title: CTL empty vector replicate 3

description: Gene expression data from sorted mouse bone marrow cells transduced with EGFP control vector

source_name: sorted mouse bone marrow cells_empty vector

tag: strain

tag: cell type

value: sorted mouse bone marrow cells

tag: construct

value: empty vector


title: 3023_T

status: Public on Jun 01 2016

type: RNA

city: Dallas

first: Luc

last: Girard

state: TX

address: 5323 Harry Hines Blvd

department: Hamon Center for Therapeutic Oncology Research

country: USA

institute: UT Southwestern Medical Center

hyb_protocol: 1.5 ug of the amplified and labeled cRNA probes was hybridized to the chip overnight at 58 degree C, then washed, blocked and detected by streptavidin-Cy3 per manufacturer's protocol.

scan_protocol: The chips were scanned by Illumina iScan system.

data_processing: Bead-level data were processed with the MBCB algorithm (Ding et al, Nucl Acids Res, 36:e58, 2008), which is a background-correction and summarization method, then quantile-normalized and log2-transformed

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Lung cancer

label_protocol: 500 ng of total RNA was used to label the cRNA probes by Ambion Illumina TotalPrep RNA Amplification kit (Cat# IL1791)

extract_protocol: After homogenization, total RNA was extracted using TRI Reagent (Life Technologies, Grand Island, NY) according to manufacturer’s protocol. The nanodrop spectrophotometer (Thermo Fisher Scientific Inc., Wilmington, DE) was used to estimate the concentration of RNA and the quality of the RNA (RIN number) was assessed on Nano Series II RNA LAB-chips using Agilent Bioanalyzer 2100 (Agilent Technologies, Inc., Santa Clara, CA)

tag: histology

value: Adenocarcinoma

tag: age (yrs)

tag: gender

value: Male

tag: race

value: Caucasian

tag: smoker

value: Current

tag: pack-years

tag: Stage

value: IA

tag: egfr

value: WT

tag: kras


title: wholeblood_830505_2

city: Toronto

first: Jan

last: Heng

state: ON

address: 25 Orde Street

country: Canada

institute: Lunenfeld-Tanenbaum Research Institute

hyb_protocol: Hybridization was performed according to standard protocols for Affymetrix HumanGene 2.1 ST (GeneTitan)

scan_protocol: Affymetrix Gene Titan

data_processing: Data were normalized using RMA and differential expression was determined using Limma with multiple hypothesis testing (Benjamini and Hochberg); Bioconductor, R

source_name: whole blood, maternal peripheral

label_protocol: Labeling was performed according to standard Affymetrix protocols (Ambion WT kit)

extract_protocol:
Sample collection protocol: Peripheral maternal blood collected using PAXgene tubes.
PAXgene Blood RNA system kit was used to isolate total RNA.

tag: individual id

tag: sample collected at time pt (17-23weeks 1, 27-33weeks 2)

tag: gest age at sampling (weeks)

tag: gest age at delivery (weeks)

tag: birth outcome (sptb 1, term 0)

tag: birthing outcome (sptl 1, pprom 2, term 3)

tag: tissue

value: peripheral maternal blood


title: IDH1_wt replicate 1

city: Hannover

first: Anuhar

last: Chaturvedi

address: Cral Neuberg Strasse-1

department: Hematology, Hemostasis, Oncology and Stem Cell Transplantation

country: Germany

institute: Hannover Medical School

description: Gene expression data from sorted mouse bone marrow cells transduced with IDH1wt vector

hyb_protocol: Samples were hybridized to an identical lot of Affymetrix GeneChip for 16 hours at 45°C on MOE430 2.0. Steps for washing and SA-PE staining were processed on the fluidics station 450 using the mini_euk2v3_FS450 protocol (Affymetrix; Santa Clara, CA)

scan_protocol: Image Analysis was performed on  GCS3000 Scanner and GCOS1.2 Software Suite (Affymetrix; Santa Clara, CA)

data_processing: RMA (Robust Multichip Average; Bioconductor)

organism: Mus musculus

source_name: sorted mouse bone marrow cells_IDH1wt

label_protocol: For biotin-labeled target synthesis starting from 3 µg of total RNA, reactions were performed using standard protocols supplied by the manufacturer (Affymetrix; Santa Clara, CA). Briefly, 3 µg total RNA were converted to dsDNA using 100 pmol of a T7T23V primer (Eurogentec; Seraing, Belgium) containing a T7 promotor. The cDNA was then used directly in an in-vitro transcription reaction in the presence of biotinylated nucleotides

growth_protocol: in vivo from C57BJ6 mice

extract_protocol: Qiagen Rneasy plus Mini Kit according to manufacturers instructions

treatment_protocol: Transduction with Retrovirus, transplantation in syngenic mice, treatment, isolation of bone marrow  four weeks post transplantation, sorting of GFP positive cells than RNA Preparation

tag: strain

tag: cell type

tag: construct


title: CTL empty vector replicate 2


title: wholeblood_830505_1


title: 1_cartilage_Health

city: Xi'an

first: Feng

last: Zhang

address: Yanta West Road 76

country: China

institute: Xi'an Jiaotong University

hyb_protocol: Following the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology), the labeled cRNA was purified using RNeasy Mini Kit (Qiagen, MD, USA). The concentration and specific activity of labeled cRNA were measured by Agilent ND-1000. 1 μg of labeled cRNA was mixed together with hybridization buffer and hybridized to the Agilent Human 4x44K Gene Expression Microarray (v2, Agilent Technologies).

scan_protocol: Hybridization signals were recorded by Agilent microarray scanner (G2505C).

data_processing: Hybridization signals were analyzed by Feature Extraction v11.0 and Agilent GeneSpring GX v12.1 software (Agilent Technologies).

source_name: cartilage, healthy control

label_protocol: Total RNA was translated into cRNA and labeled with Cy3 using the Agilent Quick Amp Labeling kit (Agilent Technologies).

extract_protocol: Frozen cartilage samples were first rapidly ground in liquid nitrogen using freezer mill. Total RNA were then isolated from cartilage samples using the Agilent Total RNA Isolation Mini kit (Agilent Technologies, Santa Clara, CA, USA) following manufacturer recommended protocol. The integrity of isolated total RNA was evaluated with 1% agarose gel electrophoresis. The concentration of isolated total RNA was determined by Agilent ND-1000 (Agilent Technologies).

tag: gender

value: male

value: hip cartilage

tag: diagnosis

value: healthy control


title: 2_cartilage_NFH

source_name: cartilage, necrosis of femoral head

value: necrosis of femoral head patient


title: B_1_R_cartilage_NFH


title: 3021_T

tag: histology

tag: age (yrs)

tag: race

tag: smoker

value: IIB

value: MUT


title: wholeblood_830478_2


title: 3022_T

tag: pack-years

tag: Stage

tag: egfr

tag: kras


title: CTL empty vector replicate 1


title: 3022_N

source_name: Non-malignant lung

value: Non-malignant


title: 3024_N


title: Bach2-deficient tumor repeat 5

city: BETHESDA

first: PING

last: JIN

state: MD

address: 9000 ROCKVILLE PIKE

department: DTM

institute: CC/DTM/NIH

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

scan_protocol: GeneChips were scanned using GeneChip Scanner G3000.

data_processing: data is log transformed intensity, Principle component analyses were performed using Partek Genomic Suite after Robust Multiarray Average normalization of microarray data

source_name: Bach2-deficient tumor

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

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

treatment_protocol: whole tumors were dissected and single cell suspensions were generated using mechanical dissociation (Miltenyi GentleMacs).

tag: strain background

tag: genotype/variation

tag: tissue type

value: B16 tumor


title: wholeblood_830478_1

tag: individual id

tag: sample collected at time pt (17-23weeks 1, 27-33weeks 2)

tag: gest age at sampling (weeks)

tag: gest age at delivery (weeks)

tag: birth outcome (sptb 1, term 0)

tag: birthing outcome (sptl 1, pprom 2, term 3)

tag: tissue


title: 3014_T

tag: histology

tag: age (yrs)

tag: gender

value: Female

value: IIIA


title: Bach2-deficient tumor repeat 3


title: wholeblood_830446_2


title: 3021_N

tag: race

tag: smoker

tag: pack-years


title: wholeblood_830446_1


title: Bach2-deficient tumor repeat 1


title: Bach2-deficient tumor repeat 2


title: wholeblood_830432_2


title: 3014_N


title: WT tumor repeat 5

source_name: WT tumor

value: wild type


title: wholeblood_830432_1


title: 3012_T

value: Adenocarcinoma

tag: Stage

tag: egfr

tag: kras


title: 3013_N

value: Caucasian


title: wholeblood_830398_1


title: wholeblood_830397_2


title: WT tumor repeat 3

tag: strain background

tag: genotype/variation

tag: tissue type


title: WT tumor repeat 4


title: 3013_T

value: Current


title: wholeblood_830398_2

tag: individual id

tag: sample collected at time pt (17-23weeks 1, 27-33weeks 2)

tag: gest age at sampling (weeks)


title: 3003_T

value: IIA


title: wholeblood_830397_1

tag: gest age at delivery (weeks)

tag: birth outcome (sptb 1, term 0)

tag: birthing outcome (sptl 1, pprom 2, term 3)


title: wholeblood_830381_2

tag: tissue


title: 3012_N

tag: histology

tag: age (yrs)

tag: gender


title: WT tumor repeat 2


title: 07L66_T

tag: race

tag: smoker

tag: pack-years

value: IA

value: WT


title: wholeblood_830381_1

value: peripheral maternal blood


title: B_2_cartilage_NFH

value: female

value: hip cartilage

tag: diagnosis


title: 3003_N


title: SIRT6 KO_HSC

city: hangzhou

first: Hu

last: Wang

address: wenyixi road 1378

institute: hangzhou normal university

description: Gene expression data from SIRT6 KO HSC.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45 degree on GeneChip 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 G2500A.

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

source_name: SIRT6 KO HSC

label_protocol: Cy3-cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

tag: age

value: 3 months

tag: cell type

value: HSC

value: SIRT6 knockout


title: wholeblood_830370_2


title: OT-II TCR-Tg CD4, Ad26, mouse #4

city: Oxford

first: Nicholas

last: Provine

state: Oxfordshire

address: John Radcliffe Hospital

department: NDM - Experimental Medicine

country: United Kingdom

institute: University of Oxford

hyb_protocol: 5 ug was hybridized following standard Nugen/Affymetrix protocols

scan_protocol: Scanned with Affymetrix using AGCC v. 1.1

data_processing: Analyzed on Affymetrix Expression Console v. 1.1 using a MAS5.0 algorithm

source_name: OT-II TCR-Tg CD4 T cell from Ad26-OVA immunized mouse, mouse #4

label_protocol: 1st and 2nd strand synthesis, followed by Spia amplification using the Nugen WT pico kit to generate cDNA. Fragmentation and biotinylation using Nugen cat# 4200 following standard Nugen/Affymetrix protocols

growth_protocol: CD45.1+ B6 mice received 5x10^3 naïve CD45.2+ OT-II TCR-Tg CD4 T cells one day prior to immunization and were immunized intramuscularly with 10^10vp of Ad5 or Ad26 expressing Ovalbumin

extract_protocol: CD45.2+ OT-II TCR-Tg CD4 T cells were isolated using a BD Biosciences Aria cell sorter. RNA extraction was performed by Phenol/Chloroform followed by Agilent RNA extraction proctol with optional DNase treatment.

treatment_protocol: Day 10 post-immunization, splenic CD4 T cells were enriched by negative selection (MACS), stained for CD4,,CD44, and CD45.2 and sort purified on a BD Biosciences Aria cell sorter.

tag: strain

value: OT-II TCR Tg

value: spleen

value: CD4 T cell

tag: vaccine

tag: timepoint

value: day 10 post-immunization


title: OT-II TCR-Tg CD4, naive, mouse #1

source_name: OT-II TCR-Tg CD4 T cell from naïve mouse, mouse #1

value: naïve


title: 07L59_T

value: Adenocarcinoma

value: Female

value: Former

tag: Stage

value: IB

tag: egfr

tag: kras

value: MUT


title: WT_HSC

description: Gene expression data from WT HSC.

source_name: wild type HSC

tag: genotype/variation

value: wild type


title: wholeblood_830356_2

tag: individual id

tag: sample collected at time pt (17-23weeks 1, 27-33weeks 2)

tag: gest age at sampling (weeks)

tag: gest age at delivery (weeks)

tag: birth outcome (sptb 1, term 0)

tag: birthing outcome (sptl 1, pprom 2, term 3)

tag: tissue

value: peripheral maternal blood


title: IDH1_wt replicate 3

value: sorted mouse bone marrow cells

tag: construct


title: OT-II TCR-Tg CD4, Ad26, mouse #3

source_name: OT-II TCR-Tg CD4 T cell from Ad26-OVA immunized mouse, mouse #3


title: wholeblood_830507_2


title: WT tumor repeat 1

tag: strain background

tag: tissue type

value: B16 tumor


title: wholeblood_830356_1


title: wholeblood_830347_2


title: 07L51_T

tag: histology

tag: age (yrs)

tag: gender

tag: race

value: Caucasian

tag: smoker

value: Current

tag: pack-years

value: IA

value: WT


title: 07L59_N

value: Non-malignant


title: AK1_cartilage_Health

value: male

value: hip cartilage

tag: diagnosis

value: healthy control


title: wholeblood_830370_1

tag: individual id


title: OT-II TCR-Tg CD4, Ad26, mouse #5

source_name: OT-II TCR-Tg CD4 T cell from Ad26-OVA immunized mouse, mouse #5

tag: strain

value: OT-II TCR Tg

value: spleen

tag: cell type

value: CD4 T cell

tag: vaccine

tag: timepoint

value: day 10 post-immunization


title: 07L66_N

value: Female


title: wholeblood_830347_1B

tag: sample collected at time pt (17-23weeks 1, 27-33weeks 2)

tag: gest age at sampling (weeks)

tag: gest age at delivery (weeks)

tag: birth outcome (sptb 1, term 0)

tag: birthing outcome (sptl 1, pprom 2, term 3)


title: OT-II TCR-Tg CD4, Ad26, mouse #1

source_name: OT-II TCR-Tg CD4 T cell from Ad26-OVA immunized mouse, mouse #1

tag: tissue


title: OT-II TCR-Tg CD4, Ad26, mouse #2

source_name: OT-II TCR-Tg CD4 T cell from Ad26-OVA immunized mouse, mouse #2


title: OT-II TCR-Tg CD4, Ad5, mouse #4

source_name: OT-II TCR-Tg CD4 T cell from Ad5-OVA immunized mouse, mouse #4


title: 3023_N

tag: histology

tag: age (yrs)

value: Male


title: Bach2-deficient tumor repeat 4

tag: strain background

tag: genotype/variation

tag: tissue type


title: OT-II TCR-Tg CD4, Ad5, mouse #5

source_name: OT-II TCR-Tg CD4 T cell from Ad5-OVA immunized mouse, mouse #5


title: 07L38_T

source_name: Lung cancer

value: Adenocarcinoma

tag: gender

tag: race

value: Asian

tag: smoker

value: Never

tag: Stage

value: IIIB

tag: egfr

value: MUT

tag: kras


title: wholeblood_818781_2A

source_name: whole blood, maternal peripheral

tag: individual id

tag: sample collected at time pt (17-23weeks 1, 27-33weeks 2)

value: peripheral maternal blood


title: 07L38_N


title: wholeblood_818827_1

tag: gest age at sampling (weeks)

tag: gest age at delivery (weeks)


title: wholeblood_818827_2

tag: birth outcome (sptb 1, term 0)

tag: birthing outcome (sptl 1, pprom 2, term 3)


title: OT-II TCR-Tg CD4, Ad5, mouse #2

source_name: OT-II TCR-Tg CD4 T cell from Ad5-OVA immunized mouse, mouse #2

tag: strain

tag: tissue

tag: cell type

tag: vaccine

tag: timepoint


title: 07L36_N

tag: histology

tag: age (yrs)

tag: gender

value: American Indian or Alaska Native

value: Current

tag: pack-years


title: 07L36_T

tag: race

tag: smoker

tag: Stage

value: IB

tag: egfr

value: WT


title: OT-II TCR-Tg CD4, Ad5, mouse #3

source_name: OT-II TCR-Tg CD4 T cell from Ad5-OVA immunized mouse, mouse #3


title: 07L32_T

value: Caucasian

value: IIB

tag: kras


title: A_cartilage_NFH

source_name: cartilage, necrosis of femoral head

value: male

value: hip cartilage

tag: diagnosis

value: necrosis of femoral head patient


title: OT-II TCR-Tg CD4, Ad5, mouse #1

source_name: OT-II TCR-Tg CD4 T cell from Ad5-OVA immunized mouse, mouse #1

value: OT-II TCR Tg

value: spleen

value: CD4 T cell

value: day 10 post-immunization


title: wholeblood_818781_1C

tag: individual id

tag: sample collected at time pt (17-23weeks 1, 27-33weeks 2)

tag: gest age at sampling (weeks)

tag: gest age at delivery (weeks)

tag: birth outcome (sptb 1, term 0)


title: wholeblood_818684_1

tag: birthing outcome (sptl 1, pprom 2, term 3)

tag: tissue


title: wholeblood_818684_2


title: 07L32_N

source_name: Non-malignant lung

tag: histology

value: Non-malignant

value: Female


title: 07L31_T

value: Adenocarcinoma

tag: age (yrs)

value: Asian

value: IA


title: Hepatocytes-IL6+HGF-12h

city: Lübeck

first: Hauke

last: Busch

state: Schleswig-Holstein

address: Ratzeburger Allee 160

department: Lübeck Institute of Experimental Dermatology

institute: University of Lübeck

hyb_protocol: 15 µg labelled cRNA were hybridized onto the Mouse Genome 2.0 GeneChip® Arrays (Affymetrix, CA, USA) for 16h at 45°C using Hybridization Wash and Stain Kit (Affymetrix)

scan_protocol: Arrays were washed and stained with GeneChip Fluidics Station 450 and scanned with GeneChip Scanner 3000 using the GeneChip Operating Software (Affymetrix).

data_processing: R/Bioconductor

label: Biotin

source_name: primary Hepatocyte

label_protocol: Biotinylated cRNA was generated from 1.5 µg total RNA using the One-Cycle Target Labeling Assay (Affymetrix).

growth_protocol: Eight to twelve weeks Male C57BL/6N mice were employed for primary hepatocyte isolation

extract_protocol: RNA was extracted at 1,2,3,4,5,6,7,8,9,10,12,24 hours under stimulated conditions and additionally at -5, 0, 4, 8, 12, 24 hours for controls using the RNeasy Mini Plus Kit (Qiagen, Hilden, Germany).

treatment_protocol: Following perfusion, the liver was withdrawn and hepatocytes were collected by disrupting the liver capsule and filtering the resulting cell suspension through a 100 μm cell strainer (BD biosciences). Cells were washed twice by centrifugation and resuspension in washing buffer. Cell yield and vitality were determined by trypan blue staining (Fluka) using a Neubauer counting chamber (Brand). Preparations with vitality greater than 70% were employed for experiments. For each experiment cells from a single animal, or, if necessary, from a cell pool from up to three animals were used. For all experiments primary mouse hepatocytes were cultivated at sub-confluence on collagen I- coated cell ware. Two million cells per dish (diameter: 10 cm) were seeded in 5 ml of full medium (phenol red-free Williams E medium (Biochrom) supplemented with 10% (v/v) FBS (Invitrogen), 100 nM dexamethasone, 10 μg/ml insulin, 2 mM L-glutamine, and 1% (v/v) penicillin/streptomycin 100x (both Invitrogen)). Following plating, cells were allowed to attach for 4 h. Subsequently, hepatocytes were washed, twice vigorously and once gently, with PBS (PAN Biotech) to remove unattached cells, and cultured in serum-free cultivation medium (phenol red-free Williams E medium supplemented with 100 nM dexamethasone, 2 mM L-glutamine, and 1% (v/v) penicillin/streptomycin 100 x) for 24 h prior to experiments. Before stimulation an additional 4 hour time interval in starvation medium(phenol red-free Williams E medium supplemented with 2 mM L-glutamine and 1% (v/v) penicillin/streptomycin 100 x) was applied

value: Liver

tag: timepoint

tag: stimulus

tag: gender

tag: age

value: 8-12 weeks

tag: strain


title: Hepatocytes-IL6+HGF-24h


title: 07L51_N

tag: race

tag: smoker

value: Current

tag: pack-years


title: 07L31_N


title: wholeblood_818670_2

tag: individual id

value: peripheral maternal blood


title: wholeblood_818626_2

tag: sample collected at time pt (17-23weeks 1, 27-33weeks 2)


title: Hepatocytes-IL6+HGF-10h


title: Hepatocytes-IL6+HGF-9h


title: 07L25_T

value: Caucasian

tag: Stage

value: IB

tag: egfr

value: WT

tag: kras

value: MUT


title: 07L28_T

value: Never

value: IIIA


title: 07L25_N


title: wholeblood_818626_1

tag: gest age at sampling (weeks)

tag: gest age at delivery (weeks)

tag: birth outcome (sptb 1, term 0)

tag: birthing outcome (sptl 1, pprom 2, term 3)


title: wholeblood_818614_2C

tag: tissue


title: wholeblood_818615_2


title: Hepatocytes-IL6+HGF-6h

tag: timepoint

tag: stimulus

value: male


title: 07L24_T

tag: histology

tag: age (yrs)

tag: gender

value: Male

value: IIA


title: wholeblood_818615_1


title: wholeblood_818670_1A


title: Hepatocytes-IL6+HGF-8h

tag: age

tag: strain


title: Hepatocytes-IL6-4h


title: wholeblood_818614_1A

tag: individual id


title: Hepatocytes-IL6+HGF-7h


title: 07L28_N

value: Non-malignant

value: Female

tag: race

tag: smoker


title: 07L22_T

value: Adenocarcinoma

value: Asian

tag: Stage

tag: egfr


title: Hepatocytes-IL6+HGF-5h

value: Liver


title: Hepatocytes-IL6-2h

value: 8-12 weeks


title: wholeblood_818481_2

tag: sample collected at time pt (17-23weeks 1, 27-33weeks 2)

tag: gest age at sampling (weeks)


title: Hepatocytes-IL6-3h


title: 07L24_N

value: Current

tag: pack-years


title: wholeblood_818481_1

tag: gest age at delivery (weeks)

tag: birth outcome (sptb 1, term 0)

tag: birthing outcome (sptl 1, pprom 2, term 3)

value: peripheral maternal blood


title: 07L22_N


title: wholeblood_818409_2

tag: tissue


title: 07L21_T

tag: histology

value: Caucasian

tag: kras


title: 07L21_N

tag: age (yrs)

tag: gender


title: wholeblood_818381_1B


title: Hepatocytes-Ctl-12h

tag: timepoint

tag: stimulus

value: Control

tag: age

tag: strain


title: Hepatocytes-Ctl-8h


title: Hepatocytes-IL6-1h


title: 07L16_T

tag: race

tag: smoker

tag: Stage

value: IA

value: WT


title: Hepatocytes-Ctl-0h


title: Hepatocytes-Ctl-24h


title: Hepatocytes-Ctl-minus5h


title: wholeblood_818368_2

tag: individual id

tag: sample collected at time pt (17-23weeks 1, 27-33weeks 2)

tag: gest age at sampling (weeks)


title: wholeblood_818409_1

tag: gest age at delivery (weeks)

tag: birth outcome (sptb 1, term 0)


title: 07L19_N

value: Never


title: Hepatocytes-Ctl-4h

tag: tissue


title: 07L19_T

tag: histology

value: IB

tag: egfr

value: MUT


title: wholeblood_818361_2A

tag: birthing outcome (sptl 1, pprom 2, term 3)


title: 07L18_N

tag: age (yrs)

tag: gender

value: Male

value: Former

tag: pack-years


title: wholeblood_818381_2A


title: wholeblood_818368_1


title: 07L14_T

tag: kras


title: Hepatocytes-IL6+HGF-32h-rep2

source_name: primary Hepatocyte stimulated with IL6+HGF

extract_protocol: RNA from three biological triplicates was extracted at 0, 0.5, 2, 4, 8, 16, 24 and 32 hours after stimulation using the RNeasy Mini Plus Kit (Qiagen, Hilden, Germany)

treatment_protocol: Following perfusion, the liver was withdrawn and hepatocytes were collected by disrupting the liver capsule and filtering the resulting cell suspension through a 100 μm cell strainer (BD biosciences). Cells were washed twice by centrifugation and resuspension in washing buffer. Cell yield and vitality were determined by trypan blue staining (Fluka) using a Neubauer counting chamber (Brand). Preparations with vitality greater than 70% were employed for experiments. For each experiment cells from a single animal, or, if necessary, from a cell pool from up to three animals were used. For all experiments primary mouse hepatocytes were cultivated at sub-confluence on collagen I- coated cell ware. Two million cells per dish (diameter: 10 cm) were seeded in 5 ml of full medium (phenol red-free Williams E medium (Biochrom) supplemented with 10% (v/v) FBS (Invitrogen), 100 nM dexamethasone, 10 μg/ml insulin, 2 mM L-glutamine, and 1% (v/v) penicillin/streptomycin 100x (both Invitrogen)). Following plating, cells were allowed to attach for 4 h. Subsequently, hepatocytes were washed, twice vigorously and once gently, with PBS (PAN Biotech) to remove unattached cells, and cultured in serum-free cultivation medium (phenol red-free Williams E medium supplemented with 100 nM dexamethasone, 2 mM L-glutamine, and 1% (v/v) penicillin/streptomycin 100 x) for 24 h prior to experiments.

value: male

tag: age

tag: strain

tag: stimulus

tag: time point


title: wholeblood_818361_1i

tag: individual id


title: 07L16_N

value: Non-malignant

tag: race

tag: smoker


title: 07L18_T

value: Adenocarcinoma

tag: Stage


title: 07L14_N


title: wholeblood_818357_1

tag: sample collected at time pt (17-23weeks 1, 27-33weeks 2)

tag: gest age at sampling (weeks)

tag: gest age at delivery (weeks)

tag: birth outcome (sptb 1, term 0)


title: Hepatocytes-IL6+HGF-32h-rep1

tag: tissue


title: wholeblood_818357_2B

tag: birthing outcome (sptl 1, pprom 2, term 3)


title: 07L13_T

tag: histology

tag: age (yrs)

tag: gender

value: Female

tag: egfr


title: Hepatocytes-IL6+HGF-24h-rep2

value: Liver

tag: age

tag: strain


title: wholeblood_818308_2


title: Hepatocytes-IL6+HGF-24h-rep1

value: 8-12 weeks

tag: stimulus

tag: time point


title: wholeblood_818257_1

tag: individual id


title: 07L6_T

tag: race

value: Asian

tag: smoker

value: IIB

tag: kras


title: Hepatocytes-IL6+HGF-8h-rep1


title: wholeblood_818308_1

tag: sample collected at time pt (17-23weeks 1, 27-33weeks 2)

tag: gest age at sampling (weeks)

value: peripheral maternal blood


title: wholeblood_818257_2

tag: gest age at delivery (weeks)

tag: birth outcome (sptb 1, term 0)


title: 06L75_N

value: Caucasian

value: Current

tag: pack-years


title: wholeblood_818246_2

tag: birthing outcome (sptl 1, pprom 2, term 3)

tag: tissue


title: Hepatocytes-IL6+HGF-16h-rep2

tag: gender


title: Hepatocytes-IL6+HGF-4h-rep2


title: Hepatocytes-IL6+HGF-16h-rep1


title: Hepatocytes-IL6+HGF-8h-rep2


title: 06L74_T

tag: histology

tag: age (yrs)

value: asian

tag: Stage

tag: egfr

value: WT


title: wholeblood_818249_2


title: 07L5_N


title: 07L5_T

value: IB


title: 06L75_T

value: IA

value: MUT


title: wholeblood_818246_1


title: 07L13_N

value: Former


title: wholeblood_818249_1


title: Hepatocytes-IL6+HGF-4h-rep1

value: male

tag: age

tag: strain

tag: stimulus

tag: time point


title: 07L6_N

value: Non-malignant

value: Male

tag: race

tag: smoker

value: Never


title: Hepatocytes-IL6+HGF-2h-rep2

value: Liver


title: 06L74_N

value: Female


title: Hepatocytes-IL6+HGF-2h-rep1

value: 8-12 weeks


title: 06L71_T

value: Adenocarcinoma

tag: kras


title: wholeblood_818241_1

tag: individual id

tag: sample collected at time pt (17-23weeks 1, 27-33weeks 2)

tag: gest age at sampling (weeks)

tag: gest age at delivery (weeks)

value: peripheral maternal blood


title: Hepatocytes-IL6+HGF-0.5h-rep2

tag: tissue


title: 06L71_N

tag: gender

value: Caucasian


title: wholeblood_818241_2

tag: birth outcome (sptb 1, term 0)

tag: birthing outcome (sptl 1, pprom 2, term 3)


title: Hepatocytes-IL6+HGF-0.5h-rep1


title: Hepatocytes-IL6-32h-rep2

source_name: primary Hepatocyte stimulated with IL6

value: 40 ng/ml rhIL-6


title: wholeblood_818224_2


title: 06L64_N

tag: histology

tag: age (yrs)


title: 06L64_T

tag: Stage

tag: egfr


title: wholeblood_818224_1


title: 06L57_T

value: Current

tag: pack-years

value: IIIA


title: Hepatocytes-IL6-32h-rep1

tag: age

tag: strain

tag: stimulus

tag: time point


title: wholeblood_818200_2

tag: individual id


title: wholeblood_818195_2

tag: sample collected at time pt (17-23weeks 1, 27-33weeks 2)


title: 06L54_T

tag: race

tag: smoker

value: WT

tag: kras


title: wholeblood_818200_1

tag: gest age at sampling (weeks)

tag: gest age at delivery (weeks)

tag: tissue


title: Hepatocytes-IL6-24h-rep1

tag: gender


title: Hepatocytes-IL6-24h-rep2


title: wholeblood_818181_2

tag: birth outcome (sptb 1, term 0)

tag: birthing outcome (sptl 1, pprom 2, term 3)


title: 06L54_N

tag: histology

tag: age (yrs)


title: Hepatocytes-IL6-8h-rep2

tag: age


title: wholeblood_818181_1


title: 06L53_T

tag: pack-years

tag: Stage

tag: egfr


title: wholeblood_818174_2

tag: individual id


title: Hepatocytes-IL6-16h-rep2

tag: strain

tag: stimulus

tag: time point


title: H3K9ac_control_6 hour_1

type: genomic

city: singapore

first: Devendra

middle: Kumar

last: Gupta

state: Singapore

address: 60 NANYANG DRIVE

department: School of Biological Sciences

country: Singapore

institute: Nanyang Technological University

hyb_protocol: Equal amounts of labelled ChIP sample and input were hybridized on the microarray chip using the Agilent hybridization system. Hybridizations were performed for 20 hours at 63.5°C in a rotating hybridization oven at 10rpm.

scan_protocol: The microarrays were scanned using GenePix scanner 400b. Data was acquired using GenePix Pro v6.0 software (Axon Instruments, USA) as described in Mok, S., M. Imwong et al (2011) Artemisinin resistance in Plasmodium falciparum is associated with an altered temporal pattern of transcription. BMC Genomics 12: 391.

data_processing: Data was lowess normalized and processed further as described in Gupta, A.P., Chin, W.H., Zhu, L., Mok, S., Luah, Y.-H., Lim, E.-H., and Bozdech, Z. (2013). Dynamic Epigenetic Regulation of Gene Expression during the Life Cycle of Malaria Parasite Plasmodium falciparum. PLoS Pathog 9, e1003170.

molecule: genomic DNA

organism: Plasmodium falciparum

source_name: ChIP DNA for H3K9ac

label_protocol: Labelling was performed as described in Bozdech, Z., Mok, S., and Gupta, A. (2013). DNA Microarray-Based Genome-Wide Analyses of Plasmodium Parasites. In Malaria, Volume 923, R. Ménard, ed. (Humana Press), pp. 189-211

extract_protocol: Chromatin immunoprecipitation was performed as described in Bozdech, Z., Mok, S., and Gupta, A. (2013). DNA Microarray-Based Genome-Wide Analyses of Plasmodium Parasites. In Malaria, Volume 923, R. Ménard, ed. (Humana Press), pp. 189-211

tag: fraction

value: ChIP

tag: agent

value: control

tag: antibody

value: whole organism

value: 6 hours

source_name: Input pool

value: Input

tag: reference

value: pool made from equal amount of amplified genomic DNA from both MMS treated and untreated samples


title: 06L53_N

value: Non-malignant

tag: gender

tag: race

tag: smoker

value: Former


title: 06L57_N

tag: histology

value: Female


title: wholeblood_818174_1

tag: sample collected at time pt (17-23weeks 1, 27-33weeks 2)

tag: gest age at sampling (weeks)

tag: gest age at delivery (weeks)

tag: birth outcome (sptb 1, term 0)

tag: birthing outcome (sptl 1, pprom 2, term 3)

tag: tissue


title: Hepatocytes-IL6-16h-rep1

value: Liver

value: male

tag: age

value: 8-12 weeks

tag: strain


title: wholeblood_818195_1

tag: individual id

value: peripheral maternal blood


title: wholeblood_818172_1


title: 06L50_T

value: Adenocarcinoma

tag: age (yrs)

value: Caucasian

tag: pack-years

tag: Stage

value: IA

tag: egfr

tag: kras

value: MUT


title: CEN.PK113-7D -Glucose-limited chemostat culture 0.1h-3

city: Delft

first: Jean-Marc

last: Daran

address: Julianalaan 67

department: Department of Biotechnology

country: Netherlands

institute: Delft University of Technology

description: S. cerevisiae CEN.PK113-7D aerobic glucose-limited chemostat with a dilution rate of 0.1h-1.

hyb_protocol: Hybridization of labelled fragmented aRNA to the microarrays and staining, washing and scanning of the microarrays was performed according to Affymetrix instructions (EukGE_WS2v5).

data_processing: The 6383 yeast open reading frames were extracted from the 9335 transcript features on the YG-S98 microarrays. To allow comparison, all expression data were normalized to a target value of 240 using the average signal from all gene features. To eliminate variation in genes that are not expressed, genes with expression values below 12 were set to 12 and the gene features for which the average expression was below 20 for all 13 arrays were discarded. The average deviation of the mean transcript data of replicate retentostats was approximately 10%, similar to the reproducibility usually observed in replicate steady state chemostat cultures [57]. The expression of housekeeping genes ACT1, HHT2, SHR3, PDA1, TPI and TFC1 [58] remained stable for both strains at all tested growth rates (average coefficient of variation 11% ± 4% see Figure S3).   To perform a differential expression analysis based on gene expression profiles across the different growth rates, EDGE version 1.1.291 [59] was used with growth rate as covariate. Genes with expression profiles with a p-value below 0.01 were considered to significantly correlate with growth rate, and were clustered with k-means clustering using Consensus Clustering (GenePattern 2.0, Broad Institute, [60]) .   Gene expression clusters were analysed for overrepresentation of functional annotation categories from the Munich Information Centre for Protein Sequences (MIPS) database (http://mips.gsf.de/genre/proj/yeast),  the Gene Ontology (GO) database (http://geneontology.org/) and transcription factor binding (TF) according to [61], based on the hypergeometric distribution analysis tool described by Knijnenburg et al [62].

label: Biotin-Streptavidin

organism: Saccharomyces cerevisiae

source_name: FS09322 Glucose-limited chemostat culture -0.025H-1

growth_protocol: Chemostat: Aerobic retentostat cultivation started with a chemostat phase, performed in 2 litre bioreactors (Applikon, Delft, the Netherlands) equipped with a level sensor to maintain a constant working volume of 1.4 L. The culture temperature was controlled at 30°C and the dilution rate of 0.025 h-1 was set by controlling the flow rate. Cultures were grown on adapted synthetic medium, containing 20 g.l-1 glucose (CS,chem), 5 g.L-1 (NH4)2SO4, 3 g.L-1 KH2PO4, 0.5 g.L-1 MgSO4∙ 7H2O, 1.5 mL. L-1 trace metals solutions, 2 mL.L-1 vitamin stock solution [50] and 0.25 g.L-1 Pluronic 6100 PE antifoaming agent (BASF, Ludwigshafen, Germany). Fresh medium was supplied to the bioreactor from a 3 L mixing reactor (Applikon, Delft, The Netherlands) equipped with a sampling port, at a working volume (VS) of 1.2 L maintained by a level sensor and stirred continuously at 500 rpm. To minimize risk of contamination, the mixing reactor was ventilated through the headspace with N2-gas. Medium was added to the mixing reactor by automatic addition from an external medium vessel controlled by a level sensor, with a flow rate of 35 mL.h-1 corresponding to the dilution rate in the bioreactor. Cultures were sparged with air (0.5 vvm) and stirred at 800 rpm. The pH was kept constant at 5.0 by automatic addition of 10% NH4OH. Chemostat cultures were assumed to be in steady state when, after at least 6 volume changes, the culture dry weight and the specific carbon dioxide production rate changed by less than 3% over 2 consecutive volume changes. Steady state carbon recoveries for independent chemostats were above 98%. Chemostat experiments performed at a dilution rate of 0.1 h-1 were performed exactly as described above, with the following modification: cultures were grown on non-adapted synthetic medium [50], with 7.5 g.L-1 glucose, 1 mL.L-1 trace metals solutions, and 1 mL.L-1 vitamin stock solution.  Retentostat: After steady-state sampling the retentostat phase was started by switching the reactor effluent to an outflow port equipped with an autoclavable Applisense filter assembly (Applikon), consisting of a hydrophobic polypropylene filter with a pore size of 0.22 um and a stainless steel hollow filter support. Prior to autoclaving, the filter was wetted by overnight incubation in 96% ethanol, and subsequent rinsing with PBS solution. To control biomass accumulation, the medium entering the mixing reactor was altered by switching to a medium vessel containing standard synthetic medium supplemented with 7.5 g.l-1 glucose and 0.25 g.l-1 pluronic 6100 PE antifoam. Consequently, the concentration of growth-limiting substrate glucose entering the bioreactor (Cs,feed in [g.l-1]) was slowly reduced in time (t in [h]). During retentostat mode, the pH was switched to automatic addition of 2M KOH. Sampling frequency and volume were minimized to limit impact on biomass accumulation inside the reactor. Culture purity was routinely checked by microscopy and by plating on synthetic agar containing 20 g.l-1 glucose and 20 mM of lithium chloride. Full biomass retention was confirmed by plating filtered effluent on yeast-peptone agar plates containing 2% glucose.

extract_protocol: Prior to RNA extraction, samples were stored in a mixture of phenol/chloroform and TEA buffer at -80°C. Total RNA extraction, isolation of mRNA, cDNA synthesis, cRNA synthesis, labelling and array hybridization was performed as described previously [Mendes et al, Appl Environ Microbiol 2013, 79:5949-5961].

treatment_protocol: Microarray analysis was performed with samples from independent duplicate steady-state chemostat and retentostat cultures of S. cerevisiae CEN.PK113-7D sampled at different growth rates. Sampling from chemostat cultures for transcriptome analysis was carried out by using liquid nitrogen for rapid quenching of mRNA turnover (Piper et al., J Biol Chem. 277:37001-8.).

tag: genetic background

value: CEN.PK113-7D (MATa MAL2-8C SUC2 )

tag: genotype/variation

value: MATa MAL2-8C SUC2

tag: c-source

value: glucose

tag: sample type


title: wholeblood_818162_2

tag: sample collected at time pt (17-23weeks 1, 27-33weeks 2)

tag: gest age at sampling (weeks)


title: wholeblood_818172_2

tag: gest age at delivery (weeks)

tag: birth outcome (sptb 1, term 0)


title: 06L52_N

tag: histology

tag: gender

value: Male

tag: race

tag: smoker


title: Hepatocytes-IL6-0.5h-rep2

tag: tissue

tag: age

tag: strain

tag: stimulus

value: 40 ng/ml rhIL-6

tag: time point


title: Hepatocytes-IL6-2h-rep2


title: wholeblood_818162_1

tag: individual id

tag: birthing outcome (sptl 1, pprom 2, term 3)


title: wholeblood_818156_2


title: Hepatocytes-IL6-2h-rep1


title: 06L50_N

tag: age (yrs)

value: Current

tag: pack-years


title: 06L46_N

value: Non-malignant


title: 06L45_N


title: Hepatocytes-HGF-24h-rep2

source_name: primary Hepatocyte stimulated with HGF

value: 40 ng/ml rmHGF


title: Hepatocytes-IL6-0.5h-rep1


title: 06L46_T

value: Female

tag: Stage

value: IB

tag: egfr

value: WT

tag: kras


title: Hepatocytes-IL6-4h-rep2

value: Liver

value: male

value: 8-12 weeks


title: 06L43_T

value: Adenocarcinoma

value: Caucasian


title: wholeblood_818153_1

tag: sample collected at time pt (17-23weeks 1, 27-33weeks 2)

tag: gest age at sampling (weeks)

tag: gest age at delivery (weeks)

tag: birth outcome (sptb 1, term 0)

value: peripheral maternal blood


title: wholeblood_818153_2A


title: Hepatocytes-HGF-32h-rep2

tag: gender


title: 06L45_T

tag: histology

tag: race

tag: smoker

value: MUT


title: wholeblood_818156_1

tag: tissue


title: Hepatocytes-HGF-24h-rep1

tag: age

tag: strain

tag: stimulus

tag: time point


title: wholeblood_818088_2

tag: individual id

tag: birthing outcome (sptl 1, pprom 2, term 3)


title: wholeblood_818125_2


title: Hepatocytes-HGF-32h-rep1


title: 06L42_N

tag: age (yrs)

value: Former


title: 06L42_T

tag: Stage

tag: egfr

tag: kras


title: 06L43_N

tag: pack-years


title: Hepatocytes-HGF-8h-rep2


title: wholeblood_818125_1

tag: sample collected at time pt (17-23weeks 1, 27-33weeks 2)

tag: gest age at sampling (weeks)

tag: gest age at delivery (weeks)

tag: birth outcome (sptb 1, term 0)


title: Hepatocytes-HGF-16h-rep1

tag: gender


title: Hepatocytes-HGF-16h-rep2

tag: tissue


title: 06L30_T

tag: histology

tag: race

value: asian

tag: smoker

value: IIB


title: Hepatocytes-HGF-8h-rep1

tag: age

tag: strain

tag: stimulus

tag: time point


title: wholeblood_818084_1

tag: individual id

tag: birthing outcome (sptl 1, pprom 2, term 3)


title: 06L39_T

tag: age (yrs)

tag: Stage

tag: egfr

tag: kras


title: Hepatocytes-HGF-2h-rep2


title: wholeblood_818084_2

tag: sample collected at time pt (17-23weeks 1, 27-33weeks 2)

tag: gest age at sampling (weeks)

tag: gest age at delivery (weeks)


title: Hepatocytes-HGF-2h-rep1

tag: tissue

tag: gender


title: Hepatocytes-HGF-4h-rep2


title: 06L39_N

tag: histology

tag: race

tag: pack-years


title: 06L30_N

value: Male

tag: smoker


title: wholeblood_818081_1

tag: birth outcome (sptb 1, term 0)


title: Hepatocytes-HGF-4h-rep1

tag: age

tag: strain

tag: stimulus

tag: time point


title: wholeblood_818081_2

tag: individual id

tag: birthing outcome (sptl 1, pprom 2, term 3)


title: wholeblood_818088_1


title: wholeblood_818070_2


title: 06L29_T

tag: age (yrs)

value: Asian

value: Never

tag: Stage

tag: egfr

tag: kras


title: wholeblood_818054_2

tag: sample collected at time pt (17-23weeks 1, 27-33weeks 2)

tag: gest age at sampling (weeks)

tag: gest age at delivery (weeks)

tag: tissue


title: 06L22_N

tag: histology

value: Non-malignant

tag: gender

tag: race

value: Current

tag: pack-years


title: Hepatocytes-HGF-0.5h-rep1

tag: age

tag: strain

value: 40 ng/ml rmHGF


title: wholeblood_818070_1

tag: birth outcome (sptb 1, term 0)


title: wholeblood_818054_1

tag: individual id


title: Hepatocytes-Ctl-32h-rep2

tag: stimulus

tag: time point


title: 06L29_N

tag: age (yrs)

value: Female

tag: smoker


title: 06L22_T

tag: Stage

value: IA

tag: egfr

tag: kras

value: WT


title: 06L20_T

value: IB


title: Hepatocytes-HGF-0.5h-rep2

value: Liver

value: male

value: 8-12 weeks


title: Hepatocytes-Ctl-32h-rep1


title: wholeblood_818046_1

tag: sample collected at time pt (17-23weeks 1, 27-33weeks 2)

tag: gest age at sampling (weeks)

tag: gest age at delivery (weeks)

tag: birthing outcome (sptl 1, pprom 2, term 3)

value: peripheral maternal blood


title: Hepatocytes-Ctl-24h-rep2

tag: tissue

tag: gender


title: 06L14_T

tag: histology

value: Adenocarcinoma

tag: race

value: Caucasian

tag: pack-years

value: MUT


title: wholeblood_818036_2

tag: individual id

tag: birth outcome (sptb 1, term 0)


title: wholeblood_818046_2


title: 06L20_N


title: Hepatocytes-Ctl-16h-rep2

tag: age

tag: strain

tag: stimulus

tag: time point


title: wholeblood_818034_2


title: Hepatocytes-Ctl-8h-rep2


title: 06L11_N

tag: age (yrs)

tag: smoker


title: 564008A10 - 6-OE-stressed_1 vs 5-OE-CTR_1

city: Orsay

first: Stéphanie

last: Pateyron

address: Rue de Noetzlin _ Batiment 630

country: France

institute: IPS2_Institute of Plant Sciences Paris-Saclay

description: Understanding the physiological role of pPLAIIα under control and drought stress conditions.

hyb_protocol: 5-OE-CTR_1 Cy5 / 6-OE-stressed_1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: Mapix, Cy3:pmt voltage 532nm,480V,laser power 35%, Cy5:635nm,pmt voltage 480V,laser power 30%

data_processing: For each array, the raw data comprised the logarithm of median feature pixel intensity at wavelengths Cy5 (red) and Cy3 (green).For each array, a global intensity-dependent normalization using the loess procedure (Yang et al., 2002) was performed to correct the dye bias.Log-ratios are then averaged over the duplicate probes to get a value per gene.

organism: Arabidopsis thaliana

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. (Labelling_protocol.txt) Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: rosette - Media:soil/vermiculite (1/1) hygrometry:60% relative humidity Temperature:23ºC day/18ºC night Light:170–190 µmol m-2 s-1

extract_protocol: 5-OE-CTR_1:250mg. (Qiagen_RNeasy.pdf)

treatment_protocol: no treatment

tag: ecotype

value: Columbia

value: Boyes et al. Plant Cell 2001:30% of flower buds to be produced have opened

treatment_protocol: Name:Drought - environmental treatment - abiotic stress,drought:time 9day . Arabidopsis thaliana (L.) Heynh seeds of the three lines (WT8, AS14 and OE4) were surface sterilized and stratified at 4 ºC for four days. Plants were grown on mixture of compost (CompoSana, Compo International) and vermiculite (1:1), previously sterilized at 190 ºC for 4 h in square polypropylene pots (200 ml). Plants were grown in a growth chamber at 23 ºC day 18 ºC night, 60 % relative humidity, a photoperiod of 10 h day/14 h night and 170–190 µmol m-2 s-1 irradiance. Water was supplied by sub-irrigation with distilled water. Drought (S) was imposed by withholding watering for a period of 9 days, 31 days after planting. Control plants (C) were watered during the treatment period and harvested in the same day as the stressed ones. Samples for RNA extraction (fully expanded rosette leaves) were collected 2 hours after the beginning of the light period. RNA was extracted from leaves, pooled from 3 plants, for each line/treatment. Samples were collected from two independent plantings (1 and 2)


title: 06L11_T

tag: Stage

tag: egfr

tag: kras


title: 564008A12 - 12-OE-stressed_2 vs 11-OE-CTR_2

hyb_protocol: 11-OE-CTR_2 Cy5 / 12-OE-stressed_2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: 11-OE-CTR_2:260mg. (Qiagen_RNeasy.pdf)


title: Hepatocytes-Ctl-8h-rep1

tag: tissue


title: Hepatocytes-Ctl-16h-rep1

tag: gender


title: Hepatocytes-Ctl-4h-rep2


title: Hepatocytes-Ctl-24h-rep1


title: 564008A11 - 11-OE-CTR_2 vs 12-OE-stressed_2

hyb_protocol: 12-OE-stressed_2 Cy5 / 11-OE-CTR_2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 06L14_N

tag: histology


title: 06L10_T

tag: race


title: wholeblood_818032_2

tag: sample collected at time pt (17-23weeks 1, 27-33weeks 2)

tag: gest age at sampling (weeks)

tag: gest age at delivery (weeks)

tag: birthing outcome (sptl 1, pprom 2, term 3)


title: wholeblood_818034_1

tag: individual id

tag: birth outcome (sptb 1, term 0)


title: wholeblood_818036_1


title: 564008A04 - 8-WT-stressed_2 vs 7-WT-CTR_2

hyb_protocol: 7-WT-CTR_2 Cy5 / 8-WT-stressed_2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: 7-WT-CTR_2:210mg. (Qiagen_RNeasy.pdf)

tag: age


title: 06L10_N

tag: age (yrs)

tag: pack-years


title: wholeblood_818032_1


title: 564008A09 - 5-OE-CTR_1 vs 6-OE-stressed_1

hyb_protocol: 6-OE-stressed_1 Cy5 / 5-OE-CTR_1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: ecotype


title: Hepatocytes-Ctl-4h-rep1

tag: strain

tag: stimulus

tag: time point


title: wholeblood_818025_2

tag: tissue


title: 06L3_N

tag: gender

tag: smoker


title: Hepatocytes-IL6-8h-rep1

value: 40 ng/ml rhIL-6


title: wholeblood_818023_1


title: Hepatocytes-Ctl-2h-rep1


title: Hepatocytes-Ctl-2h-rep2


title: 564008A01 - 1-WT-CTR_1 vs 2-WT-stressed_1

hyb_protocol: 2-WT-stressed_1 Cy5 / 1-WT-CTR_1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: 1-WT-CTR_1:250mg. (Qiagen_RNeasy.pdf)


title: 06L52_T

tag: histology

value: Male

tag: race

value: Former

tag: Stage

tag: egfr

tag: kras


title: Hepatocytes-IL6-4h-rep1


title: Hepatocytes-Ctl-0.5h-rep1


title: wholeblood_818023_2

tag: individual id

tag: sample collected at time pt (17-23weeks 1, 27-33weeks 2)

tag: gest age at sampling (weeks)

tag: gest age at delivery (weeks)

tag: birthing outcome (sptl 1, pprom 2, term 3)


title: wholeblood_818025_1

tag: birth outcome (sptb 1, term 0)


title: 06L3_T

tag: age (yrs)

value: Current

tag: pack-years

value: IIB


title: 05L54_T

value: Female

value: Asian

value: Never

value: IA


title: Hepatocytes-Ctl-0.5h-rep2

value: Liver

value: male

tag: age

tag: strain

tag: stimulus

tag: time point


title: 564008A02 - 2-WT-stressed_1 vs 1-WT-CTR_1

hyb_protocol: 1-WT-CTR_1 Cy5 / 2-WT-stressed_1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: ecotype


title: 05L54_N

hyb_protocol: 1.5 ug of the amplified and labeled cRNA probes was hybridized to the chip overnight at 58 degree C, then washed, blocked and detected by streptavidin-Cy3 per manufacturer's protocol.

tag: histology

value: Non-malignant

tag: gender

tag: race

tag: smoker


title: 564008A07 - 9-AS-CTR_2 vs 10-AS-stressed_2

hyb_protocol: 10-AS-stressed_2 Cy5 / 9-AS-CTR_2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: 9-AS-CTR_2:240mg. (Qiagen_RNeasy.pdf)


title: 564008A08 - 10-AS-stressed_2 vs 9-AS-CTR_2

hyb_protocol: 9-AS-CTR_2 Cy5 / 10-AS-stressed_2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 05L49_T

value: Adenocarcinoma

tag: Stage

value: IB

tag: egfr

value: WT

tag: kras


title: wholeblood_818022_2

hyb_protocol: Hybridization was performed according to standard protocols for Affymetrix HumanGene 2.1 ST (GeneTitan)

tag: individual id

tag: sample collected at time pt (17-23weeks 1, 27-33weeks 2)

tag: gest age at sampling (weeks)

tag: gest age at delivery (weeks)

tag: tissue

value: peripheral maternal blood


title: wholeblood_818022_1

tag: birth outcome (sptb 1, term 0)

tag: birthing outcome (sptl 1, pprom 2, term 3)


title: Hepatocytes-Ctl-0h-rep3

tag: age

value: 8-12 weeks

tag: strain

tag: stimulus


title: 564008A05 - 3-AS-CTR_1 vs 4-AS-stressed_1

hyb_protocol: 4-AS-stressed_1 Cy5 / 3-AS-CTR_1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: ecotype

value: Columbia

value: Boyes et al. Plant Cell 2001:30% of flower buds to be produced have opened

extract_protocol: 3-AS-CTR_1:290mg. (Qiagen_RNeasy.pdf)


title: Hepatocytes-Ctl-0h-rep4

tag: gender

tag: time point


title: wholeblood_815219_2


title: 05L52_N

tag: histology

tag: age (yrs)

tag: race

value: Caucasian

tag: smoker

tag: pack-years


title: 564008A06 - 4-AS-stressed_1 vs 3-AS-CTR_1

hyb_protocol: 3-AS-CTR_1 Cy5 / 4-AS-stressed_1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 05L52_T

value: Current

tag: Stage

tag: egfr

tag: kras

value: MUT


title: ORC2 ChIP-seq N-terminus antibody

type: SRA

city: Chicago

first: Zhe

last: Ji

state: ILLINOIS

address: 303 E Superior St, Lurie 6-107

institute: Northwestern University

library_source: genomic

data_processing:
Libraries sequence reads obtained were aligned to the UCSC human genome assembly hg19 using the Bowtie application (Illumina), allowing no more than two mismatches per sequence.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig

source_name: genomic DNA

growth_protocol: Human K562 erythroid cells were obtained from American Type Culture Collection (lot no. 4607240) and cultured according to ENCODE procedurses.

extract_protocol: After pre-clearing with protein A sepharose beads (4C for 1 hours), the chromatin from an equivalent of 5x107 cells was used for immunoprecipitation with an ORC2 antibody (Santa Cruz, sc-28742 or BD Biosciences, bd-6875) or IgG as a control. After 4C overnight incubation, beads were washed, eluted in buffer E (25mM Tris-HCl pH 7.5; 5mM EDTA; 0.5% SDS) and cross-links reversed at 65C with proteinase K for 6 hours. ChIP libraries were created using 15 cycles of amplification according to the Illumina manufacturer protocol. Libraries were run on a 2% agarose gel, and the 150-450 bp fraction was extracted and purified using DNA gel extraction kit (QIAGEN). To estimate the yield of library and its relative amplification value, library DNA was quantitated using a Nanodrop. Quality of the library was access by qPCR monitoring at known origins (see primers above).

treatment_protocol: Cells were crosslinked in 1% formaldehyde, nuclei isolated and the chromatin shredded by sonication in buffer to obtain chromatin fragments of ~200-300bp. Note that our samples were prepared using the same set of chromatin and procedures as those used for transcription factors mapping and presented on the genome browser as YaleTracks (ENCODE, 2012).

tag: cell line

tag: chip antibody

value: ORC2 antibody (BD Biosciences, bd-6875)


title: PorcineDC_PRRSV_rep4

city: Mississauga

first: Claude

last: Lachance

state: Ontario

address: 1329 Meyerside Drive

institute: Bio-Rad

description: Pig11-PRRSV_MGK187-1_US09473739_252644010677_S01_GE1_107_Sep09_1_1

hyb_protocol: Standard Agilent hybridization protocol

scan_protocol: Standard Agilent scanning protocol

data_processing: The data were normalised with VSN method using Flexarray 1.6.2

label: Cyanine 3

organism: Sus scrofa

label_protocol: cDNA was labelled with Cyanine 3 Labeling Master Mix according to Manufacturer's protocol.

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

treatment_protocol: Cells were plated at 1 x 10^6 cells/ml in 1 ml of complete RPMI and rested 3 h before use. For PRRSV infection, medium was removed and replaced with 300 μl of serum-free complete RPMI with PRRSV IAF-Klop (MOI of 0.1) for 2 h. The wells were washed with PBS twice to remove free virus and 1 ml of complete RPMI was added to each well.For co-infection experiments, cells were infected with PRRSV as described above. After 2 h infection, cells were washed with PBS. Then, S. suis P1/7 was added at a MOI of 0.1 (1 x 105 CFU) for the microarray assay. Bacteria were left in culture with the cells for 12 h. In parallel studies, virus-infected cells were left without bacterial infection (virus infection alone) or were virus-mock infected, similarly incubated and then infected with S. suis (bacterial infection alone).

tag: cell type

value: Dendritic cells

tag: infected with

value: porcine reproductive and respiratory syndrome virus


title: 05L49_N

extract_protocol: After homogenization, total RNA was extracted using TRI Reagent (Life Technologies, Grand Island, NY) according to manufacturer’s protocol. The nanodrop spectrophotometer (Thermo Fisher Scientific Inc., Wilmington, DE) was used to estimate the concentration of RNA and the quality of the RNA (RIN number) was assessed on Nano Series II RNA LAB-chips using Agilent Bioanalyzer 2100 (Agilent Technologies, Inc., Santa Clara, CA)

value: Female

value: Asian

value: Never


title: wholeblood_815219_1

extract_protocol:
Sample collection protocol: Peripheral maternal blood collected using PAXgene tubes.
PAXgene Blood RNA system kit was used to isolate total RNA.

tag: individual id

tag: sample collected at time pt (17-23weeks 1, 27-33weeks 2)

tag: gest age at sampling (weeks)

tag: gest age at delivery (weeks)

tag: birth outcome (sptb 1, term 0)

tag: birthing outcome (sptl 1, pprom 2, term 3)

tag: tissue


title: Hepatocytes-Ctl-0h-rep2

hyb_protocol: 15 µg labelled cRNA were hybridized onto the Mouse Genome 2.0 GeneChip® Arrays (Affymetrix, CA, USA) for 16h at 45°C using Hybridization Wash and Stain Kit (Affymetrix)

value: Liver

tag: gender

value: male

tag: age

tag: strain

tag: stimulus

tag: time point


title: 05L47_N

tag: histology

value: Non-malignant

tag: age (yrs)

tag: race

tag: smoker


title: PorcineDC_S.suis_rep4

description: Pig11-P1_7_MGK183-1_US09473739_252644010675_S01_GE1_107_Sep09_1_1

tag: cell type

tag: infected with

value: Streptococcus suis strain P1/7


title: 05L46_T

value: Adenocarcinoma

value: Former

tag: pack-years

tag: Stage

value: IIB

tag: egfr

value: WT

tag: kras


title: Hepatocytes-Ctl-0h-rep1

value: 8-12 weeks


title: wholeblood_815218_2

tag: individual id

tag: sample collected at time pt (17-23weeks 1, 27-33weeks 2)

tag: gest age at sampling (weeks)

tag: gest age at delivery (weeks)

tag: birth outcome (sptb 1, term 0)

tag: birthing outcome (sptl 1, pprom 2, term 3)

value: peripheral maternal blood


title: 05L47_T

tag: gender


title: wholeblood_815218_1

tag: tissue


title: PorcineDC_PRRSV_rep3

description: Pig3-PRRSV_MGK186-1_US09473739_252644010665_S01_GE1_107_Sep09_1_3


title: PorcineDC_PRRSV&S.suis_rep4

description: Pig11-Coinf_MGK191-1_US09473739_252644010665_S01_GE1_107_Sep09_1_2

value: porcine reproductive and respiratory syndrome virus & Streptococcus suis strain P1/7


title: PorcineDC_S.suis_rep3

description: Pig3-P1_7_MGK182-1_US09473739_252644010665_S01_GE1_107_Sep09_1_4


title: PorcineDC_mock-infected_rep4

description: Pig11-CTL_MGK179-1_US09473739_252644010675_S01_GE1_107_Sep09_1_3

value: Mock-infected


title: 05L45_T

tag: histology

tag: age (yrs)

value: IA


title: 05L45_N

tag: race

tag: smoker


title: PorcineDC_mock-infected_rep3

description: Pig3-CTL_MGK178-1_US09473739_252644010677_S01_GE1_107_Sep09_1_4

tag: cell type

value: Dendritic cells

tag: infected with


title: wholeblood_815200_1


title: wholeblood_815196_2


title: wholeblood_815200_2


title: PorcineDC_PRRSV_rep2

description: Pig2-PRRSV_MGK185-1_US09473739_252644010676_S01_GE1_107_Sep09_1_4

value: porcine reproductive and respiratory syndrome virus


title: wholeblood_815194_2


title: 05L43_N

value: Female

value: Caucasian

value: Current

tag: pack-years


title: 05L46_N


title: wholeblood_815196_1


title: PorcineDC_PRRSV&S.suis_rep3

description: Pig3-Coinf_MGK190-1_US09473739_252644010676_S01_GE1_107_Sep09_1_1


title: wholeblood_815194_1B


title: 05L43_T

tag: Stage

value: IB

tag: egfr

value: MUT


title: Non-relapsing_DLBCL_primary (case31)

city: Basel

first: Darius

last: Juskevicius

address: Schoenbeinstr. 40

department: Molecuar Pathology

country: Switzerland

institute: Institute of Pathology

hyb_protocol: Labeled DNAs were hybridized in an ozone free environment in a rotisserie oven at 25 rpm for at least 24 hours then washed according to array supplier's (Agilent)protocol

scan_protocol: All arrays were scanned using an Agilent 2565C Scanner and default settings for CGH.

data_processing: Data was extracted from the TIFF files using Agilent FE 10.5. The data quality was assessed using the QC Report output in F.E. 10.5. All arrays that passed the experimental Q.C. were then visulaized and analyzed using Agilent Genomic Workbench v7.0 and the ADM2 algorithm.

source_name: FFPE tissue biopsy

label_protocol: A 100-500 nanogram aliquot of each sample and reference DNA was heat digested then labeled with a fluorescent nucleotide (Cy5 for tumor and Cy3 for normal reference) using the BioPrime labeling kit (Invitrogen)according to manufacturer's protocol.

extract_protocol: H&E- and CD20-stained sections of FFPE blocks or fresh-frozen tissue were reviewed to evaluate tumor content. Only tissues with >70% tumor content were used. Depending on the distribution of tumor cells, 25µm-thick sections were cut or punches were taken from the tumor-rich tissue areas. Prior to overnight Proteinase K digestion, paraffin sections were deparaffinized and rehydrated by serial xylene and ethanol washes, respectively. Genomic DNA (gDNA) was extracted by automation using Maxwell® 16 FFPE plus LEV DNA Purification Kit. gDNA from samples with extremely scarce tumor material was isolated by the phenol-chloroform extraction as described previously22. Yields were quantified by the Qubit assay.

tag: disease state

value: Diffuse large B cell lymphoma (DLBCL)

tag: specimen

value: Non-relapsing DLBCL primary

tag: case

source_name: Reference pooled 46XX

value: pooled normal (46,XX) reference (Promega)


title: wholeblood_815189_2

tag: individual id

tag: sample collected at time pt (17-23weeks 1, 27-33weeks 2)

tag: gest age at sampling (weeks)

tag: gest age at delivery (weeks)


title: PorcineDC_S.suis_rep2

description: Pig2-P1_7_MGK181-1_US09473739_252644010677_S01_GE1_107_Sep09_1_2

value: Streptococcus suis strain P1/7


title: 564008A03 - 7-WT-CTR_2 vs 8-WT-stressed_2

hyb_protocol: 8-WT-stressed_2 Cy5 / 7-WT-CTR_2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: ecotype

value: Columbia

tag: age

value: Boyes et al. Plant Cell 2001:30% of flower buds to be produced have opened


title: 05L39_T

source_name: Lung cancer

tag: histology

value: Adenocarcinoma

tag: age (yrs)

tag: gender

value: Asian

value: Never

value: WT

tag: kras


title: PorcineDC_mock-infected_rep2

description: Pig2-CTL_MGK177-1_US09473739_252644010676_S01_GE1_107_Sep09_1_2

tag: cell type

value: Dendritic cells

tag: infected with

value: Mock-infected


title: 05L40_T

value: Female

tag: race

tag: smoker

tag: Stage

value: IA


title: 05L40_N

value: Non-malignant


title: PorcineDC_PRRSV_rep1

description: Pig1-PRRSV_MGK184-1_US09473739_252644010675_S01_GE1_107_Sep09_1_2

value: porcine reproductive and respiratory syndrome virus


title: wholeblood_815179_2

source_name: whole blood, maternal peripheral

tag: birth outcome (sptb 1, term 0)

tag: birthing outcome (sptl 1, pprom 2, term 3)

tag: tissue

value: peripheral maternal blood


title: wholeblood_815189_1

tag: individual id

tag: sample collected at time pt (17-23weeks 1, 27-33weeks 2)


title: 05L38_T

value: Caucasian

value: Former

tag: pack-years

value: IV

tag: egfr

value: MUT


title: PorcineDC_S.suis_rep1

description: Pig1-P1_7_MGK180-1_US09473739_252644010676_S01_GE1_107_Sep09_1_3

value: Streptococcus suis strain P1/7


title: PorcineDC_PRRSV&S.suis_rep2

description: Pig2-Coinf_MGK189-1_US09473739_252644010677_S01_GE1_107_Sep09_1_3

value: porcine reproductive and respiratory syndrome virus & Streptococcus suis strain P1/7


title: wholeblood_815183_1

tag: gest age at sampling (weeks)

tag: gest age at delivery (weeks)


title: wholeblood_815183_2


title: 05L38_N

tag: histology

tag: age (yrs)


title: 05L39_N

tag: gender


title: Non-relapsing_DLBCL_primary (case28)

source_name: Frozen tissue biopsy

tag: disease state

value: Diffuse large B cell lymphoma (DLBCL)

tag: specimen

value: Non-relapsing DLBCL primary

tag: case

value: pooled normal (46,XX) reference (Promega)


title: PorcineDC_mock-infected_rep1

description: Pig1-CTL_MGK176-1_US09473739_252644010665_S01_GE1_107_Sep09_1_1

tag: cell type

tag: infected with


title: Non-relapsing_DLBCL_primary (case27)


title: 05L34_T

value: Adenocarcinoma

tag: race

value: Asian

tag: smoker

value: Never

tag: Stage

value: IB

tag: kras

value: WT


title: Non-relapsing_DLBCL_primary (case30)

tag: tissue


title: Non-relapsing_DLBCL_primary (case25)


title: PorcineDC_PRRSV&S.suis_rep1

description: Pig1-Coinf_MGK188-1_US09473739_252644010675_S01_GE1_107_Sep09_1_4

value: Monocytes


title: wholeblood_815179_1

tag: individual id

tag: sample collected at time pt (17-23weeks 1, 27-33weeks 2)

tag: birth outcome (sptb 1, term 0)

tag: birthing outcome (sptl 1, pprom 2, term 3)


title: Non-relapsing_DLBCL_primary (case23)


title: 05L34_N

tag: histology

value: Non-malignant

value: Female


title: wholeblood_815168_2

tag: gest age at sampling (weeks)

tag: gest age at delivery (weeks)

value: peripheral maternal blood


title: Porcinemonocytes_PRRSV&S.suis_rep4

description: PRRSV-P1_7-V_MGK175-1_US09473739_252644010640_S01_GE1_1100_Jul11_1_3.txt


title: Non-relapsing_DLBCL_primary (case24)

tag: disease state


title: Porcinemonocytes_PRRSV&S.suis_rep2

description: PRRSV-P1_7-T_MGK173-1_US09473739_252644010643_S01_GE1_1100_Jul11_1_2.txt


title: 05L33_T

tag: age (yrs)

tag: gender

value: Male

value: Caucasian

value: Former

tag: pack-years

tag: egfr


title: Non-relapsing_DLBCL_primary (case22)

tag: specimen

tag: case


title: wholeblood_815168_1


title: wholeblood_815163_2


title: 05L32_T

tag: race

tag: smoker

value: Current

tag: Stage

value: IIB


title: Porcinemonocytes_PRRSV&S.suis_rep3

description: PRRSV-P1_7-U_MGK174-1_US09473739_252644010642_S01_GE1_1100_Jul11_1_3.txt

tag: cell type

tag: infected with

value: porcine reproductive and respiratory syndrome virus & Streptococcus suis strain P1/7


title: wholeblood_815163_1

tag: individual id

tag: sample collected at time pt (17-23weeks 1, 27-33weeks 2)

tag: birth outcome (sptb 1, term 0)

tag: tissue


title: Porcinemonocytes_PRRSV&S.suis_rep1

description: PRRSV-P1_7-D_MGK172-1_US09473739_252644010643_S01_GE1_1100_Jul11_1_1.txt


title: Relapsing_DLBCL_relapse (case20)

value: Diffuse large B cell lymphoma (DLBCL)

value: Relapsing DLBCL relapse


title: Non-relapsing_DLBCL_primary (case21)

value: Non-relapsing DLBCL primary

value: pooled normal (46,XX) reference (Promega)


title: Porcinemonocytes_PRRSV_rep4

description: PRRSV-V_MGK171-1_US09473739_252644010640_S01_GE1_1100_Jul11_1_1.txt

value: porcine reproductive and respiratory syndrome virus


title: wholeblood_815154_1

tag: gest age at sampling (weeks)

tag: gest age at delivery (weeks)

tag: birthing outcome (sptl 1, pprom 2, term 3)


title: 05L33_N

tag: histology

tag: age (yrs)

tag: gender


title: Non-relapsing_DLBCL_primary (case26)

tag: disease state

tag: specimen


title: wholeblood_815154_2


title: 05L27_N

tag: race

value: Asian

value: Never


title: 05L27_T

value: Adenocarcinoma

tag: smoker

tag: egfr

value: MUT

tag: kras

value: WT


title: 05L32_N

value: Non-malignant

tag: pack-years


title: Porcinemonocytes_PRRSV_rep2

description: PRRSV-T_MGK169-1_US09473739_252644010640_S01_GE1_1100_Jul11_1_2.txt

tag: cell type

value: Monocytes

tag: infected with


title: Relapsing_DLBCL_relapse (case19)

tag: case


title: Porcinemonocytes_PRRSV_rep3

description: PRRSV-U_MGK170-1_US09473739_252644010641_S01_GE1_1100_Jul11_1_2.txt


title: Porcinemonocytes_S.suis_rep4

description: P1_7-V_MGK167-1_US09473739_252644010641_S01_GE1_1100_Jul11_1_3.txt

value: Streptococcus suis strain P1/7


title: wholeblood_815149_2

tag: individual id

tag: sample collected at time pt (17-23weeks 1, 27-33weeks 2)

tag: birth outcome (sptb 1, term 0)

tag: tissue

value: peripheral maternal blood


title: wholeblood_815149_1

tag: gest age at sampling (weeks)

tag: gest age at delivery (weeks)

tag: birthing outcome (sptl 1, pprom 2, term 3)


title: wholeblood_815137_2


title: wholeblood_815137_1


title: Relapsing_DLBCL_relapse (case18)

tag: disease state


title: Porcinemonocytes_S.suis_rep3

description: P1_7-U_MGK166-1_US09473739_252644010641_S01_GE1_1100_Jul11_1_1.txt


title: Porcinemonocytes_PRRSV_rep1

description: PRRSV-D_MGK168-1_US09473739_252644010640_S01_GE1_1100_Jul11_1_4.txt


title: 05L19_N

tag: histology

tag: age (yrs)

tag: gender

value: Female

value: Caucasian

value: Current


title: 05L19_T

tag: race

tag: smoker

tag: Stage

value: IV

tag: egfr


title: wholeblood_815127_2


title: 05L13_N

value: Male


title: 05L12_T

value: IIIA

tag: kras


title: Non-relapsing_DLBCL_primary (case29)

value: Diffuse large B cell lymphoma (DLBCL)

tag: specimen

value: Non-relapsing DLBCL primary

tag: case

value: pooled normal (46,XX) reference (Promega)


title: Relapsing_DLBCL_relapse (case14)

value: Relapsing DLBCL relapse


title: wholeblood_815127_1

tag: individual id

tag: sample collected at time pt (17-23weeks 1, 27-33weeks 2)


title: Porcinemonocytes_S.suis_rep2

description: P1_7-T_MGK165-1_US09473739_252644010641_S01_GE1_1100_Jul11_1_4.txt

tag: cell type

tag: infected with


title: Porcinemonocytes_S.suis_rep1

description: P1_7-D_MGK164-1_US09473739_252644010643_S01_GE1_1100_Jul11_1_3.txt


title: Relapsing_DLBCL_relapse (case16)

tag: tissue


title: Relapsing_DLBCL_relapse (case15)


title: 05L13_T

value: Adenocarcinoma

value: Asian

value: Never

value: IB


title: Porcinemonocytes_mock-infected_rep4

description: Mock-V_MGK163-1_US09473739_252644010642_S01_GE1_1100_Jul11_1_2.txt

value: Monocytes

value: Mock-infected


title: wholeblood_815116_2

tag: gest age at sampling (weeks)

tag: gest age at delivery (weeks)

tag: birth outcome (sptb 1, term 0)

tag: birthing outcome (sptl 1, pprom 2, term 3)

value: peripheral maternal blood


title: 05L10_T

tag: histology

tag: age (yrs)

tag: gender

value: Female

value: Former

value: IA

value: WT

value: MUT


title: 05L12_N

value: Non-malignant

value: Male

tag: race

tag: smoker


title: Relapsing_DLBCL_relapse (case17)

tag: disease state

value: Diffuse large B cell lymphoma (DLBCL)


title: Relapsing_DLBCL_relapse (case12)

tag: specimen

value: pooled normal (46,XX) reference (Promega)


title: Relapsing_DLBCL_relapse (case13)

value: Relapsing DLBCL relapse

tag: case


title: Relapsing_DLBCL_relapse (case11)


title: Porcinemonocytes_mock-infected_rep2

description: Mock-T_MGK161-1_US09473739_252644010642_S01_GE1_1100_Jul11_1_1.txt


title: 05L9_T

value: Adenocarcinoma

value: Caucasian

value: Current

tag: pack-years

tag: Stage

tag: egfr

tag: kras


title: Porcinemonocytes_mock-infected_rep1

description: Mock-D_MGK160-1_US09473739_252644010642_S01_GE1_1100_Jul11_1_4.txt

tag: cell type

tag: infected with


title: wholeblood_815123_1

tag: individual id

tag: sample collected at time pt (17-23weeks 1, 27-33weeks 2)

tag: gest age at sampling (weeks)

tag: gest age at delivery (weeks)

tag: tissue


title: wholeblood_815123_2

tag: birth outcome (sptb 1, term 0)

tag: birthing outcome (sptl 1, pprom 2, term 3)


title: 05L10_N

tag: histology

tag: age (yrs)

tag: gender

tag: race

tag: smoker


title: Porcinemonocytes_mock-infected_rep3

description: Mock-U_MGK162-1_US09473739_252644010643_S01_GE1_1100_Jul11_1_4.txt


title: 05L7_T

value: Asian

value: Never

tag: Stage

value: IB


title: wholeblood_815094_2

value: peripheral maternal blood


title: PML-/- MEF 3h stimulation rep2

city: Glasgow

first: Ruaidhri

last: Carmody

address: Sir Graeme Davies Building, 120 University Place

department: Institute of Infection, Immunity and Inflammation

institute: University of Glasgow

description:
KO TNF 2
This sample is of PML knockout  mouse embryonic fibroblasts treated with TNFalpha for 3 hours. It is the second of three TNFalpha treated PML knockout  biological replicates used in this experiment, each from separate cultures.

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

source_name: PML-/- MEF 3h stimulation

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol:
WT MEFs, PML -/- MEFs cells were maintained in tissue culture dishes and/or flasks (Iwaki) in Dulbecco’s modified eagle medium (DMEM) at 37˚C, 5% CO₂. Cell maintenance medium was as follows: 500ml DMEM (GIBCO; 41966), 10% v/v foetal bovine serum (FBS;), 5ml 1,000U/ml penicillin-streptomycin (Invitrogen), 5ml Glycine (Sigma)
Cells were treated with a final concentration of 10ng/ul mouse TNFα for 3 hours

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer at the Harvard-Partners Center for Genetics and Genomics (Harvard Medical School, Cambridge, MA USA).

tag: strain background

tag: genotype/variation

value: PML-/-

value: mouse embryonic fibroblasts (MEFs)

tag: stimulated with

value: 10ng/ul mouse TNFα for 3hrs


title: PML-/- MEF unstimulated rep3

description:
KO UNT 3
This sample is of untreated PML knockout  mouse embryonic fibroblasts. It is the third of three untreated PML knockout biological replicates used in this experiment, each from separate cultures.

source_name: PML-/- MEF unstimulated

tag: cell type

value: none (unstimulated control)


title: Relapsing_DLBCL_relapse (case10)

tag: disease state

tag: specimen

tag: case


title: wholeblood_815116_1

tag: individual id

tag: sample collected at time pt (17-23weeks 1, 27-33weeks 2)

tag: gest age at sampling (weeks)

tag: gest age at delivery (weeks)


title: Relapsing_DLBCL_relapse (case9)

tag: tissue


title: wholeblood_815102_1

tag: birth outcome (sptb 1, term 0)

tag: birthing outcome (sptl 1, pprom 2, term 3)


title: 05L9_N

tag: histology

tag: age (yrs)

tag: gender

value: Female

tag: race

tag: pack-years


title: PML-/- MEF 3h stimulation rep3

description:
KO TNF 3
This sample is of PML knockout  mouse embryonic fibroblasts treated with TNFalpha for 3 hours. It is the third of three TNFalpha treated PML knockout  biological replicates used in this experiment, each from separate cultures.

tag: strain background

tag: genotype/variation

tag: stimulated with


title: wholeblood_815102_2


title: 05L7_N

value: Non-malignant

tag: smoker


title: PML-/- MEF 3h stimulation rep1

description:
KO TNF 1
This sample is of PML knockout  mouse embryonic fibroblasts treated with TNFalpha for 3 hours. It is the first of three TNFalpha treated PML knockout  biological replicates used in this experiment, each from separate cultures.

tag: cell type


title: 05L6_T

tag: Stage

tag: egfr

value: WT

tag: kras

value: MUT


title: wholeblood_815094_1

tag: individual id

tag: sample collected at time pt (17-23weeks 1, 27-33weeks 2)

tag: gest age at sampling (weeks)

tag: gest age at delivery (weeks)


title: wholeblood_815082_1

tag: birth outcome (sptb 1, term 0)

tag: birthing outcome (sptl 1, pprom 2, term 3)

tag: tissue


title: Relapsing_DLBCL_relapse (case5)

tag: disease state

value: Diffuse large B cell lymphoma (DLBCL)

tag: specimen

tag: case

value: pooled normal (46,XX) reference (Promega)


title: Relapsing_DLBCL_relapse (case7)

value: Relapsing DLBCL relapse


title: Relapsing_DLBCL_relapse (case6)


title: Relapsing_DLBCL_relapse (case8)


title: Relapsing_DLBCL_relapse (case4)


title: Relapsing_DLBCL_relapse (case3)


title: wholeblood_815076_2


title: 05L6_N

tag: histology

tag: age (yrs)

tag: gender

tag: race


title: 05L4_T

value: Adenocarcinoma

tag: smoker

tag: Stage

value: IIB


title: WT MEF 3h stimulation rep3

description:
WT TNF 3
This sample is of wild-type mouse embryonic fibroblasts treated with TNFalpha for 3 hours. It is the third of three TNFalpha treated wild-type biological replicates used in this experiment, each from separate cultures.

source_name: WT MEF 3h stimulation

tag: strain background

tag: genotype/variation

value: wild type

tag: cell type

tag: stimulated with


title: wholeblood_815076_1

tag: individual id

tag: sample collected at time pt (17-23weeks 1, 27-33weeks 2)

tag: gest age at sampling (weeks)

tag: gest age at delivery (weeks)


title: 05L4_N

source_name: Non-malignant lung

value: Asian

value: Never


title: T4P38b

city: Düsseldorf

first: Wasco

last: Wruck

address: Moorenstr. 5

institute: Universitätsklinikum Düsseldorf

description: replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using rank invariant normalisation after background subtraction using the Gene Expression Module 1.8.0 of GenomeStudio V2010.3 (Illumina).

source_name: Cells with high bone forming capacity in vivo

label_protocol: Illumina Gene Expression protocols contain a first- and second-strand   reverse transcription step, followed by a single in vitro transcription   (IVT) amplification that incorporates biotin-labeled nucleotides.   Subsequent steps include array hybridization, washing, blocking, and   streptavadin-Cy3 staining. Fluorescence emission by Cy3 is quantitatively   detected for downstream analysis.

extract_protocol: The RNA was isolated using the RNeasy Mini Kit (Qiagen), including RNase-free Dnase (Qiagen) digestion   (RNase-free DNase Set, Quiagen) has been applied on the columns during   isolation.

value: Bone marrow derived stromal cells immortalized with telomerase gene

tag: treatment

value: No treatment basal culture condition

tag: passage


title: WT MEF 3h stimulation rep1

description:
WT TNF 1
This sample is of wild-type mouse embryonic fibroblasts treated with TNFalpha for 3 hours. It is the first of three TNFalpha treated wild-type biological replicates used in this experiment, each from separate cultures.

value: mouse embryonic fibroblasts (MEFs)


title: wholeblood_815072_1

tag: birth outcome (sptb 1, term 0)

tag: birthing outcome (sptl 1, pprom 2, term 3)

tag: tissue

value: peripheral maternal blood


title: Relapsing_DLBCL_relapse (case2)

tag: disease state

tag: specimen

tag: case


title: wholeblood_815073_2


title: wholeblood_815072_2


title: WT MEF 3h stimulation rep2

description:
WT TNF 2
This sample is of wild-type mouse embryonic fibroblasts treated with TNFalpha for 3 hours. It is the second of three TNFalpha treated wild-type biological replicates used in this experiment, each from separate cultures.

value: 10ng/ul mouse TNFα for 3hrs


title: T4P74b

description: replicate 2

source_name: Cells with low bone forming capacity in vivo


title: Relapsing_DLBCL_relapse (case1.2)


title: PML-/- MEF unstimulated rep2

description:
KO UNT 2
This sample is of untreated PML knockout mouse embryonic fibroblasts. It is the second of three untreated PML knockout  biological replicates used in this experiment, each from separate cultures.

value: PML-/-

value: none (unstimulated control)


title: wholeblood_815073_1


title: WT MEF unstimulated rep2

description:
WT UNT 2
This sample is of untreated wild-type mouse embryonic fibroblasts. It is the second of three untreated wild-type biological replicates used in this experiment, each from separate cultures.

source_name: WT MEF unstimulated


title: DD8P6b

description: replicate 2


title: Relapsing_DLBCL_relapse (case1.1)


title: wholeblood_812590_2


title: WT MEF unstimulated rep1

description:
WT UNT 1
This sample is of untreated wild-type mouse embryonic fibroblasts. It is the first of three untreated wild-type biological replicates used in this experiment, each from separate cultures.


title: Relapsing_DLBCL_primary (case19)

value: Relapsing DLBCL primary


title: BB10b

description: replicate 2


title: Relapsing_DLBCL_primary (case17)


title: wholeblood_812590_1


title: WT MEF unstimulated rep3

description:
WT UNT 3
This sample is of untreated wild-type mouse embryonic fibroblasts. It is the third of three untreated wild-type biological replicates used in this experiment, each from separate cultures.


title: Relapsing_DLBCL_primary (case20)


title: PML-/- MEF unstimulated rep1

description:
KO UNT 1
This sample is of untreated PML knockout mouse embryonic fibroblasts. It is the first of three untreated PML knockout  biological replicates used in this experiment, each from separate cultures.


title: HDm-/HD-

city: Gosselies

first: Christiane

last: Christophe-Hobertus

address: Biopark Charleroi Brussels South,

department: IBMM

country: Belgium

institute: Université Libre de Bruxelles

description:
the miRNA transcriptome variation between 8505c cells expressing the TTF1 antagonist (Engr HD– Dox) versus the cells expressing the control protein (Engr HDm – Dox)
Slide 4 is the dye swap

hyb_protocol: Samples were hybridized using Corning Pronto! Microarray Hybridization Kit.

scan_protocol: The slides were scanned using a GenePix 4000B scanner (Axon, Sunnyvale, CA).

data_processing: A Normex + offset background correction and LOESS normalization were carried out by using functions of the LIMMA 3.18.13 package for the R 2.13.1 language. Data points were removed when intensity values for both dyes were below 200% of the background and absent calls were removed before subsequent statistical analyses. Dye-swaped signals were averaged before computing log2 Fold-change.

source_name: Human 8505c cells expressing Engr HD (–Dox)

label_protocol: Total RNA was labelled using the miRCURY LNA microRNA Power Labelling Kit (Hy3/Hy5) (Exiqon, Copenhagen, Denmark), according to the manufacturer’s protocol. Labeled RNA was purified on a miRNeasy column (Qiagen).

growth_protocol: 8505-C cells were cultured as described by van Staveren and coworkers [9] at 37°C in a water-saturated 95% air/5% CO2 atmosphere.

extract_protocol: Total RNA was obtained from cells at about 80-90 % confluency maintained in the presence or absence of doxycycline for one week using the miRNeasy mini kit from Qiagen. 1µg of total RNA was engaged for the hybridization reaction.

treatment_protocol: The DNA constructs and transfection conditions used to transform the cells have been described previously [3,16]. Transformed 8505C cells expressing the doxycycline-dependent tTA transactivator from a pEFIN4 construct [3] were selected in the presence of 400µg/mL geneticin (GIBCO) and maintained in culture medium supplemented with 200µg/mL of the agent. The pTRE2hyg-Luc construct (Clontech) was used to select the tTA-expressing 8505C clone displaying the best response to doxycycline withdrawal. For the isolation of the clones transformed with the pTRE2hyg construct driving the conditional expression of EngrHD or EngrHDm [3], cells were transfected in culture medium supplemented with 200 µg/mL of geneticin and 2 µg/mL of doxycycline (Sigma-Aldrich) and then selected in the presence of 200 µg/mL of both geneticin and hygromycin (HygroGold, InvivoGen) and 2 µg/mL of doxycycline.

tag: cell line

value: thyroid

tag: construct

value: Engr-HD-producing construct

tag: doxycycline status

value: absent

tag: construct expression status

value: expressed

source_name: Human 8505c cells expressing Engr HDm (–Dox)

value: Engr-HDm-producing construct

tag: construct expression


title: CB8b

description: replicate 2

tag: cell type


title: HD+/HD-

description:
the miRNA transcriptome variation between 8505c cells expressing a TTF1 antagonist (Engr HD –Dox) versus non-expressing cells (Engr HD +Dox)
Slide 2 is the dye swap

source_name: Human 8505c cells not expressing Engr HD (+Dox)

value: present

value: not expressed


title: HDm+/HDm-

description:
the miRNA transcriptome variation between 8505c cells expressing the control protein (Engr HDm – Dox) versus non-expressing cells (Engr HDm + Dox)
Slide 6 is the dye swap

source_name: Human 8505c cells not expressing Engr HDm (+Dox)


title: Relapsing_DLBCL_primary (case18)

value: Diffuse large B cell lymphoma (DLBCL)

value: pooled normal (46,XX) reference (Promega)


title: Relapsing_DLBCL_primary (case16)


title: Relapsing_DLBCL_primary (case15)


title: T4P74a

description: replicate 1

value: Bone marrow derived stromal cells immortalized with telomerase gene


title: CB4b

description: replicate 2

value: No treatment basal culture condition


title: Relapsing_DLBCL_primary (case14)


title: wholeblood_812581_2

tag: individual id

tag: sample collected at time pt (17-23weeks 1, 27-33weeks 2)


title: AD10b

description: replicate 2


title: Relapsing_DLBCL_primary (case12)


title: T4P38a

description: replicate 1


title: wholeblood_812587_2

tag: gest age at sampling (weeks)

tag: gest age at delivery (weeks)


title: Relapsing_DLBCL_primary (case11)


title: BB10a

description: replicate 1

tag: treatment

tag: passage


title: E34VZ replicate 3

city: San Juan de Alicante

first: Victor

last: Borrell

state: Alicante

address: Av Ramon y Cajal s/n

department: Institute of Neuroscience

country: Spain

institute: CSIC

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 100%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.

organism: Mustela putorius furo

source_name: Repl.3_Ventricular Zone Embryonic day 34

label_protocol: 85ng 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 LowInputQuick 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

tag: developmental stage

value: Embryonic day 34


title: wholeblood_812586_2

city: Toronto

first: Jan

last: Heng

address: 25 Orde Street

institute: Lunenfeld-Tanenbaum Research Institute

data_processing: Data were normalized using RMA and differential expression was determined using Limma with multiple hypothesis testing (Benjamini and Hochberg); Bioconductor, R

tag: birth outcome (sptb 1, term 0)

tag: birthing outcome (sptl 1, pprom 2, term 3)

tag: tissue

value: peripheral maternal blood


title: wholeblood_812574_2


title: CF1b

description: replicate 2


title: Relapsing_DLBCL_primary (case13)

source_name: FFPE tissue biopsy

tag: disease state

tag: specimen

tag: case


title: wholeblood_812574_1


title: P15VZ replicate 1

source_name: Repl.1_Ventricular Zone Postnatal day 1.5

value: Postnatal day 1.5


title: wholeblood_812586_1


title: wholeblood_812587_1


title: E34VZ replicate 1

source_name: Repl.1_Ventricular Zone Embryonic day 34