title: Female_0.1_rep8

city: Victoria

first: Ben

middle: F

last: Koop

state: BC

address: PO Box 3020 STN CSC

department: Biology

country: Canada

institute: The University of Victoria

description:
raw data files: 10086_cy5_70txt; 10086_cy3_75txt
10086_Block2

hyb_protocol: Samples were hybridized to oligonucleotide microarrays as per manufacturers' instructions for Low-Input Quick Amp kits (Agilent; v6.5). Arrays were designed using previously annotated ESTs from both Pacific and Atlantic L. salmonis (Yasuike et al. 2012; eArray design ID 024389; Agilent).

scan_protocol: Scanned at 5 micrometer resolution on a ScanArray Express (Perkin Elmer) and quantified on Imagene (v8.1; BioDiscovery).

data_processing: For each probe on the microarray, the background median was subtracted from the foreground median. Data analysis was performed in GeneSpring GX11 (Agilent). Each array was normalized using an intensity-dependent Lowess normalization. All entities on the array are presented in the attached matrix file here, however, for the analysis, quality control filters for each of the three experiments retained probes that pass the following criteria in at least 65% of the samples in any one condition: raw signal ≥ 500 in both channels and no poor quality flags.

organism: Lepeophtheirus salmonis

source_name: Female_pre-adult lice_0.1

label_protocol: Labeled cRNA was generated from 825ng total RNA using Low-Input Quick Amp kits (Agilent; v6.5). A Cy3-cRNA reference pool to hybridize alongside samples was created for each of the above experiments, ensuring each experimental condition was included in the pool.

growth_protocol: Pacific: L. salmonis egg strings were obtained from adult female lice infecting Atlantic salmon in a salmon farm near Broughton Archipegalo, British Columbia (BC) in 2010. Eggs were hatched in a static sea water hatch system, grown to copepodids, and then grown on Atlantic salmon in house at Pacific Biological Station, Nanaimo, BC, Canada. Pre-adult lice were removed from Atlantic salmon sedated with Metomidate hydrochloride (Aquacalm, Syndel Laboratories Ltd.) A total of 40 pre-adult I and II stage L. salmonis individuals were randomly distributed into  beakers containing 500 ml filtered seawater (10C; 30 parts per thousand salinity; one air stone per beaker).

extract_protocol: Lice were flash frozen individually and kept at -80 degrees Celcius until RNA extraction (n = 40 individuals). Total RNA was extracted from frozen tissue using TRIzol reagent® (Life Technologies), on-column DNase digestion (QIAGEN) followed by RNEasy column purification as per manufacturers’ instructions (QIAGEN). Purified total RNA was tested by agarose gel and automated electrophoresis (Experion; Bio-Rad) and spec.

treatment_protocol: Stock emamectin benzoate (EMB; PESTANAL®, Sigma-Aldrich) was prepared to 100 mg/L in methanol, then diluted to working concentrations in seawater. EMB dilutions were prepared to final concentrations of 0, 0.01, and 0.01 parts per billion (n = 6-8 individuals for each sex/dose combination). Exposure time was 24 hours before collection and flash freezing.

tag: Sex

value: Female

tag: age

value: pre-adult lice

tag: population

value: Pacific Canada

tag: microsporidian identification (facilispora margolisi)

value: Negative

tag: emb concentration (ppb)

source_name: all condition pool

tag: sample type

value: pooled reference


title: SporadicPRCC2_TumorTissue7

status: Public on Jun 01 2016

type: RNA

city: Singapore

first: Weng Khong

last: Lim

state: Singapore

address: 11 Hospital Drive

department: Department of Medical Sciences

country: Singapore

institute: National Cancer Centre Singapore

description: Gene expression profiling of hereditary and sporadic Type 2 Papillary Renal Cell Carcinoma (PRCC2) and adjacent normal tissue from PRCC2 patients

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 7G

data_processing: CEL files were loaded into R and then preprocessed and normalized using RMA. A custom CDF (GPL16311) was used to reannotate the probes.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Tumor tissue from sporadic PRCC2

label_protocol: Standard Affymetrix protocol, 10ug of RNAeasy-purified total RNA

extract_protocol: Trizol extraction of total RNA was performed according to manufacturer's instructions, followed by purification using the Qiagen RNAeasy kit.

tag: tissue type

value: Cancer

tag: disease status

value: sporadic PRCC2


title: Male_0_rep7

description:
raw data files: 10086_cy5_70txt; 10086_cy3_75txt
10086_Block4txt

source_name: Male_pre-adult lice_0

value: Male

value: Positive


title: Male_0_rep6

description:
raw data files: 10086_cy5_70txt; 10086_cy3_75txt
10086_Block1


title: Female_0_rep6

description:
raw data files: 10086_cy5_70txt; 10086_cy3_75txt
10086_Block3

source_name: Female_pre-adult lice_0


title: E249-Tp1

city: Bethesda

first: Perwez

middle: S

last: Hussain

state: MD

address: 37 Convent Drive, Building 37, Room3044B

country: USA

institute: National Cancer Institute

hyb_protocol: Hybrdization reactions were performed according to the manufacturer's instructions (NanoString).

scan_protocol: standard Nanostring protocol

data_processing:
The data were normalized for lane-to-lane variation with a dilution series of six spike-in positive controls using code count normalization according to manufacturer's protocol (Nanostring). Log2 normalized data was imported to Parkek Genomic Suite 6 and batch effect was removed before analysis.
NanoString Technologies v1.6.0
miRBase Identifier (miRBase 16)

source_name: pancreatic ductual adenocarcinoma_38

extract_protocol: Tissues were flash frozen immediately after surgery.RNA from frozen tissue samples was extracted using standard TRIZOL (Invitrogen) protocol. RNA quality was confirmed with the Agilent 2100 Bioanalyzer (Agilent Technologies) before the microarray gene expression profiling

tag: tissue

value: Tumor

tag: survival months

tag: survival status

tag: mif status

value: High


title: E186-Tp2

source_name: pancreatic ductual adenocarcinoma_32


title: E246-Tp1

source_name: pancreatic ductual adenocarcinoma_37

value: Low


title: E209-Tp2

source_name: pancreatic ductual adenocarcinoma_34


title: E218-Tp1

source_name: pancreatic ductual adenocarcinoma_35


title: E208-Tp1

source_name: pancreatic ductual adenocarcinoma_33


title: E245-Tp1

source_name: pancreatic ductual adenocarcinoma_36


title: F1_0168_1

city: San Francisco

first: David

last: Quigley

state: CA

address: 1450 Third St. Room 207

department: Helen Diller Comprehensive Cancer Center

institute: UCSF

description: Gene expression from F1 dorsal skin exposed to TPA

hyb_protocol: 90 microliters of hybridization sample were incubated in the Affymetrix GeneTitan Hybridization Oven instrument for 16 hours at 48C

scan_protocol: Arrays were processed with the Affymetrix GeneTitan Fluidics Station instrument, using the MoGene-1_1-st-v1-96 fluidics script and GeneTitan Hybridization, Wash, and Stain Kit for WT Array Plates. Arrays were scanned in the Affymetrix GeneTitan Multi-Channel (MC) instrument with the AGCC GeneTitan Instrument Control.

data_processing: CEL files were background corrected and normalized with RMA using oligo in R and then log2 transformed

organism: Mus musculus

source_name: dorsal skin

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA

growth_protocol: Mice were aged to 8 weeks, housed in standard conditions with standard chow and water ad libitum.

extract_protocol: Trizol followed by Qiagen RNEasy clean-up

treatment_protocol: For TPA treatment, the dorsal skins of FVB/N, Spret/Ei, and FVB/N x Spret/Ei mice were shaved and two days later treated with a single dose of TPA (200 ml of 10-4 M solution in acetone) or vehicle alone. Mice were sacrificed at 0, 2, 4, 6, 24, 48, and 72 hours, and after one week.

tag: hours

tag: genotype

tag: batch

value: dorsal skin

tag: treatment

value: TPA


title: E181-Tp1

source_name: pancreatic ductual adenocarcinoma_30


title: F1_0048_2


title: F1_0012_1


title: F1_0048_3


title: Female_0.1_rep7

description:
raw data files: 10085_cy5_70txt; 10085_cy3_75txt
10085_Block3


title: F1_0006_2


title: Female_0_rep3

description:
raw data files: 10082_cy5_70txt; 10082_cy3_75txt
10082_Block1


title: Female_0.01_rep5

description:
raw data files: 10082_cy5_70txt; 10082_cy3_75txt
10082_Block2

source_name: Female_pre-adult lice_0.01


title: Female_0.01_rep7

description:
raw data files: 10084_cy5_70txt; 10084_cy3_75txt
10084_Block3


title: Female_0.1_rep6

description:
raw data files: 10083_cy5_70txt; 10083_cy3_75txt
10083_Block2


title: Female_0.01_rep6

description:
raw data files: 10083_cy5_70txt; 10083_cy3_75txt
10083_Block3


title: E182-Tp2

source_name: pancreatic ductual adenocarcinoma_31


title: E179-Tp1

source_name: pancreatic ductual adenocarcinoma_29


title: Male_0_rep5

description:
raw data files: 10085_cy5_70txt; 10085_cy3_75txt
10085_Block4


title: F1_0072_1


title: E058-Tc7

source_name: pancreatic ductual adenocarcinoma_28


title: F1_0048_1


title: E042-Tc10

source_name: pancreatic ductual adenocarcinoma_27


title: E005-Tc8

source_name: pancreatic ductual adenocarcinoma_26


title: E041-Tc7

source_name: pancreatic ductual adenocarcinoma_25


title: E021-Tc8

source_name: pancreatic ductual adenocarcinoma_24


title: Male_0.1_rep5

description:
raw data files: 10081_cy5_70txt; 10081_cy3_75txt
10081_Block4

source_name: Male_pre-adult lice_0.1

source_name: all condition pool


title: E012-Tp2

source_name: pancreatic ductual adenocarcinoma_23


title: F1_0024_1


title: Male_0_rep4

description:
raw data files: 10084_cy5_70txt; 10084_cy3_75txt
10084_Block1

source_name: Male_pre-adult lice_0


title: F1_0072_2


title: F1_0000_2

description: Gene expression data from untreated F1 dorsal skin

value: untreated


title: Female_0_rep4

description:
raw data files: 10082_cy5_70txt; 10082_cy3_75txt
10082_Block3

source_name: Female_pre-adult lice_0


title: 9728T

source_name: pancreatic ductual adenocarcinoma_22


title: F1_0000_1


title: Male_0_rep3

description:
raw data files: 10081_cy5_70txt; 10081_cy3_75txt
10081_Block3


title: F1_0000_4


title: Female_0.01_rep4

description:
raw data files: 10080_cy5_70txt; 10080_cy3_75txt
10080_Block3


title: F1_0004_2


title: Female_0.1_rep5

description:
raw data files: 10080_cy5_70txt; 10080_cy3_75txt
10080_Block1

source_name: Female_pre-adult lice_0.1


title: Female_0_rep2

description:
raw data files: 10081_cy5_70txt; 10081_cy3_75txt
10081_Block1


title: F1_0024_2

source_name: dorsal skin


title: F1_0006_1


title: FVB_1008_3

description: Gene expression from FVB dorsal skin exposed to TPA

value: FVB


title: F1_0004_1

description: Gene expression from F1 dorsal skin exposed to TPA


title: Male_0.1_rep6

description:
raw data files: 10083_cy5_70txt; 10083_cy3_75txt
10083_Block1


title: Male_0.1_rep7

description:
raw data files: 10084_cy5_70txt; 10084_cy3_75txt
10084_Block2


title: 9233

source_name: pancreatic ductual adenocarcinoma_21


title: Female_0_rep1

description:
raw data files: 10080_cy5_70txt; 10080_cy3_75txt
10080_Block4


title: FVB_1008_1


title: F1_0000_3


title: Male_0.01_rep4

description:
raw data files: 10079_cy5_70txt; 10079_cy3_75txt
10079_Block4

source_name: Male_pre-adult lice_0.01


title: Female_0_rep5

description:
raw data files: 10084_cy5_70txt; 10084_cy3_75txt
10084_Block4


title: 34245T

source_name: pancreatic ductual adenocarcinoma_20


title: 32175T

source_name: pancreatic ductual adenocarcinoma_19


title: FVB_1008_2


title: 31393T

source_name: pancreatic ductual adenocarcinoma_18


title: Male_0.01_rep5

description:
raw data files: 10081_cy5_70txt; 10081_cy3_75txt
10081_Block2


title: Male_0.1_rep4

description:
raw data files: 10080_cy5_70txt; 10080_cy3_75txt
10080_Block2


title: F1_0002_1


title: 31263T

source_name: pancreatic ductual adenocarcinoma_17


title: F1_0012_2


title: 29827T

source_name: pancreatic ductual adenocarcinoma_16


title: 29818T

source_name: pancreatic ductual adenocarcinoma_15


title: Male_0.01_rep3

description:
raw data files: 10079_cy5_70txt; 10079_cy3_75txt
10079_Block3


title: 29261T

source_name: pancreatic ductual adenocarcinoma_14


title: FVB_0168_3


title: 29164T

source_name: pancreatic ductual adenocarcinoma_13


title: Female_0.1_rep3

description:
raw data files: 10078_cy5_70txt; 10078_cy3_75txt
10078_Block4

source_name: all condition pool


title: FVB_0168_1


title: 27881T

source_name: pancreatic ductual adenocarcinoma_11


title: 29102T

source_name: pancreatic ductual adenocarcinoma_12


title: FVB_0168_2


title: Female_0.01_rep3

description:
raw data files: 10079_cy5_70txt; 10079_cy3_75txt
10079_Block2

source_name: Female_pre-adult lice_0.01


title: Female_0.1_rep4

description:
raw data files: 10079_cy5_70txt; 10079_cy3_75txt
10079_Block1


title: FVB_0072_1


title: FVB_0048_2


title: FVB_0072_3


title: FVB_0048_3


title: 26576T

source_name: pancreatic ductual adenocarcinoma_9


title: FVB_0072_2


title: 26172T

source_name: pancreatic ductual adenocarcinoma_8


title: Female_0.1_rep2

description:
raw data files: 10078_cy5_70txt; 10078_cy3_75txt
10078_Block2

source_name: Female_pre-adult lice_0.1


title: Male_0.01_rep2

description:
raw data files: 10078_cy5_70txt; 10078_cy3_75txt
10078_Block1


title: Female_0.01_rep1

description:
raw data files: 10077_cy5_70txt; 10077_cy3_75txt
10077_Block2


title: Male_0.1_rep3

description:
raw data files: 10077_cy5_70txt; 10077_cy3_75txt
10077_Block4

source_name: Male_pre-adult lice_0.1


title: Male_0.1_rep1

description:
raw data files: 10077_cy5_70txt; 10077_cy3_75txt
10077_Block1


title: Female_0.01_rep2

description:
raw data files: 10078_cy5_70txt; 10078_cy3_75txt
10078_Block3


title: Male_0.1_rep2

description:
raw data files: 10077_cy5_70txt; 10077_cy3_75txt
10077_Block3


title: 22506T

source_name: pancreatic ductual adenocarcinoma_7


title: 27775T

source_name: pancreatic ductual adenocarcinoma_10


title: FVB_0012_3

description: Gene expression from FVB dorsal skin exposed to TPA

source_name: dorsal skin


title: FVB_0024_1


title: 19927T

source_name: pancreatic ductual adenocarcinoma_6


title: FVB_0048_1


title: 18590T

source_name: pancreatic ductual adenocarcinoma_5


title: Female_0.1_rep1

description:
raw data files: 10043_cy5_70txt; 10043_cy3_75txt
10043_Block3


title: FVB_0024_2


title: FVB_0024_3


title: FVB_0012_2


title: Male_0_rep2

description:
raw data files: 10043_cy5_70txt; 10043_cy3_75txt
10043_Block4

source_name: Male_pre-adult lice_0


title: 17531T

source_name: pancreatic ductual adenocarcinoma_3


title: 17798T

source_name: pancreatic ductual adenocarcinoma_4


title: FVB_0006_3


title: Male_0_rep1

description:
raw data files: 10043_cy5_70txt; 10043_cy3_75txt
10043_Block2


title: FVB_0012_1


title: 17529T

source_name: pancreatic ductual adenocarcinoma_2


title: FVB_0006_1


title: FVB_0006_2


title: Male_0.01_rep1

description:
raw data files: 10043_cy5_70txt; 10043_cy3_75txt
10043_Block1

source_name: Male_pre-adult lice_0.01

source_name: all condition pool


title: H99 3 kGy-2 120 min

city: Jeongeup

first: Kwang-Woo

last: Jung

address: 29 Geumgu-gil

country: South Korea

institute: Korea Atomic Energy Research Institute

description: The chips we used for this study is Mycoarray.com Cryptococcus neoformans JEC21 3X20K.

hyb_protocol: Labeled cDNAs were mixed with hybridization solution (MYcroarray.com), and the hybridization mixtures were heated at 65℃ for 5 min and then immediately cooled on ice for 5 min. Hybridization mixtures were directly loaded onto assembled MYcroarray.com microarray. The arrays hybridized at 50℃ for 16 hr using Agilent Hybridization oven (Agilent Technology, USA).

scan_protocol: The hybridization images were analyzed by GenePix Pro 6.0 (Axon Instruments, CA).

data_processing: The average fluorescence intensity for each spot was calculated and local background was subtracted. All data normalization and selection of fold-changed genes were performed using GenoWiz 4.0 (Ocimumbiosolutions, India).

organism: Cryptococcus neoformans H99

source_name: Cryptococcus neoformans H99_3 kGy_120 min

label_protocol: Labeling reactions were performed with a Bioprime labeling kit (Invitrogen) in a volume of 50 μl with a modified dNTP pool containing 120 μM each of dATP, dGTP, and dCTP; 60 μM dTTP; and 60 μM Cy5-dUTP (for all)

growth_protocol: The WT H99 stain was grown in 50 ml YPD medium at 30oC for 16h. Then, 2.5 ml of overnight cell culture was inoculated into the 50 ml of fresh YPD medium and further incubated at 30℃ until it approximately reaches an optical density at 600 nm of 1.0.

extract_protocol: For total RNA isolation, 1 ml RiboEx solution (Geneall) was added to cell pellet and resuspended without bubbling. It allowed to incubate at room temperature for 5 min. Cells was poured into the chilled screw cap tube containing 1 ml zirconium beads (biospec, #11079105Z). Cells were homogenized by 4 times bead-beating at 6000X for 30 sec with intermittent cooling at -20℃. Next, cells were treated with 200 µl chloroform and mixed vigorously for 3 min. After mixing, samples are kept at RT for 2 min and then centrifugated at 14,000 rpm at 4℃ for 15 min. The aqueous phase was collected into the fresh tube. For purification of the extracted total RNA, we used Rneasy spin column (Qiagen) following the manufacturer’s protocol.

treatment_protocol: The grown cells were transferred into the falcon tubes and irradiated at 3 kGy for 1h. After gamma irradiation, cells were transferred into the flask and incubated at 30℃ for the required recovery time points (30 min, 60 min, and 120 min).

tag: strain


title: FVB_0002_3


title: T cell_WT_media_rep2

city: Daejeon

first: Ji-Hwan

last: Park

address: 125 Gwahak-ro, Yuseong-gu

institute: Korea Research Institute of Bioscience and Biotechnology (KRIBB)

description: WT T cells (media)

hyb_protocol: Following the standard Agilent protocols, RNA was reverse-transcribed, amplified, and then hybridized onto the Agilent SurePrint G3 Mouse GE 8x60K microarray

scan_protocol: cRNA on SurePrint G3 Mouse GE 8x60K microarray chip was scanned by SureScan Microarray Scanner

data_processing: Quantile-normalization was performed for the log2-value of gMedianSignal

source_name: Splenic T cells

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared, followed by RNAeasy Mini Kit (QIAGEN).

growth_protocol: Mice genetically deficient in Lsp1 (Lsp1 –/– mice) were backcrossed onto the C57BL/6 background (generation N10). Age and sex-matched wild-type C57BL/6 mice (Lsp1+/+) were used as controls. All mice were 8-12 weeks of age unless specified otherwise. The mice were maintained in specific pathogen-free conditions and were used according to guidelines of the Institutional Animal Care Committee

extract_protocol: Total RNA was isolated from splenic T cells of Lsp1-deficient and wild-type mice, which were stimulated with anti-CD3/CD28 Abs for 6 hours. The total RNA integrity was evaluated by Bioanalyzer 2100 (Agilent, Santa Clara, CA). The RNA integrity number in all the samples was larger than 9.5.

tag: cell type

value: Splenic T cells

tag: genotype/variation

value: WT


title: T cell_KO_CD3/28_rep1

description: Lsp1 KO T cells (anti-CD3/28 Abs)

source_name: Splenic T cells, Lsp1 KO, anti-CD3/28 Abs stimulation

treatment_protocol: Total RNA was isolated from splenic T cells of Lsp1-deficient and wild-type mice, which were stimulated with anti-CD3/CD28 Abs for 6 hours.

value: Lsp1 KO


title: FVB_0002_2


title: FVB_0000_2

description: Gene expression data from untreated FVB dorsal skin


title: T cell_WT_CD3/28_rep2

description: WT T cells (anti-CD3/28 Abs)

source_name: Splenic T cells, anti-CD3/28 Abs stimulation


title: FVB_0000_1


title: T cell_KO_CD3/28_rep2

description: Lsp1 KO T cells (anti-CD3/28 Abs)


title: T cell_KO_media_rep2

description: Lsp1 KO T cells (media)

source_name: Splenic T cells, Lsp1 KO


title: FVB_0002_1


title: T cell_WT_media_rep1

description: WT T cells (media)


title: T cell_KO_media_rep1

description: Lsp1 KO T cells (media)


title: T cell_WT_CD3/28_rep1

description: WT T cells (anti-CD3/28 Abs)


title: H99 0 kGy-3 0 min

source_name: Cryptococcus neoformans H99_0 kGy_0 min


title: H99 3 kGy-3 120 min


title: BRAFV600E_CRISPR untreated 3

city: Amsterdam

first: Sander

middle: Roeland

last: van Hooff

address: Meibergdreef 9

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

country: Netherlands

institute: AUMC

description: Gene expression from BRAF-V600E mutant organoid untreated

hyb_protocol: Hybridization was performed according to the standard protocols of the Cologne Center for Genomics (CCG), University of Cologne, Germany.

scan_protocol: Samples were scanned using the Gene Titan Affymetrix instrument according to the standard protocols of the Cologne Center for Genomics (CCG), University of Cologne, Germany.

data_processing: Data were normalized by RMA using the Affy R package and batch effects were removed using the Combat algorithm as implemented in the sva R package

source_name: BRAFV600E_CRISPR untreated

label_protocol: Labeling was performed according to the standard protocols of the Cologne Center for Genomics (CCG), University of Cologne, Germany.

growth_protocol: Organoid cultures were isolated from patient material and cultured accodring to standard protocols.

extract_protocol: Total RNA was extracted using the NucleoSpin RNA II kit from Macherey-Nagel.

treatment_protocol: Organoid cultures were treated for 5 days with A83-01 (control condition/untreated) or 5 ng/ml recombinant human TGF-β1.

value: organoid culture

tag: organoid

value: control


title: BRAFV600E_CRISPR treated with TGFβ 2

description: Gene expression from BRAF-V600E mutant organoid treated with TGFβ

source_name: BRAFV600E_CRISPR treated with TGFβ

value: TGFβ


title: H99 0 kGy-1 0 min


title: FVB_0000_3

source_name: dorsal skin


title: H99 0 kGy-2 0 min


title: A375 HA15

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

description: A375 HA15

hyb_protocol: Agilent : 600.0 ng at 65 degree_C during 17 hours

scan_protocol: Arrays were scanned using the Agilent SureScan High Resolution Scanner.

data_processing: Quantile normalization and paired differential analysis in R / Bioconductor.

label_protocol: Agilent - Low RNA input QuickAmp

extract_protocol: Qiagen - RNeasy

tag: cell line

tag: agent

tag: rin number

tag: amount in (microg)


title: H99 3 kGy-3 60 min

source_name: Cryptococcus neoformans H99_3 kGy_60 min


title: H99 3 kGy-2 30 min

source_name: Cryptococcus neoformans H99_3 kGy_30 min


title: H99 3 kGy-2 60 min


title: 22Rv1_OBP-801

city: Nagoya

first: Keisuke

last: Katsushima

address: 1 Kawasumi, Mizuho-cho, Mizuho-ku

department: Department of Epigenomics

country: Japan

institute: Nagoya City University Graduate School of Medical Sciences

description: miRNA expression after 48hr in induction of OBP-801

hyb_protocol: Labeled samples were purified with MicroBio-Spin 6 columns (Bio-Rad, Richmond, CA) and hybridized to microarray at 55 °C with rotation at 20 rpm for 20 hours.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol miRNA_107_Sep09_patch) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Prostate cancer cell, 48hr, OBP-801, replicate 1

label_protocol: One hundred ng of total RNA was labeled with pCp-Cy3 (Agilent Technologies) and 15 units of T4 RNA ligase (GE Healthcare, Little Chalfont, Buckinghamshire, UK) at 16°C for 2 hours.

growth_protocol: 22Rv1 cell line was purchased from ATCC (Manassas, VA, USA) and cultured in RPMI 1640 (Life Technologies, Carlsbad, CA) supplemented with 10% heat-inactivated fetal bovine serum at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: Total RNA was isolated using TRIzol (Life Technologies) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-2000.

treatment_protocol: 22Rv1 cells were added 10nM OBP and incubated for 48 hours at 37 ºC in a humidified incubator with 5% CO2.

tag: gender

value: male


title: 22Rv1_DMSO

description: miRNA expression after 48hr in induction of DMSO

source_name: Prostate cancer cell, 48hr, DMSO, replicate 1


title: BRAFV600E_CRISPR treated with TGFβ 1

tag: tissue


title: H99 3 kGy-1 30 min


title: H99 3 kGy-1 60 min


title: A375 DMSO

description: A375 DMSO

source_name: A375 DMSO

value: DMSO


title: Mel501 DMSO

description: Mel501 DMSO

source_name: Mel501 DMSO


title: H99 3 kGy-3 30 min


title: N3 treated with TGFβ

description: Gene expression from normal colon organoid N3 treated with TGFβ

source_name: N3 treated with TGFβ

value: normal colon


title: BRAFV600E_CRISPR untreated 2


title: N3 untreated

description: Gene expression from normal colon organoid N3 untreated

source_name: N3 untreated


title: G3_IB_ENEG_GNEG_1

city: Paris

first: Geoffroy

last: CANLORBE

address: 4, rue de la Chine

department: Department of Obstetrics and Gynaecology

institute: Tenon University Hospital, Assistance Publique des Hôpitaux de Paris (AP-HP), University Pierre and Marie Curie, Paris 6

hyb_protocol: Following fragmentation, mirRNA targets were hybridized for 20 hr at 48C on mirRNA-40 Affymetrix. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GCS 3000 scanner (Affymetrix)

data_processing: The data were preprocessed and analyzing using Partek Genomic Suite.

source_name: Endometrium cancer, FPPE section

label_protocol: After validation of the RNA quality with Bioanalyzer 2100, 1 µg of total RNA was biotin labelled following the FlashTag Biotin HSR RNA labelling kit (Affymetrix).

extract_protocol: Total RNA was extracted using the miRNeasy FFPE Kit (Qiagen, Courtaboeuf, France), according to the manufacturer's instructions.

tag: disease state

value: Endometrium cancer

tag: grade

tag: figo stage

tag: lymphovascular space invasion status

value: LVSI-

tag: lymph node status

value: Nodal -

tag: sample origin

value: FPPE section


title: Mel501 HA15

description: Mel501 HA15

source_name: Mel501 HA15


title: G3_IB_EPOS_GNEG_2

value: LVSI+


title: TA2 untreated 1

description: Gene expression from colon tumor organoid TA2 untreated

source_name: TA2 untreated

value: organoid culture of tubular adenoma

tag: treatment

tag: batch


title: SKMel28 DMSO

description: SKMel28 DMSO

source_name: SKMel28 DMSO


title: N2 untreated

description: Gene expression from normal colon organoid N2 untreated

source_name: N2 untreated


title: TA2 untreated 2


title: SKMel28 HA15

description: SKMel28 HA15

source_name: SKMel28 HA15


title: TA2 treated with TGFβ 4

description: Gene expression from colon tumor organoid TA2 treated with TGFβ

source_name: TA2 treated with TGFβ


title: BRAFV600E_CRISPR untreated 1

source_name: BRAFV600E_CRISPR untreated


title: N2 treated with TGFβ

description: Gene expression from normal colon organoid N2 treated with TGFβ

source_name: N2 treated with TGFβ


title: TA2 treated with TGFβ 3


title: G3_IB_EPOS_GNEG_1


title: H99 3 kGy-1 120 min

source_name: Cryptococcus neoformans H99_3 kGy_120 min

tag: strain


title: G2_IB_EPOS_GNEG_2


title: G2_IA_EPOS_GNEG_1


title: TA1 treated with TGFβ 1

description: Gene expression from colon tumor organoid TA1 treated with TGFβ

source_name: TA1 treated with TGFβ


title: G1_IA_ENEG_GNEG_1


title: TA3 untreated 2

description: Gene expression from colon tumor organoid TA3 untreated

source_name: TA3 untreated


title: TA1 untreated 1

description: Gene expression from colon tumor organoid TA1 untreated

source_name: TA1 untreated


title: G2_IB_EPOS_GNEG_1


title: G1_IB_ENEG_GNEG_2


title: G2_IA_ENEG_GNEG_2


title: TA2 treated with TGFβ 2


title: TA2 treated with TGFβ 1


title: TA3 treated with TGFβ 1

description: Gene expression from colon tumor organoid TA3 treated with TGFβ

source_name: TA3 treated with TGFβ


title: G3_IB_ENEG_GPOS_1

value: Nodal +


title: G3_IB_EPOS_GPOS_1


title: TA8

description: Gene expression from tubular adenoma

extract_protocol: Total RNA was extracted using the AllPrep DNA/RNA/miRNA Universal Kit from Qiagen.

treatment_protocol: 5x20 μm frozen tissue sections were cut using a cryotome and stored at -80°C until further use.

value: tubular adenomas

tag: braf

value: wt

tag: cimp

value: neg

tag: cms


title: G2_IB_EPOS_GPOS_1


title: TA15

description: Gene expression from tubular adenoma

value: low


title: G1_IB_ENEG_GNEG_1


title: G2_IB_EPOS_GPOS_2


title: G2_IA_EPOS_GPOS_1


title: TA13

description: Gene expression from tubular adenoma


title: TA14

description: Gene expression from tubular adenoma


title: 48H_H006

city: Beijing

first: Sun

last: Lidong

state: Beijing

address: Dong zhi men nei nan xiao jie 16

country: China

institute: China Academy of Traditional Chinese Medicine

description: 48H-H006, technical repeat of H005

hyb_protocol: Phalanx HOA 5.1 arrays were pre-heat at 60℃ for 10 mins, rehydrated by 100% ethanol following with deionized water. The slides were pre-hybridized with 5x SSPE, 0.1% SDS and 1% BSA at 42℃ for 2 hour. After the pre-hybridization, 5 µg Cy5-labeled aRNA was hybridize on HOA in the presentation of the Phalanx OneArray hybridization buffer in duplication.

scan_protocol: HOA 5.1 arrays were scanned by Axon 4000B [F635(PMT520,power100),F532(PMT460.power10)] and quantify the fluoresence intensity.

data_processing: Data processing was performed and calculated by Rosetta Resolver® (Rosetta Biosoftware). The probes that ﬂag <0 in all samples were filtered out, then normalized by median scaling method between technical replicates. Pair-wise comparisons between samples were calculated by Rosetta error model and presented by log2 ratio and p-value.

label_protocol: 1 µg of total RNA was reverse-transcribed and amplified using MessageAmpTM aRNA Amplification Kit (Ambion).  Indirect labeling the aa-UTP whereon by NHS-CyDye (Cy5, Amershan).

growth_protocol: The breast cancer cell lines MDA-MB-231 were purchased from the American Type Culture Collection (Maryland, USA) and cultured with RPMI-1640 medium supplemented with 10% fatal bovine serum and 1% Pen/Strep in a humid incubator with 5% CO2.

extract_protocol: RNA extraction by Trizol Reagent (Invitrogen). RNA purity was checked by optical density of NanoDrop ND-1000 and agarose electrophoresis with the result of A260/A280≧1.8, A260/A230≧1.5, no gDNA contamination. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧6).

treatment_protocol: MDA-231 cells were plated onto 6-well plate and cultured for 24 hours. After that, the cells were  treated with 5 ng/ml  (2 wells / time point) PTX for 24 and 48 hours respectively and then the cell lysates were prepared by TRIzol reagent.

tag: cell line

value: female

tag: pathological type

value: high-invasive breast adenocarcinoma cells derived from metastatic site:pleural effusion

tag: cell type

value: adherent epithelial cells

tag: origin

value: 51 years adult,Caucasian


title: ET 48h-1+CK-3

city: Danzhou

first: Zhiyi

last: Nie

state: Hainan

address: Baodao New Village

department: Rubber Research Institute

institute: Chinese Academy of Tropical Agricultural Sciences

description: compare gene expression profiles of control cells

hyb_protocol: standard CapitalBio Methods

scan_protocol: Luxscan 10K (CapitalBio)

data_processing: After background correction and removal of bad spots, a space and intensity-dependent normalization based on a LOWESS program was employed. For each test and control sample, two hybridizations were performed by using a reversal fluorescent strategy, the geometric mean of lowess normalized log2 ratio (test/control) of two dye-swap slides was calculated.

organism: Hevea brasiliensis

source_name: ET stimulated rubber tree latex 48h-3

label_protocol: Fluorescent dye (Cy5 and Cy3-dCTP, Amersham Pharmacia Biotech, Piscataway, NJ) labeled DNA was produced through Eberwine's linear RNA amplification method and subsequent enzymatic reaction. the amplified RNA (aRNA) was purified with NucleoSpin Extract II (MN). We took a cDNA labeling approach with Klenow enzyme after reverse transcription.

growth_protocol: Field experiments were performed using mature, 7-year-old virgin rubber trees (Clone Reyan  7–33–97) that had never been tapped.

extract_protocol: ET stimulated rubber tree and control Rubber tree latex were harvest, Total RNA was extracted from the fresh latex by SDS  method.

treatment_protocol: 0.5% (w/w) Ethephon (Sigma-Aldrich, USA) in water was applied to the bark below the half-spiral of the tapping cut. Water was used as the mock stimulation for the control samples. The trunks of the treated trees were wrapped with black plastic film around the tapping cut and stimulated for 8, 24 or 48 h, after which they were tapped for latex early in the morning on the same day. Each sample included three independent biological replicates, and each replicate comprised the latex collected from six trees.

tag: clone id

value: Reyan 7–33–97

tag: tissue

value: latex

tag: age

value: 7 years

source_name: control rubber tree latex


title: G2_IB_ENEG_GPOS_1

tag: disease state

value: Endometrium cancer

tag: grade

tag: figo stage

value: LVSI-


title: SSA17

description: Gene expression from sessile serrated adenoma

value: sessile serrated adenomas

value: mut

value: pos


title: TA12

description: Gene expression from tubular adenoma


title: G3_IB_EPOS_GPOS_2

tag: lymphovascular space invasion status

value: LVSI+

tag: lymph node status

value: Nodal +

tag: sample origin

value: FPPE section


title: G2_IB_ENEG_GNEG_1

value: Nodal -


title: TA11

description: Gene expression from tubular adenoma

value: tubular adenomas

value: wt

value: neg


title: ET 48h-1+CK-1

source_name: ET stimulated rubber tree latex 48h-1


title: TA10

description: Gene expression from tubular adenoma


title: 48H_H005

tag: gender

value: female

value: high-invasive breast adenocarcinoma cells derived from metastatic site:pleural effusion

value: adherent epithelial cells


title: G1_IB_ENEG_GPOS_2

source_name: Endometrium cancer, FPPE section


title: TA3 untreated 1

value: organoid culture of tubular adenoma

tag: organoid

tag: treatment

value: control

tag: batch


title: ET 48h-1+CK-2

source_name: ET stimulated rubber tree latex 48h-2

value: Reyan 7–33–97

value: latex

value: 7 years


title: TA9

description: Gene expression from tubular adenoma

tag: braf

tag: cimp

value: low

tag: cms


title: SSA14

value: sessile serrated adenomas

value: mut

value: pos


title: G1_IB_ENEG_GPOS_1

value: Endometrium cancer

value: LVSI-

value: Nodal +

value: FPPE section


title: SSA12


title: SSA15


title: 24H_H004

description: 24H_H004, technical repeat of H003

tag: cell line

tag: pathological type

tag: cell type

tag: origin

value: 51 years adult,Caucasian


title: SSA9

tag: tissue


title: ET 24h-3+CK-3

source_name: ET stimulated rubber tree latex 24h-3

tag: clone id

tag: age


title: G2_IA_ENEG_GNEG_1

tag: disease state

tag: grade

tag: figo stage

tag: lymphovascular space invasion status

value: Nodal -


title: G2_IA_ENEG_GPOS_1

tag: lymph node status

tag: sample origin


title: 24H_H003

tag: gender

value: female

value: high-invasive breast adenocarcinoma cells derived from metastatic site:pleural effusion


title: TA16

description: Gene expression from tubular adenoma

value: tubular adenomas

tag: braf

value: wt

value: neg


title: SSA13

tag: cimp


title: G2_IA_ENEG_GPOS_2


title: NC_H002

description: NC-H002, technical repeat of H001

source_name: MDA-non-treated

value: adherent epithelial cells


title: G1_IA_ENEG_GPOS_1


title: SSA10

tag: cms


title: NC_H001

tag: cell line


title: ET 24h-2+CK-2

source_name: ET stimulated rubber tree latex 24h-2

value: Reyan 7–33–97

value: latex

value: 7 years


title: Hypoxia 24h-3

city: Wuxi

first: sun

last: shengming

state: Jiangsu

address: No.9, Shanshui Rd East

institute: Freshwater Fisheries Research Center (FFRC) of Chinese Academy of Fishery Sciences (CAFS),

description: hypoxic conditions (2.0 ± 0.1 mg O2 L−1) within the treatment tanks were maintained for 24 h by bubbling with N2 gas until the desired O2

hyb_protocol: Hybridization was performed overnight on a μParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies) (1). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://www.mirbase.org/) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry. The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 L 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C.

scan_protocol: Fluorescence images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics)

data_processing: Data were analyzed by first subtracting the background, then the signals were normalized using a Lowess (locally weighted regression) filter. The raw microarray data set was filtered according to a standard procedure to exclude spots with minimum intensity. It was arbitrarily set to an intensity parameter of P100 for the miRNA microarray data. Spots with diameters less than 10 μm and flagged spots were also excluded from the analyses.

organism: Macrobrachium nipponense

source_name: tissue

label_protocol: Labeling of total RNA was performed according to the protocol from LC Science for a single-color experiment with no modification.

extract_protocol: Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA), and then treated with RNase-free DNase I (TianGen, Beijing, China) to remove genomic DNA contamination. The quality of RNA was examined using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).

value: gill, hepatopancreas, muscle and hemocytes


title: ET 8h-1+CK-1

source_name: ET stimulated rubber tree latex 8h-1


title: ET 8h-3+CK-3

source_name: ET stimulated rubber tree latex 8h-3


title: ET 8h-2+CK-2

source_name: ET stimulated rubber tree latex 8h-2


title: Hypoxia 24h-1


title: Normoxia 24h-3

description: maintained under normoxic conditions (6.5 ± 0.2 mg O2 L−1)


title: Normoxia 24h-2


title: Control_90 min

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

description: Control_90 min

hyb_protocol: 2000ng of Cy3 labeled cRNA samples were mixed and hybridized on the array using the Gene Expression Hybridization kit (Part Number 5190-0404; Agilent) in Sure hybridization Chambers (Agilent) at 65º C for 16 hours. Hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327).

scan_protocol: Scanned using the Agilent Microarray Scanner

data_processing: Images were quantified using Feature Extraction Software ( Agilent). Feature extracted raw data was analyzed using GeneSpring GX software from Agilent. Normalization of the data was done in GeneSpring GX using the 75th percentile shift

organism: Escherichia coli str. K-12 substr. MG1655

source_name: pMMB206 90 mins after induction

label_protocol: The samples were labeled using Agilent Quick Amp Kit (Part number: 5190-0442). 500ng of total RNA was reverse transcribed using Random hexamer primer tagged to T7 promoter sequence. cDNA thus obtained was converted to double stranded cDNA in the same reaction. Further the cDNA was converted to cRNA in the in-vitro transcription step using T7 RNA polymerase enzyme and Cy3 dye was added into the reaction mix. During cRNA synthesis Cy3 dye was incorporated into the newly synthesized cRNA strands. cRNA obtained was cleaned up using Qiagen RNeasy columns(Qiagen, Cat No: 74106). Concentration and amount of dye incorporated was determined using Nanodrop. Samples that pass the QC for specific activity were taken for hybridization

growth_protocol: M9 minimal salts media+ Glucose, grown at 37 degrees

extract_protocol: Total RNA was extracted at 0, 30, 90 and 180 minutes using TRIZOL method

treatment_protocol: Induced with 1 µM IPTG at 30 degrees for 3 hours

tag: plasmid

value: only vector (pMMB206)


title: Hypoxia 24h-2


title: Replicate 1

city: Giessen

first: Jochen

last: Wilhelm

state: Hessen

address: Aulweg 132

department: Institute for Lung Health

country: Germany

institute: Justus-Liebig University Giessen

hyb_protocol: Agilent Two-color Microarray-Based Gene Expression Analysis, Version 5.7, March 2008

scan_protocol: Slides were scanned with Innoscan 900F1 using Mapix V. 6.0.1 at 2µm resolution

data_processing: Intensities were background-corrected using the normexp-model on the negative control spots. Corrected intensities were quantile normalized beween arrays. See: Nucleic Acids Research 38, e204.

organism: Rattus norvegicus

source_name: control

label_protocol: Agilent QuickAmp labelling kit (two-color)

growth_protocol: Rats were grown under stadrad growth conditions.

extract_protocol: total RNA was extracted using QIAgen Mini Kit

treatment_protocol: Lew rats after successful allogenic kidney transplantation were treated with ApoE-mimetic peptide (6mg/kg body weight) or control peptide by daily i.v. injections for four days starting from the day of renal transplantation. On day four animals were sacrificed. Renal allografts were explanted, cut into slices and shock frozen in liquid nitrogen.

tag: strain

value: Lew

tag: agent

value: control

value: renal allograft

source_name: ApoE

value: ApoE


title: Control_180 min

description: Control_180 min

source_name: pMMB206 180 mins after induction


title: Normoxia 24h-1

tag: tissue


title: Non-relapsing_DLBCL_primary (case39)

type: genomic

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.

molecule: genomic DNA

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.

value: Diffuse large B cell lymphoma (DLBCL)

tag: specimen

value: Non-relapsing DLBCL primary

source_name: Reference pooled 46XX

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


title: Non-relapsing_DLBCL_primary (case37)


title: Replicate 4


title: Non-relapsing_DLBCL_primary (case40)


title: Combination: 44

type: protein

city: Houston

first: Joseph

middle: A.

last: Ludwig

state: Texas

department: Sarcoma Medical Oncology

institute: UT-MD-Anderson Cancer Center

description: RPPA

hyb_protocol: Protein-lysed-spots were probed with 179 validated primary antibodies and detected using a DakoCytomation-catalyzed system with secondary antibodies.

scan_protocol: Slides were scanned on a flatbed scanner to produce 16-bit tiff images. Spots from tiff images were identified and their densities were quantified by MicroVigene. Relative protein levels for each sample were determined by interpolation of each dilution curve from the standard curve (supercurve) of the slide (antibody). Supercurve is constructed from a script in R written by the informatics department. These raw values are given as log2 values.  MicroVigene software program (VigeneTech) was used for automated spot identification, background correction, and individual spot-intensity determination.

data_processing: Expression data was normalized for possible unequal protein loading, taking into account the signal intensity for each sample for all antibodies tested. Log2 values were median-centered by protein to account for variability in signal intensity by time and were calculated using the formula log2 signal – log2 median. Principal component analysis was used to check for a batch effect and feature-by-feature two-sample t-tests were used to assess differences between treatment and control groups. We also used feature-by-feature one-way analysis of variance (ANOVA) followed by the Tukey test to perform pair comparisons for all groups. Beta-uniform mixture models were used to fit the resulting p value distributions to adjust for multiple comparisons. The cutoff p values and number of significant proteins were computed for several different false discovery rates (FDRs).  Biostatistical analyses comparing two groups were performed using an unpaired t-test with Gaussian distribution followed by the Welch correction. To distinguish between treatment groups, we used one-way ANOVA with the Geisser-Greenhouse correction. Differences with p values <0.05 were considered significant. Within clustered image maps (CIM), unsupervised double hierarchical clustering used the Pearson correlation distance and Ward’s linkage method as the clustering algorithm to link entities (proteins or genes) and samples.

label: 179 Primary Antibodies

molecule: protein

source_name: EW5 xenograft of Ewing Sarcoma

label_protocol: Using a 2470 Arrayer (Aushon BioSystems), sample arrays were were processed, spotted onto nitrocellulose-coated FAST slides.

growth_protocol: Male non-obese diabetic (NOD)-SCID-IL-2Rgnull mice were used to generate EW5 explants (2 mm). Mice bearing subcutaneous tumors were randomized into treatment and control groups when their tumors reached a diameter of 6 mm

extract_protocol: Protein extraction from xenograft tumors was performed by homogenizing an approximate 10 mg of frozen tissue in 500 ul of the lysis buffer containing protease and phosphatase inhibitors using an electric tissue homogenizer (Pro Scientific). Total lysed proteins were quantified using BCA protein assay kit and stored for further analyses for RPPA.

treatment_protocol: Mice bearing tumors, when their tumors reached a diameter of 6 mm, they received MK-8669 (Ridaforolimus, mTOR inhibitor, 5mg/kg per dose, once weekly), MK-0646 (Dalotuzumab, IGF-1R inhibitor monoclonal antibody, 0.5mg IP twice weekly), or a placebo control (sterile buffer). Animals were treated either until their tumors reached 1500 mm3 in volume.

value: Ewing Sarcoma human Tumor

tag: xenograft host


title: ET 24h-1+CK-1

source_name: ET stimulated rubber tree latex 24h-1

tag: clone id

tag: age

source_name: control rubber tree latex


title: Control: 58

description: RPPA

value: Male non-obese diabetic (NOD)-SCID-IL-2Rgnull mice


title: Dalotuzumab: 21

description: RPPA


title: Control_0 min

description: Control_0 min

source_name: pMMB206 before induction


title: Replicate 3


title: Non-relapsing_DLBCL_primary (case38)

tag: disease state


title: Test_180 min

description: Test_180 min

source_name: pSDP10 180 mins after induction

value: pSDP10, generated by cloning orf306 under the control of tac promoter of broad host range expression vector pMMB206.


title: Non-relapsing_DLBCL_primary (case35)


title: Control_30 min

description: Control_30 min

source_name: pMMB206 30 mins after induction


title: Replicate 2


title: Test_90 min

description: Test_90 min

source_name: pSDP10 90 mins after induction


title: Non-relapsing_DLBCL_primary (case33)


title: Non-relapsing_DLBCL_primary (case36)


title: Non-relapsing_DLBCL_primary (case34)


title: Ridaforolimus: 61

description: RPPA


title: Test_30 min

description: Test_30 min

source_name: pSDP10 30 mins after induction


title: Test_0 min

description: Test_0 min

source_name: pSDP10 before induction


title: Combination: 52

description: RPPA


title: Combination: 66

description: RPPA


title: Control: 55

description: RPPA


title: Combination: 51

description: RPPA


title: Non-relapsing_DLBCL_primary (case32)

source_name: Frozen tissue biopsy


title: Dalotuzumab: 17

description: RPPA


title: Ridaforolimus: 49

description: RPPA


title: Dd2_schizont_MMS_6 hour_2

city: singapore

first: Devendra

middle: Kumar

last: Gupta

address: 60 NANYANG DRIVE

department: School of Biological Sciences

institute: Nanyang Technological University

hyb_protocol: Equal amounts of labelled sample and reference cDNA were hybridized on the microarray chip using the Agilent hybridization system. Hybridizations were performed for 20 hours at 65°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: Features with flag>0 and with median foreground intensity greater than 1.5 fold median background intensity for either channel passed quality control and were accepted. Local  background correction using normexp, followed by lowess normalization across all features were carried out to generate the normalized Log2 gene expression ratios.

organism: Plasmodium falciparum

source_name: Dd2_schizont_MMS_6 hour_2

label_protocol: Synthesis of aminoallyl-coupled cDNA by reverse transcription and labeling of samples with cy fluorophore were carried out as described in Bozdech, Z., S. Mok & A. P. Gupta, (2013) DNA microarray-based genome-wide analyses of Plasmodium parasites. Methods in molecular biology 923: 189-211.

extract_protocol: Total RNA was extracted using Trizol following manufacturer's instructions and as described in Bozdech, Z., S. Mok & A. P. Gupta, (2013) DNA microarray-based genome-wide analyses of Plasmodium parasites. Methods in molecular biology 923: 189-211.

tag: culture

value: In vitro culture

tag: laboratory strain

tag: Stage

value: asexual blood stage:schizont

source_name: P. falciparum 3D7 RNA reference pool

value: asexual blood stage

tag: composition

value: mixture of equal amounts of RNA harvested every 6 hours over the 48-hour parasite's intraerythrocytic life cycle


title: Dd2_schizont_MMS_6 hour_1

source_name: Dd2_schizont_MMS_6 hour_1


title: 3D7_schizont_MMS_6 hour_1

source_name: 3D7_schizont_MMS_6 hour_1


title: Dd2_schizont_control for MMS_6 hour_2

source_name: Dd2_schizont_control for MMS_6 hour_2


title: 3D7_schizont_MMS_6 hour_2

source_name: 3D7_schizont_MMS_6 hour_2


title: Dalotuzumab: 45

description: RPPA


title: Ridaforolimus: 42

description: RPPA


title: Dd2_schizont_control for MMS_6 hour_1

source_name: Dd2_schizont_control for MMS_6 hour_1


title: Control: 39

description: RPPA

source_name: EW5 xenograft of Ewing Sarcoma


title: 3D7_schizont_control for MMS_6 hour_2

source_name: 3D7_schizont_control for MMS_6 hour_2


title: Dalotuzumab: 30

description: RPPA


title: 3D7_schizont_control for MMS_6 hour_1

source_name: 3D7_schizont_control for MMS_6 hour_1


title: Dalotuzumab: 62

description: RPPA


title: Ridaforolimus: 25

description: RPPA


title: W2_MMS_6 hour_1

source_name: W2_MMS_6 hour_1

value: asexual blood stage:trophozoite


title: Combination: 23

description: RPPA


title: TC71: Ridaforolimus-Selected-C1.4

description: RPPA

hyb_protocol: Protein-lysed-spots were probed with 167 validated primary antibodies and detected using a DakoCytomation-catalyzed system with secondary antibodies.

label: 167 Primary Antibodies

source_name: Resistant Ewing Sarcoma Cell line to mTOR blockade

growth_protocol: Ewing Sarcoma cell lines sensitive or resistant to ridaforolimus grown in 2D-monolayer cultures were maintained in RPMI 1640 medium (Mediatech) containing 10% (vol/vol) fetal bovine serum (Gemini Bio-Products) and antibiotics (100 IU/ml penicillin and 100 mg/ml streptomycin [Mediatech]) in a humidified incubator at 37°C in a 5% CO2 atmosphere.

extract_protocol: Protein extraction from cell lines was performed by homogenizing an approximate 10 mg of frozen tissue in 500 ul of the lysis buffer containing protease and phosphatase inhibitors using an electric tissue homogenizer (Pro Scientific). Total lysed proteins were quantified using BCA protein assay kit and stored for further analyses for RPPA.

treatment_protocol: TC32 and TC71 ES clones with acquired resistance to ridaforolimus were generated by maintaining the corresponding parental cell lines with increasing concentrations of the agents (up to 50 μM) for 7 months. All parental and acquired drug resistant cell lines were tested twice per year for mycoplasma contamination using the MycoAlert Detection Kit (Lonza Group Ltd.) according to the manufacturer’s protocol and validated using short-tandem repeat fingerprinting with an AmpFLSTR Identifier kit as previously described. Herein, we determine subtle differences in acquired mechanism of resistance by ridaforolimus which inhibits only mTORC1 in ewing sarcoma cell lines using RPPA.

tag: cell type

value: Ewing Sarcoma cell line

value: TC71 clone


title: 95_BUCAtlantic_Control

city: Basking Ridge

first: Deanne

middle: M

last: Taylor

state: NJ

address: 140 Allen Road

institute: Reproductive Medicine Associates of New Jersey

hyb_protocol: Fragmented DNA is labeled with biotin, hybridized 16-18 hours at 49 degrees C in the GeneChip Hybridization Oven 640, washed and stained on the GeneChip Fluidics station 450, and scanned on the GeneChip Scanner 7G according to the standard Affymetrix protocol.

scan_protocol: Scanned on GeneChip Scanner 3000 (GCS 3000) using Affymetrix GCOS 1.4.0

data_processing: Data was processed with Affymetrix GCOS 1.4.0

source_name: Buccal

label_protocol: Extracted buccal DNA is processed according to the Affymetrix GeneChip Mapping 500K Assay Manual (Affymetrix Inc., Santa Clara, CA), using only the NspI Digestion, Ligation, and PCR reactions.

extract_protocol: Buccal gDNA was extracted after an overnight incubation in Qiagen Cell Lysis Solution and Puregene Proteinase K by adding the samples to spin columns and treating wit ethanol-based washes. Samples are subsequently eluted with 50uL Qiagen AE Buffer into 1.5mL microfuge tubes.

tag: gender

value: female

tag: case status

tag: source

value: buccal sample


title: 75_BUCAtlantic_Control

value: control


title: 29_BUCAtlantic_Control


title: 67_BUCAtlantic_Control


title: TC71: Ridaforolimus-Selected-C1.3

description: RPPA

tag: cell line


title: TC71: Ridaforolimus-Selected-C1.2

description: RPPA


title: 9_BUCAtlantic_Case

value: case


title: 87_BUCAtlantic_Control


title: 79_BUCAtlantic_Control


title: W2_control for MMS_6 hour_2

source_name: W2_control for MMS_6 hour_2


title: TC71: Ridaforolimus-Selected-C1.1

description: RPPA


title: W2_control for MMS_6 hour_1

source_name: W2_control for MMS_6 hour_1


title: TC32: Ridaforolimus-Selected-C9

description: RPPA

value: TC32 clone


title: W2_MMS_6 hour_2

source_name: W2_MMS_6 hour_2


title: D6_MMS_6 hour_1

source_name: D6_MMS_6 hour_1


title: D6_MMS_6 hour_2

source_name: D6_MMS_6 hour_2


title: D6_control for MMS_6 hour_1

source_name: D6_control for MMS_6 hour_1

source_name: P. falciparum 3D7 RNA reference pool


title: Dd2_MMS_6 hour_2

source_name: Dd2_MMS_6 hour_2


title: TC32: Ridaforolimus-Selected-C8

description: RPPA


title: D6_control for MMS_6 hour_2

source_name: D6_control for MMS_6 hour_2


title: Dd2_MMS_6 hour_1

source_name: Dd2_MMS_6 hour_1


title: 41_BUCAtlantic_Control


title: TC32: Parental_Rep2

description: RPPA

source_name: TC32: Parental Sensitive Ewing Sarcoma


title: TC32: Ridaforolimus-Selected-C7

description: RPPA


title: 31_BUCAtlantic_Control


title: 81_BUCAtlantic_Control


title: Dd2_control for MMS_6 hour_2

source_name: Dd2_control for MMS_6 hour_2


title: 19_BUCAtlantic_Case


title: TC32: Ridaforolimus-Selected-C6

description: RPPA


title: 3D7_DMSO for ART_6 hours_ 3

source_name: 3D7_DMSO for ART_6 hours_ 3


title: 65_BUCAtlantic_Control


title: 73_BUCAtlantic_Control


title: 97_BUCAtlantic_Control


title: 61_BUCAtlantic_Control


title: 49_BUCAtlantic_Control


title: 25_BUCAtlantic_Control


title: Dd2_control for MMS_6 hour_1

source_name: Dd2_control for MMS_6 hour_1


title: TC32: Parental_Rep1

description: RPPA


title: 51_BUCAtlantic_Control


title: 3_BUCAtlantic_Case


title: TC32: Parental-Ridaforolimus-72hrs

description: RPPA

source_name: TC32: Parental treated Sensitive Ewing Sarcoma


title: 3D7_DMSO for ART_6 hours_ 1

source_name: 3D7_DMSO for ART_6 hours_ 1


title: 89_BUCAtlantic_Control

source_name: Buccal


title: 3D7_DMSO for ART_6 hours_ 2

source_name: 3D7_DMSO for ART_6 hours_ 2


title: 3D7_ART_6 hours_3

source_name: 3D7_ART_6 hours_3


title: 3D7_ART_6 hours_2

source_name: 3D7_ART_6 hours_2


title: 57_BUCAtlantic_Control


title: TC71: Parental_Rep-1

description: RPPA

source_name: TC71: Parental Sensitive Ewing Sarcoma


title: 3d7_MMS_3 hour_2

source_name: 3d7_MMS_3 hour_2


title: 3D7_ART_6 hours_1

source_name: 3D7_ART_6 hours_1


title: 3d7_MMS_3 hour_1

source_name: 3d7_MMS_3 hour_1

source_name: P. falciparum 3D7 RNA reference pool


title: 3D7_control for MMS_3 hour_2

source_name: 3D7_control for MMS_3 hour_2


title: Differentiated 24h [10454NPCS173]

city: Ramat-Gan

first: Michael

last: Gurevich

address: Tel-Hashomer

department: Multiple Sclerosis Center

country: Israel

institute: Sheba Medical Center

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400. Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila 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. 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.
Following scanning of the arrays, the microarray raw data were initially normalized by R Bioconductor Packages, all arrays were normalized serially using a single sample microarray normalization approach designed for personal medicine workflows (SCAN Normalization)
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: SVZ-NSCs_Differentiated 24h

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

growth_protocol: SVZ was dissected from adult C57Bl6/J mice and enzymatically and mechanically dissociated. Single-cell suspension were plated (3500 cells/cm2) in 75 cm2 tissue-culture flasks, in Neurospheres medium. Fresh media was added every 4 days to maintain the cells as proliferating neurospheres, which were then passaged every 6 days and re-plated as single cells using Accutase for continued growth. Cells used in the study were from passages 5-7, and were enriched for neurosphere generating cells through consecutive passages every 3 days.

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

treatment_protocol:
SVZ-NSCs were harvested at time points 0 (undifferentiated cells; grown in presence of growth factors) or 12 and 24 hrs after induction of differentiation in presence of 5% serum on poly-D-lysine and in absence of growth factors.
PBMC were purified from  Ficoll hypaque gradient (Invitrogen, USA)

tag: strain background

value: 6 months

value: subventricular zone-neural stem cells (SVZ-NSCs)

tag: growth condition

value: no growth factors added. In the presence of 5% FCS

tag: time point


title: Differentiated 24h [10410NPCS170]

value: 24 hrs after induction of differentiation


title: Differentiated 24h [10406NPCS170]


title: Differentiated 24h [10450NPCS173]


title: TC71: Parental-Ridaforolimus-72hrs

description: RPPA

source_name: TC71: Parental treated Sensitive Ewing Sarcoma


title: 39_BUCAtlantic_Control


title: 3D7_MMS_1 hour_2

source_name: 3D7_MMS_1 hour_2


title: Differentiated 12h [10453NPCS173]

source_name: SVZ-NSCs_Differentiated 12h

value: 12 hrs after induction of differentiation


title: 43_BUCAtlantic_Control


title: 3D7_control for MMS_3 hour_1

source_name: 3D7_control for MMS_3 hour_1

value: In vitro culture


title: Differentiated 12h [10409NPCS170]


title: 3D7_MMS_1 hour_1

source_name: 3D7_MMS_1 hour_1


title: 21_BUCAtlantic_Control


title: 3D7_control for MMS_1 hour_2

source_name: 3D7_control for MMS_1 hour_2


title: Differentiated 12h [10405NPCS170]


title: wholeblood_830909_2

city: Toronto

first: Jan

last: Heng

state: ON

address: 25 Orde Street

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: Differentiated 12h [10281NPCS166]

tag: age


title: 53_BUCAtlantic_Control

source_name: Buccal


title: 3D7_control for MMS_1 hour_1

source_name: 3D7_control for MMS_1 hour_1

tag: culture

tag: laboratory strain

tag: Stage

value: asexual blood stage

tag: composition


title: Differentiated 24h [10282NPCS166]

tag: gender

tag: cell type


title: Differentiated 12h [10273NPCS166]

tag: strain background


title: wholeblood_830909_1


title: 71_BUCAtlantic_Control

tag: case status

tag: source


title: 45_BUCAtlantic_Control


title: 1_BUCAtlantic_Case


title: 3D7_control for MMS_6 hours_2

source_name: 3D7_control for MMS_6 hours_2

value: mixture of equal amounts of RNA harvested every 6 hours over the 48-hour parasite's intraerythrocytic life cycle


title: Undifferentiated [10408NPCS170]

tag: growth condition

value: In the presence of growth factors

tag: time point

value: time points 0 (undifferentiated cells)


title: Undifferentiated [10452NPCS173]


title: wholeblood_830872_2A

tag: individual id

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

tag: gest age at sampling (weeks)


title: Undifferentiated [10404NPCS170]


title: wholeblood_830790_2

tag: gest age at delivery (weeks)

tag: birth outcome (sptb 1, term 0)

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


title: 3D7_control for MMS_6 hours_1

source_name: 3D7_control for MMS_6 hours_1

tag: culture

value: asexual blood stage:trophozoite


title: 3D7_MMS_6 hours_3

source_name: 3D7_MMS_6 hours_3

tag: laboratory strain


title: 3D7_control for MMS_6 hours_3

source_name: 3D7_control for MMS_6 hours_3

tag: Stage


title: 13_BUCAtlantic_Case

value: female


title: 83_BUCAtlantic_Control

value: buccal sample


title: Undifferentiated [10280NPCS166]

tag: age


title: 63_BUCAtlantic_Control

tag: gender

value: control


title: 3D7_MMS_6 hours_1

source_name: 3D7_MMS_6 hours_1

tag: composition


title: 11_BUCAtlantic_Case

value: case


title: wholeblood_830872_1A

tag: tissue


title: Undifferentiated [10272NPCS166]

tag: strain background

tag: cell type


title: 33_BUCAtlantic_Control

tag: case status

tag: source


title: wholeblood_830790_1

tag: individual id


title: 15_BUCAtlantic_Case


title: wholeblood_830762_2

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


title: 85_BUCAtlantic_Control


title: 91_BUCAtlantic_Control


title: 5_BUCAtlantic_Case


title: wholeblood_830762_1

tag: gest age at sampling (weeks)


title: wholeblood_830741_2

tag: gest age at delivery (weeks)


title: 47_BUCAtlantic_Control


title: 99_BUCAtlantic_Control


title: 93_BUCAtlantic_Control


title: 3D7_TSA_6 hours_2

source_name: 3D7_TSA_6 hours_2

source_name: P. falciparum 3D7 RNA reference pool


title: Donor number 3 treated by ENO or control. Testl time : H45

city: Rouen cedex

first: Celine

last: Derambure

address: 22 Bvd Gambetta

institute: INSERM U905

description: Biological replicate 3 of 3 harvested at H45 of the treatment (ENO or Control)

hyb_protocol: Hybridization was performed according to the Agilent instructions for Gene Expression Hybridization Kit (catalog number 5188-5242). Samples were applied to microarrays enclosed in Agilent SureHyb hybridization chambers (65°C, 17H). After hybridization, slides were washed and dried in acetonitril.

scan_protocol: Scanned on an Agilent G2565CA scanner. Images were quantified using Agilent Feature Extraction Software (v 10.5.1.1)

data_processing: Agilent Feature Extraction Software (v 10.5.1.1) was used for LOWESS normalization.

source_name: ENO  PBMC H45

label_protocol: Agilent Low input QuickAmp Labeling kit was used according to the manufacturer instructions (catalog number 5190-2306) with 100ng of total RNA.

extract_protocol: Total RNA from PBMC were extracted using RNAqueous-4PCR kit (Ambion, #AM1914) following manufacturer's instructions. RNA Integrity Number was obtained by BioAnalyzer 2100 (Agilent).

treatment_protocol: PBMCs from total blood for each donor (n=3) were isolated by Ficoll. ENO or BSA (50µg/mL of culture medium) was added to 1.106 PBMC. PBMC were harvested at H0, H5, H20 or H45 after the treatment onset and total RNA extraction was immediately performed.

tag: cell

value: PBMC

tag: treatment

value: a-Enolase

tag: time

source_name: CONTROL(BSA)  PBMC H45

value: BSA (Control)


title: 27_BUCAtlantic_Control


title: wholeblood_830741_1

tag: birth outcome (sptb 1, term 0)

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


title: 3D7_DMSO_6 hours_2

source_name: 3D7_DMSO_6 hours_2

tag: culture

tag: laboratory strain

tag: Stage


title: 3D7_DMSO_6 hours_3

source_name: 3D7_DMSO_6 hours_3

tag: composition


title: wholeblood_830692_1

tag: tissue


title: 59_BUCAtlantic_Control

tag: gender


title: Donor number 3 treated by ENO or control. Test time : H20

description: Biological replicate 3 of 3 harvested at H20 of the treatment (ENO or Control)

source_name: ENO  PBMC H20

source_name: CONTROL(BSA)  PBMC H20


title: wholeblood_830692_2


title: wholeblood_830656_2


title: Donor number 3 treated by ENO or control. Control time : H0

description: Biological replicate 3 of 3 harvested at the onset of the treatment (ENO or Control)

source_name: ENO  PBMC H0

value: Control H0

source_name: CONTROL(BSA)  PBMC H0


title: 7_BUCAtlantic_Case

source_name: Buccal

tag: case status


title: Donor number 2 treated by ENO or control. Testl time : H45

description: Biological replicate 2 of 3 harvested at H45 of the treatment (ENO or Control)


title: 35_BUCAtlantic_Control

tag: source


title: 3D7_TSA_6 hours_1

source_name: 3D7_TSA_6 hours_1


title: 3D7_Etoposide_6 hours_1

source_name: 3D7_Etoposide_6 hours_1


title: 3D7_Etoposide_6 hours_2

source_name: 3D7_Etoposide_6 hours_2


title: Donor number 3 treated by ENO or control. Test time : H5

description: Biological replicate 3 of 3 harvested at H5 of the treatment (ENO or Control)

source_name: ENO  PBMC H5

source_name: CONTROL(BSA)  PBMC H5


title: 3D7_Etoposide_6 hours_3

source_name: 3D7_Etoposide_6 hours_3


title: Donor number 2 treated by ENO or control. Test time : H20

description: Biological replicate 2 of 3 harvested at H20 of the treatment (ENO or Control)


title: Donor number 2 treated by ENO or control. Test time : H5

description: Biological replicate 2 of 3 harvested at H5 of the treatment (ENO or Control)


title: wholeblood_830607_2

source_name: whole blood, maternal peripheral

tag: individual id


title: 55_BUCAtlantic_Control


title: wholeblood_830607_1

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


title: Donor number 2 treated by ENO or control. Control time : H0

description: Biological replicate 2 of 3 harvested at the onset of the treatment (ENO or Control)


title: 37_BUCAtlantic_Control


title: wholeblood_830597_1

tag: gest age at sampling (weeks)


title: 3D7_DMF_6 hours_2

source_name: 3D7_DMF_6 hours_2

source_name: P. falciparum 3D7 RNA reference pool


title: wholeblood_830597_2A

tag: gest age at delivery (weeks)


title: L15_T

city: Dallas

first: Luc

last: Girard

state: TX

address: 5323 Harry Hines Blvd

department: Hamon Center for Therapeutic Oncology Research

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

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)

value: Female

tag: race

value: Asian

tag: smoker

value: Never

value: IB

tag: egfr

value: MUT

tag: kras

value: WT


title: wholeblood_830590_2

tag: birth outcome (sptb 1, term 0)

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

value: peripheral maternal blood


title: 3D7_DMF_6 hours_1

source_name: 3D7_DMF_6 hours_1

tag: culture

value: In vitro culture

tag: laboratory strain

tag: Stage

value: asexual blood stage:trophozoite

value: asexual blood stage

tag: composition

value: mixture of equal amounts of RNA harvested every 6 hours over the 48-hour parasite's intraerythrocytic life cycle


title: wholeblood_830590_1

tag: tissue


title: L12_T

tag: gender

value: Male

value: Caucasian

value: Current

tag: pack-years

value: IIIA


title: wholeblood_830656_1

tag: individual id

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

tag: gest age at sampling (weeks)


title: 3D7_DMF_6 hours_3

source_name: 3D7_DMF_6 hours_3


title: Donor number 1 treated by ENO or control. Test time : H5

description: Biological replicate 1 of 3 harvested at H5 of the treatment (ENO or Control)

tag: cell

value: PBMC

tag: treatment

value: a-Enolase

tag: time

value: BSA (Control)


title: wholeblood_830587_2

tag: gest age at delivery (weeks)


title: 3D7_Cispaltin_6 hours_ 2

source_name: 3D7_Cispaltin_6 hours_ 2


title: 17_BUCAtlantic_Case

value: female

tag: case status

value: case

tag: source

value: buccal sample


title: 3D7_Cispaltin_6 hours_ 1

source_name: 3D7_Cispaltin_6 hours_ 1


title: 23_BUCAtlantic_Control

value: control


title: 3D7_MMS_6 hours_2

source_name: 3D7_MMS_6 hours_2


title: L15_N

source_name: Non-malignant lung

tag: histology

value: Non-malignant

tag: age (yrs)

value: Female

tag: race

value: Asian

tag: smoker

value: Never


title: Donor number 1 treated by ENO or control. Testl time : H45

description: Biological replicate 1 of 3 harvested at H45 of the treatment (ENO or Control)

source_name: ENO  PBMC H45

source_name: CONTROL(BSA)  PBMC H45


title: Donor number 1 treated by ENO or control. Control time : H0

description: Biological replicate 1 of 3 harvested at the onset of the treatment (ENO or Control)

source_name: ENO  PBMC H0

value: Control H0

source_name: CONTROL(BSA)  PBMC H0


title: H3K56ac_MMS_6 hour_3

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.

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.

source_name: ChIP DNA for H3K56ac

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: MMS

tag: antibody

value: whole organism

tag: time point

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: wholeblood_830587_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)

tag: tissue

value: peripheral maternal blood


title: CEN.PK113-7D -Glucose-limited retentostat culture sample R8A

city: Delft

first: Jean-Marc

last: Daran

address: Julianalaan 67

department: Department of Biotechnology

institute: Delft University of Technology

description: S. cerevisiae CEN.PK113-7D aerobic glucose-limited retentostat sampled after 16 days after switching the effluent

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: CEN.PK113-7D Glucose-limited chemostat culture -0.05H-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: strain

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_830584_2

source_name: whole blood, maternal peripheral

tag: gest age at sampling (weeks)

tag: gest age at delivery (weeks)


title: 69_BUCAtlantic_Control

source_name: Buccal

tag: gender

value: female

tag: case status

tag: source

value: buccal sample


title: L9_N

tag: histology

value: Non-malignant

tag: age (yrs)

value: Male

tag: race

value: Caucasian

tag: smoker

value: Former

tag: pack-years


title: L9_T

value: Adenocarcinoma

tag: Stage

value: IA

tag: egfr

value: WT

tag: kras


title: CEN.PK113-7D -Glucose-limited retentostat culture sample R5B

description: S. cerevisiae CEN.PK113-7D aerobic glucose-limited retentostat sampled after 8 days after switching the effluent

scan_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).

source_name: CEN.PK113-7D Glucose-limited chemostat culture -0.025H-1

label_protocol: 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].

tag: strain

tag: genetic background


title: H3K56ac_MMS_6 hour_2

tag: fraction

value: ChIP

tag: agent

value: MMS

tag: antibody

tag: tissue

value: whole organism

tag: time point

tag: reference


title: 3D7_DMSO_6 hours_1

source_name: 3D7_DMSO_6 hours_1

tag: culture

value: In vitro culture

tag: laboratory strain

value: asexual blood stage:trophozoite

source_name: P. falciparum 3D7 RNA reference pool

value: asexual blood stage

tag: composition

value: mixture of equal amounts of RNA harvested every 6 hours over the 48-hour parasite's intraerythrocytic life cycle


title: wholeblood_830584_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)

value: peripheral maternal blood


title: H3K56ac_MMS_6 hour_1

value: 6 hours

value: Input

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


title: 3D7_Cispaltin_6 hours_ 3

source_name: 3D7_Cispaltin_6 hours_ 3

tag: Stage


title: 78_BUCAtlantic_Control

tag: gender

value: female

tag: case status

value: control

tag: source

value: buccal sample


title: H3K56ac_control_6 hour_3

tag: fraction

tag: agent

tag: antibody


title: H3K56ac_control_6 hour_2

tag: tissue

tag: time point

tag: reference


title: CEN.PK113-7D -Glucose-limited retentostat culture sample R3A

description: S. cerevisiae CEN.PK113-7D aerobic glucose-limited retentostat sampled after 3.5 days after switching the effluent

source_name: FS09322 Glucose-limited chemostat culture -0.15H-1

tag: strain

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: Donor number 1 treated by ENO or control. Test time : H20

description: Biological replicate 1 of 3 harvested at H20 of the treatment (ENO or Control)

source_name: ENO  PBMC H20

tag: cell

value: PBMC

tag: treatment

value: a-Enolase

tag: time

source_name: CONTROL(BSA)  PBMC H20

value: BSA (Control)


title: H3K56ac_control_6 hour_1

value: ChIP

value: whole organism


title: L1_N

source_name: Non-malignant lung

tag: histology

value: Non-malignant

tag: age (yrs)

tag: gender

value: Male

tag: race

value: Caucasian

tag: smoker

value: Current

tag: pack-years


title: wholeblood_830575_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

value: peripheral maternal blood


title: CEN.PK113-7D -Glucose-limited retentostat culture sample R1A

description: S. cerevisiae CEN.PK113-7D aerobic glucose-limited retentostat sampled after 1.5 days after switching the effluent

source_name: FS09322 Glucose-limited chemostat culture -0.1H-1

tag: strain

tag: genetic background

tag: genotype/variation

tag: c-source

tag: sample type


title: wholeblood_830561_2


title: CEN.PK113-7D -Glucose-limited chemostat culture 0.025h-6

description: S. cerevisiae CEN.PK113-7D aerobic glucose-limited chemostat with a dilution rate of 0.025h-1.

source_name: FS09322 Glucose-limited chemostat culture -0.05H-1


title: wholeblood_830575_2


title: L1_T

source_name: Lung cancer

tag: histology

value: Adenocarcinoma

tag: age (yrs)

tag: Stage

value: IB

tag: egfr

value: WT

tag: kras

value: MUT


title: 3039_T

tag: gender

value: Female

tag: race

tag: smoker

value: Never

value: IIB


title: 3039_N


title: L2_T

value: Asian

value: IIIA


title: wholeblood_830561_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: H3K9ac_MMS_6 hour_1

source_name: ChIP DNA for H3K9ac

tag: fraction

tag: agent

value: MMS

tag: antibody

tag: tissue

tag: time point

value: 6 hours

value: Input

tag: reference

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


title: L2_N

tag: histology

value: Non-malignant

tag: age (yrs)


title: CEN.PK113-7D -Glucose-limited retentostat culture sample R1B

tag: strain

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

value: retentostat sampled after 1.5 days after switching the effluent


title: H3K9ac_control_6 hour_3

value: ChIP

value: control

value: whole organism


title: H3K9ac_control_6 hour_2


title: wholeblood_830576_2A

tag: individual id

tag: birth outcome (sptb 1, term 0)

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

value: peripheral maternal blood


title: CEN.PK113-7D -Glucose-limited chemostat culture 0.1h-5

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

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


title: CEN.PK113-7D -Glucose-limited chemostat culture 0.025h-1

value: chemostat with a dilution rate of 0.025h-1.


title: wholeblood_830560_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: wholeblood_830560_1


title: 3036_N

tag: gender

value: Female

tag: race

tag: smoker

value: Never


title: wholeblood_830576_1

tag: tissue


title: 3035_N

tag: histology

value: Male

value: Caucasian


title: 3036_T

value: Adenocarcinoma

tag: age (yrs)

value: Asian

tag: Stage

value: IIB

tag: egfr

value: MUT

tag: kras

value: WT


title: H4K8ac_MMS_6 hours_3

source_name: ChIP DNA for H4K8ac

tag: fraction

tag: agent

value: MMS

tag: antibody

tag: time point

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: wholeblood_830544_2

source_name: whole blood, maternal peripheral

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: 3035_T

tag: gender

tag: race

value: IA


title: CEN.PK113-7D -Glucose-limited retentostat culture sample R8B

source_name: CEN.PK113-7D Glucose-limited chemostat culture -0.05H-1

tag: strain

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

value: retentostat sampled after 16 days after switching the effluent


title: H4K8ac_MMS_6 hours_2

value: ChIP

tag: tissue

value: whole organism


title: 3033_T

tag: histology

tag: age (yrs)

value: Female

value: Caucasian

tag: smoker

value: Never

tag: Stage

tag: egfr

tag: kras


title: wholeblood_830554_2A

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: 3033_N

value: Non-malignant

tag: gender

tag: race


title: CEN.PK113-7D -Glucose-limited chemostat culture 0.1h-1

tag: strain

tag: genetic background

value: chemostat with a dilution rate of 0.1h-1.


title: H3K9ac_MMS_6 hour_2

tag: fraction

tag: agent

value: MMS

tag: antibody

tag: time point

tag: reference


title: L12_N

tag: histology

tag: age (yrs)

value: Male

tag: smoker

value: Current

tag: pack-years


title: CEN.PK113-7D -Glucose-limited retentostat culture sample R5A

source_name: CEN.PK113-7D Glucose-limited chemostat culture -0.025H-1

tag: genotype/variation

tag: c-source

tag: sample type

value: retentostat sampled after 8 days after switching the effluent


title: wholeblood_830554_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)

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

tag: tissue


title: 3032_T

value: Adenocarcinoma

tag: gender

tag: race

tag: Stage

value: IIIA

tag: egfr

value: WT

tag: kras


title: CTL R-2HG replicate3

city: Hannover

first: Anuhar

last: Chaturvedi

address: Cral Neuberg Strasse-1

department: Hematology, Hemostasis, Oncology and Stem Cell Transplantation

institute: Hannover Medical School

description: Gene expression data from sorted mouse bone marrow cells transduced with IDH1mut 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)

source_name: sorted mouse bone marrow cells_empty vector_R-2HG

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

value: sorted mouse bone marrow cells

tag: construct

value: empty vector


title: H4K8ac_MMS_6 hours_1

tag: fraction

value: ChIP

tag: agent

tag: antibody

tag: time point

value: 6 hours

value: Input

tag: reference

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


title: H4K8ac_control_6 hours_3

value: control

value: whole organism


title: wholeblood_830538_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)

value: peripheral maternal blood


title: 3032_N

tag: histology

value: Non-malignant

tag: age (yrs)

tag: gender

value: Female

value: Caucasian

tag: smoker

value: Never


title: CTL R-2HG replicate2


title: CEN.PK113-7D -Glucose-limited retentostat culture sample R3B

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

value: retentostat sampled after 3.5 days after switching the effluent


title: wholeblood_830544_1

tag: birth outcome (sptb 1, term 0)

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

tag: tissue


title: H4K8ac_control_6 hours_1

tag: fraction

tag: agent

tag: antibody

tag: time point


title: CTL R-2HG replicate1

tag: strain

tag: cell type

value: sorted mouse bone marrow cells

tag: construct


title: IDH1_mut replicate 3

source_name: sorted mouse bone marrow cells_IDH1mut


title: wholeblood_830538_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: 3031_T

tag: histology

value: Adenocarcinoma

tag: age (yrs)

tag: gender

tag: race

tag: smoker

tag: Stage

value: IIA

tag: egfr

value: MUT

tag: kras

value: WT


title: H4K8ac_control_6 hours_2

tag: fraction

value: ChIP

tag: agent

tag: antibody

tag: tissue

value: 6 hours

value: Input

tag: reference

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


title: IDH1_mut replicate 2

tag: strain

tag: cell type

tag: construct


title: 3030_T

value: Current

tag: pack-years

value: IIB


title: 3030_N

tag: histology

value: Non-malignant

value: Female

value: Caucasian


title: IDH1_mut replicate 1


title: wholeblood_830518_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: wholeblood_830515_2


title: IDH1_wt replicate 2

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

source_name: sorted mouse bone marrow cells_IDH1wt


title: wholeblood_830515_1


title: B_9_28_cartilage_Health

city: Xi'an

first: Feng

last: Zhang

address: Yanta West Road 76

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: female

value: hip cartilage

tag: diagnosis

value: healthy control


title: 3024_T

value: Adenocarcinoma

tag: age (yrs)

value: Male

tag: race

tag: smoker

tag: Stage

value: III

tag: egfr

tag: kras


title: wholeblood_830518_1

tag: tissue


title: 3031_N

value: Never


title: wholeblood_830507_1


title: B_9_16_cartilage_Health

value: male