title: HN04.138T

description:
U133Plus2_091108_SR26_HN05-138T

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).


title: HN04.172N

status: Public on Aug 03 2011

type: RNA

city: Boston

first: Levi

last: Waldron

state: MA

address: 655 Huntington Avenue

department: Biostatistics

country: USA

institute: Harvard School of Publich Health

description:
U133Plus2_091108_SR30_HN05-172N

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).

hyb_protocol: Labeling and hybridization to arrays were performed by The Centre for Applied Genomics, Medical and Related Sciences Centre (MaRS), Toronto, ON, Canada, using standard Affymetrix procedures.

scan_protocol: Microarray slides were scanned using the GeneArray 2500 scanner (Agilent Technologies).

data_processing: Data were processed using the BrainArray Entrez-gene centric alternative CDF, with GC-RMA background correction and normalization.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Normal

label_protocol: Amplification and biotin labeling of antisense cRNA was performed using the Enzo BioArray High YieldTM RNA transcript labeling kit (Enzo Diagnostics, Farmingdale, NY, USA), according to the manufacturer’s instructions.

extract_protocol: Total RNA was extracted from all tissues using Trizol reagent (Life Technologies, Inc., Burlington, ON, Canada), followed by purification using the Qiagen RNeasy kit/DNase RNase-free set (Qiagen, Valencia, CA, USA), according to manufacturer’s instructions. RNA was quantified by spectrophotometry and its quality was assessed using the 2100 Bioanalyzer (Firmware v.A.01.16, Agilent Technologies, Canada). All samples were of sufficient quantity and quality for arrays and quantitative real-time PCR (QRT-PCR) analyses.

tag: patient identifier

tag: disease state

value: squamous cell carcinoma of the tongue

tag: tissue location

value: tongue

tag: Stage

value: IV

tag: grade

value: invasive poorly diff

tag: site

value: margin

tag: site detail

value: normal

tag: recurrence

value: no

tag: outcome

value: ANED


title: HN04.105A

description:
U133Plus2_091108_SR24_HN04-105A

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).

source_name: Anterior margin

value: invasive mod diff

value: anterior margin


title: HN04.141PI

description:
U133Plus2_091108_SR28_HN05-141PI

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).

source_name: Posterior Inferior margin

value: posterior Inferior margin

value: yes

value: regional and distant

value: DOD


title: Control Human Kidney 81, Tubuli

city: Bronx

first: Karolina

last: Woroniecka

state: NY

address: 1300 Morris Park Ave

institute: AECOM

description:
HK81T
KS1-HG_U133A_2-2920

hyb_protocol: Biotinylated cRNA was hybridized onto Affymetrix Human Genome U133A 2.0 Arrays (Affymetrix, USA).

scan_protocol: The data were scanned using a GeneChip scanner in accordance with the Affymetrix protocol.

data_processing: Data were normalized in GeneSpring GZ software (Agilent) using the RMA16 summarization algorithm. Baseline is the median of all samples.

label: Biotin

source_name: Tubuli of control kidney

label_protocol: Labeling was performed using the Two-Cycle Target Labeling Kit (Affymetrix) as per the manufacturer's protocol. The GeneChip IVT labeling kit performed the final in vitro transcription reaction to produce biotinylated cRNA for the microarray.

extract_protocol: 1mm x 1mm biopsy tissues were placed under an Olympus model SZX12 stereomicroscope using 90x magnification. The biopsy tissue was manually microdissected at 4C in RNALater for glomerular and tubular compartments using fine tip forceps. In general, 5 glomeruli that readily released from the capsule were collected and placed into cold RLT solution (Qiagen RNeasey kit). The corresponding tubulointerstitial and vascular compartment was placed into RLT solution also. For easier designation we called this component tubules. Dissected tissue was homogenized using a Powergen125 (Fisher) homogenizer and stored at -80C. RNA was prepared using RNAeasy mini columns (Qiagen) according to manufacterer's instructions. RNA quality and quantity was determined using a Lab-on-Chip Total RNA PicoKit (Agilent BioAnalyzer).

tag: tissue

value: kidney

tag: tissue subregion

value: tubules

value: control


title: HN04.140AL

description:
U133Plus2_091108_SR27_HN05-140AL

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).

source_name: Antero-lateral margin

value: squamous cell carcinoma of the tongue

value: antero-lateral margin


title: Control Human Kidney 82, Tubuli

description:
HK82T
KS1-HG_U133A_2-2922


title: Control Human Kidney 172, Tubuli

description:
HK172T
KS1-HG_U133A_2-6466


title: Cyclin T2 shRNA-biological replicate 2

city: Houston

first: Andrew

middle: P

last: Rice

state: TX

address: MS BCM385,One Baylor Plaza

department: Molecular Virology & Microbiology

institute: Baylor College of Medicine

hyb_protocol: standard Affymetrix protocol

scan_protocol: Affymetrix Gene Chip Scanner 3100

data_processing: CEL files for each array were uploaded into GeneSifter and the data normalized and log transformed using the GC-RMA algorithm.

source_name: HeLa cells

label_protocol: standard Affymetrix protocol

growth_protocol: HeLa cells were maintained in DMEM (Invitrogen) supplemented with 10% fetal bovine serum (Invitrogen)

extract_protocol: RNA was isolated using the Qiagen Rneasy kit according to the manufacturer's protocol and RNA quality was determined using an Aligent 2100 Bioanalyzer

treatment_protocol: HeLa cells were transduced with shRNA virus against Cyclin T2 or Cyclin T1 or MM control for five days.

tag: cell line

value: HeLa

tag: treatment

value: Cyclin T2 knockdown


title: Control Human Kidney 160, Tubuli

description:
HK160T
KS1-HG_U133A_2-6375


title: HN04.104N

description:
U133Plus2_091108_SR23_HN04-104N

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).

value: tongue

value: IV

value: margin


title: Control Human Glomeruli 33

description:
HK33G
KS1-HG_U133A_2-2772

source_name: Glomerulus of control kidney

value: glomerulus

tag: individual


title: Control Human Kidney 177, Tubuli

description:
HK177T
KS1-HG_U133A_2-6573


title: Control Human Kidney 70, Tubuli

description:
HK70T
KS1-HG_U133A_2-2906


title: Control Human Kidney 77, Tubuli

description:
HK77T
KS1-HG_U133A_2-2914


title: Control Human Kidney 76, Tubuli

description:
HK76T
KS1-HG_U133A_2-2912


title: HN04.103T

description:
U133Plus2_091108_SR22_HN04-103T

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).

source_name: Tumor

value: invasive mod diff

value: tumor

value: no

value: ANED


title: HN04.102L

description:
U133Plus2_091108_SR21_HN04-102L

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).

source_name: Lateral margin

value: lateral margin


title: Control Human Kidney 64, Tubuli

description:
HK64T
KS1-HG_U133A_2-2903


title: Control Human Kidney 53, Tubuli

description:
HK53T
KS1-HG_U133A_2-2741


title: MM control shRNA- biological replicate 2

value: mismatch MM control


title: Cyclin T1 shRNA-biological replicate 2

value: Cyclin T1 knockdown


title: HN04.84N

description:
U133Plus2_091108_SR20_HN04-84N

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).

value: II

value: invasive poorly diff

value: normal

value: DOC


title: Cyclin T1 shRNA-biological replicate 1

value: HeLa


title: Cyclin T2 shRNA-biological replicate 1

value: Cyclin T2 knockdown


title: MM control shRNA- biological replicate 1


title: IGT_DM2_7

first: Mary Elizabeth

last: Patti

address: 1 Joslin Place

department: Research Division

institute: Joslin Diabetes Center

description: Gene expression from skeletal muscle of obese subject with IGT or DM2

hyb_protocol: 15ug of biotinylated cRNA were hybridized for 16hr at 45C to the Affymetrix GeneChip Human Genome U133 Plus 2.0 array.  Following hybridization, arrays were washed and stained on the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneArray Scanner G2500.

data_processing: Data were analyzed using Affymetrix GCOS v.1.3, MAS5.0 algorithm, and globally scaled with the trimmed mean target intensity set to 50.

source_name: skeletal muscle

label_protocol: Biotinylated cRNA were prepared from total RNA according to the standard Affymetrix protocol.

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

tag: subject

tag: age

tag: fasting glucose

tag: fasting insulin

tag: total cholesterol

tag: hdl

tag: total triglycerides

tag: bmi


title: CONTROL_9

description: Gene expression from skeletal muscle of control subject

value: control


title: CONTROL_10


title: Control Human Kidney 17, Tubuli

description:
HK17T
KS1-HG_U133A_2-2898

value: kidney

value: tubules

tag: disease state


title: Diabetic Human Kidney 178, Tubuli

description:
HK178T
KS1-HG_U133A_2-6575

source_name: Tubuli of DKD kidney

value: diabetic kidney disease (DKD)


title: HN04.80S

description:
U133Plus2_091108_SR18_HN04-80S

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).

source_name: Superior margin

tag: patient identifier

value: squamous cell carcinoma of the tongue

tag: tissue location

value: tongue

tag: Stage

tag: grade

tag: site

value: margin

tag: site detail

value: superior margin


title: Control Human Kidney 37, Tubuli

description:
HK37T
KS1-HG_U133A_2-2868

tag: tissue

tag: tissue subregion


title: HN04.79A

description:
U133Plus2_091108_SR17_HN04-79A

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).

value: anterior margin

tag: recurrence

value: no

tag: outcome

value: ANED


title: HN04.78I

description:
U133Plus2_091108_SR16_HN04-78I

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).

source_name: Inferior margin

value: II

value: Inferior margin


title: IGT_DM2_5

tag: subject

tag: age

tag: fasting glucose


title: CONTROL_8

tag: fasting insulin

tag: total cholesterol

tag: hdl


title: control

city: Jacksonville

first: Tushar

last: Patel

state: FL

address: 4500 San Pablo Road

institute: Mayo Clinic

description: gene expression data from cells treated with control

hyb_protocol: microarrays were hybridized overnight with 5 mg biotin labelled ss-cDNA, and washed in fluidics station wash protocol: MES_EukGE-WS2v5_450

scan_protocol: Genechip scanner 3000 7G

data_processing:
Normalization: The input files were normalized with full quantile normalization (Irizarry et al 2003).  For each input array, for each probe expression value, the array ith percentile probe value was replaced with the average of all array ith percentile points.
Background Correction: Arrays are corrected for background the method described in Robust Multi-array Average (RMA).  (Irrizary, et al 2003).  After normalization, the array probe values are adjusted for background by assuming that Perfect Match (PM) probe scores are distributed as the sum of independent Exponential (S=Signal) and Normal (B=Background) distributions.  Or
PM = S + B ~ Exp(Lambda) + N(Mu,Sigma^2)
The signal Exponential distribution has parameter lambda and the normal distribution has parameters mu, and sigma^2.  For each array (hybridization) These parameters are estimated from an estimated probability density function (PDF) as follows.  For a single array (or hybridization) let M_PM be the overall mode (the highest point) of the estimated CDF:
Mu = mode of PM values such that PM is less than M_PM (PM<M_PM),
Sigma^2 = (2 * Sum{PM<Mu}(PM-Mu)^2) / ({# of probes such that PM < Mu} - 1) ,
Lambda = mode of PM-Mu (for PM values greater than Mu - Mu).
For each PM probe, the background corrected value is the Expected value of S given the observed PM which is given by Irrizary et al as
E(S|PM) = PM - Mu - Lambda * Sigma^2 + (Sigma * StdNormPDF(a) / (StdNormCDF(a) - 1) )
Where StdNormPDF is the probability density function of the standard Normal distribution and StdNormCDF(a) is the integral from negative infinity to a of StdNormPDF.  The variable a=(PM-Mu-Lambda*Sigma^2)/Sigma.
The PDF estimate used for parameter estimation is a kernel density estimate using the Epanechnikov kernel and 2^14 data points.
Transformation: Probe scores were then transformed by taking the Base-2 Logarithm of 0 plus the probe score.
Estimating Gene (probe-set) Expression From Probe Scores (Summarization)
After normalization, background correction, and transformation, the perfect match (PM) probe scores were combined to estimate a gene level for each chip by means of median polish developed by Tucky and applied to microarray analysis by Irrizary et al.  Specifically, Let TO be a table where, for a particular gene, the rows are chips and the columns are probes so that TO(i,j) is the score of the jth probe on the ith chip.  First let T = TO and then alternately sweep rows and columns of T until a stopping criteria is met.
Sweep Rows: For each chip i subtract the median of row i, R(i), from T (i.e. T(i,j)=T(i,j)-R(i))
Sweep Columns: For each chip i subtract the median of column j, C(j), from T (i.e. T(i,j)=T(i,j)-R(j))
Until stop criteria: Max Number Iteration = 5 or all medians less than 0.05
The values remaining in T are residuals after probe and chip effects have been removed and the final estimate of the expression of chip i is the row i average of TO-T.  Mismatch (MM) probes are not used in this step.

source_name: MzChA1 cells treated with diluent

label_protocol: labelling was performed according to the Affymetrix (Santa Clara, CA) GeneChip Whole Transcript (WT) Sense Target Labelling Assay manual

growth_protocol: MzChA1 cells were cultured in 100mm dishes with CMRL medium

extract_protocol: RNA was extracted with RNeasy mini kit (Qiagen, Valencia, CA)

treatment_protocol: MzChA1 cells were treated with felodipine (20uM) or diluent control for 24 hrs and then collected for RNA extraction

tag: cell line

tag: condition

value: control diluent


title: HN04.83T

description:
U133Plus2_091108_SR19_HN04-83T

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).

tag: patient identifier

tag: disease state

tag: tissue location

value: invasive poorly diff

value: tumor


title: Diabetic Human Kidney 187, Tubuli

description:
HK187T
KS1-HG_U133A_2-7682


title: IGT_DM2_6

tag: total triglycerides

tag: bmi


title: CGH: Soy wild type/no obvious phenotype FN mutant R32C04 vs. Reference

type: genomic

city: Saint Paul

first: Robert

middle: M

last: Stupar

state: MN

address: 1991 Upper Buford Circle

department: Agronomy and Plant Genetics

institute: University of Minnesota

hyb_protocol: Genomic DNA were hybridized to the microarray according to the manufacturer instructions (NimbleGen CGH User Guide Ver 5.1)

scan_protocol: Slides were scanned on the GenePix4000B Scanner (Molecular Devices, Sunnyvale, CA) according to the array manufacturer instructions (NimbleGen CGH User Guide Ver 5.1)

data_processing: The segMNT algorithm in the NimbleScan software (verison 2.5) was used to extract the raw data and normalize into log2 ratio value according to the default settings.

molecule: genomic DNA

organism: Glycine max

source_name: FN mutant R32C04

label_protocol: 1ug of genomic DNA was labeled and amplified using the NimbleGen Dual-Color Labeling Kit according to the NimbleGen CGH User Guide Ver 5.1.

extract_protocol: Qiagen DNeasy

tag: tissue

value: Leaf sample

tag: genotype

value: fast neutron mutant

tag: phenotype

value: Mutant shows no obvious phenotype.

tag: cultivar

value: M92-220 background

source_name: FN pooled reference

value: Leaf samples

value: 30 pooled soybean fast neutron mutants


title: CONTROL_6

tag: subject

value: control


title: CGH: Soy wild type/no obvious phenotype FN mutant R07C12-1-Rep2 vs. Reference

source_name: FN mutant R07C12-1-Rep2


title: Diabetic Human Kidney 168, Tubuli

description:
HK168T
KS1-HG_U133A_2-6396

value: kidney

tag: tissue subregion

value: tubules

value: diabetic kidney disease (DKD)


title: CGH: Soy wild type/no obvious phenotype FN mutant R02C55-9 vs. Reference

source_name: FN mutant R02C55-9


title: HN04.68P

description:
U133Plus2_091108_SR15_HN04-68P

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).

source_name: Posterior margin

value: squamous cell carcinoma of the tongue

value: anterior alveoli

tag: Stage

tag: grade

value: invasive mod diff

tag: site

value: margin

tag: site detail

value: posterior margin

tag: recurrence

value: no

tag: outcome


title: HN04.67P

description:
U133Plus2_091108_SR14_HN04-67P

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).

tag: patient identifier

value: II

value: ANED


title: CGH: Soy wild type/no obvious phenotype FN mutant R02C28-7 vs. Reference

source_name: FN mutant R02C28-7

value: Leaf sample

value: fast neutron mutant


title: CONTROL_5

tag: age

tag: fasting glucose

tag: fasting insulin

tag: total cholesterol

tag: hdl


title: IGT_DM2_4

tag: total triglycerides

tag: bmi


title: felodipine

description: gene expression data from cells treated with felodipine

source_name: MzChA1 cells treated with felodipine

tag: cell line

tag: condition

value: treated with felodipine


title: CONTROL_3

tag: subject


title: Diabetic Human Kidney 148, Tubuli

description:
HK148T
KS1-HG_U133A_2-7680

tag: tissue

tag: tissue subregion

tag: disease state


title: HN04.66T

description:
U133Plus2_091108_SR13_HN04-66T

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).

tag: tissue location

tag: Stage

tag: grade

tag: site

value: tumor

tag: site detail


title: IGT_DM2_2

tag: age

tag: fasting glucose


title: CONTROL_4

tag: fasting insulin

tag: total cholesterol


title: CONTROL_2

tag: hdl

tag: total triglycerides


title: Diabetic Human Kidney 162, Tubuli

description:
HK162T
KS1-HG_U133A_2-6377


title: CGH: Soy wild type/no obvious phenotype FN mutant R01C42 vs. Reference

source_name: FN mutant R01C42

tag: genotype

tag: phenotype

value: Mutant shows no obvious phenotype.

tag: cultivar

value: M92-220 background

value: Leaf samples

value: 30 pooled soybean fast neutron mutants


title: IGT_DM2_1

tag: subject

tag: bmi


title: CGH: Soy wild type/no obvious phenotype FN mutant R05C50 vs. Reference

source_name: FN mutant R05C50

tag: tissue


title: CGH: Soy wild type/no obvious phenotype FN mutant R07C12-1-Rep1 vs. Reference

source_name: FN mutant R07C12-1-Rep1


title: CGH: Soy wild type/no obvious phenotype FN mutant R30C54 vs. Reference

source_name: FN mutant R30C54


title: CGH: Soy wild type/no obvious phenotype FN mutant R06C22 vs. Reference

source_name: FN mutant R06C22


title: CGH: Soy wild type/no obvious phenotype FN mutant R09C16 vs. Reference

source_name: FN mutant R09C16


title: CGH: Soy wild type/no obvious phenotype FN mutant R05C22-6 vs. Reference

source_name: FN mutant R05C22-6


title: IGT_DM2_3

source_name: skeletal muscle


title: HN02.174N

description:
U133Plus2_091108_SR10_HN02-174N

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).

source_name: Normal

tag: patient identifier

tag: disease state

tag: tissue location

value: anterior floor of mouth

value: III

value: invasive poorly diff

value: normal

tag: recurrence

tag: outcome

value: DOC


title: C (24hr) Rep 3

city: Brisbane

first: Charles

last: Wan

state: Queensland

address: 60 Musk Ave

country: Australia

institute: QUT

description: replicate 3

hyb_protocol: Standard conditions and protocol for the Sentrix HumanREF-8 v1.1 expression beadchips were used

scan_protocol: Beadchips were scanned using the Illumina Bead Station, as per pre-defined protocols.

data_processing: Image capture and processing was facilitated using BeadScan ver3.5.11, and were normalised using the Cubic Spline method.

label: biotin-uridine triphosphate

label_protocol: Target labellign was facilitated using Illumina's TotalPrep RNA amplification kit (Applied Biosystems).

growth_protocol: A human endometrium-derived, hormone-responsive cell line ECC-1 was cultured in vitro for 26 weeks with activated charcoal medium prior to the addition of female reproductive hormones and Chlamydia trachomatis serovar D.

extract_protocol: Total RNA was extracted using the Rneasy mini kit (QIAgen) according to the manufacturer's instructions.

treatment_protocol: The pre-treated cells were administered with average physiological concentrations of Female Reproductive Hormones (17b-estradiol alone, progesterone alone, or a 1:1 combination of both hormones) and were added to respective wells until the cells reached full confluence. Cells were supplemented with a continuous supply of hormones for 24 hours prior to infection with C.trachomatis D.

tag: cell line

tag: timepoint

tag: hormone

tag: infected with

value: Chlamydia trachomatis D


title: HN04.65N

description:
U133Plus2_091108_SR12_HN04-65N

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).

value: squamous cell carcinoma of the tongue

value: anterior alveoli

tag: Stage

tag: grade

value: invasive mod diff

tag: site

value: margin

tag: site detail

value: no


title: HN02.173L

description:
U133Plus2_091108_SR09_HN02-173L

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).

source_name: Lateral margin

value: lateral margin


title: HN02.171T

description:
U133Plus2_091108_SR08_HN02-171T

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).

source_name: Tumor

value: tumor


title: HN04.60P

description:
U133Plus2_091108_SR11_HN04-60P

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).

value: II

value: posterior margin

value: ANED


title: C (24hr) Rep 1

description: replicate 1


title: Diabetic Human Kidney 67, Tubuli

description:
HK67T
KS1-HG_U133A_2-2876

source_name: Tubuli of DKD kidney

value: kidney

tag: tissue subregion

value: tubules

value: diabetic kidney disease (DKD)


title: Diabetic Human Kidney 120, Tubuli

description:
HK120T
KS1-HG_U133A_2-9417


title: CONTROL_1

tag: subject

value: control

tag: age

tag: fasting glucose

tag: fasting insulin

tag: total cholesterol

tag: hdl

tag: total triglycerides


title: C (24hr) Rep 2

description: replicate 2


title: E+P+C (24hr) Rep 3

description: replicate 3

value: 17b-estradiol and Progesterone


title: CONTROL_7

tag: bmi


title: E+P+C (24hr) Rep 2

description: replicate 2

tag: cell line


title: Diabetic Human Kidney 62, Tubuli

description:
HK62T
KS1-HG_U133A_2-2902

tag: tissue

tag: disease state


title: Diabetic Human Kidney 43, Tubuli

description:
HK43T
KS1-HG_U133A_2-2765


title: HN02.162N

description:
U133Plus2_091108_SR07_HN02-162N

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).

tag: patient identifier

tag: tissue location

value: tongue

value: superficially invasive

value: normal

tag: recurrence

tag: outcome


title: P+C (24hr) Rep 3

description: replicate 3

tag: timepoint

tag: hormone

value: Progesterone

tag: infected with

value: Chlamydia trachomatis D


title: E+P+C (24hr) Rep 1

description: replicate 1


title: HN02.160L

description:
U133Plus2_091108_SR06_HN02-160L

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).

value: squamous cell carcinoma of the tongue

tag: Stage

tag: grade

tag: site

value: margin

tag: site detail


title: P+C (24hr) Rep 1

description: replicate 1


title: Control Human Kidney 150, Glomeruli

description:
HK150G
KS1-HG_U133A_2-5116

source_name: Glomerulus of control kidney

tag: tissue subregion

value: glomerulus

tag: individual


title: P+C (24hr) Rep 2

description: replicate 2


title: Control Human Kidney 154, Glomeruli

description:
HK154G
KS1-HG_U133A_2-5118


title: E+C (24hr) Rep 3

description: replicate 3


title: E+C (24hr) Rep 1

description: replicate 1


title: E+C (24hr) Rep 2

description: replicate 2


title: Control Human Kidney 123, Glomeruli

description:
HK123G
KS1-HG_U133A_2-5111


title: HN02.159M

description:
U133Plus2_091108_SR05_HN02-159M

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).

source_name: Medial margin

value: medial margin

value: no


title: Control (24hr) Rep 3

description: replicate 3


title: Control Human Kidney 119, Glomeruli

description:
HK119G
KS1-HG_U133A_2-3470


title: HN02.158A

description:
U133Plus2_091108_SR04_HN02-158A

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).

source_name: Anterior margin

value: II

value: anterior margin


title: Control (24hr) Rep 2

description: replicate 2


title: Control (24hr) Rep 1

description: replicate 1


title: E+P (24hr) Rep 3

description: replicate 3


title: HN02.134I

description:
U133Plus2_091108_SR02_HN02-134I

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).

source_name: inferior margin

value: invasive mod diff

value: Inferior margin

value: yes

value: local

value: AWD


title: E+P (24hr) Rep 2

description: replicate 2

value: 17b-estradiol and Progesterone


title: Control Human Kidney 83, Glomeruli

description:
HK83G
KS1-HG_U133A_2-2923

value: kidney

value: control


title: HN02.135N

description:
U133Plus2_091108_SR03_HN02-135N

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).

value: tongue

value: normal


title: HN05.216A

description:
U133Plus2_073008L_SR21_HNO5 216A

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).

value: squamous cell carcinoma of the tongue

value: IV

value: ANED


title: E+P (24hr) Rep 1

description: replicate 1


title: Control Human Kidney 100, Glomeruli

description:
HK100G
KS1-HG_U133A_2-3427

value: glomerulus


title: HN02.129T

description:
U133Plus2_091108_SR01_HN02-129T

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).

value: tumor


title: Diabetic Human Kidney 164, Tubuli

description:
HK164T
KS1-HG_U133A_2-6394

value: tubules

value: diabetic kidney disease (DKD)


title: P (24hr) Rep 2

description: replicate 2

value: Progesterone


title: P (24hr) Rep 3

description: replicate 3


title: Control Human Kidney 82, Glomeruli

description:
HK82G
KS1-HG_U133A_2-2921


title: E (24hr) Rep 3

description: replicate 3


title: HN05.214T

description:
U133Plus2_073008L_SR20_HNO5 214T

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).

value: invasive mod diff

value: no


title: C (12hr)

description: replicate 1

value: Chlamydia trachomatis D


title: E (24hr) Rep 1

description: replicate 1


title: Control Human Kidney 81, Glomeruli

description:
HK81G
KS1-HG_U133A_2-2919


title: Control (12hr)

description: replicate 1


title: E+P+C (12hr)

description: replicate 1


title: Control Human Kidney 76, Glomeruli

description:
HK76G
KS1-HG_U133A_2-2911


title: HN05.197SP

description:
U133Plus2_073008L_SR18_HNO5 197SP

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).

source_name: Superior margin

value: keratinizing mod diff

value: margin

value: superior margin

value: yes

value: regional and distant

value: DOD


title: E+C (12hr)

description: replicate 1


title: Control Human Kidney 110, Glomeruli

description:
HK110G
KS1-HG_U133A_2-3467

value: kidney

value: control


title: E (24hr) Rep 2

description: replicate 2


title: P (24hr) Rep 1

description: replicate 1


title: HN05.213N

description:
U133Plus2_073008L_SR19_HNO5 213N

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).

value: squamous cell carcinoma of the tongue

value: tongue

value: IV

value: normal

value: ANED


title: HN05.196P

description:
U133Plus2_073008L_SR17_HNO5 196P

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).

source_name: Posterior margin

value: posterior margin


title: Control Human Kidney 34, Glomeruli

description:
HK34G
KS1-HG_U133A_2-2784

value: glomerulus


title: HN05.193M

description:
U133Plus2_073008L_SR16_HNO5 193M

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).

value: medial margin


title: Control Human Kidney 77, Glomeruli

description:
HK77G
KS1-HG_U133A_2-2913


title: Control Human Kidney 33, Glomeruli

description:
HK33G
KS1-HG_U133A_2-2772


title: E+P (12hr)

description: replicate 1

value: 17b-estradiol and Progesterone


title: E (12hr)

description: replicate 1


title: HN05.191N

description:
U133Plus2_073008L_SR14_HNO5 191N

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).

value: keratinizing mod diff


title: HN05.192T

description:
U133Plus2_073008L_SR15_HNO5 192T

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).

value: tumor


title: Diabetic Human Kidney 164, Glomeruli

description:
HK164G
KS1-HG_U133A_2-6393

source_name: Glomerulus of DKD kidney

value: diabetic kidney disease (DKD)


title: HN05.190P

description:
U133Plus2_073008L_SR13_HNO5 190P

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).

value: upper alveolus

value: margin

value: no


title: Diabetic Human Kidney 178, Glomeruli

description:
HK178G
KS1-HG_U133A_2-6574

value: kidney


title: P (12hr)

description: replicate 1

value: Progesterone


title: HN05.188L

description:
U133Plus2_073008L_SR12_HNO5 188L

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).

value: squamous cell carcinoma of the tongue

value: lateral margin


title: Diabetic Human Kidney 151, Glomeruli

description:
HK151G
KS1-HG_U133A_2-5117


title: HN05.187LP

description:
U133Plus2_073008L_SR11_HNO5 187LP

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).

source_name: Left posterior margin

value: IV

value: left posterior margin


title: Diabetic Human Kidney 168, Glomeruli

description:
HK168G
KS1-HG_U133A_2-6395


title: Diabetic Human Kidney 158, Glomeruli

description:
HK158G
KS1-HG_U133A_2-6372


title: HN05.182S

description:
U133Plus2_073008L_SR10_HNO5 182S

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).

value: superior margin

value: ANED


title: Diabetic Human Kidney 67, Glomeruli

description:
HK67G
KS1-HG_U133A_2-2905

value: glomerulus


title: po13_vs_po14

city: Barcelona

first: Arcadi

last: Navarro

address: Plaça Charles Darwin, 1

country: Spain

institute: University Pompeu Fabra

hyb_protocol: Performed by NimbleGen according to manufacturer's direction

data_processing: Normalization was performed using NimbleScan 2.4.

organism: Pongo sp.

source_name: Tissue sampled after natural death

growth_protocol: Tissue were maintained in -20C freezer before DNA extraction

extract_protocol: genomic DNA extracted by standard phenol chloroform extraction protocol

tag: sample type

value: po13 test sample

value: po14 reference sample


title: Diabetic Human Kidney 48, Glomeruli

description:
HK48G
KS1-HG_U133A_2-2871


title: HN05.181T

description:
U133Plus2_073008L_SR09_HNO5 181T

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).

value: keratinizing mod diff


title: Diabetic Human Kidney 62, Glomeruli

description:
HK62G
KS1-HG_U133A_2-2901


title: HN05.180N

description:
U133Plus2_073008L_SR08_HNO5 180N

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).

value: normal


title: AG05252_vs_Susie

scan_protocol: Performed by NimbleGen according to manufacturer's direction

organism: Pongo pygmaeus

value: AG05252 test sample

value: Susie reference sample


title: po12_vs_po14

label_protocol: Performed by NimbleGen according to manufacturer's direction

value: po12 test sample


title: PPY6_vs_Susie

value: PPY6 test sample


title: PPY10_vs_po14

value: PPY10 test sample


title: HN04.96P

description:
U133Plus2_073008L_SR07_HNO4 96P

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).

value: tongue

value: II

value: invasive mod diff

value: margin

value: posterior margin

value: no


title: Hati_vs_Susie

value: Hati test sample


title: P+C (12hr)

description: replicate 1

tag: cell line

value: Progesterone

value: Chlamydia trachomatis D


title: Diabetic Human Kidney 40, Glomeruli

description:
HK40G
KS1-HG_U133A_2-2757

tag: tissue

value: kidney

value: glomerulus

value: diabetic kidney disease (DKD)


title: HN04.94T

description:
U133Plus2_073008L_SR06_HNO4 94T

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).

tag: disease state

value: squamous cell carcinoma of the tongue

value: tumor

value: ANED


title: PPY9_vs_Susie

value: PPY9 test sample

value: Susie reference sample


title: HN04.93N

description:
U133Plus2_073008L_SR05_HNO4 93N

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).

tag: patient identifier

value: tongue

value: normal


title: po14_vs_po13

organism: Pongo abelii

value: po14 reference sample

value: po13 test sample


title: Tengku_vs_Susie

value: Tengku test sample


title: HN04.38P

description:
U133Plus2_073008L_SR04_HNO4 38P

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).

tag: tissue location

value: floor of mouth

value: IV

value: invasive poorly diff

value: margin

value: posterior margin

value: no


title: Susie_vs_Tengku


title: po14_vs_po12

value: po12 test sample


title: Susie_vs_PPY6

value: PPY6 test sample


title: HN04.37LL

description:
U133Plus2_073008L_SR03_HNO4 37LL

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).

source_name: Left lateral margin

value: squamous cell carcinoma of the tongue

value: left lateral margin

tag: recurrence


title: HN04.34T

description:
U133Plus2_073008L_SR02_HNO4 34T

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).

value: tumor

tag: outcome

value: ANED


title: AG1256_vs_Susie

value: AG1256 test sample

value: Susie reference sample


title: Tsc2-/- MEFs, Tfeb shRNA, vehicle, rep2

city: Dallas

first: Samuel

last: Peña-Llopis

address: 6000 Harry Hines Blvd., NB5.102

department: Internal Medicine - Oncology Division

institute: UT Southwestern Medical Center

description: Gene expression profiling from Tsc2-deficient MEFs stably expressing a Tfeb shRNA vector and treated with low serum (0.1% FBS) and vehicle (methanol) for 24h

hyb_protocol: Standard Illumina procedure using Illumina MouseWG-6 v2.0 expression beadchips

scan_protocol: Standard Illumina scanning protocol

data_processing: Arrays were preprocessed with an RMA-like background correction using the MBCB package and quantile normalized with the Affy package in R/Bioconductor. The presence/absence of calls was assessed using GenomeStudio (Illumina)

organism: Mus musculus

source_name: Tsc2-/- MEFs expressing a Tfeb shRNA vector and treated with low serum and vehicle for 24h, replicate 2

label_protocol: Standard Illumina procedure

growth_protocol: Cells were maintained under 10% FBS DMEM and 1% (v/v) penicillin/streptomycin in a humidified incubator at 37 °C and 5% CO2

extract_protocol: RNA was extracted using the RNeasy Mini kit (Qiagen, Valencia, CA) with on-column DNase digestion

treatment_protocol: Cells were transduced with lentiviruses containing a pLKO.1 vector encoding a scrambled or a Tfeb shRNA sequence (TRCN0000085548). Cells were selected with 2 µg/ml puromycin for one week to make stable cell lines knocking down Tfeb (or a scrambled sequence). Cells at a confluency ~70% were washed twice with PBS and treated with 25 nM rapamycin or vehicle (methanol) under 0.1% FBS for 24 h

tag: cell type

value: immortalized mouse embryo fibroblast (MEF) cell line

tag: genotype

tag: knockdown

value: Tfeb shRNA

tag: treatment

value: vehicle


title: Susie_vs_PPY9

value: PPY9 test sample


title: Susie_vs_Hati

value: Hati test sample


title: Tsc2-/- MEFs, Tfeb shRNA, rapamycin, rep2

description: Gene expression profiling from Tsc2-deficient MEFs stably expressing a Tfeb shRNA vector and treated with low serum (0.1% FBS) and 25 nM rapamycin for 24h

source_name: Tsc2-/- MEFs expressing a Tfeb shRNA vector and treated with low serum and rapamycin for 24h, replicate 2

value: rapamycin


title: OR1166_vs_LB502

organism: Pan paniscus

value: OR1166 test sample

value: LB502 reference sample


title: Tsc2-/- MEFs, Tfeb shRNA, vehicle, rep1

source_name: Tsc2-/- MEFs expressing a Tfeb shRNA vector and treated with low serum and vehicle for 24h, replicate 1


title: KB1650_vs_LB502

value: KB1650 test sample


title: wt MEFs, Tfeb shRNA, rapamycin, rep2

description: Gene expression profiling from wild-type MEFs stably expressing a Tfeb shRNA vector and treated with low serum (0.1% FBS) and 25 nM rapamycin for 24h

source_name: Wild-type MEFs expressing a Tfeb shRNA vector and treated with low serum and rapamycin for 24h, replicate 2


title: Tsc2-/- MEFs, Tfeb shRNA, vehicle, rep3

source_name: Tsc2-/- MEFs expressing a Tfeb shRNA vector and treated with low serum and vehicle for 24h, replicate 3


title: HN04.33N

description:
U133Plus2_073008L_SR01_HNO4 33N

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).

source_name: Normal

value: floor of mouth

tag: Stage

value: IV

tag: grade

value: invasive poorly diff

value: margin

value: normal

value: no


title: HN08.435

description:
U133Plus2_060508L_SR13_HNO8-435

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).

source_name: Margin

value: squamous cell carcinoma of the tongue

value: midline floor of mouth

value: unknown

tag: site

tag: site detail

value: ANED


title: OR310_vs_LB502

value: OR310 test sample


title: wt MEFs, Tfeb shRNA, rapamycin, rep1

source_name: Wild-type MEFs expressing a Tfeb shRNA vector and treated with low serum and rapamycin for 24h, replicate 1

value: immortalized mouse embryo fibroblast (MEF) cell line

value: Tfeb shRNA


title: LB502_vs_KB4229

value: KB4229 test sample


title: Susie_vs_AG05252

value: Susie reference sample

value: AG05252 test sample


title: KB7036_vs_LB502

value: KB7036 test sample

value: LB502 reference sample


title: KB4229_vs_LB502


title: wt MEFs, Tfeb shRNA, vehicle, rep2

description: Gene expression profiling from wild-type MEFs stably expressing a Tfeb shRNA vector and treated with low serum (0.1% FBS) and vehicle (methanol) for 24h

source_name: Wild-type MEFs expressing a Tfeb shRNA vector and treated with low serum and vehicle for 24h, replicate 2

value: vehicle


title: HN08.434

description:
U133Plus2_060508L_SR12_HNO8-434

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).

source_name: Tumor

value: tumor


title: po14_vs_PPY10

value: po14 reference sample

value: PPY10 test sample


title: HN08.433

description:
U133Plus2_060508L_SR11_HNO8-433

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).

value: margin

value: normal

value: no


title: Susie_vs_AG1256

value: AG1256 test sample


title: wt MEFs, Tfeb shRNA, vehicle, rep1

source_name: Wild-type MEFs expressing a Tfeb shRNA vector and treated with low serum and vehicle for 24h, replicate 1


title: LB502_vs_KB1650

value: KB1650 test sample


title: LB502_vs_KB7036


title: Tsc2-/- MEFs, scrambled shRNA, rapamycin, rep2

description: Gene expression profiling from Tsc2-deficient MEFs stably expressing a scrambled shRNA vector and treated with low serum (0.1% FBS) and 25 nM rapamycin for 24h

source_name: Tsc2-/- MEFs expressing a scrambled shRNA vector and treated with low serum and rapamycin for 24h, replicate 2

value: scrambled shRNA

value: rapamycin


title: Tsc2-/- MEFs, Tfeb shRNA, rapamycin, rep1

source_name: Tsc2-/- MEFs expressing a Tfeb shRNA vector and treated with low serum and rapamycin for 24h, replicate 1

value: immortalized mouse embryo fibroblast (MEF) cell line

value: Tfeb shRNA


title: HN08.430T

description:
U133Plus2_060508L_SR09_HNO8-430

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).

value: squamous cell carcinoma of the tongue

value: tongue

value: unknown

value: ANED


title: LB502_vs_OR310

value: LB502 reference sample

value: OR310 test sample


title: Tsc2-/- MEFs, scrambled shRNA, rapamycin, rep1

source_name: Tsc2-/- MEFs expressing a scrambled shRNA vector and treated with low serum and rapamycin for 24h, replicate 1


title: KB7973_vs_pg20

organism: Gorilla gorilla gorilla

value: KB7973 test sample

organism: Gorilla gorilla

value: pg20 reference sample


title: HN08.428M

description:
U133Plus2_060508L_SR07_HNO8-428

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).

source_name: Medial margin

value: margin

value: medial margin


title: KB5829_vs_pg20

source_name: Tissue sampled after natural death

value: KB5829 test sample


title: HN08.429N

description:
U133Plus2_060508L_SR08_HNO8-429

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).

value: normal

value: no


title: HN08.426TB

description:
U133Plus2_060508L_SR06_HNO8-426

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).

source_name: Tongue base margin

value: tongue base margin


title: HN08.425T

description:
U133Plus2_060508L_SR05_HNO8-425

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).

value: tumor


title: LB502_vs_OR1166

value: OR1166 test sample


title: Tsc2-/- MEFs, scrambled shRNA, vehicle, rep3

description: Gene expression profiling from Tsc2-deficient MEFs stably expressing a scrambled shRNA vector and treated with low serum (0.1% FBS) and vehicle (methanol) for 24h

source_name: Tsc2-/- MEFs expressing a scrambled shRNA vector and treated with low serum and vehicle for 24h, replicate 3

value: immortalized mouse embryo fibroblast (MEF) cell line

value: scrambled shRNA

value: vehicle


title: Tsc2-/- MEFs, scrambled shRNA, vehicle, rep1

source_name: Tsc2-/- MEFs expressing a scrambled shRNA vector and treated with low serum and vehicle for 24h, replicate 1


title: HepG2.2.15

city: Wuhan

first: Xing-Xing

last: He

state: Hubei

address: 1095# Jie-Fang Avenue

department: Institute of Liver and Gastrointestinal Diseases

country: China

institute: Tongji Hospital

hyb_protocol: see manufacturer's web site at http://www.agilent.com/

scan_protocol: Images were scanned with the Agilent microarray scanner and the results were obtained by Agilent feature extraction software, Scan resolution 5μm, PMT 100%，5%

data_processing: The scanned images were analyzed with  Agilent Feature Extraction Software, the raw intensity data were further analyzed using GeneSpring10.0 software.

growth_protocol: HepG2.2.15 cells (human hepatoma cell line HepG2 stably transfected with HBV genome, kindly provided by Prof. Y.C. Cheng) were cultured and intained in Dulbecco’s modified Eagle’s medium (DMEM), supplemented with 100 ml/l fetal calf serum (FCS), 100 IU/ml penicillin, 100 lg/ml streptomycin, and 200 lg/ml G418 at 37  C in a humidified incubator with 5% CO2.

extract_protocol: The MirVanaTM miRNA Isolation Kit (Ambion, AM1560) was used to isolate total RNA (including miRNA) from all cell lines according to the manufacturer’s protocol.


title: KB3456_vs_pg20

value: KB3456 test sample


title: OR934_vs_pg20

value: OR934 test sample


title: HN08.384T

description:
U133Plus2_060508L_SR02_HNO8-384

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).

value: squamous cell carcinoma of the tongue

value: buccal

value: unknown

value: ANED


title: HN08.385P

description:
U133Plus2_060508L_SR03_HNO8-385

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).

source_name: Posterior margin

value: margin

value: posterior margin


title: Tsc2-/- MEFs, scrambled shRNA, vehicle, rep2

source_name: Tsc2-/- MEFs expressing a scrambled shRNA vector and treated with low serum and vehicle for 24h, replicate 2


title: wt MEFs, scrambled shRNA, rapamycin, rep1

description: Gene expression profiling from wild-type MEFs stably expressing a scrambled shRNA vector and treated with low serum (0.1% FBS) and 25 nM rapamycin for 24h

source_name: Wild-type MEFs expressing a scrambled shRNA vector and treated with low serum and rapamycin for 24h, replicate 1

value: rapamycin


title: wt MEFs, scrambled shRNA, vehicle, rep1

description: Gene expression profiling from wild-type MEFs stably expressing a scrambled shRNA vector and treated with low serum (0.1% FBS) and vehicle (methanol) for 24h

source_name: Wild-type MEFs expressing a scrambled shRNA vector and treated with low serum and vehicle for 24h, replicate 1

growth_protocol: Cells were maintained under 10% FBS DMEM  and 1% (v/v) penicillin/streptomycin in a humidified incubator at 37 °C and 5% CO2


title: wt MEFs, scrambled shRNA, rapamycin, rep2

source_name: Wild-type MEFs expressing a scrambled shRNA vector and treated with low serum and rapamycin for 24h, replicate 2


title: Tsc2-/- MEFs, rapamycin, rep2

description: Gene expression data from Tsc2-/- MEFs treated with low serum (0.1% FBS) and 25 nM rapamycin for 24h

hyb_protocol: Following fragmentation, 10 µg of cRNA were hybridized on Affymetrix MOE430A chips according to standard methodology

scan_protocol: Standard Affymetrix procedure

data_processing: CEL files were preprocessed and normalized using the RMA algorithm through the Affy package of R/Bioconductor. The presence/absence of calls was assessed using MAS5 (Affymetrix)

source_name: Tsc2-/- MEFs treated with low serum and rapamycin for 24h, replicate 2

label_protocol: Standard Affymetrix procedure

extract_protocol: RNA was extracted with NucleoSpin RNA II (Clontech, Mountain View, CA)

treatment_protocol: Cells at a confluency ~70% were washed twice with PBS and treated with 25 nM rapamycin or vehicle (methanol) under 0.1% FBS for 24 h


title: wt MEFs, scrambled shRNA, vehicle, rep2

source_name: Wild-type MEFs expressing a scrambled shRNA vector and treated with low serum and vehicle for 24h, replicate 2


title: KB5712_vs_pg20

value: KB5712  test sample

value: pg20 reference sample


title: pg20_vs_OR934

value: OR934  test sample


title: Tsc2-/- MEFs, rapamycin, rep1

source_name: Tsc2-/- MEFs treated with low serum and rapamycin for 24h, replicate 1


title: KB3784_vs_pg20

value: KB3784 test sample


title: HNO5-140AL

description:
U133Plus2_033109L_KR17_HNO5-140AL

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).

source_name: Margin

value: yes

value: local

value: DOD


title: HN08.383N

description:
U133Plus2_060508L_SR01_HNO8-383

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).

source_name: Normal

value: normal

value: no


title: HN08.432LP

description:
U133Plus2_060508L_SR10_HNO8-432

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).

source_name: Left posterior margin

value: tongue

value: left posterior margin


title: wt MEFs, rapamycin, rep2

description: Gene expression data from wild-type MEFs treated with low serum (0.1% FBS) and 25 nM rapamycin for 24h

source_name: Wild-type MEFs treated with low serum and rapamycin for 24h, replicate 2

value: immortalized mouse embryo fibroblast (MEF) cell line


title: HNO5-144S

description:
U133Plus2_033109L_KR16_HNO5-144S

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).

value: squamous cell carcinoma of the tongue

value: unknown


title: HNO5-143LS

description:
U133Plus2_033109L_KR15_HNO5-143LS

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).

value: margin


title: Tsc2-/- MEFs, vehicle, rep2

description: Gene expression data from Tsc2-/- MEFs treated with low serum (0.1% FBS) and vehicle (methanol) for 24h

source_name: Tsc2-/- MEFs treated with low serum and vehicle for 24h, replicate 2

value: vehicle


title: pg20_vs_5829

source_name: Tissue sampled after natural death

value: 5829 test sample


title: pg20_vs_KB5712

value: KB5712  test sample


title: CD8-M-3

city: Ribeirao Preto

first: Rodrigo

middle: Alexandre

last: Panepucci

state: São Paulo

address: R. Tenente Catao Roxo, 2501

country: Brazil

institute: Regional Blood Center of Ribeirâo Preto (FUNDHERP, HC-FMRP-USP)

description:
251485036483_CD8-M
All samples were obtained by positive selection (using MACS Kits, from Miltenyi Biotec) to purities above 95% (% of CD4 or CD8+ cells, determined by flow cytometry).

hyb_protocol: The cRNA was purified on an RNeasy column and 10µg were fragmented and hybridized to microarrays overnight (17h at 65C and 4 RPM) in SureHyb chambers placed in a rotator oven incubator (Agilent, G2534A, G2530-60029 and G2545A), using the 'Gene Expression Hybridization Kit' (Agilent, 5188-5242). After posthybridization washes ('Wash Buffers 1 and 2 Kit', Agilent, 5188-5327), arrays were dried and analyzed.

scan_protocol: After processing, microarray slides were scanned at 535 nm and 5um/pixel resolution using a GenePix 4000B scanner and the software 'GenePix Pro 6.0' (Molecular Devices, Sunnyvale, CA, USA).

data_processing: Images were analyzed with the software 'Agilent Feature Extraction 8.5' and extracted expression values (gProcessedSignal) were further normalized to the 75 percentile expression value, considering all non-control features (ControlType=0). Following normalization, replicate probes were averaged, resulting in the final set of 41,000 unique probes.

source_name: CD8+ T-lymphocytes, cocultured 5 days with MSCs following activation

label_protocol: Cy3-labelled cRNA was generated using the 'Quick Amp Labeling Kit, one-color' (Agilent, 5190-0442), following the manufacturer’s protocol. Briefly, 1µg total RNA from each studied sample was spiked with a control RNA ('One Color RNA Spike-In Kit', Agilent, 5188-5282) and reverse transcribed using T7 oligo(dT) primers, followed by synthesis of the second complementary DNA (cDNA) strand and purification of double-strand cDNA with QIAquick columns (Qiagen). Cy3-labelled cRNA was then generated by an in vitro transcription reaction using T7 RNA polymerase and Cyanine 3-CTP and labeling efficiency was measured using a NanoDrop 1000 spectrophotometer.

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated from the blood of healthy volunteers by centrifugation using Ficoll-Paque PLUS, and CD3+ T-cells were immunomagnetically purified using the Pan T cell Isolation Kit (Miltenyi Biotec). Following isolation, CD3+ T-cells were activated (see treatment protocol) and cultured (RPMI, 10% FCS) in three 100-mm plates (7.5x10^6 cells/plate): two containing 1.5x10^6 MSCs (adhered 24 h earlier) and one without MSCs.

extract_protocol: Total RNA was extracted using TRIZOL-LS (Invitrogen), treated with DNase and purified using the RNAeasy kit (Qiagen, Valencia, CA, USA). RNA quality was assessed by agarose gel electrophoresis and quantified using a NanoDrop 1000 spectrophotometer (NanoDrop, Wilmington, DE, USA).

treatment_protocol: Anti-biotin magnetic beads pre-loaded with biotinylated antibodies against human CD2, CD3, and CD28 (T Cell Activation/Expansion Kit, Miltenyi Biotec) were used (1 - 2 beads/cell) to mimic antigen-presenting cells and to activate resting T cells isolated from PBMCs or purified CD3+ T cells. Following activation, cells were cultured in RPMI (Invitrogen), and on the 3rd day, 20 U/ml of human recombinant IL-2 (Peprotech) was added to the culture. Cultures were maintained for two additional days before final evaluation.

tag: gender

value: male

tag: tissue origin

value: peripheral blood

tag: source cell type

value: CD3+ T-cells from peripheral blood mononuclear cells (PBMCs)


title: pg20_vs_7973

tag: sample type

value: pg20 reference sample

value: 7973 test sample


title: pg20_vs_3784

value: KB3784 test sample


title: Tsc2-/- MEFs, vehicle, rep1

source_name: Tsc2-/- MEFs treated with low serum and vehicle for 24h, replicate 1


title: pg20_vs_KB3456

value: KB3456 test sample


title: CD4-L-3

description:
251485036483_CD4-L
All samples were obtained by positive selection (using MACS Kits, from Miltenyi Biotec) to purities above 95% (% of CD4 or CD8+ cells, determined by flow cytometry).

source_name: CD4+ T-lymphocytes, cultured 5 days following activation


title: CD4-M-3

description:
251485036483_CD4-M
All samples were obtained by positive selection (using MACS Kits, from Miltenyi Biotec) to purities above 95% (% of CD4 or CD8+ cells, determined by flow cytometry).

source_name: CD4+ T-lymphocytes, cocultured 5 days with MSCs following activation


title: CD4-L-2

description:
251485036481_CD4-L
All samples were obtained by positive selection (using MACS Kits, from Miltenyi Biotec) to purities above 95% (% of CD4 or CD8+ cells, determined by flow cytometry).


title: CD8-L-3

description:
251485036483_CD8-L
All samples were obtained by positive selection (using MACS Kits, from Miltenyi Biotec) to purities above 95% (% of CD4 or CD8+ cells, determined by flow cytometry).

source_name: CD8+ T-lymphocytes, cultured 5 days following activation


title: wt MEFs, rapamycin, rep1

source_name: Wild-type MEFs treated with low serum and rapamycin for 24h, replicate 1

value: rapamycin


title: HNO5-141PI

description:
U133Plus2_033109L_KR14_HNO5-141PI

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).

tag: disease state

value: yes

value: local

value: DOD


title: px27_vs_px14

organism: Pan troglodytes troglodytes

value: px27 test sample

organism: Pan troglodytes

value: Px14 reference sample


title: HNO5-138T

description:
U133Plus2_033109L_KR13_HNO5-138T

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).

source_name: Tumor

tag: patient identifier

value: squamous cell carcinoma of the tongue

value: unknown

value: tumor


title: PR01009_vs_Clint

value: PR01009 test sample

value: Clint reference sample


title: px31_vs_px14

value: px31 test sample


title: HNO4-105A

description:
U133Plus2_033109L_KR09_HNO4-105A

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).

tag: tissue location

value: margin


title: PR01105_vs_Clint

value: PR01105 test sample


title: wt MEFs, vehicle, rep1

description: Gene expression data from wild-type MEFs treated with low serum (0.1% FBS) and vehicle (methanol) for 24h

source_name: Wild-type MEFs treated with low serum and vehicle for 24h, replicate 1

value: immortalized mouse embryo fibroblast (MEF) cell line

value: vehicle


title: HN08.424N

description:
U133Plus2_060508L_SR04_HNO8-424

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).

value: tongue

value: normal

tag: recurrence

value: no

value: ANED


title: PR00496_vs_Clint

value: PR00496 test sample


title: HNO4-106P

description:
U133Plus2_033109L_KR10_HNO4-106P

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).

value: yes

value: local

tag: outcome

value: DOD


title: CD8-L-2

description:
251485036481_CD8-L
All samples were obtained by positive selection (using MACS Kits, from Miltenyi Biotec) to purities above 95% (% of CD4 or CD8+ cells, determined by flow cytometry).

value: male

value: peripheral blood

value: CD3+ T-cells from peripheral blood mononuclear cells (PBMCs)


title: HNO4-107T

description:
U133Plus2_033109L_KR11_HNO4-107T

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).

value: squamous cell carcinoma of the tongue

value: unknown

value: tumor


title: CD4-M-2

description:
251485036481_CD4-M
All samples were obtained by positive selection (using MACS Kits, from Miltenyi Biotec) to purities above 95% (% of CD4 or CD8+ cells, determined by flow cytometry).


title: CCR4b RNAi

city: San Antonio

first: Masahiro

last: Morita

state: Texas

address: 4939 Charles Katz Drive

department: Department of Molecular Medicine

institute: University of Texas Health Science Center at San Antonio

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16hr at 45C on Gene Chip Mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with Affymetrix GCOS (GeneChipOperating Software) software.

source_name: CCR4b-depleted NIH3T3 cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA.

extract_protocol: Total RNA were extracted with ISOGEN according to manufacture's protocol (Nippon Gene) and purified with RNeasy Kit (Qiagen).

treatment_protocol: shRNA-expressing retrovirus infection

tag: cell line

value: NIH3T3 cells

value: CCR4b RNAi


title: HNO4-104N

description:
U133Plus2_033109L_KR08_HNO4-104N

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).

value: margin


title: Control RNAi

source_name: Control-depleted NIH3T3 cells

value: Control RNAi


title: wt MEFs, vehicle, rep2

source_name: Wild-type MEFs treated with low serum and vehicle for 24h, replicate 2

tag: cell type

value: immortalized mouse embryo fibroblast (MEF) cell line

tag: genotype

value: vehicle


title: CD8-L-1

description:
251485036480_CD8-L
All samples were obtained by positive selection (using MACS Kits, from Miltenyi Biotec) to purities above 95% (% of CD4 or CD8+ cells, determined by flow cytometry).


title: CD4-M-1

description:
251485036480_CD4-M
All samples were obtained by positive selection (using MACS Kits, from Miltenyi Biotec) to purities above 95% (% of CD4 or CD8+ cells, determined by flow cytometry).


title: CD4-L-1

description:
251485036480_CD4-L
All samples were obtained by positive selection (using MACS Kits, from Miltenyi Biotec) to purities above 95% (% of CD4 or CD8+ cells, determined by flow cytometry).


title: HNO5-137N

description:
U133Plus2_033109L_KR12_HNO5-137N

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).

value: normal


title: CD8-M-2

description:
251485036481_CD8-M
All samples were obtained by positive selection (using MACS Kits, from Miltenyi Biotec) to purities above 95% (% of CD4 or CD8+ cells, determined by flow cytometry).


title: T_28 RNA INF7

city: Braunschweig

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

country: Germany

institute: HCI - Helmholtz Centre for Infection Research

description: T_28 RNA INF7

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at conditions recommended by the manufacturer. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GCS 3000.

data_processing: RMA summarization, log2

source_name: kidney infected with Staphylococcus aureus

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

extract_protocol: RNeasy Midi Kit

tag: infection phase

tag: tissue

value: kidney


title: px25_vs_px14

value: px25 test sample

value: Px14 reference sample


title: T_28 RNA INF6

description: T_28 RNA INF6


title: HNO4-89M

description:
U133Plus2_033109L_KR06_HNO4-89M

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).

source_name: Margin

tag: Stage

tag: grade

value: yes

value: locoregional

value: DOD


title: HNO4-88A

description:
U133Plus2_033109L_KR05_HNO4-88A

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).

tag: site

tag: site detail


title: HNO2-19916T

description:
U133Plus2_033109L_KR02_HNO2-19916T

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).

value: local

value: AWD


title: HNO4-86T

description:
U133Plus2_033109L_KR07_HNO4-86T

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).

value: squamous cell carcinoma of the tongue

value: unknown


title: HNO4-87N

description:
U133Plus2_033109L_KR04_HNO4-87N

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).

source_name: Normal


title: T_2 RNA INF1

description: T_2 RNA INF1


title: HNO2-127I

description:
U133Plus2_033109L_KR03_HNO2-127I

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).


title: HNO2-19916N

description:
U133Plus2_033109L_KR01_HNO2-19916N

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).


title: T_28 RNA CTL4

description: T_28 RNA CTL4

source_name: kidney uninfected


title: Clint_vs_PR01009

value: Clint reference sample

value: PR01009 test sample


title: T_28 RNA INF1

description: T_28 RNA INF1


title: T_2 RNA INF4

description: T_2 RNA INF4


title: T_28 RNA CTL1

description: T_28 RNA CTL1


title: human DLBCL tumoral sample, gene expr, case 27

status: Public on Aug 02 2011

city: Madrid

first: Santiago

last: Montes-Moreno

state: Madrid

address: C/ Melchor Fernández Almagro, 3

department: Molecular Pathology

institute: CNIO

description: US22502553_251239139148_S01_GE2-v4_95_Feb07.txt

hyb_protocol: cRNA product was hybridized overnight following the manufacturer’s instructions.

scan_protocol: Scanning was carried out immediately using the Agilent G2565AA Microarray Scanner System (Agilent Technologies) and data were collected with Feature Extraction v9.5 software (Agilent Technologies).

data_processing: For gene-expression profiling, microarray background subtraction was carried out using the normexp tool available in Bioconductor’s limma package (http://www.bioconductor.org). To normalize the dataset, loess within-array normalization and quartile between-array normalization were performed.

source_name: human DLBCL tumoral sample

label_protocol: 500 ng of mRNA were amplified and fluorescence-labeled with Agilent’s Low RNA Input Fluorescence Linear Amplification kit (Agilent Technologies). The sample was labeled with Cy5 and the reference Universal Human Reference RNA (Stratagene, La Jolla, CA, USA) was labeled with Cy3

extract_protocol: RNA extracted with Trizol was purified by RNase-free DNase I RNeasy kit (Qiagen Inc., Valencia, CA) following the standard procedure. mRNA quality was assessed with the Agilent 2100 Bioanalyzer (Agilent Technologies).

tag: case id

value: tumoral sample

value: diffuse large B cell lymphoma (DLBCL)

tag: status os (0 alive; 1 death)

tag: status pfs (0

tag: time os (months)

tag: time pfs (months)

tag: reference


title: px20_vs_px14

source_name: Tissue sampled after natural death

tag: sample type

value: px20 test sample


title: human DLBCL tumoral sample, gene expr, case 28

description: US22502553_251239150234_S01_GE2-v4_95_Feb07.txt

source_name: Universal Human Reference RNA (Stratagene, La Jolla, CA, USA)


title: px 22_vs_px14

value: px22 test sample


title: T_28 RNA CTL2

description: T_28 RNA CTL2


title: CD8-M-1

description:
251485036480_CD8-M
All samples were obtained by positive selection (using MACS Kits, from Miltenyi Biotec) to purities above 95% (% of CD4 or CD8+ cells, determined by flow cytometry).

source_name: CD8+ T-lymphocytes, cocultured 5 days with MSCs following activation

tag: gender

value: male

tag: tissue origin

value: peripheral blood

tag: source cell type

value: CD3+ T-cells from peripheral blood mononuclear cells (PBMCs)


title: T_2 RNA INF3

description: T_2 RNA INF3

value: kidney


title: human DLBCL tumoral sample, gene expr, case 29

description: US22502553_251239150233_S01_GE2-v4_95_Feb07.txt

tag: cell type

value: Universal Human Reference RNA (Stratagene, La Jolla, CA, USA)


title: Clint_vs_PR00496

value: PR00496 test sample


title: Clint_vs_PR01105

value: PR01105 test sample


title: px1_vs_px14

value: px1 test sample

value: Px14 reference sample


title: px14_vs_px20


title: human DLBCL tumoral sample, gene expr, case 21

description: US22502553_251239139152_S01_GE2-v4_95_Feb07.txt


title: human DLBCL tumoral sample, gene expr, case 25

description: US22502553_251239150235_S01_GE2-v4_95_Feb07.txt


title: human DLBCL tumoral sample, gene expr, case 24

description: US22502553_251239150627_S01_GE2-v4_95_Feb07.txt


title: human DLBCL tumoral sample, gene expr, case 19

description: US22502553_251239150236_S01_GE2-v4_95_Feb07.txt


title: human DLBCL tumoral sample, gene expr, case 23

description: US22502553_251239147719_S01_GE2-v4_95_Feb07.txt


title: px14_vs_px1


title: human DLBCL tumoral sample, gene expr, case 20

description: US22502553_251239152177_S02_GE2-v4_95_Feb07.txt


title: human DLBCL tumoral sample, gene expr, case 16

description: US22502553_251239152872_S01_GE2-v4_95_Feb07.txt


title: human DLBCL tumoral sample, gene expr, case 13

description: US22502553_251239152874_S01_GE2-v4_95_Feb07.txt


title: human DLBCL tumoral sample, gene expr, case 17

description: US22502553_251239152878_S01_GE2-v4_95_Feb07.txt


title: human DLBCL tumoral sample, gene expr, case 11

description: US22502553_251239139137_S01_GE2-v4_95_Feb07.txt


title: human DLBCL tumoral sample, gene expr, case 18

description: US22502553_251239152661_S01_GE2-v4_95_Feb07.txt


title: human DLBCL tumoral sample, gene expr, case 14

description: US22502553_251239139136_S01_GE2-v4_95_Feb07.txt


title: human DLBCL tumoral sample, gene expr, case 22

description: US22502553_251239147842_S01_GE2-v4_95_Feb07.txt


title: human DLBCL tumoral sample, gene expr, case 15

description: US22502553_251239152882_S01_GE2-v4_95_Feb07.txt


title: px14_vs_px22


title: px14_vs_px31

value: px31 test sample


title: human DLBCL tumoral sample, gene expr, case 10

description: US22502553_251239152176_S01_GE2-v4_95_Feb07.txt


title: human DLBCL tumoral sample, gene expr, case 9

description: US22502553_251239139135_S01_GE2-v4_95_Feb07.txt


title: human DLBCL tumoral sample, gene expr, case 8

description: US22502553_251239152665_S01_GE2-v4_95_Feb07.txt


title: px14_vs_px25

value: px25 test sample


title: human DLBCL tumoral sample, gene expr, case 7

description: US22502553_251239152175_S01_GE2-v4_95_Feb07.txt


title: human DLBCL tumoral sample, gene expr, case 4

description: US22502553_251239139129_S01_GE2-v4_95_Feb07.txt


title: px14_vs_px27

value: px27 test sample


title: human DLBCL tumoral sample, gene expr, case 6

description: US22502553_251239152174_S01_GE2-v4_95_Feb07.txt


title: human DLBCL tumoral sample, gene expr, case 3

description: US22502553_251239139130_S01_GE2-v4_95_Feb07.txt


title: human DLBCL tumoral sample, gene expr, case 5

description: US22502553_251239139128_S01_GE2-v4_95_Feb07.txt


title: Tobacco normal plant, biological rep 1

city: New delhi

first: Padmalatha

state: Delhi

address: Pusa campus

department: Plant Biotechnology

country: India

institute: NRCPB

description: Gene expression data from normal tobacco plant

hyb_protocol: Following fragmentation, 10 µg of cRNA were hybridized for 16 hr at 45°C on tomato GeneChip Genome Array. The arrays were washed and stained using streptavidin phycoerythrin on an Affymetrix fluidics station 450.

scan_protocol: The tomato GeneChip Genome arrays were scanned on a GeneChip scanner 3000.

data_processing: After scanning, CEL files were analyzed using GeneSpring GX 11.0 sotware. The GeneChip-Robust Multiarray Average (GC-RMA) algorithm was used for the back ground correction, quantile normalization and median polished probe set summarization to generate single expression value for each probe set. Normalized expression values were log2-transformed.

organism: Nicotiana tabacum

source_name: Tobacco normal plant

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5.0 µg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Plants were grown in tissue culture bottles in the selection medium containing spectinomycin (500 mg/L), kept in dim light (25-30 mmol photons m-2 sec-1) 16h (light/8h (dark). Leaves harvested from the plants subcultred for 2-3 weeks were used in transcriptomic studies.

extract_protocol: Total RNA was isolated using Spectrum Plant Total RNA Kit (Sigma, USA) from tobacco leaf samples of wild type, psaA and psbA mutants according to the manufacturer’s protocol

treatment_protocol: Leaf samples were collected from the wild, psaA and psbA mutant tobacco plants and immediately frozen in liquid nitrozen.

value: leaf

tag: genotype/variation

value: normal

tag: cultivar

value: Petit Havanna


title: Tobacco psaA deletion mutant, biological rep 1

description: Gene expression data from psaA mutant tobacco plant

source_name: Tobacco psaA deletion mutant plant

tag: tissue

value: psaA mutant


title: Tobacco psbA deletion mutant, biological rep 1

description: Gene expression data from psbA mutant tobacco plant

source_name: Tobacco psbA deletion mutant plant

value: psbA mutant


title: Tobacco normal plant, biological rep 2


title: Recurrent mammary tumor D419

city: boston

first: jean

last: zhao

address: 450 Brookline Ave

department: cancer biology

institute: dana-farber cancer institute

hyb_protocol: At least 225 ug of biotinylated, fragmented PCR products were hybridized for 16 hr at 50C on Affymetrix Mouse Diversity Genotyping Arrays. The arrays were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: The arrays were scanned using an Affymetrix GeneChip Scanner 3000.

data_processing: CEL files were generated using the GeneChip software (Affymetrix). Data was analyzed using the SNP array data processing modules of the software suite, dChip (http://www.biostat.harvard.edu/complab/dchip/snp.htm). Data processing on model-based expression was performed using the PM/MM model. Permutation using Hidden Markov Model (HMM) score and normalization was performed using the reference normalization algorithm developed at St. Jude (Nature 2007;446:758-764 [PMID 17344859]).

source_name: recurrent mammary tumor

label_protocol: Biotinylated, fragmented PCR products were prepared according to the Affymetrix Genome-Wide Human SNP Nsp/Sty 6.0 User Guide (P/N 702504, Rev 3) starting with 500 ug of mouse genomic DNA.

growth_protocol: Tumor biopsies.

extract_protocol: Genomic DNAs were extracted from frozen tumor biopsies using Qiagen's All Prep DNA kit. DNA quality and quantity were assessed using a Nanodrop Spectrophotometer.

treatment_protocol: None.

value: mammary tumor


title: Tobacco psaA deletion mutant, biological rep 2


title: Recurrent mammary tumor C658


title: human DLBCL tumoral sample, gene expr, case 2

description: US22502553_251239139131_S01_GE2-v4_95_Feb07.txt

value: tumoral sample

value: diffuse large B cell lymphoma (DLBCL)


title: Recurrent mammary tumor E302


title: Tobacco psbA deletion mutant, biological rep 2


title: Recurrent mammary tumor E473


title: 35S:HaHB1 TGB-2

city: Santa Fe

first: Agustin

middle: Lucas

last: Arce

state: Santa Fe

address: Ciudad Universitaria

country: Argentina

institute: Instituto de Agrobiotecnología del Litoral

description: Biological replicate 2 of 4. 35S:HaHB1 transgenic plants, line B, vs WT

hyb_protocol: Agilent GE2-v5_95_Feb07 protocol.

scan_protocol: Scanned on an Agilent Technologies scanner G2505B US22502618. Protocol name: GE2-v5_95_Feb07. FeatureExtractor_PatternName: Agilent-015059.

data_processing: Agilent Feature Extraction Software (v 9.5.3.1) was used for background subtraction and LOWESS normalization.

organism: Arabidopsis thaliana

source_name: 35S:HaHB1 Transgenic line B Replicate 2

label_protocol: Agilent GE2-v5_95_Feb07 protocol.

growth_protocol: Arabidopsis thaliana Heyhn. ecotype Columbia (Col-0) were grown directly on soil in a growth chamber at 22-24 ºC under long-day photoperiods (16 h of illumination with a mixture of cool-white and GroLux fluorescent lamps) at an intensity of approximately 150 µE m-2 s-1 in 8 cm diameter x 7 cm height pots during 21 days.

extract_protocol: Total RNA was extracted from the vegetative aerial part of 3-week-old plants using RNeasy® Plant Mini Kit (QIAGEN) following manufacturer's instructions.

tag: ecotype

value: 35S:HaHB1 Transgenic line

value: Shoot system (whole rosette at vegetative stage)

tag: age

value: 21 days

source_name: Col-0 WT plant

value: wild type


title: 35S:HaHB1 TGA-2

description: Biological replicate 2 of 4. 35S:HaHB1 transgenic plants, line A, vs WT

source_name: 35S:HaHB1 Transgenic line A Replicate 2


title: Ri4 technical replicate 2

first: Salvador

middle: Aznar

last: Benitah

address: Baldiri Reixac 10

department: Oncology

institute: Institute for Research in Biomedicine (IRB, Barcelona)

hyb_protocol: After fragmentation, 1650 ng of labeled cRNA from each sample was hybridized in in situ hybridization oven (Agilent) for 17 h at 65ºC and washed during 1 min at rt in Gene Expression Wash Buffer 1 (Agilent) and 1 min at 37 ºC with Gene Expression Wahs buffer 2 (Agilent).

scan_protocol: Scanned on an Agilent G2539A scanner at 5um resolution and 110%PMT The intensity data of each individual hybridization were extracted and the quality was assessed with the Feature Extraction software 10.7 (Agilent).

data_processing: Raw data was corrected for background noise using the normexp method. Quantile normalization was applied to assure comparability across samples.

source_name: Primary human keratinocytes

label_protocol: 500 ng of total RNA from each sample were amplified by Oligo-dT-T7 reverse transcription and labeled by in vitro transcription with T7 RNA polymerase in the presence of Cy3-CTP using the Quick Amp Labeling kit (Agilent) and purified using RNAeasy columns (Qiagen, Hilden, Germany)

extract_protocol: Total RNAs were prepared with Qiagen Rneasy minikit according to manufacturer’s protocol

value: Primary human keratinocytes

value: Cbx4 knock-down


title: 35S:HaHB1 TGB-1

description: Biological replicate 1 of 4. 35S:HaHB1 transgenic plants, line B, vs WT

source_name: 35S:HaHB1 Transgenic line B Replicate 1


title: RND technical replicate 3

value: pRSP control (for knockdown)


title: RND technical replicate 2


title: human DLBCL tumoral sample, gene expr, case 1

description: US22502553_251239139133_S01_GE2-v4_95_Feb07.txt

value: Universal Human Reference RNA (Stratagene, La Jolla, CA, USA)


title: Ri4 technical replicate 4


title: Diseased ureter

city: Sapporo

first: Osamu

last: Ichii

state: Hokkaido

address: Kita 18-Nishi 9

department: Faculty of Veterinary Medicine

country: Japan

institute: Hokkaido University

hyb_protocol: Labeled samples (10μg) and 5 x fragmentation buffer were heated at 94℃ 20min and chilled on ice. Hybridization buffer (260μL) was prepared from 78μL hybridization buffer component A, 130μL hybridization buffer component B, 27μL nuclease-free water, and 25μL fragmented aRNA. Hybridization buffer were heated at 90℃ 5min, cooled at room temperature, and applied on the microarray. These were incubated 37℃ 18h (300 rpm), and washed by 0.75 x TNT buffer at 46℃ 60min. These array were incubated with Cy5-streptavidine working solution at 25℃ 30min. These array were washed by 1 x TNT buffer at 25℃ 5min, 4 times. Finally, these array were washed by 0.1 x SSC/0.05% Tween 20 solution at 25℃ 30min.

scan_protocol: The arrays were scanned by GenePix4000BR （Molecular devices）.

data_processing: By using CodeLink TM Expression Analysis v5.0 (Applied Microarray), the fluorescence intensity in each spot was quantitated from the scanned image (Tiff, 16bit). In this process, “Net intensity” was calculated by the deduction of background values from each fluorescence intensity (Raw intensity).

source_name: ureter

label_protocol: From 1 micro gram of total RNA, aRNA was synthesized by using MessageAmpTM II-Biotin Enhanced Kit (Ambion).

extract_protocol: Whole ureters were prepared for the extraction of total RNA by using Trizol reagents (invitrogen).

value: ureter

tag: strain

tag: disease state

value: ureteritis


title: Recurrent mammary tumor E565


title: Ri4 technical replicate 3


title: RND technical replicate 1


title: Normal ureter

value: normal


title: 35S:HaHB1 TGA-1

description: Biological replicate 1 of 4. 35S:HaHB1 transgenic plants, line A, vs WT

source_name: 35S:HaHB1 Transgenic line A Replicate 1


title: Ri4 technical replicate 1


title: Recurrent mammary tumor D782


title: WT technical replicate 3

value: Cbx4 WT


title: Normal mammary tissue

description: Control

source_name: normal mammary tissue

value: mammary tissue


title: WT technical replicate 4


title: WT technical replicate 2


title: WT technical replicate 1


title: PBP technical replicate 2

value: pBABE control


title: DC technical replicate 4

value: Cbx4 CDM mutant


title: DC technical replicate 1


title: PBP technical replicate 1


title: DC technical replicate 2


title: PBP technical replicate 4


title: human DLBCL tumoral sample, gene expr, case 26

description: US22502553_251239147841_S01_GE2-v4_95_Feb07.txt

tag: case id

value: tumoral sample

tag: status os (0 alive; 1 death)


title: liver_WT_ 28w_rep2

city: Cincinnati

first: nupur

last: dasgupta

state: OH

address: 3333 Burnet Ave.

institute: Cincinnati Children's Hopital Medical Center

description: Wildtype control mice

hyb_protocol: cRNAs were hybridized to Affymetrix GeneChip Mouse Genome 430 2.0 Array.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: The data were analyzed with GeneChip Operating Software 1.1 (GCOS 1.1) using Affymetrix default analysis settings and global scaling to the same target intensity value.

label: biotinylate

source_name: WILDTYPE liver at 28 weeks

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

extract_protocol: Total RNA was extracted using TOTALLY RNA kit (Ambion Inc.) according to the manufacturer's instructions.

value: wild-type

value: liver

value: 28 weeks


title: PBP technical replicate 3


title: lung_WT_ 28w_rep3

description: Wildtype control mice

source_name: WILDTYPE lung at 28 weeks

value: lung


title: DC technical replicate 3


title: liver_WT_ 28w_rep1

description: Wildtype control mice


title: liver_WT_ 28w_rep3

description: Wildtype control mice


title: human DLBCL tumoral sample, gene expr, case 12

description: US22502553_251239152876_S01_GE2-v4_95_Feb07.txt

source_name: human DLBCL tumoral sample

value: diffuse large B cell lymphoma (DLBCL)

tag: status pfs (0

tag: time os (months)


title: liver_4L_ 28w_rep2

description: V394L/V394L GCase point-mutated mice

source_name: 4L liver at 28 weeks


title: lung_WT_ 28w_rep2

description: Wildtype control mice


title: lung_WT_ 28w_rep1

description: Wildtype control mice


title: lung_WT_ 28w_rep4

description: Wildtype control mice


title: liver_4L_ 18w_rep1

description: V394L/V394L GCase point-mutated mice

source_name: 4L liver at 18 weeks

value: 18 weeks


title: liver_4L_ 12w_rep2

description: V394L/V394L GCase point-mutated mice

source_name: 4L liver at 12 weeks

value: 12 weeks


title: liver_4L_ 18w_rep2

description: V394L/V394L GCase point-mutated mice


title: liver_4L_ 12w_rep1

description: V394L/V394L GCase point-mutated mice


title: Case 01 distinct site Right Bronchus 6

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

country: Netherlands

institute: Vrije Universiteit Medical Center

description: Pooled DNA from the blood of 18 healthy individuals was used as reference in the aCGH experiments; across array CGH comparisons were made as described by Buffart et al, Genes, Chromosomes description =  Cancer 2008, 47(11): 994-1004

hyb_protocol: Hybridization protocol available via www.agilent.com

scan_protocol: Slides were scanned using the Agilent G2505B micro-array scanner. Image data acquisition was performed in feature extraction software v9.5.1 (Agilent Technologies) using the Agilent CGH-v4_95 protocol with default settings

data_processing: Median Signal intensity minus median Background intensity; excluding negative values. To overcome potential wave bias due to differences in GC-content of the different chromosomal regions, a smoothing algorithm was applied on our dataset as described by van de Wiel et al, Bioinformatics 2009; 25(9):1099-1104.

source_name: Bronchial tissue, AFB-visualized

label_protocol: DNA labeling protocol according to Enzo Life Sciences

extract_protocol: DNA isolation protocol as described by van Zeeburg et al, Cancer Res 2005; 65(4):1271-1276

tag: case number

value: Case 01

tag: tissue type

value: distinct site Right Bronchus 6

value: bronchial

value: female

source_name: blood, pooled DNA from 19 individuals

value: blood


title: Case 05 distinct site Left Main Bronchus

value: Case 05

value: distinct site Left Main Bronchus

tag: gender


title: CGH: Soy yellow phenotype FN mutant R27C28r223aMN10 vs. Reference

hyb_protocol: Genomic DNA were hybridized to the microarray according to the manufacturer instructions (NimbleGen CGH User Guide Ver 5.1)

scan_protocol: Slides were scanned on the GenePix4000B Scanner (Molecular Devices, Sunnyvale, CA) according to the array manufacturer instructions (NimbleGen CGH User Guide Ver 5.1)

data_processing: The segMNT algorithm in the NimbleScan software (verison 2.5) was used to extract the raw data and normalize into log2 ratio value according to the default settings.

source_name: FN mutant R27C28r223aMN10

extract_protocol: Qiagen DNeasy

value: Leaf sample

tag: genotype

value: fast neutron mutant

tag: phenotype

value: Mutant shows yellow phenotype.

value: M92-220 background

source_name: FN parental line M92-220

value: Leaf samples

value: FN parental line M92-220.


title: CGH: Soy NIL line IsoClark#1 vs. recurrent parent Clark

scan_protocol: Slides were scanned on the NimbleGen MS200 microarray Scanner (Roche) according to the array manufacturer instructions (NimbleGen MS200 microarray scanner Operator's manual version 1.0)

source_name: NIL line IsoClark#1

value: Leaf sample from soybean NIL line IsoClark#1

value: an iron-inefficient NIL line of Soybean, IsoClark#1 (PI547430)

source_name: Clark

value: Leaf sample from Clark

value: Clark (PI548533) an iron-efficient line, is a recurrent parent for NIL line IsoClark#1


title: CGH: Soy wild type/no obvious phenotype FN mutant R27C28r223bMN10 vs. Reference

source_name: FN mutant R27C28r223bMN10

value: Mutant shows no obvious phenotype.


title: liver_4L_ 4w_rep2

description: V394L/V394L GCase point-mutated mice

source_name: 4L liver at 4 weeks

value: liver

value: 4 weeks


title: CGH: Soy NIL line IsoClark#3 vs. recurrent parent Clark

source_name: NIL line IsoClark#3

value: Leaf sample from  soybean NIL line IsoClark#3

value: an iron-inefficient NIL line of Soybean, IsoClark#3 (PI547430)

value: Clark (PI548533) an iron-efficient line, is a recurrent parent for NIL line IsoClark#3


title: liver_4L_ 28w_rep1

description: V394L/V394L GCase point-mutated mice

value: 28 weeks


title: Case 06 Squamous Cell Cancer

value: Case 06

value: Squamous Cell Cancer

value: bronchial

value: female

value: blood


title: Case 02 distinct site Right Middle Lobe

value: Case 02

value: distinct site Right Middle Lobe

value: male


title: Case 02 distinct site Left Carina 2

value: distinct site Left Carina 2


title: CGH: Soy wild type/no obvious phenotype FN mutant R27C28r223cMN10 vs. Reference

source_name: FN mutant R27C28r223cMN10

value: Leaf sample

value: fast neutron mutant

value: M92-220 background

value: Leaf samples

value: FN parental line M92-220.


title: Case 04 distinct site trachea

value: Case 04

value: distinct site trachea


title: CGH: Soy NIL recurrent parent Clark vs donor parent T203

source_name: recurrent parent Clark

value: Leaf sample from Clark

value: Clark (PI548533) an iron-efficient line, is a recurrent parent for NIL line IsoClark

source_name: donor parent T203

value: Leaf sample from T203

value: T203 (PI54619) is a donor parent for NIL line IsoClark


title: CGH: Soy wild type/no obvious phenotype FN mutant R17C34r202cMN10 vs. Reference

source_name: FN mutant R17C34r202cMN10

value: Mutant shows no obvious phenotype.


title: CGH: Soy NIL line IsoClark#4 vs. recurrent parent Clark

source_name: NIL line IsoClark#4

value: Leaf sample from  soybean NIL line IsoClark#4

value: an iron-inefficient NIL line of Soybean, IsoClark#4 (PI547430)

value: Clark (PI548533) an iron-efficient line, is a recurrent parent for NIL line IsoClark#4


title: CGH: Soy NIL line HiPro vs. NIL line LoPro

source_name: NIL line HiPro

value: Leaf sample from  soybean NIL line HiPro

value: an High Protein NIL line of Soybean, HiPro (LD04-15154)

source_name: NIL line LoPro

value: Leaf sample from  soybean NIL line LoPro

value: a Low Protein NIL line of Soybean, LoPro (LD04-15146)


title: Case 05 distinct site Left Bronchus 6

value: Case 05

value: distinct site Left Bronchus 6

value: bronchial

value: female

value: blood


title: CGH: Soy yellow phenotype FN mutant R17C34r202aMN10 vs. Reference

source_name: FN mutant R17C34r202aMN10

value: Leaf sample

value: fast neutron mutant

value: Mutant shows yellow phenotype.

value: M92-220 background

value: Leaf samples

value: FN parental line M92-220.


title: CGH: Soy NIL line IsoClark#5 vs. recurrent parent Clark

source_name: NIL line IsoClark#5

value: Leaf sample from  soybean NIL line IsoClark#5

value: an iron-inefficient NIL line of Soybean, IsoClark#5 (PI547430)

value: Leaf sample from Clark

value: Clark (PI548533) an iron-efficient line, is a recurrent parent for NIL line IsoClark#5


title: CGH: Soy NIL line IsoClark#2 vs. recurrent parent Clark

source_name: NIL line IsoClark#2

value: Leaf sample from  soybean NIL line IsoClark#2

value: an iron-inefficient NIL line of Soybean, IsoClark#2 (PI547430)

value: Clark (PI548533) an iron-efficient line, is a recurrent parent for NIL line IsoClark#2


title: NT09/296 Normal_Colon (1699538181_G)

city: Singapore

first: Sherry

last: Wang

address: 21 Lower Kent Ridge Road

department: Biochemistry

country: Singapore

institute: National University of Singapore

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Scanner used: Illumina BeadArray Reader Scanning protocol: Scan factor of 1, PMT525 Software: Illumina Beadscan version 3.0

data_processing:
Data is extracted using Illumina Genomestudio version 2010.2, Expression Module version 1.7.0
Data were analyzed using Partek GS6.4 Ver 6.09.0922.
Normalization algorithm: RMA
Analysis was performed using ANOVA.

source_name: Colon Tissue

label_protocol: Standard Illumina label protocol

growth_protocol: Cells were cultured in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% heat inactivated fetal bovine serum (HIFBS) (Gibco, Invitrogen) and 100U/ml penicillin and streptomycin (Gibco, Invitrogen).

extract_protocol: Total RNA was extracted from cells using RNeasy Mini Kit (Qiagen) with modifications. Cells were first washed with PBS twice and then lysed in TRIzol (Invitrogen) before purification using RNA extraction columns and buffers provided in the kit. The RNA concentration was quantified using Nanodrop (Thermo Scientific). 500ng total RNA was used for cRNA amplification using Illumina TotalPrep RNA Amplification kit (Ambion). Steps were carried out by following the instructional manual in the kit.

treatment_protocol: Not Applicable

tag: sample type

value: patient Sample

tag: disease

value: normal colon epithelial tissues


title: CGH: Soy wild type/no obvious phenotype FN mutant 6R44C72Dr116fMN10 vs. Reference

address: 1991 Upper Buford Circle

institute: University of Minnesota

source_name: FN mutant 6R44C72Dr116fMN10

label_protocol: 1ug of genomic DNA was labeled and amplified using the NimbleGen Dual-Color Labeling Kit according to the NimbleGen CGH User Guide Ver 5.1.

value: Mutant shows no obvious phenotype.

tag: cultivar

source_name: FN parental line M92-220


title: CGH: Soy yellow  phenotype FN mutant R17C34r202dMN10 vs. Reference

source_name: FN mutant R17C34r202dMN10

tag: tissue


title: CGH: Soy yellow phenotype FN mutant R17C34r202bMN10 vs. Reference

source_name: FN mutant R17C34r202bMN10


title: CGH: Soy wild type/no obvious phenotype FN mutant 6R44C72Dr116hMN10 vs. Reference

source_name: FN mutant 6R44C72Dr116hMN10


title: Case 03 Squamous Cell Cancer

source_name: Bronchial tissue, AFB-visualized

value: Case 03

value: Squamous Cell Cancer

value: bronchial

value: male

source_name: blood, pooled DNA from 19 individuals

value: blood

value: female


title: lung_4L_ 28w_rep1

description: V394L/V394L GCase point-mutated mice

source_name: 4L lung at 28 weeks

tag: genotype/variation

value: lung

value: 28 weeks


title: lung_4L_ 28w_rep2

description: V394L/V394L GCase point-mutated mice

tag: age


title: Control 23 follow up Severe Dysplasia

value: Control 23

tag: baseline/follow-up

value: follow up

tag: disease status

value: Severe Dysplasia


title: NT09/296 Normal_Colon (1699538181_E)

value: colorectal cancer


title: liver_4L_ 4w_rep1

description: V394L/V394L GCase point-mutated mice

source_name: 4L liver at 4 weeks

value: liver

value: 4 weeks


title: CGH: Soy yellow/green phenotype FN mutant R11C54r187aMN10 vs. Reference

source_name: FN mutant R11C54r187aMN10

value: Leaf sample

value: fast neutron mutant

value: Mutant shows yellow/green phenotype.

value: M92-220 background

value: Leaf samples

value: FN parental line M92-220.


title: CGH: Soy christmas tree phenotype FN mutant 6R44C72Dr116cMN10 vs. Reference

source_name: FN mutant 6R44C72Dr116cMN10

value: Mutant shows christmas tree phenotype.


title: Control 22 follow up Squamous Metaplasia

value: Control 22

value: Squamous Metaplasia

value: bronchial

value: male

value: blood


title: CGH: Soy christmas tree phenotype FN mutant 6R44C72Dr116bMN10 vs. Reference

source_name: FN mutant 6R44C72Dr116bMN10


title: Schizont stage, replicate 3

city: Pathumthani

first: Philip

middle: James

last: Shaw

state: Pathumthani

address: 113 Phahonyothin Road

department: National Center for Genetic Engineering and Biotechnology

country: Thailand

institute: National Science and Technology Development Agency

description: Laboratory strain K1.

hyb_protocol: Purified Cy3- and Cy5-labelled cDNA were mixed in a Short Oligo Hybridization Solution (Corning Inc.), and hybridized to P. falciparum spotted 70-mer oligo microarrays for 16-18 hr at 45°C. Arrays were washed at room temperature in a solution of 2x SSC (Sodium Saline Citrate) containing 0.2% SDS, and then in 0.1x SSC.

scan_protocol: The array was dried by centrifugation and immediately scanned using a GenePix 4000B scanner. The .tif images were analyzed using GenePixPro 6.1.0.4 software and data were extracted as .gpr files.

data_processing: Features flagged as bad spots (Flags <0), low intensity features (SNR 635 <3 and SNR 532 <3) and saturated features (F635 % Sat. >50 and F532 % Sat. >50) were excluded from further data analysis. The filtered features were normalized within the array by global lowess in the Aroma package in R 2.8.1 and across replicate arrays using the normalizeAcrossArrays algorithm in the Aroma package.

organism: Plasmodium falciparum

source_name: Schizont stage synchronized

label_protocol: 10-15 µg of total RNA were annealed with 5 µg of oligo (dT)21 and reverse transcribed to produce aminoallyl-dUTP(Ambion)-containing cDNA using StratascriptTM reverse transcriptase (Stratagene). The cDNA was then labelled with monoreactive Cy5 (GE Healthcare).

growth_protocol: Parasites were cultured in vitro using the standard method of Trager and Jensen (1976). The parasite culture was composed of human erythrocytes type O Rh+ in RPMI 1640 supplemented with 25 mM HEPES pH 7.4, 0.2% NaHCO3 0.2% glucose, 0.025 mg/ml hypoxanthine, 40 µg/ml gentamicin and 8% (v/v) pooled human serum. The culture was maintained in a 3% CO2 incubator at 37°C. Culture synchronization was obtained by lysing mature parasites with 5% sorbitol for two consecutive cell cycles. The culture was continued for 36h after the second synchronization before harvesting of parasites.

tag: strain

tag: developmental stage

value: schizont

source_name: Pooled mixed stage (ring, trophozoite, schizont)

label_protocol: 10-15 µg of pooled total RNA were annealed with 5 µg of oligo (dT)21 and reverse transcribed to produce aminoallyl-dUTP(Ambion)-containing cDNA using StratascriptTM reverse transcriptase (Stratagene). The cDNA was then labelled with monoreactive Cy3 (GE Healthcare).

extract_protocol:
Parasites were harvested and liberated from erythrocytes by saponin lysis. Total RNA was extracted immediately from parasites using TRIzol reagent (Invitrogen) in accordance with the manufacturer’s recommendations.

A pooled reference RNA was made by combining extracted total RNA from ring, trophozite and schizont stage parasites in equal amounts.

value: mixed (ring, trophozoite, schizont)

value: reference


title: CGH: Soy wild type/no obvious phenotype FN mutant 6R44C72Dr116gMN10 vs. Reference

city: Saint Paul

first: Robert

last: Stupar

source_name: FN mutant 6R44C72Dr116gMN10

value: Mutant shows no obvious phenotype.


title: Control 21 follow up Squamous Metaplasia

value: Control 21

value: follow up

value: female


title: NT09/296 Normal_Colon (1699538181_B)

value: patient Sample

value: colorectal cancer


title: NT09/296 Normal_Colon (1699538181_A)

value: normal colon epithelial tissues


title: Schizont stage, replicate 2

description: Laboratory strain K1.

extract_protocol: Parasites were harvested and liberated from erythrocytes by saponin lysis. Total RNA was extracted immediately from parasites using TRIzol reagent (Invitrogen) in accordance with the manufacturer’s recommendations.

growth_protocol: Parasites were cultured in vitro using the standard method of Trager and Jensen (1976). The parasite culture was composed of human erythrocytes type O Rh+ in RPMI 1640 supplemented with 25 mM HEPES pH 7.4, 0.2% NaHCO3 0.2% glucose, 0.025 mg/ml hypoxanthine, 40 µg/ml gentamicin and 8% (v/v) pooled human serum. The culture was maintained in a 3% CO2 incubator at 37°C. Culture synchronization was obtained by lysing mature parasites with 5% sorbitol for two consecutive cell cycles.


title: Control 20 follow up Squamous Metaplasia

value: Control 20


title: lung_4L_ 18w_rep1

description: V394L/V394L GCase point-mutated mice

source_name: 4L lung at 18 weeks

value: lung

value: 18 weeks


title: lung_4L_ 12w_rep2

description: V394L/V394L GCase point-mutated mice

source_name: 4L lung at 12 weeks

value: 12 weeks


title: Schizont stage, replicate 1

description: Laboratory strain K1.


title: lung_4L_ 12w_rep1

description: V394L/V394L GCase point-mutated mice