gc responder type

value: low

value: whole blood

tag: cell type

tag: treatment

value: allergen plus treatment


title: normal tissue from patient 51

description: normal tissue from patient 51

source_name: normal tissue from patient 51

tag: patient id

tag: Sex

value: male

tag: tobacco use

value: yes

tag: alcohol use

value: moderately

tag: adjuvant therapy

tag: survival time(months)

tag: disease state

value: normal tissue from patient 51


title: normal tissue from patient 61

description: normal tissue from patient 61

source_name: normal tissue from patient 61

tag: age

value: female

value: no

tag: tumor loation

value: upper

tag: tumor grade

tag: t stage

tag: n stage

tag: tnm stage

value: III

tag: arrhythmia

value: normal tissue from patient 61


title: cancer tissue from patient 49

description: cancer tissue from patient 49

source_name: cancer tissue from patient 49

value: lower

tag: pneumonia

tag: anastomotic leak

tag: death at fu

tag: tissue

value: cancer tissue from patient 49


title: normal tissue from patient 46

description: normal tissue from patient 46

source_name: normal tissue from patient 46

tag: patient id

tag: Sex

value: middle

value: II

value: esophageal squamous cell carcinoma

value: normal tissue from patient 46


title: normal tissue from patient 49

description: normal tissue from patient 49

source_name: normal tissue from patient 49

tag: tobacco use

tag: alcohol use

value: normal tissue from patient 49


title: LR_P3_D

source_name: Low responder, P3, diluent

tag: patient

tag: disease status

value: seasonal allergic rhinitis (SAR)

tag: gc responder type

value: low

value: whole blood

tag: cell type

value: CD4+ T cells

tag: treatment

value: diluent


title: cancer tissue from patient 46

description: cancer tissue from patient 46

source_name: cancer tissue from patient 46

tag: age

value: male

value: yes

tag: tumor loation

tag: tumor grade

value: moderately

tag: t stage

tag: adjuvant therapy

tag: survival time(months)

tag: disease state

value: cancer tissue from patient 46


title: LR_P2_A

source_name: Low responder, P2, allergen

tag: tissue

value: allergen


title: cancer tissue from patient 45

description: cancer tissue from patient 45

source_name: cancer tissue from patient 45

tag: patient id

value: no

tag: n stage

tag: tnm stage

tag: arrhythmia

tag: pneumonia

tag: anastomotic leak

tag: death at fu

value: cancer tissue from patient 45


title: LR_P1_D

source_name: Low responder, P1, diluent

tag: patient

tag: disease status

tag: gc responder type

tag: cell type


title: cancer tissue from patient 52

description: cancer tissue from patient 52

source_name: cancer tissue from patient 52

tag: age

tag: Sex

tag: tobacco use

tag: alcohol use

tag: tumor loation

value: lower

tag: tumor grade

value: well

value: I

value: cancer tissue from patient 52


title: cancer tissue from patient 51

description: cancer tissue from patient 51

source_name: cancer tissue from patient 51

tag: patient id

tag: t stage

value: II

tag: adjuvant therapy

tag: survival time(months)

tag: disease state

value: esophageal squamous cell carcinoma

tag: tissue

value: cancer tissue from patient 51


title: normal tissue from patient 36

description: normal tissue from patient 36

source_name: normal tissue from patient 36

value: middle

value: poorly

tag: n stage

tag: tnm stage

value: III

tag: arrhythmia

tag: pneumonia

tag: anastomotic leak

tag: death at fu

value: normal tissue from patient 36


title: cancer tissue from patient 42

description: cancer tissue from patient 42

source_name: cancer tissue from patient 42

tag: age

tag: Sex

value: male

value: yes

value: cancer tissue from patient 42


title: normal tissue from patient 42

description: normal tissue from patient 42

source_name: normal tissue from patient 42

tag: tobacco use

tag: alcohol use

value: normal tissue from patient 42


title: LR_P4_D

source_name: Low responder, P4, diluent

tag: patient

tag: disease status

value: seasonal allergic rhinitis (SAR)

tag: gc responder type

value: low

value: whole blood

tag: cell type

value: CD4+ T cells

tag: treatment

value: diluent


title: normal tissue from patient 32

description: normal tissue from patient 32

source_name: normal tissue from patient 32

tag: patient id

tag: tumor loation

tag: tumor grade

value: moderately

tag: t stage

value: no

tag: adjuvant therapy

tag: survival time(months)

tag: disease state

value: normal tissue from patient 32


title: cancer tissue from patient 36

description: cancer tissue from patient 36

source_name: cancer tissue from patient 36

tag: n stage

tag: tnm stage

tag: arrhythmia

tag: pneumonia

tag: anastomotic leak

tag: death at fu

value: esophageal squamous cell carcinoma

tag: tissue

value: cancer tissue from patient 36


title: LR_P3_T

source_name: Low responder, P3, allergen plus treatment

tag: patient

tag: disease status

tag: gc responder type

value: allergen plus treatment


title: normal tissue from patient 31

description: normal tissue from patient 31

source_name: normal tissue from patient 31

tag: patient id

tag: age

tag: Sex

tag: tobacco use

tag: alcohol use

value: middle

value: II

value: unknown

value: normal tissue from patient 31


title: LR_P2_D

source_name: Low responder, P2, diluent

tag: cell type

tag: treatment


title: HR_P15_T

source_name: High responder, P15, allergen plus treatment

value: high


title: cancer tissue from patient 28

description: cancer tissue from patient 28

source_name: cancer tissue from patient 28

value: male

value: yes

tag: tumor loation

tag: tumor grade

tag: t stage

tag: n stage

value: III

tag: adjuvant therapy

tag: survival time(months)

tag: disease state

value: cancer tissue from patient 28


title: cancer tissue from patient 32

description: cancer tissue from patient 32

source_name: cancer tissue from patient 32

tag: tnm stage

tag: arrhythmia

tag: pneumonia

tag: anastomotic leak

tag: death at fu

tag: tissue

value: cancer tissue from patient 32


title: cancer tissue from patient 31

description: cancer tissue from patient 31

source_name: cancer tissue from patient 31

tag: patient id

tag: age

tag: Sex

tag: tobacco use

value: cancer tissue from patient 31


title: normal tissue from patient 27

description: normal tissue from patient 27

source_name: normal tissue from patient 27

tag: alcohol use

tag: tumor loation

value: lower

value: well

value: normal tissue from patient 27


title: HR_P13_T

source_name: High responder, P13, allergen plus treatment

tag: patient

tag: disease status

value: seasonal allergic rhinitis (SAR)

tag: gc responder type

value: whole blood

tag: cell type

value: CD4+ T cells

tag: treatment


title: cancer tissue from patient 26

description: cancer tissue from patient 26

source_name: cancer tissue from patient 26

value: middle

tag: tumor grade

value: poorly

tag: t stage

tag: n stage

tag: tnm stage

value: no

tag: adjuvant therapy

tag: survival time(months)

tag: disease state

value: esophageal squamous cell carcinoma

value: cancer tissue from patient 26


title: normal tissue from patient 26

description: normal tissue from patient 26

source_name: normal tissue from patient 26

tag: patient id

tag: age

value: male

tag: arrhythmia

tag: pneumonia

tag: anastomotic leak

tag: death at fu

tag: tissue

value: normal tissue from patient 26


title: normal tissue from patient 25

description: normal tissue from patient 25

source_name: normal tissue from patient 25

tag: Sex

value: female

tag: tobacco use

tag: alcohol use

tag: tumor loation

value: III

value: yes

value: unknown

value: normal tissue from patient 25


title: cancer tissue from patient 27

description: cancer tissue from patient 27

source_name: cancer tissue from patient 27

value: lower

tag: tumor grade

value: well

tag: t stage

value: cancer tissue from patient 27


title: LR_P1_A

source_name: Low responder, P1, allergen

tag: patient

tag: disease status

value: seasonal allergic rhinitis (SAR)

tag: gc responder type

value: low

value: whole blood

tag: cell type

tag: treatment

value: allergen


title: HR_P11_A

source_name: High responder, P11, allergen

value: high

value: CD4+ T cells


title: normal tissue from patient 28

description: normal tissue from patient 28

source_name: normal tissue from patient 28

tag: patient id

tag: age

value: middle

value: moderately

tag: n stage

tag: tnm stage

value: no

tag: adjuvant therapy

tag: survival time(months)

tag: disease state

value: esophageal squamous cell carcinoma

value: normal tissue from patient 28


title: HR_P12_D

source_name: High responder, P12, diluent

tag: tissue

value: diluent


title: normal tissue from patient 13

description: normal tissue from patient 13

source_name: normal tissue from patient 13

tag: Sex

value: male

tag: tobacco use

value: yes

tag: alcohol use

value: upper

value: poorly

value: I

tag: arrhythmia

tag: pneumonia

tag: anastomotic leak

tag: death at fu

value: normal tissue from patient 13


title: LR_P14_A

source_name: Low responder, P14, allergen

tag: patient

tag: disease status

value: seasonal allergic rhinitis (SAR)

tag: gc responder type

value: low

tag: cell type


title: normal tissue from patient 23

description: normal tissue from patient 23

source_name: normal tissue from patient 23

tag: patient id

tag: age

value: female

tag: tumor loation

tag: tumor grade

tag: t stage

tag: n stage

value: II

value: unknown

value: normal tissue from patient 23


title: normal tissue from patient 12

description: normal tissue from patient 12

source_name: normal tissue from patient 12

tag: Sex

value: middle

value: moderately

tag: tnm stage

tag: adjuvant therapy

tag: survival time(months)

tag: disease state

tag: tissue

value: normal tissue from patient 12


title: cancer tissue from patient 11

description: cancer tissue from patient 11

source_name: cancer tissue from patient 11

tag: tobacco use

tag: alcohol use

value: no

value: lower

value: III

tag: arrhythmia

tag: pneumonia

tag: anastomotic leak

tag: death at fu

value: esophageal squamous cell carcinoma

value: cancer tissue from patient 11


title: cancer tissue from patient 23

description: cancer tissue from patient 23

source_name: cancer tissue from patient 23

tag: patient id

tag: age

value: cancer tissue from patient 23


title: cancer tissue from patient 25

description: cancer tissue from patient 25

source_name: cancer tissue from patient 25

tag: tumor loation

tag: tumor grade

value: poorly

value: yes

value: cancer tissue from patient 25


title: cancer tissue from patient 13

description: cancer tissue from patient 13

source_name: cancer tissue from patient 13

value: male

value: upper

tag: t stage

tag: n stage

value: I

value: cancer tissue from patient 13


title: cancer tissue from patient 12

description: cancer tissue from patient 12

source_name: cancer tissue from patient 12

tag: Sex

tag: tnm stage

value: II

value: unknown

value: cancer tissue from patient 12


title: normal tissue from patient 11

description: normal tissue from patient 11

source_name: normal tissue from patient 11

tag: adjuvant therapy

tag: survival time(months)

value: normal tissue from patient 11


title: cancer tissue from patient 297

description: cancer tissue from patient 297

source_name: cancer tissue from patient 297

value: no

value: middle

value: well

tag: disease state

tag: tissue

value: cancer tissue from patient 297


title: HR_P9_A

source_name: High responder, P9, allergen

tag: patient

tag: disease status

value: seasonal allergic rhinitis (SAR)

tag: gc responder type

value: high

value: whole blood

tag: cell type

value: CD4+ T cells

tag: treatment

value: allergen


title: normal tissue from patient 10

description: normal tissue from patient 10

source_name: normal tissue from patient 10

tag: patient id

value: male

tag: tobacco use

value: yes

tag: alcohol use

value: poorly

tag: arrhythmia

tag: pneumonia

tag: anastomotic leak

tag: death at fu

value: esophageal squamous cell carcinoma

value: normal tissue from patient 10


title: cancer tissue from patient 290

description: cancer tissue from patient 290

source_name: cancer tissue from patient 290

tag: age

tag: Sex

tag: tumor loation

value: lower

tag: tumor grade

tag: t stage

tag: n stage

tag: tnm stage

value: III

value: unknown

value: cancer tissue from patient 290


title: LR_P10_D

source_name: Low responder, P10, diluent

tag: patient

tag: disease status

tag: gc responder type

value: low

tag: tissue

value: diluent


title: HR_P16_D

source_name: High responder, P16, diluent

tag: cell type

tag: treatment


title: HR_P9_T

source_name: High responder, P9, allergen plus treatment

value: allergen plus treatment


title: cancer tissue from patient 10

description: cancer tissue from patient 10

source_name: cancer tissue from patient 10

tag: patient id

tag: tobacco use

tag: alcohol use

value: middle

value: II

tag: arrhythmia

value: no

tag: adjuvant therapy

tag: survival time(months)

tag: disease state

value: cancer tissue from patient 10


title: normal tissue from patient 290

description: normal tissue from patient 290

source_name: normal tissue from patient 290

tag: age

tag: Sex

tag: tumor loation

tag: tumor grade

value: well

tag: pneumonia

tag: anastomotic leak

tag: death at fu

value: normal tissue from patient 290


title: HR_P15_A

source_name: High responder, P15, allergen

tag: patient

tag: disease status

value: seasonal allergic rhinitis (SAR)

tag: gc responder type

value: high

tag: tissue

value: whole blood

value: CD4+ T cells

value: allergen


title: normal tissue from patient 217

description: normal tissue from patient 217

source_name: normal tissue from patient 217

tag: patient id

value: male

tag: tobacco use

value: yes

value: moderately

tag: t stage

tag: n stage

tag: tnm stage

value: III

value: esophageal squamous cell carcinoma

value: normal tissue from patient 217


title: normal tissue from patient 297

description: normal tissue from patient 297

source_name: normal tissue from patient 297

tag: alcohol use

value: middle

tag: arrhythmia

tag: adjuvant therapy

value: unknown

tag: survival time(months)

tag: disease state

value: normal tissue from patient 297


title: cancer tissue from patient 9

description: cancer tissue from patient 9

source_name: cancer tissue from patient 9

tag: age

tag: Sex

tag: tumor loation

value: lower

tag: tumor grade

value: no

tag: pneumonia

value: cancer tissue from patient 9


title: HR_P13_D

source_name: High responder, P13, diluent

tag: patient

tag: disease status

value: seasonal allergic rhinitis (SAR)

tag: gc responder type

tag: cell type

tag: treatment

value: diluent


title: LR_P14_T

source_name: Low responder, P14, allergen plus treatment

value: low

tag: tissue

value: whole blood

value: allergen plus treatment


title: HR_P16_T

source_name: High responder, P16, allergen plus treatment

value: high

value: CD4+ T cells


title: normal tissue from patient 9

description: normal tissue from patient 9

source_name: normal tissue from patient 9

tag: patient id

value: male

tag: tobacco use

value: yes

value: moderately

tag: t stage

tag: n stage

tag: tnm stage

tag: anastomotic leak

tag: death at fu

value: normal tissue from patient 9


title: LR_P10_T

source_name: Low responder, P10, allergen plus treatment


title: normal tissue from patient 201

description: normal tissue from patient 201

source_name: normal tissue from patient 201

tag: age

tag: Sex

value: female

tag: alcohol use

value: upper

value: III

tag: arrhythmia

tag: adjuvant therapy

tag: survival time(months)

tag: disease state

value: esophageal squamous cell carcinoma

value: normal tissue from patient 201


title: normal tissue from patient 45

description: normal tissue from patient 45

source_name: normal tissue from patient 45

value: no

tag: tumor loation

value: middle

tag: tumor grade

value: II

tag: pneumonia

value: normal tissue from patient 45


title: HR_P12_A

source_name: High responder, P12, allergen

tag: patient

tag: disease status

value: seasonal allergic rhinitis (SAR)

tag: gc responder type

tag: tissue

value: whole blood

tag: cell type

tag: treatment

value: allergen


title: HR_P11_D

source_name: High responder, P11, diluent

value: high

value: CD4+ T cells

value: diluent


title: cancer tissue from patient 268

description: cancer tissue from patient 268

source_name: cancer tissue from patient 268

tag: patient id

value: male

tag: tobacco use

value: yes

value: moderately

tag: t stage

tag: n stage

tag: tnm stage

tag: anastomotic leak

tag: death at fu

value: cancer tissue from patient 268


title: cancer tissue from patient 217

description: cancer tissue from patient 217

source_name: cancer tissue from patient 217

tag: age

tag: Sex

tag: alcohol use

value: III

tag: arrhythmia

tag: adjuvant therapy

tag: survival time(months)

tag: disease state

value: cancer tissue from patient 217


title: cancer tissue from patient 117

description: cancer tissue from patient 117

source_name: cancer tissue from patient 117

tag: tumor loation

tag: tumor grade

tag: pneumonia

value: esophageal squamous cell carcinoma

tag: tissue

value: cancer tissue from patient 117


title: Liver_low forage allowance_purebred_-165 days_replicate 4

city: Montevideo

first: Mariana

last: Carriquiry

address: Ave Garzon 780

department: Department of Animal Sciences and Pastures

country: Uruguay

institute: Facultad de Agronomía, UdelaR

description:
Liver gene expression of mature cow in , low forage allowance, purebred, -165 days, replicate 4
1160 -165

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

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 023647_D_F_20090518) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Bos taurus

source_name: Liver, low forage allowance, purebred, -165 days, replicate 4

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: Total RNA was isolated using TRIZOL (Invitrogen, Life Technologies, Carlsbad, CA, USA) followed by precipitation with lithium chloride and DNase-treatment (Applied Biosystems/Ambion, Austin,TX, USA). RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Liver biopsies were collected using a 14-gauge biopsy needle (Tru-Core-II Automatic Biopsy Instrument; Angiotech, Lausanne, Switzerland), at -165 and -15 ± 8 (gestation), +15 and +60 ± 3 (early lactation) days ± SD. Samples were immediately frozen in liquid nitrogen and stored at -80°C until analyzed.

tag: genotype

value: AA

value: liver

tag: developmental stage

value: mature cow

tag: herbage allowance

value: low forage allowance

tag: time

value: -165 days (gestation)


title: Liver_low forage allowance_purebred_+15 days_replicate 4

description:
Liver gene expression of mature cow in , low forage allowance, purebred, +15 days, replicate 4
1160 +15

source_name: Liver, low forage allowance, purebred, +15 days, replicate 4

value: +15 days (early lactation)


title: Liver_low forage allowance_purebred_+60 days_replicate 4

description:
Liver gene expression of mature cow in , low forage allowance, purebred, +60 days, replicate 4
1160 +60

source_name: Liver, low forage allowance, purebred, +60 days, replicate 4

value: +60 days (early lactation)


title: normal tissue from patient 102

description: normal tissue from patient 102

source_name: normal tissue from patient 102

tag: patient id

value: female

tag: tobacco use

value: no

value: lower

value: well

tag: t stage

tag: n stage

tag: tnm stage

value: I

tag: anastomotic leak

value: unknown

value: normal tissue from patient 102


title: normal tissue from patient 112

description: normal tissue from patient 112

source_name: normal tissue from patient 112

tag: age

tag: Sex

value: male

value: yes

tag: alcohol use

value: poorly

value: III

tag: arrhythmia

tag: adjuvant therapy

tag: death at fu

value: normal tissue from patient 112


title: normal tissue from patient 117

description: normal tissue from patient 117

source_name: normal tissue from patient 117

tag: tumor loation

value: middle

tag: tumor grade

value: moderately

tag: pneumonia

tag: survival time(months)

tag: disease state

value: esophageal squamous cell carcinoma

tag: tissue

value: normal tissue from patient 117


title: Liver_low forage allowance_purebred_-15 days_replicate 4

description:
Liver gene expression of mature cow in , low forage allowance, purebred, -15 days, replicate 4
1160 -15

source_name: Liver, low forage allowance, purebred, -15 days, replicate 4

tag: genotype

value: AA

value: liver

tag: developmental stage

value: mature cow

tag: herbage allowance

value: low forage allowance

tag: time

value: -15 days (gestation)


title: Liver_low forage allowance_crossbred_+60 days_replicate 4

description:
Liver gene expression of mature cow in , low forage allowance, crossbred, +60 days, replicate 4
4030 +60

source_name: Liver, low forage allowance, crossbred, +60 days, replicate 4

value: AH

value: +60 days (early lactation)


title: cancer tissue from patient 129

description: cancer tissue from patient 129

source_name: cancer tissue from patient 129

tag: patient id

tag: tobacco use

value: no

value: well

tag: t stage

tag: n stage

tag: tnm stage

value: II

tag: anastomotic leak

value: cancer tissue from patient 129


title: normal tissue from patient 268

description: normal tissue from patient 268

source_name: normal tissue from patient 268

tag: age

tag: Sex

value: male

value: yes

tag: alcohol use

value: upper

tag: arrhythmia

tag: adjuvant therapy

tag: death at fu

value: normal tissue from patient 268


title: HR_P12_T

source_name: High responder, P12, allergen plus treatment

tag: patient

tag: disease status

value: seasonal allergic rhinitis (SAR)

tag: gc responder type

value: high

tag: tissue

value: whole blood

tag: cell type

value: CD4+ T cells

tag: treatment

value: allergen plus treatment


title: normal tissue from patient 129

description: normal tissue from patient 129

source_name: normal tissue from patient 129

tag: patient id

tag: tobacco use

tag: tumor loation

value: middle

tag: tumor grade

tag: pneumonia

tag: survival time(months)

tag: disease state

value: esophageal squamous cell carcinoma

value: normal tissue from patient 129


title: cancer tissue from patient 112

description: cancer tissue from patient 112

source_name: cancer tissue from patient 112

tag: age

tag: Sex

tag: alcohol use

value: lower

value: poorly

tag: t stage

tag: n stage

tag: tnm stage

value: III

tag: anastomotic leak

value: cancer tissue from patient 112


title: cancer tissue from patient 87

description: cancer tissue from patient 87

source_name: cancer tissue from patient 87

value: no

value: well

tag: arrhythmia

tag: adjuvant therapy

value: unknown

tag: death at fu

tag: tissue

value: cancer tissue from patient 87


title: LR_P14_D

source_name: Low responder, P14, diluent

tag: patient

tag: disease status

tag: gc responder type

value: low

tag: cell type

tag: treatment

value: diluent


title: cancer tissue from patient 201

description: cancer tissue from patient 201

source_name: cancer tissue from patient 201

tag: patient id

value: female

tag: tobacco use

tag: tumor loation

value: upper

tag: tumor grade

value: moderately

tag: pneumonia

value: yes

tag: survival time(months)

tag: disease state

value: cancer tissue from patient 201


title: normal tissue from patient 234

description: normal tissue from patient 234

source_name: normal tissue from patient 234

tag: age

tag: Sex

value: male

tag: alcohol use

value: middle

tag: t stage

tag: n stage

tag: tnm stage

tag: anastomotic leak

value: esophageal squamous cell carcinoma

value: normal tissue from patient 234


title: cancer tissue from patient 102

description: cancer tissue from patient 102

source_name: cancer tissue from patient 102

value: lower

value: I

tag: arrhythmia

tag: adjuvant therapy

tag: death at fu

tag: tissue

value: cancer tissue from patient 102


title: Liver_low forage allowance_crossbred_+15 days_replicate 4

description:
Liver gene expression of mature cow in , low forage allowance, crossbred, +15 days, replicate 4
4030 +15

source_name: Liver, low forage allowance, crossbred, +15 days, replicate 4

tag: genotype

value: AH

value: liver

tag: developmental stage

value: mature cow

tag: herbage allowance

value: low forage allowance

tag: time

value: +15 days (early lactation)


title: Liver_low forage allowance_crossbred_-15 days_replicate 4

description:
Liver gene expression of mature cow in , low forage allowance, crossbred, -15 days, replicate 4
4030 -15

source_name: Liver, low forage allowance, crossbred, -15 days, replicate 4

value: -15 days (gestation)


title: HR_P11_T

source_name: High responder, P11, allergen plus treatment

tag: patient

tag: disease status

value: seasonal allergic rhinitis (SAR)

tag: gc responder type

value: high

value: whole blood

tag: cell type

value: CD4+ T cells

tag: treatment

value: allergen plus treatment


title: cancer tissue from patient 234

description: cancer tissue from patient 234

source_name: cancer tissue from patient 234

tag: patient id

tag: age

tag: Sex

value: male

tag: tobacco use

value: yes

tag: alcohol use

value: no

tag: tumor loation

value: middle

tag: tumor grade

value: well

tag: t stage

value: III

tag: pneumonia

tag: survival time(months)

tag: disease state

value: cancer tissue from patient 234


title: HR_P9_D

source_name: High responder, P9, diluent

tag: tissue

value: diluent


title: cancer tissue from patient 229

description: cancer tissue from patient 229

source_name: cancer tissue from patient 229

value: lower

value: moderately

tag: n stage

tag: tnm stage

tag: arrhythmia

tag: anastomotic leak

tag: adjuvant therapy

tag: death at fu

value: esophageal squamous cell carcinoma

value: cancer tissue from patient 229


title: Liver_low forage allowance_crossbred_-165 days_replicate 4

description:
Liver gene expression of mature cow in , low forage allowance, crossbred, -165 days, replicate 4
4030 -165

source_name: Liver, low forage allowance, crossbred, -165 days, replicate 4

tag: genotype

value: AH

value: liver

tag: developmental stage

value: mature cow

tag: herbage allowance

value: low forage allowance

tag: time

value: -165 days (gestation)


title: Liver_high forage allowance_purebred_-165 days_replicate 4

description:
Liver gene expression of mature cow in , high forage allowance, purebred, -165 days, replicate 4
1306 -165

source_name: Liver, high forage allowance, purebred, -165 days, replicate 4

value: AA

value: high forage allowance


title: Liver_high forage allowance_purebred_+60 days_replicate 4

description:
Liver gene expression of mature cow in , high forage allowance, purebred, +60 days, replicate 4
1306 +60

source_name: Liver, high forage allowance, purebred, +60 days, replicate 4

value: +60 days (early lactation)


title: cancer tissue from patient 249

description: cancer tissue from patient 249

source_name: cancer tissue from patient 249

tag: patient id

tag: age

tag: Sex

value: male

tag: tobacco use

value: yes

tag: alcohol use

tag: tumor loation

value: middle

value: poorly

value: II

value: no

value: cancer tissue from patient 249


title: cancer tissue from patient 231

description: cancer tissue from patient 231

source_name: cancer tissue from patient 231

tag: tumor grade

value: moderately

tag: t stage

tag: pneumonia

tag: survival time(months)

tag: disease state

value: esophageal squamous cell carcinoma

tag: tissue

value: cancer tissue from patient 231


title: HR_P13_A

source_name: High responder, P13, allergen

tag: patient

tag: disease status

value: seasonal allergic rhinitis (SAR)

tag: gc responder type

value: high

value: whole blood

tag: cell type

value: CD4+ T cells

tag: treatment

value: allergen


title: LR_P10_A

source_name: Low responder, P10, allergen

value: low


title: cancer tissue from patient 247

description: cancer tissue from patient 247

source_name: cancer tissue from patient 247

tag: patient id

value: lower

tag: n stage

tag: tnm stage

value: III

tag: arrhythmia

tag: anastomotic leak

tag: adjuvant therapy

value: unknown

tag: death at fu

value: cancer tissue from patient 247


title: normal tissue from patient 246

description: normal tissue from patient 246

source_name: normal tissue from patient 246

tag: age

tag: Sex

value: male

tag: tobacco use

value: yes

tag: alcohol use

tag: tumor loation

value: middle

tag: tumor grade

tag: t stage

value: normal tissue from patient 246


title: normal tissue from patient 228

description: normal tissue from patient 228

source_name: normal tissue from patient 228

value: no

value: moderately

tag: pneumonia

tag: survival time(months)

tag: disease state

tag: tissue

value: normal tissue from patient 228


title: Liver_high forage allowance_purebred_+15 days_replicate 4

description:
Liver gene expression of mature cow in , high forage allowance, purebred, +15 days, replicate 4
1306 +15

source_name: Liver, high forage allowance, purebred, +15 days, replicate 4

tag: genotype

value: AA

value: liver

tag: developmental stage

value: mature cow

tag: herbage allowance

value: high forage allowance

tag: time

value: +15 days (early lactation)


title: Liver_high forage allowance_purebred_-15 days_replicate 4

description:
Liver gene expression of mature cow in , high forage allowance, purebred, -15 days, replicate 4
1306 -15

source_name: Liver, high forage allowance, purebred, -15 days, replicate 4

value: -15 days (gestation)


title: Liver_high forage allowance_crossbred_+60 days_replicate 4

description:
Liver gene expression of mature cow in , high forage allowance, crossbred, +60 days, replicate 4
2037 +60

source_name: Liver, high forage allowance, crossbred, +60 days, replicate 4

value: AH

value: +60 days (early lactation)


title: cancer tissue from patient 246

description: cancer tissue from patient 246

source_name: cancer tissue from patient 246

tag: patient id

tag: n stage

tag: tnm stage

value: III

tag: arrhythmia

tag: anastomotic leak

tag: adjuvant therapy

value: esophageal squamous cell carcinoma

value: cancer tissue from patient 246


title: normal tissue from patient 245

description: normal tissue from patient 245

source_name: normal tissue from patient 245

tag: age

tag: Sex

value: male

tag: tobacco use

value: yes

tag: alcohol use

tag: tumor loation

tag: death at fu

value: normal tissue from patient 245


title: cancer tissue from patient 245

description: cancer tissue from patient 245

source_name: cancer tissue from patient 245

value: middle

tag: tumor grade

tag: t stage

value: no

tag: pneumonia

tag: survival time(months)

tag: disease state

tag: tissue

value: cancer tissue from patient 245


title: normal tissue from patient 231

description: normal tissue from patient 231

source_name: normal tissue from patient 231

tag: patient id

value: moderately

tag: n stage

value: II

value: normal tissue from patient 231


title: Liver_high forage allowance_crossbred_+15 days_replicate 4

description:
Liver gene expression of mature cow in , high forage allowance, crossbred, +15 days, replicate 4
2037 +15

source_name: Liver, high forage allowance, crossbred, +15 days, replicate 4

tag: genotype

value: liver

tag: developmental stage

value: mature cow

tag: herbage allowance

value: high forage allowance

tag: time


title: normal tissue from patient 229

description: normal tissue from patient 229

source_name: normal tissue from patient 229

tag: age

tag: Sex

value: lower

tag: tnm stage

tag: arrhythmia

tag: anastomotic leak

tag: adjuvant therapy

value: normal tissue from patient 229


title: normal tissue from patient 243

description: normal tissue from patient 243

source_name: normal tissue from patient 243

tag: tobacco use

tag: alcohol use

tag: tumor loation

tag: tumor grade

tag: t stage

tag: death at fu

value: normal tissue from patient 243


title: normal tissue from patient 249

description: normal tissue from patient 249

source_name: normal tissue from patient 249

tag: patient id

value: poorly

tag: n stage

tag: pneumonia

tag: survival time(months)

tag: disease state

value: esophageal squamous cell carcinoma

tag: tissue

value: normal tissue from patient 249


title: cancer tissue from patient 228

description: cancer tissue from patient 228

source_name: cancer tissue from patient 228

tag: age

tag: Sex

value: male

value: yes

value: III

value: cancer tissue from patient 228


title: normal tissue from patient 247

description: normal tissue from patient 247

source_name: normal tissue from patient 247

tag: tnm stage

tag: arrhythmia

value: no

value: unknown

value: normal tissue from patient 247


title: HR_P16_A

source_name: High responder, P16, allergen

tag: patient

tag: disease status

value: seasonal allergic rhinitis (SAR)

tag: gc responder type

value: high

value: whole blood

tag: cell type

value: CD4+ T cells

tag: treatment

value: allergen


title: cancer tissue from patient 241

description: cancer tissue from patient 241

source_name: cancer tissue from patient 241

value: female

tag: tobacco use

tag: alcohol use

tag: tumor loation

value: upper

tag: tumor grade

value: moderately

tag: t stage

value: II

tag: anastomotic leak

tag: adjuvant therapy

value: cancer tissue from patient 241


title: normal tissue from patient 223

description: normal tissue from patient 223

source_name: normal tissue from patient 223

tag: patient id

value: male

value: lower

value: well

tag: n stage

tag: pneumonia

tag: death at fu

tag: survival time(months)

tag: disease state

value: esophageal squamous cell carcinoma

tag: tissue

value: normal tissue from patient 223


title: normal tissue from patient 241

description: normal tissue from patient 241

source_name: normal tissue from patient 241

tag: age

tag: Sex

value: no

tag: tnm stage

tag: arrhythmia

value: yes

value: normal tissue from patient 241


title: cancer tissue from patient 222

description: cancer tissue from patient 222

source_name: cancer tissue from patient 222

tag: tobacco use

tag: alcohol use

value: middle

value: cancer tissue from patient 222


title: Liver_low forage allowance_purebred_+60 days_replicate 3

description:
Liver gene expression of mature cow in , low forage allowance, purebred, +60 days, replicate 3
3227 +60

source_name: Liver, low forage allowance, purebred, +60 days, replicate 3

tag: genotype

value: HH

value: liver

tag: developmental stage

value: mature cow

tag: herbage allowance

value: low forage allowance

tag: time

value: +60 days (early lactation)


title: Liver_low forage allowance_purebred_+15 days_replicate 3

description:
Liver gene expression of mature cow in , low forage allowance, purebred, +15 days, replicate 3
3227 +15

source_name: Liver, low forage allowance, purebred, +15 days, replicate 3

value: +15 days (early lactation)


title: Liver_high forage allowance_crossbred_-165 days_replicate 4

description:
Liver gene expression of mature cow in , high forage allowance, crossbred, -165 days, replicate 4
2037 -165

source_name: Liver, high forage allowance, crossbred, -165 days, replicate 4

value: AH

value: high forage allowance

value: -165 days (gestation)


title: Liver_low forage allowance_purebred_-15 days_replicate 3

description:
Liver gene expression of mature cow in , low forage allowance, purebred, -15 days, replicate 3
3227 -15

source_name: Liver, low forage allowance, purebred, -15 days, replicate 3

value: -15 days (gestation)


title: Liver_low forage allowance_crossbred_+60 days_replicate 3

description:
Liver gene expression of mature cow in , low forage allowance, crossbred, +60 days, replicate 3
2151 +60

source_name: Liver, low forage allowance, crossbred, +60 days, replicate 3

value: HA


title: normal tissue from patient 239

description: normal tissue from patient 239

source_name: normal tissue from patient 239

tag: patient id

value: female

tag: tumor loation

value: lower

tag: tumor grade

value: moderately

tag: t stage

value: III

tag: anastomotic leak

tag: adjuvant therapy

value: esophageal squamous cell carcinoma

value: normal tissue from patient 239


title: cancer tissue from patient 236

description: cancer tissue from patient 236

source_name: cancer tissue from patient 236

value: male

value: yes

value: no

value: poorly

tag: n stage

tag: pneumonia

tag: death at fu

tag: survival time(months)

tag: disease state

tag: tissue

value: cancer tissue from patient 236


title: normal tissue from patient 222

description: normal tissue from patient 222

source_name: normal tissue from patient 222

tag: age

tag: Sex

tag: tobacco use

tag: alcohol use

value: middle

tag: tnm stage

value: II

tag: arrhythmia

value: normal tissue from patient 222


title: cancer tissue from patient 223

description: cancer tissue from patient 223

source_name: cancer tissue from patient 223

tag: patient id

tag: tumor loation

value: well

value: cancer tissue from patient 223


title: cancer tissue from patient 243

description: cancer tissue from patient 243

source_name: cancer tissue from patient 243

tag: tumor grade

tag: t stage

value: cancer tissue from patient 243


title: normal tissue from patient 236

description: normal tissue from patient 236

source_name: normal tissue from patient 236

tag: anastomotic leak

tag: adjuvant therapy

value: normal tissue from patient 236


title: cancer tissue from patient 221

description: cancer tissue from patient 221

source_name: cancer tissue from patient 221

tag: n stage

tag: pneumonia

value: unknown

value: cancer tissue from patient 221


title: Liver_high forage allowance_crossbred_-15 days_replicate 4

description:
Liver gene expression of mature cow in , high forage allowance, crossbred, -15 days, replicate 4
2037 -15

source_name: Liver, high forage allowance, crossbred, -15 days, replicate 4

tag: genotype

value: AH

value: liver

tag: developmental stage

value: mature cow

tag: herbage allowance

value: high forage allowance

tag: time

value: -15 days (gestation)


title: Liver_low forage allowance_purebred_-165 days_replicate 3

description:
Liver gene expression of mature cow in , low forage allowance, purebred, -165 days, replicate 3
3227 -165

source_name: Liver, low forage allowance, purebred, -165 days, replicate 3

value: HH

tag: tissue

value: low forage allowance

value: -165 days (gestation)


title: normal tissue from patient 218

description: normal tissue from patient 218

source_name: normal tissue from patient 218

tag: age

tag: Sex

value: male

tag: tobacco use

value: yes

value: lower

value: poorly

value: III

value: no

tag: death at fu

tag: survival time(months)

tag: disease state

value: esophageal squamous cell carcinoma

value: normal tissue from patient 218


title: Liver_low forage allowance_crossbred_+15 days_replicate 3

description:
Liver gene expression of mature cow in , low forage allowance, crossbred, +15 days, replicate 3
2151 +15

source_name: Liver, low forage allowance, crossbred, +15 days, replicate 3

value: HA

value: +15 days (early lactation)


title: normal tissue from patient 221

description: normal tissue from patient 221

source_name: normal tissue from patient 221

tag: patient id

tag: alcohol use

tag: tumor loation

value: middle

tag: tumor grade

value: well

tag: tnm stage

value: II

tag: arrhythmia

value: unknown

value: normal tissue from patient 221


title: normal tissue from patient 220

description: normal tissue from patient 220

source_name: normal tissue from patient 220

value: moderately

tag: t stage

tag: n stage

tag: pneumonia

tag: anastomotic leak

tag: adjuvant therapy

value: normal tissue from patient 220


title: cancer tissue from patient 220

description: cancer tissue from patient 220

source_name: cancer tissue from patient 220

tag: age

value: male

tag: tissue

value: cancer tissue from patient 220


title: cancer tissue from patient 239

description: cancer tissue from patient 239

source_name: cancer tissue from patient 239

tag: Sex

value: female

tag: tobacco use

value: lower

value: yes

value: cancer tissue from patient 239


title: cancer tissue from patient 219

description: cancer tissue from patient 219

source_name: cancer tissue from patient 219

value: no

tag: death at fu

tag: survival time(months)

value: esophageal squamous cell carcinoma

value: cancer tissue from patient 219


title: Liver_low forage allowance_crossbred_-165 days_replicate 3

description:
Liver gene expression of mature cow in , low forage allowance, crossbred, -165 days, replicate 3
2151 -165

source_name: Liver, low forage allowance, crossbred, -165 days, replicate 3

tag: genotype

value: HA

value: liver

tag: developmental stage

value: mature cow

tag: herbage allowance

value: low forage allowance

tag: time

value: -165 days (gestation)


title: HR_P15_D

source_name: High responder, P15, diluent

tag: patient

tag: disease status

value: seasonal allergic rhinitis (SAR)

tag: gc responder type

value: high

value: whole blood

tag: cell type

value: CD4+ T cells

tag: treatment

value: diluent


title: normal tissue from patient 216

description: normal tissue from patient 216

source_name: normal tissue from patient 216

tag: patient id

value: male

tag: alcohol use

tag: tumor loation

tag: tumor grade

value: well

tag: t stage

tag: n stage

tag: tnm stage

value: III

tag: arrhythmia

tag: pneumonia

tag: anastomotic leak

tag: disease state

value: normal tissue from patient 216


title: cancer tissue from patient 218

description: cancer tissue from patient 218

source_name: cancer tissue from patient 218

tag: age

tag: Sex

tag: tobacco use

value: yes

value: lower

value: poorly

value: no

tag: adjuvant therapy

tag: death at fu

tag: survival time(months)

tag: tissue

value: cancer tissue from patient 218


title: Liver_high forage allowance_purebred_+15 days_replicate 3

description:
Liver gene expression of mature cow in , high forage allowance, purebred, +15 days, replicate 3
3178 +15

source_name: Liver, high forage allowance, purebred, +15 days, replicate 3

tag: genotype

value: HH

value: liver

tag: developmental stage

value: mature cow

tag: herbage allowance

value: high forage allowance

tag: time

value: +15 days (early lactation)


title: cancer tissue from patient 215

description: cancer tissue from patient 215

source_name: cancer tissue from patient 215

tag: patient id

tag: alcohol use

tag: tumor loation

value: middle

tag: tumor grade

value: moderately

tag: t stage

tag: n stage

value: unknown

value: esophageal squamous cell carcinoma

value: cancer tissue from patient 215


title: Liver_high forage allowance_purebred_+60 days_replicate 3

description:
Liver gene expression of mature cow in , high forage allowance, purebred, +60 days, replicate 3
3178 +60

source_name: Liver, high forage allowance, purebred, +60 days, replicate 3

value: +60 days (early lactation)


title: cancer tissue from patient 216

description: cancer tissue from patient 216

source_name: cancer tissue from patient 216

tag: age

value: male

value: well

tag: tnm stage

value: III

tag: arrhythmia

tag: pneumonia

tag: anastomotic leak

tag: disease state

value: cancer tissue from patient 216


title: cancer tissue from patient 211

description: cancer tissue from patient 211

source_name: cancer tissue from patient 211

tag: Sex

tag: tobacco use

value: yes

value: poorly

value: no

tag: adjuvant therapy

tag: death at fu

tag: survival time(months)

tag: tissue

value: cancer tissue from patient 211