title: CD19-enriched CLL patient sample, patient #5001

description:
CD19-enriched CLL clinical sample
A0018470

value: relapsed chronic lymphocytic leukemia (CLL) patient

value: patient #5001


title: T1DM_11

status: Public on Jul 30 2014

type: protein

city: Pohang, Gyungbuk

first: Sehyun

last: Chae

address: San 31, Hyoja-Dong, Nam-Gu

department: Department of Interdisciplinary Bioscience and Bioengineering(I-BIO)

country: South Korea

institute: POSTECH

description: Auto-antibodies from serum samples were profiled using a high-density, fluorescence-based protein microarray containing duplicate spots of 9,480 human proteins derived from the Ultimate ORF collection

hyb_protocol: Following the manufacturers’ instructions, serum diluted 1:500 in PBST buffer was incubated on the microarray slides for 90 minutes.

scan_protocol: The array slides were scanned with a GenePix® 4000B Fluorescent Scanner (Molecular Devices).

data_processing:
Signal intensities were acquired using ProtoArray™ Prospector, a software tool developed for ProtoArray data by Invitrogen.
Protein microarray used for this study contains 18,960 protein spots and >4,000 control spots. Raw data (gpr file) obtained from GenePix image quantification software contains all the information of intensities about protein and control spots. Analysing the gpr file containing 23,232 spot intensities (18,960 protein spots + >4,000 control spots), ProtoArray Prospector software provides 18,960 intensity values of signal from protein features. Please note that the output of ProtoArray Prospector v5.2 contains Database ID (e.g. NM_024548.2, BC011414.1 etc), Ultimate ORF ID (e.g. IOH27601, IOH9720 etc) which corresponds to Ultimate ORFs provided in a Gateway entry vector, and Array ID (e.g. B01R01C01). The sample data table is formatted using Database IDs.
The signal intensities were converted to log2-intensities and then normalized using the quantile normalization method

label: Alexa Fluor 647

molecule: protein

organism: Homo sapiens

label_protocol: standard Invitrogen protocol

extract_protocol: The serum was collected from 16 T1DM, 16 type 2 diabetes (T2DM) patients, and 27 healthy controls with normal glucose tolerance (NGT)

tag: disease state

value: type 1 diabetes mellitus (T1DM)

tag: age (yrs)

tag: tissue

value: Serum


title: cHF+Phospholipids+Rosi, replicate 8

type: RNA

city: Wageningen

first: Evert

middle: M.

last: van Schothorst

address: De Elst 1

country: Netherlands

institute: Wageningen University

description: Cy3 samples were pooled on a equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.

hyb_protocol: Individual Cy5-labelled samples were hybridized against the Cy3-labelled reference pool according to the manufacturers' procedure using Agilent In Situ Hybridization Kit Plus and GEx Hybridization Buffer HI-RPM. Samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers and hybridized at 65C for 17 hours at 10rpm rotation. After hybridization, slides were washed sequential following Agilents' recommendations and finally covered with Ozone-barrier slides.

scan_protocol: Scanned with an Agilent Technologies Scanner G2505B with 10 and 100% laser-power intensities.

data_processing: Images were quantified using Agilent Feature Extraction Software (v 10.5.1.1) to obtain raw median signal and background values for both Cy5 and Cy3. Spots with a mean signal higher than twice the background value over all arrays were considered to be expressed. Data was normalized according to Pellis et al., (Physiol Genomics 2003; 16:99-106) based on the Cy3-reference pool, and log2 transformation.

molecule: total RNA

organism: Mus musculus

source_name: cHF+Phospholipids+Rosi, replicate 8

label_protocol: 1,000 ng of purified individual total RNA was used for cDNA synthesis, splitted in two equal fractions and used for subsequent cRNA labeling and synthesis using Cy5 and Cy3 dyes and the Agilent low RNA input fluorescent lineair amplification protocol, as described previously (Van Helden et al., Carcinogenesis 2010).

extract_protocol: Total RNA was isolated from liver tissue stored in RNAlater Solution using TRIZol Reagent (Sigma-Aldrich) according to the manufacturer’s instruction. After extraction, RNA was purified by using RNeasy columns (Qiagen). RNA concentration and purity were measured using the NanoDrop spectrophotometer (IsoGen Life Science). The integrity of RNA was checked with Experion automated electrophoresis system (BioRad).

treatment_protocol: Animals were fed a control corn oil-based high-fat diet (cHF), or one of the cHF supplementations: 1) ~7 % of dietary lipids was replaced by the EPA and DHA concentrate in the form of omega-3 phospholipids rich in phosphatidylcholine (PC); 2) low dose rosiglitazone (R); and 3) both PC and rosiglitazone (PC+R). All  groups received the diet ad-libitum during 7 weeks intervention.

tag: strain

tag: gender

value: male

tag: age

value: adult

value: liver

source_name: reference pool


title: CD19-enriched CLL patient sample, patient #606

city: South San Francisco

first: Ru-Fang

last: Yeh

state: CA

address: 1 DNA Way

country: USA

institute: Genentech

description:
CD19-enriched CLL clinical sample
A0018467

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials per manufacturers recommendation. Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 (fluidics protocol FS450_0001).

scan_protocol: Arrays were scanned using the Affymetrix GCS 3000 7G and Gene-Chip Operating Software v.1.3.0 to produce .CEL intensity files.

data_processing:
.CEL files were background adjusted, quantile normalized and summarized at the transcript level using only core probesets that mapped to RefSeq transcripts, by apt (Affymetrix Power Tool version 1.12.0) software that used the RMA algorithm.
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.na29.hg18.probeset.csv

label: biotin

source_name: CLL clinical sample, CD19-enriched

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: Pretreatment specimens from relapsed chronic lymphocytic leukemia patients

extract_protocol: CLL samples were positively enriched by magnetic cell sorting using CD19 microbeads and MACS columns (Miltenyi Biotec Ltd, Surrey, UK). Total RNA was isolated using Trizol (Invitrogen) and RNeasy kit (QIAGEN).

treatment_protocol: not applicable

tag: subject status

tag: patient id

value: patient #606

tag: binet stage

value: C

value: CD19-enriched CLL patient sample


title: T1DM_10


title: cHF+Phospholipids+Rosi, replicate 7

source_name: cHF+Phospholipids+Rosi, replicate 7


title: CD19-enriched CLL patient sample, patient #9222

description:
CD19-enriched CLL clinical sample
A0018466

value: patient #9222

value: B


title: CD19-enriched CLL patient sample, patient #9608

description:
CD19-enriched CLL clinical sample
A0018464

value: patient #9608


title: LCL_untreated [N306]

city: Haifa

first: Tamar

last: Paperna

address: Efron St. 1

department: Faculty of Medicine

country: Israel

institute: Technion

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Genome Studio software-detected intensity for values in sample columns and detection P values in the non-normalized matrix sheet. The data was log2 transformed and batch normalized using JMP genomics batch normalization application.

label_protocol: Illumina Protocol

growth_protocol: LCLs were cultured in RPMI-1640 supplemented with 10% FBS, 2 mM L-glutamine, penicillin (100 U/ml), streptomycin (100μg/ml), and nystatin (12.5U/ml, Biological Industries).

extract_protocol: RNA was extracted from LCL cultures using the Roche RNA isolation kit. All RNA samples were checked for quality using Experion (Bio-Rad).

treatment_protocol: LCLs (1.4 million cells/ml) were incubated with 100 units/ml recombinant human IFN-β1a (InterferonSource) for 4 hours. Untreated cells were cultured in parallel and under identical culture conditions for comparison.

tag: in vitro treated ifnb

value: NO

value: Female

tag: ms subtype

value: Relapsing Remitting

tag: treatment status at phlebotomy

value: Naïve

tag: ethnicity (jewish/arab)

value: A


title: T1DM_7


title: CD19-enriched CLL patient sample, patient #5403

description:
CD19-enriched CLL clinical sample
A0018460

value: relapsed chronic lymphocytic leukemia (CLL) patient

value: patient #5403


title: LCL_untreated [N206]

value: Male

value: Treated


title: CD19-enriched CLL patient sample, patient #8006

description:
CD19-enriched CLL clinical sample
A0018455

value: patient #8006


title: T1DM_9

value: type 1 diabetes mellitus (T1DM)

value: Serum


title: CD19-enriched CLL patient sample, patient #9215

description:
CD19-enriched CLL clinical sample
A0018457

value: patient #9215


title: cHF+Phospholipids+Rosi, replicate 2

source_name: cHF+Phospholipids+Rosi, replicate 2

value: male

value: adult

value: liver


title: cHF+Phospholipids+Rosi, replicate 5

source_name: cHF+Phospholipids+Rosi, replicate 5


title: cHF+Phospholipids+Rosi, replicate 4

source_name: cHF+Phospholipids+Rosi, replicate 4


title: LCL_untreated [N4605]


title: cHF+Phospholipids+Rosi, replicate 6

source_name: cHF+Phospholipids+Rosi, replicate 6


title: T1DM_8


title: cHF+Phospholipids+Rosi, replicate 3

source_name: cHF+Phospholipids+Rosi, replicate 3


title: LCL_untreated [N13605]


title: cHF+Phospholipids+Rosi, replicate 1

source_name: cHF+Phospholipids+Rosi, replicate 1


title: LCL_untreated [N12705]

value: Secondary Progressive


title: LCL_IFN-β treated_4hr [Y306]

source_name: LCL_IFN-β treated_4hr

value: Yes


title: CD19-enriched CLL patient sample, patient #4214

description:
CD19-enriched CLL clinical sample
A0018458

value: patient #4214

value: B

value: CD19-enriched CLL patient sample


title: LCL_untreated [N6305]

value: NO

value: Female

value: A


title: cHF+Phospholipids, replicate 8

source_name: cHF+Phospholipids, replicate 8


title: CD19-enriched CLL patient sample, patient #1406

description:
CD19-enriched CLL clinical sample
A0018454

value: relapsed chronic lymphocytic leukemia (CLL) patient

value: patient #1406


title: LCL_IFN-β treated_4hr [Y13605]

value: Male

value: Relapsing Remitting

value: Treated


title: cHF+Phospholipids, replicate 7

source_name: cHF+Phospholipids, replicate 7


title: T1DM_4

value: type 1 diabetes mellitus (T1DM)

value: Serum


title: T1DM_5


title: LCL_IFN-β treated_4hr [Y206]


title: CD19-enriched CLL patient sample, patient #7107

description:
CD19-enriched CLL clinical sample
A0018453

value: patient #7107


title: T1DM_3


title: CD19-enriched CLL patient sample, patient #6905

description:
CD19-enriched CLL clinical sample
A0018452

value: patient #6905

value: C


title: T1DM_6


title: T1DM_1


title: T1DM_2


title: LCL_IFN-β treated_4hr [Y4605]

value: Yes


title: cHF+Phospholipids, replicate 6

source_name: cHF+Phospholipids, replicate 6

value: male

value: adult

value: liver


title: CD19-enriched CLL patient sample, patient #2905

description:
CD19-enriched CLL clinical sample
A0018448

value: patient #2905

value: CD19-enriched CLL patient sample


title: cHF+Phospholipids, replicate 5

source_name: cHF+Phospholipids, replicate 5


title: LCL_IFN-β treated_4hr [Y6305]

value: Female

value: Secondary Progressive

value: A


title: CD19-enriched CLL patient sample, patient #3204

description:
CD19-enriched CLL clinical sample
A0018449

value: relapsed chronic lymphocytic leukemia (CLL) patient

value: patient #3204


title: LCL_IFN-β treated_4hr [Y12705]

value: Male

value: Treated


title: LCL_untreated [NM06707]

value: NO

value: Relapsing Remitting

value: J


title: cHF+Phospholipids, replicate 3

source_name: cHF+Phospholipids, replicate 3


title: CD19-enriched CLL patient sample, patient #1405

description:
CD19-enriched CLL clinical sample
A0018451

value: patient #1405

value: B


title: LCL_untreated [NM08207]


title: cHF+Phospholipids, replicate 4

source_name: cHF+Phospholipids, replicate 4

value: male


title: H460_cells-24h-differentiation-REP2

city: Cantoblanco

first: Juan

middle: Carlos

last: Oliveros

state: Madrid

address: Darwin 3

country: Spain

institute: CNB, CSIC

hyb_protocol: For each hybridization 600 ng of Cy3 probes were mixed and added to 5 ul of 10x Blocking Agent, 1 ul of 25x Fragmentation Buffer and Nuclease free water in a 25 ul reaction, incubated at 60¼C for 30 minutes to fragment RNA and stopped with  25 ul of 2x Hybridization Buffer. The samples were placed on ice and quickly loaded onto arrays, hybridized at 65¼C for 17 hours in a Hybridization oven rotator and then washed in GE wash buffer 1 at room temperature (1 minute) and in GE Wash Buffer 2 at 37¼C (1 minute). Arrays were dried by centrifugation at 2000 rpm for 2 minutes.

scan_protocol: Raw GPR files were obtained by Axon's GenePix 4000B scanner and GenePixPro 5.1 software.

data_processing: Local background was corrected by normexp method of limma package with an offset of 50 (Smyth, 2004). Background corrected intensities were transformed to log scale (base 2). To have similar intensity distribution across all arrays, background-corrected-intensity values were normalized by adjusting their quantiles (Bolstad et al., 2003).

label_protocol: Total RNA (200 ng) was amplified using One Color Low Input Quick Amp Labeling Kit (Agilent Technologies) and purified with RNeasy Mini Kit (Qiagen).

growth_protocol: H460C (CSC) cells were grown in DMEM/F12 (1:1) media supplemented with 2mM glutamine, 5mM Hepes, 0.4% BSA, N2 supplement (Gibco) and 20ng/mm of EGF and FGF-b growth factors

extract_protocol: Total RNA was extracted using Trizol according to the manufacturer's instructions

treatment_protocol: H460C cells were differentiated by culture in RPMI media supplemented with 10% Foetal Bovine Serum under adherent conditions.

tag: cell line

value: Lung cancer (NSCL) H460 cells

tag: time culture (hours)


title: NGT_26

value: healthy controls with normal glucose tolerance (NGT)

value: Serum


title: CD19-enriched CLL patient sample, patient #3903

description:
CD19-enriched CLL clinical sample
A0018447

value: patient #3903

value: C

value: CD19-enriched CLL patient sample


title: NGT_25


title: NGT_23


title: NGT_24


title: CD19-enriched CLL patient sample, patient #9605

description:
CD19-enriched CLL clinical sample
A0018445

value: patient #9605

value: A


title: cHF+Phospholipids, replicate 1

source_name: cHF+Phospholipids, replicate 1

value: adult

value: liver


title: LCL_untreated [NM03509]

value: Female

value: Treated


title: NGT_22

description: Auto-antibodies from serum samples were profiled using a high-density, fluorescence-based protein microarray containing duplicate spots of 9,480 human proteins derived from the Ultimate ORF collection


title: NGT_21


title: CD19-enriched CLL patient sample, patient #8102

description:
CD19-enriched CLL clinical sample
A0018442

value: relapsed chronic lymphocytic leukemia (CLL) patient

value: patient #8102


title: CD19-enriched CLL patient sample, patient #9808

description:
CD19-enriched CLL clinical sample
A0018446

value: patient #9808


title: cHF+Phospholipids, replicate 2

description: Cy3 samples were pooled on a equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.

source_name: cHF+Phospholipids, replicate 2

source_name: reference pool


title: LCL_untreated [NM04707]

value: NO

value: Male

value: Relapsing Remitting

value: J


title: LCL_untreated [NM1009]

value: Naïve


title: CD19-enriched CLL patient sample, patient #8101

description:
CD19-enriched CLL clinical sample
A0018440

source_name: CLL clinical sample, CD19-enriched

value: patient #8101

value: B


title: cHF+Rosi, replicate 5

source_name: cHF+Rosi, replicate 5

value: male


title: cHF+Rosi, replicate 6

source_name: cHF+Rosi, replicate 6


title: LCL_untreated [N3811]


title: NGT_20

value: healthy controls with normal glucose tolerance (NGT)

value: Serum


title: CD19-enriched CLL patient sample, patient #5008

description:
CD19-enriched CLL clinical sample
A0018439

value: patient #5008

value: CD19-enriched CLL patient sample


title: cHF+Rosi, replicate 3

source_name: cHF+Rosi, replicate 3

value: adult

value: liver


title: CD19-enriched CLL patient sample, patient #7104

description:
CD19-enriched CLL clinical sample
A0018436

value: relapsed chronic lymphocytic leukemia (CLL) patient

value: patient #7104

value: A


title: LCL_untreated [NM1208]

value: NO

value: Female

value: Relapsing Progressive

value: Treated


title: cHF+Rosi, replicate 2

source_name: cHF+Rosi, replicate 2


title: cHF+Rosi, replicate 1

source_name: cHF+Rosi, replicate 1


title: CD19-enriched CLL patient sample, patient #8203

description:
CD19-enriched CLL clinical sample
A0018444

value: patient #8203

value: C


title: LCL_untreated [NM2209]

value: Relapsing Remitting

value: J


title: cHF+Rosi, replicate 4

source_name: cHF+Rosi, replicate 4

value: male


title: LCL_untreated [NM0206]

value: Naïve


title: NGT_19

value: healthy controls with normal glucose tolerance (NGT)

value: Serum


title: CD19-enriched CLL patient sample, patient #2807

description:
CD19-enriched CLL clinical sample
A0018435

value: patient #2807

value: B

value: CD19-enriched CLL patient sample


title: LCL_IFN-β treated_4hr [YM06707]

source_name: LCL_IFN-β treated_4hr

value: Yes


title: cHF control, replicate 7

source_name: cHF control, replicate 7

value: adult

value: liver


title: NGT_17


title: NGT_16


title: NGT_18


title: CD19-enriched CLL patient sample, patient #1801

description:
CD19-enriched CLL clinical sample
A0018433

value: relapsed chronic lymphocytic leukemia (CLL) patient

value: patient #1801


title: CD19-enriched CLL patient sample, patient #1802

description:
CD19-enriched CLL clinical sample
A0018434

value: patient #1802


title: NGT_15


title: CD19-enriched CLL patient sample, patient #4208

description:
CD19-enriched CLL clinical sample
A0018432

value: patient #4208


title: cHF control, replicate 6

source_name: cHF control, replicate 6


title: cHF control, replicate 5

source_name: cHF control, replicate 5


title: LCL_IFN-β treated_4hr [YM08207]

value: Female

value: Treated


title: NGT_13


title: NGT_14


title: NGT_12


title: LCL_IFN-β treated_4hr [YM03509]

value: Relapsing Remitting

value: J


title: CD19-enriched CLL patient sample, patient #4207

description:
CD19-enriched CLL clinical sample
A0018428

value: patient #4207

value: C


title: CD19-enriched CLL patient sample, patient #9003

description:
CD19-enriched CLL clinical sample
A0018430

value: patient #9003


title: CD19-enriched CLL patient sample, patient #9203

description:
CD19-enriched CLL clinical sample
A0018427

value: patient #9203


title: LCL_IFN-β treated_4hr [YM04707]

value: Male


title: cHF control, replicate 2

source_name: cHF control, replicate 2

value: male


title: NGT_11

value: healthy controls with normal glucose tolerance (NGT)

value: Serum


title: CD19-enriched CLL patient sample, patient #2901

description:
CD19-enriched CLL clinical sample
A0018426

value: patient #2901

value: B

value: CD19-enriched CLL patient sample


title: cHF control, replicate 3

source_name: cHF control, replicate 3

value: adult

value: liver


title: cHF control, replicate 1

source_name: cHF control, replicate 1


title: LCL_IFN-β treated_4hr [Y3811]

value: Yes

value: A


title: L10-24B

city: HangZhou

first: zhenxing

last: zhou

state: Zhejiang

address: 388* Yuhang Tang Road

country: China

institute: zhejiang university

description:
W24B_NS
Gene expression after 24h.

hyb_protocol: Each Slide was hybridized with 600ng Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent Technologies, Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent Technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit (Cat#5188-5327, Agilent Technologies, Santa Clara, CA, US), following the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent Technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=5μm, PMT 100%, 10%, 16bit.

data_processing: Raw data were normalized by Quantile algorithm, GeneSpring Software 11.0 (Agilent Technologies, Santa Clara, CA, US).

organism: Streptomyces chattanoogensis

source_name: Mycelium, wild type, 24h

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat#5190-2305, Agilent Technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

growth_protocol: Grown in YEME for 12 hours, 16 hours, or 24 hours at 200 r/min, 30℃.

extract_protocol: Total RNA was isolated using the RNA extract kit (QIAGEN, Germany), according to the manufacturer’s instructions, and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: Mycelium was collected from YEME culture by centrifugation, the supernatant was discarded, and the mycelium was washed twice by PBS buffer.

tag: strain/background

tag: genotype/variation

value: wild type

value: mycelium

tag: developmental stage

value: exponential phase

tag: culture

value: YEME

tag: time


title: L10-24C

description:
W24C_NS
Gene expression after 24h.

tag: tissue


title: LCL_IFN-β treated_4hr [YM1208]

tag: gender

value: Female

value: Relapsing Progressive

value: Treated

value: J


title: cHF control, replicate 4

source_name: cHF control, replicate 4

tag: strain

value: male

tag: age


title: NGT_10

tag: disease state

value: healthy controls with normal glucose tolerance (NGT)

tag: age (yrs)

value: Serum


title: CD19-enriched CLL patient sample, patient #5006

description:
CD19-enriched CLL clinical sample
A0018425

tag: subject status

value: relapsed chronic lymphocytic leukemia (CLL) patient

tag: patient id

value: patient #5006

tag: binet stage

value: B


title: NGT_9

description: Auto-antibodies from serum samples were profiled using a high-density, fluorescence-based protein microarray containing duplicate spots of 9,480 human proteins derived from the Ultimate ORF collection


title: CD19-enriched CLL patient sample, patient #5005

description:
CD19-enriched CLL clinical sample
A0018424

value: patient #5005

value: CD19-enriched CLL patient sample


title: L10-24A

description:
W24A_NS
Gene expression after 24h.


title: LCL_IFN-β treated_4hr [YM1009]

tag: in vitro treated ifnb

value: Yes

tag: ms subtype

value: Relapsing Remitting

tag: treatment status at phlebotomy

value: Naïve

tag: ethnicity (jewish/arab)


title: Sle1.3/het #3

city: New York City

first: Vanjs

last: Sisirak

state: NY

address: 701 west 168th street

department: Microbiology and Immunology

institute: Columbia University

description: Spleen Sle1.3/E2-2het #3; Sle1.3/het#3

hyb_protocol: Biotinylated DNA probe was made according to the standard Affymetrix protocol.

scan_protocol: Arrays were scanned according to the Affymetrix protocol.

data_processing: Gene level RMA using Affymetrix expression console software

label: Biotin

source_name: splenocytes from sle1.3/E2-2het mice

label_protocol: We used the Ambion WT Labelling Kit as per manufacturer's instructions. We used 250 ng/sample of starting total RNA.

extract_protocol: Total RNA was extracted from Trizol LS according to manufacturer's instructions.

treatment_protocol: Collagenase/DnaseI digestion of the spleen

tag: strain background

tag: genotype/variation

value: sle1.3/E2-2het; Sle1.3 mice haplodeficient for E2-2

value: female

value: spleen

tag: cell type

value: splenocytes


title: LCL_IFN-β treated_4hr [Y5707]

value: Female

value: A


title: LCL_IFN-β treated_4hr [YM0206]

value: J


title: NGT_8

value: healthy controls with normal glucose tolerance (NGT)


title: NGT_7

value: Serum


title: CD19-enriched CLL patient sample, patient #3304

description:
CD19-enriched CLL clinical sample
A0018423

source_name: CLL clinical sample, CD19-enriched

value: relapsed chronic lymphocytic leukemia (CLL) patient

value: patient #3304


title: L10-16B

description:
W16B_NS
Gene expression after 16h.

source_name: Mycelium, wild type, 16h

tag: strain/background

value: wild type

value: mycelium

tag: developmental stage

value: exponential phase

tag: culture

value: YEME

tag: time


title: CD19-enriched CLL patient sample, patient #8704

description:
CD19-enriched CLL clinical sample
A0018420

value: patient #8704

value: C

tag: tissue

value: CD19-enriched CLL patient sample


title: L10-16D

description:
W16D_NS
Gene expression after 16h.


title: CD19-enriched CLL patient sample, patient #202

description:
CD19-enriched CLL clinical sample
A0018421

value: patient #202

value: B


title: NGT_5

tag: disease state


title: CD19-enriched CLL patient sample, patient #8705

description:
CD19-enriched CLL clinical sample
A0018419

value: patient #8705


title: NGT_4

tag: age (yrs)


title: Sle1.3/het #2

description: Spleen Sle1.3/E2-2het #2; Sle1.3/E2-2het #2

value: sle1.3/E2-2het; Sle1.3 mice haplodeficient for E2-2

tag: gender

value: male

value: spleen

value: splenocytes


title: L10-12D

description:
W12D_NS
Gene expression after 12h.

source_name: Mycelium, wild type, 12h


title: CD19-enriched CLL patient sample, patient #9603

description:
CD19-enriched CLL clinical sample
A0018418

tag: subject status

tag: patient id

value: patient #9603


title: L10-16A

description:
W16A_NS
Gene expression after 16h.


title: Sle1.3/het #1

description: Spleen Sle1.3/E2-2het #1; Sle1.3/E2-2het #1


title: LCL_IFN-β treated_4hr [YM2209]

tag: in vitro treated ifnb

value: Yes

value: Female

value: Relapsing Remitting

value: Treated

tag: age

value: J


title: CD19-enriched CLL patient sample, patient #903

description:
CD19-enriched CLL clinical sample
A0018414

value: relapsed chronic lymphocytic leukemia (CLL) patient

value: patient #903

tag: binet stage


title: NGT_2

value: healthy controls with normal glucose tolerance (NGT)

value: Serum


title: L10-12B

description:
W12B_NS
Gene expression after 12h.

value: wild type

value: mycelium

value: exponential phase

value: YEME


title: Sle1.3 #2

description: Spleen Sle1.3 #2; Sle1.3 #2

source_name: splenocytes from sle1.3 mice

value: Sle1.3; lupus mice

value: female


title: ZJUD7-24B

description:
D24B_NS
Gene expression after 24h.

source_name: Mycelium, ∆scgA, 24h

value: ∆scgA


title: L10-12A

description:
W12A_NS
Gene expression after 12h.


title: Sle1.3 #3

description: Spleen Sle1.3 #3; Sle1.3 #3

value: male

value: spleen

value: splenocytes


title: Wild Type #2

description: Spleen Wild Type #2; WT #2

source_name: splenocytes from Wild Type mice


title: Sle1.3 #1

description: Spleen Sle1.3 #1; Sle1.3 #1


title: NGT_3


title: NGT_27


title: NGT_1


title: ZJUD7-24C

description:
D24C_NS
Gene expression after 24h.


title: ZJUD7-16D

description:
D16D_NS
Gene expression after 16h.

source_name: Mycelium, ∆scgA, 16h


title: ZJUD7-24A

description:
D24A_NS
Gene expression after 24h.


title: ZJUD7-16C

description:
D16C_NS
Gene expression after 16h.


title: CD19-enriched CLL patient sample, patient #6005

description:
CD19-enriched CLL clinical sample
A0018410

value: patient #6005

value: A

value: CD19-enriched CLL patient sample


title: CD19-enriched CLL patient sample, patient #5601

description:
CD19-enriched CLL clinical sample
A0018411

value: relapsed chronic lymphocytic leukemia (CLL) patient

value: patient #5601

value: C


title: CD19-enriched CLL patient sample, patient #3201

description:
CD19-enriched CLL clinical sample
A0018409

value: patient #3201

value: B


title: Wild Type #1

description: Spleen Wild Type #1; WT #1

value: wild type


title: CD19-enriched CLL patient sample, patient #4204

description:
CD19-enriched CLL clinical sample
A0018408

value: patient #4204


title: CD19-enriched CLL patient sample, patient #4004

description:
CD19-enriched CLL clinical sample
A0018412

value: patient #4004


title: ZJUD7-16B

description:
D16B_NS
Gene expression after 16h.

value: mycelium

value: exponential phase

value: YEME


title: ZJUD7-12C

description:
D12C_NS
Gene expression after 12h.

source_name: Mycelium, ∆scgA, 12h

value: ∆scgA


title: CD19-enriched CLL patient sample, patient #6004

description:
CD19-enriched CLL clinical sample
A0018406

value: patient #6004


title: CD19-enriched CLL patient sample, patient #1602

description:
CD19-enriched CLL clinical sample
A0018407

value: patient #1602


title: ZJUD7-12B

description:
D12B_NS
Gene expression after 12h.


title: Mel 290/T+

city: Copenhagen

first: Tina

last: Jehs

address: Blegdamsvej 3

country: Denmark

institute: University of Copenhagen

description: Gene expression data grown with activated T cells

hyb_protocol: Standard protocol, Affymetrix Core center, Rigshospitalet, Copenhagen, Denmark

data_processing:
The data was analyzed with the Expression Console
affymetrix-algorithm = rma-gene-default (v.1.0)
program-name = Expression Console (v.1.2.0.20)

source_name: uveal melanoma_after co-culture

label_protocol: Biotinylated cRNA was prepared according to the strandard Affymetrix one-cycle protocol from RNA (Expression Analysis Technical Manual 2001, Affymetrix)

growth_protocol: The uveal melanoma (UM) cell lines 92.1, Mel 270 and Mel 290 were maintained in Roswell Park Memorial Institute medium 1640 (RPMI) supplemented with 2 mg/mL sodium hydrogen carbonate (Substrate Department at the Panum Institute, Copenhagen, Denmark), with 10% Fetal Calf Serum (FCS) (Seralab, West Sussex, UK), 300 µg/mL L-glutamine and 200 µg/mL penicillin/streptomycin (Gibco, Paisley, UK). 100,000 cells of Mel 290 and Mel 270 and 80,000 cells of 92.1 were plated into 6-well plates (Becton Dickinson, Le Pont De Claix, France). When Mel 290 was confluent and Mel 270 and 92.1 were subconfluent, medium was changed for all the experiments to X-VIVO 15 serum-free medium (Lonza BioWhittaker, Verviers, Belgium) containing 300 µg/mL L-glutamine, 100 µg/mL penicillin/streptomycin and 2.5 µg/mL amphotericin B (Gibco, Paisley, UK), which did not have an effect on the further growth of the UM cells as they grew until confluency. Cells were grown in X-VIVO 15 serum-free medium for 64 h at 37 °C and 5% CO2.

extract_protocol: Uveal melanoma cells were removed using a cell scraper. RNA was purified from the UM cell lines using the NucleoSpin® RNA II Kit (Macherey-Nagel, Düren, Germany) in accordance with manufacturer’s instructions.

treatment_protocol: T cells were purified from fresh whole blood from healthy young volunteers. T cells were cultured in 0.4 µm polyethylene terephthalate membrane inserts (BD Biosciences, Franklin Lakes, NJ) over UM cell lines. A fixed number of T cells was added to each culture (1.5 x 106 T cells/well in a total volume of 3 ml), to ensure comparable levels of T cell derived soluble factors in the medium. T cells had been activated using Dynabeads® CD3/CD28 T cell Expander (Invitrogen, Oslo, Norway) and cells were co-cultured with UM cells for 64 h at 37 °C and 5% CO2. The ratio of T cells to beads was 1:1

tag: cell line

value: Mel 290

value: human choroidal uveal melanoma

tag: cocultured with

value: activated T cells from healthy volunteers


title: 92.1

description: Gene expression data grown alone

scan_protocol: Standard protocol, Affymetrix Core center, Rigshospitalet, Copenhagen, Denmark

source_name: uveal melanoma_before co-culture

value: none (control)


title: AEH CK IT 2

status: Public on Jul 29 2014

city: Frankfurt

first: Claudia

last: Döring

address: Theodor Stern Kai 7

department: Medical School, Institite of Pathology

country: Germany

institute: Johann Wolfgang-Goethe University Frankfurt a.M.

hyb_protocol: Human Gene 1.0 ST arrays (Affymetrix) were hybridized with 2.5 mg labelled cDNA.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Statistical analysis was done with the statistical computing environment R. Additional software packages (affy, geneplotter, multtest, and vsn) were taken from the Bioconductor project.  Microarray preprocessing: Probe level normalization was conducted using the variance stabilization method (vsn) from Huber et al..
Unsupported Human Gene 1.0 ST Array CDF Files
HuGene-1_0-st-v1 Probeset Annotations, CSV Format, Release 30 (11 MB 01/22/10)

source_name: U937 cells expressing a C-terminal truncated form of RUNX1-ETO and c-KIT(N822K)

label_protocol: Samples were labelled with Encore biotin module (NUGEN) washed and stained using the HWS Kit (Affymetrix).

growth_protocol: U937 cells were cultured in RPMI 1640 containing 10% FCS

extract_protocol: RNA was extracted with the RNeasy Micro Kit from Qiagen.RNA was amplified using the Ovation Pico WTA System V2 from NUGEN applied for 50ng total RNA

treatment_protocol: U937 cells were transduced with retroviral vectors encoding REtr or c-KIT(N822K) and FACS selected prior to analysis

tag: phenotype


title: Mel 270

description: Gene expression data grown alone

value: Mel 270

tag: cell type


title: AEH CK IT 3

value: expressing a C-terminal truncated form of RUNX1-ETO and c-KIT(N822K)


title: AEH CK IT 1


title: 92.1/T+


title: Mel 290

description: Gene expression data grown alone


title: WT 2

source_name: U937 wild type cells (ATCC # CRL-1593.2)


title: CK IT 3

source_name: U937 cells expressing c-KIT(N822K)

value: expressing c-KIT(N822K)


title: Mel 270/T+


title: AEH 1

source_name: U937 cells expressing a C-terminal truncated form of RUNX1-ETO


title: AEH 3

value: expressing a C-terminal truncated form of RUNX1-ETO


title: WT 3

value: wild type


title: CK IT 2


title: 18_HCC

hyb_protocol: GeneChip® miRNA 1.0 arrays (Affymetrix) were hybridized with 50 ng labelled microRNA, Hybridisation time was 40 hours.

data_processing:
Statistical analysis was done with the statistical computing environment R. Additional software packages (affy, geneplotter, multtest, and vsn) were taken from the Bioconductor project.  Microarray preprocessing: Probe level normalization was conducted using the variance stabilization method (vsn) from Huber et al..
UnsupportedGeneChip® miRNA 1.0 Array CDF Files
miRNA 1.0 Annotations, Unsupported, CSV format from Affymetrix

source_name: tumor cells HCC

label_protocol: miRNA was labeled with the Affymetrix FlashTag Biotin HSR RNA Labeling Kit

extract_protocol: miRNA was extracted with the miRNeasy FFPE Kit from Qiagen

treatment_protocol: Cells were microdissected from H&E stained FFPE sections

tag: gender (m=1, f=2)

tag: etiology of liver cirrhosis  (1=viral, 2=non-viral)

tag: histology

tag: overall survival (days)

tag: overall survival (low_<or=median=1, high_>median=2)

tag: response (recist) (pr or sd=1, pd=2)


title: 12_HCC


title: 19_HCC


title: 13_HCC


title: 16_HCC


title: 1_HCC_tech

source_name: tumor cells HCC (biological replicate from sample 1_HCC)


title: 17_HCC


title: 14_HCC


title: CK IT 1


title: WT 1


title: 15_HCC


title: 7_HCC


title: 8_HCC


title: 11_HCC


title: 9_HCC


title: 10_HCC


title: 5_HCC


title: 3_HCC


title: 4_HCC


title: 6_HCC


title: 2_HCC


title: 1_HCC


title: miR212/132_Dox-_rep2

city: Freiburg

first: Yoko

middle: Fukuda

last: Yuzawa

address: Stübeweg 51

institute: Max-Planck Institute of Immunobiology

hyb_protocol: Hybridization and washing were done using Agilent Gene Expression Hybridization Kit (Agilent, 5188-5242) and Agilent Wash Buffer Kit (Agilent, 5188-5327) according to manufacturer's protocols (One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling, v6.5 May 2010).

scan_protocol: Slides were scanned after washing on the Agilent Microarray Scanner (G2565CA) using one color scan setting for 4x44k array slides (Profile: AgilentHD_GX1col, Resolution: 5 μm).

data_processing: The scanned images were analyzed with Feature Extraction Software using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Further data processing was done using GeneSpring GX Software v11.0.

source_name: Tet-ON miR-212/132 MCF7 cells, DOX-, replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared using Low Input Quick Amp Labeling Kit, One-Color (Agilent, 5190-2305) according to manufacturer's instructions (One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling, v6.5, May 2010), followed by RNAeasy column purification (Qiagen, 4106).

growth_protocol: Doxycycline-dependent gene inducible MCF7 cells were grown in EMEM medium containing 10% FCS, 0.01 mg/ml bovine insulin, Antibiotics, 100μg/ml of G418 and 100μg/ml at 37℃ in a humidified incubator with 5% CO2.Doxycycline-dependent gene inducible MCF7 cells were grown in EMEM medium containing 10% FCS, 0.01 mg/ml bovine insulin, Antibiotics, 100μg/ml of G418 and 100μg/ml at 37℃ in a humidified incubator with 5% CO2.

extract_protocol: Total RNA was prepared using the RNeasy Kit (QIagen) following the manufacturer’s recommendations. The protocol includes on-column DNase digestion. RNA was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: Either Tet-ON miR-212/132 MCF7 or Tet-ON HIC1 MCF7 were treated with 1μg/ml of Doxycycline and incubated for 36 hours

tag: organ

value: mammary gland; breast

tag: disease

value: adenocarcinoma

value: epithelial

tag: treatment

value: Tet-ON miR-212/132 MCF7 cells treated without DOX


title: Cell line SH-2

city: Cambridge

first: Shih-Min

middle: A

last: Huang

state: MA

address: 640 Memorial Drive

department: Discovery and Early Development

institute: Sanofi Oncology

description: Gene expression data from AML cell line

hyb_protocol: cRNA is purified using magnetic beads and quantitated using spectrophotometry. Next, 11ug of purified cRNA is fragmented using a 5X Fragmentation buffer, then a hybridization cocktail is prepared and added to the fragmentation product using the Hybridization, Wash and Stain kit (Affymetrix), applied to Human U133_Plus2.0 arrays, and incubated at 45°C for 16 hours.

scan_protocol: Following hybridization, arrays are washed and stained using standard Affymetrix procedures before scanning on the Affymetrix GeneChip Scanner

data_processing: Data extraction was performed using Expression Console

source_name: Cell line SH-2

label_protocol: RNA samples are converted into labeled target antisense RNA (cRNA) using the Single-Round RNA Amplification and Biotin Labelling System (Enzo).

growth_protocol: NOMO1, KG1, PLB985, ML2, HL-60, EOL1, FKH1, GDM1, HNT34, THP1, SKM1, PL21, ME-1, KMOE-2, GF-D8, HEL, SET2, KG1?, KASUMI-1, MO7e and NB4 were grown in RPMI 1640 medium supplemented with 10% or 20% FBS; F-36P was cultured in RPMI 1640 medium supplemented with 10% FBS and 5ng/ml human IL-3; OCI-M1, OCI-M2, SHI-1, and SH-2 were cultured in IMDM medium supplemented with 20% FBS. OCI-AML2, OCI-AML5, OCI-AML3 were cultured in alpha-MEM medium supplemented with 10% or 20% FBS and GM-CSF or SCF. All cell lines were placed in a 37C humidified incubator containing 5% CO2. 10x10^6 cells were washed with 1xPBS and the cell pellets were stored at -80C before sending out for Microarray analysis.

extract_protocol: Total RNA is isolated using the Qiagen miRNeasy Mini Kit (Qiagen, #217004).


title: Cell line SHI-1

description: Gene expression data from AML cell line

source_name: Cell line SHI-1


title: miR212/132_Dox+_rep2

source_name: Tet-ON miR-212/132 MCF7 cells, DOX+, replicate 2

value: Tet-ON miR-212/132 MCF7 cells treated with DOX


title: HIC_Dox-_rep1

source_name: Tet-ON HIC1 MCF7 cells, DOX-, replicate 1

value: Tet-ON HIC1 MCF7 cells treated without DOX


title: miR212/132_Dox-_rep1

source_name: Tet-ON miR-212/132 MCF7 cells, DOX-, replicate 1


title: Cell line OCI-M2

description: Gene expression data from AML cell line

source_name: Cell line OCI-M2


title: Cell line HEL

description: Gene expression data from AML cell line

source_name: Cell line HEL

value: HEL


title: HIC_Dox-_rep2

source_name: Tet-ON HIC1 MCF7 cells, DOX-, replicate 2


title: VPA  (reisolated CD34+ cells (Day7)) 2

city: New York,

first: Pratima

last: Chaurasia

state: New York

address: One Gustave  L Levy Place

department: Medicine

institute: Icahn School of Medicine at Mount Sinai

data_processing: The data were normalised using quantile normalisation with Illumina GUI in R

label: Biotin labeled cRNA

source_name: Cord Blood

label_protocol: Double stranded cDNA and biotin-labeled cRNA will be synthesized and purified from  total RNA.

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

treatment_protocol: CB-CD34+ primary  HSC cells were  primed with cytokines ( SCF, FLT3, IL3 and TPO) for 16 hr and cultures were continued for a week in the presence and absence of individual HDACI.

tag: ID

value: VPA  reisolated CD34+ cells Day7


title: miR212/132_Dox+_rep1

source_name: Tet-ON miR-212/132 MCF7 cells, DOX+, replicate 1


title: HIC_Dox+_rep2

source_name: Tet-ON HIC1 MCF7 cells, DOX+, replicate 2

value: Tet-ON HIC1 MCF7 cells treated with DOX


title: Cell line GF-D8

description: Gene expression data from AML cell line

source_name: Cell line GF-D8


title: HIC_Dox+_rep1

source_name: Tet-ON HIC1 MCF7 cells, DOX+, replicate 1


title: Scriptaid (reisolated CD34+ cells (day7)) 2

value: Scriptaid reisolated CD34+ cells day7


title: Scriptaid (reisolated CD34+ cells (day7)) 1


title: Control (reisolated CD34+ cells (day7)) 2

value: Control reisolated CD34+ cells day7


title: VPA  (reisolated CD34+ cells (Day7)) 1


title: Control (reisolated CD34+ cells (day7)) 1


title: Cell line SET2

description: Gene expression data from AML cell line

source_name: Cell line SET2


title: Cell line FKH-1

description: Gene expression data from AML cell line

source_name: Cell line FKH-1


title: NGT_6

description: Auto-antibodies from serum samples were profiled using a high-density, fluorescence-based protein microarray containing duplicate spots of 9,480 human proteins derived from the Ultimate ORF collection

tag: disease state

value: healthy controls with normal glucose tolerance (NGT)

tag: age (yrs)

tag: tissue

value: Serum


title: Cell line HNT-34

description: Gene expression data from AML cell line

source_name: Cell line HNT-34

tag: cell line


title: Cell line NOMO-1

description: Gene expression data from AML cell line

source_name: Cell line NOMO-1


title: Streptomyces_36h_W36B

city: Hangzhou

first: Pin

last: Yu

state: Zhejiang Province

address: College of Life Sciences, Institute of Biochemistry, Zhejiang University, 866 Yuhangtang Road, Hangzhou, Zhejiang 310058, China

department: College of Life Sciences

institute: Zhejiang University

description: Gene expression at 36h in the S.  chattanoogensis L10

hyb_protocol: Each Slide was hybridized with 600ng Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=5μm, PMT 100%, 10%, 16bit.

data_processing: Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

source_name: Mycelium

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat#5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

growth_protocol: Grow in YEME for 16,24,36 hours,respectively, 200 r/min, 30℃

extract_protocol: Total RNA was isolated using the RNA extract kit (QIAGEN, Germany), according to the manufacturer’s instructions, and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: Mycelium was collected from YEME culture by centrifugation, discard the supernatant, wash the mycelium twice by PBS buffer.

tag: genotype/variation

value: L10 (wild type)

tag: time point

tag: culture

value: YEME


title: Streptomyces_24h_W24C

description: Gene expression at 24h in the S.  chattanoogensis L10


title: Cell line PL-21

description: Gene expression data from AML cell line

source_name: Cell line PL-21


title: Streptomyces_36h_W36D


title: Streptomyces_16h_W16B

description: Gene expression at 16h in the S.  chattanoogensis L10


title: Primary cells (CD34+ cells (HSC) day0) 1

tag: cell type

value: Primary CD34+ cord cells


title: Primary cells (CD34+ cells (HSC) day0) 2


title: Streptomyces_24h_W24B


title: Cell line ME-1

description: Gene expression data from AML cell line

source_name: Cell line ME-1


title: Cell line OCI-AML2

description: Gene expression data from AML cell line

source_name: Cell line OCI-AML2


title: Cell line OCI-AML5

description: Gene expression data from AML cell line

source_name: Cell line OCI-AML5


title: Cell line KG-1A

description: Gene expression data from AML cell line

source_name: Cell line KG-1A


title: Streptomyces_36h_W36C


title: CeO2 treated germinant rep3

city: Bethesda

first: Laxminath

last: Tumburu

state: MD

address: 9000 Rockville Pike

institute: National Institutes of Health

description: Gene expression data from 12 days old seedlings exposed to 500mg/L CeO2

hyb_protocol: Following fragmentation, quality of cRNA was evaluated on 2100 bionanalyzer, and  hybridized for overnight at 45°C to Affymetrix ATH1 GeneChips in an Affymetrix Model 640 GeneChip hybridization oven. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Arrays were washed and stained using an Affymetrix 450 fluidics station as per the manufacturer and then scanned on an Affymetrix Model 3000 scanner

data_processing: Raw scanning data files (Affymetrix.cel) were obtained using Affymetrix GeneChip Operating Software, v1.4, and then files were analyzed by Bioconductor SimpleAffy to assess data quality.  Data were normalized by quantile normalization and gene calls were generated using a robust multichip average algorithm.

organism: Arabidopsis thaliana

source_name: Arabidopsis germinant, 12 days old

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 15 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Seeds surface sterilized with 70% v/v ethanol, 50% bleach, washed 4 times in water, cold-stratified (4°C, 48 hours), placed on filter paper and grown in growth chamber for seed germination and initial germinant growth (22°C,light 100 μmol m-2 s-1, photoperiod 16 h/8 h light/dark).

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

treatment_protocol: Germinants for and microarray analyses (n = 3) were produced by placing 50 sterilized, stratified seeds on a sterile 9 cm glass microfiber filter disc (Whatman GF/A paper) held in a sterile 100 mm x 15 mm polystyrene Petri dishes (Fisher Scientific).  Discs were wetted with 2 mL of solution (nano-ceria control: sterilized millipore water; nano-titania control: 0.1m M KCl; ENP treatments: 500 mg ENPs L-1).

value: seedling

tag: ecotype

value: Columbia (Col-0)

tag: age

value: 12 days old seedlings


title: Cell line KMOE-2

description: Gene expression data from AML cell line

source_name: Cell line KMOE-2


title: Streptomyces_16h_W16A


title: CeO2 treated germinant rep2


title: Streptomyces_16h_W16D


title: Cell line KASUMI-1

description: Gene expression data from AML cell line

source_name: Cell line KASUMI-1


title: Cell line PLB-985

description: Gene expression data from AML cell line

source_name: Cell line PLB-985


title: Cell line MV4-11

description: Gene expression data from AML cell line

source_name: Cell line MV4-11


title: CeO2 treated germinant rep1


title: Cell line KG-1

description: Gene expression data from AML cell line

source_name: Cell line KG-1


title: Streptomyces_24h_W24A


title: ZJUD7-12A

description:
D12A_NS
Gene expression after 12h.

source_name: Mycelium, ∆scgA, 12h

tag: strain/background

value: ∆scgA

value: mycelium

tag: developmental stage

value: exponential phase

tag: time


title: Millipore Water treated germinant rep3

description: Gene expression data from 12 days old seedlings exposed to millipore water

value: Millipore Water


title: Millipore Water treated germinant rep2


title: AEH 2

source_name: U937 cells expressing a C-terminal truncated form of RUNX1-ETO

tag: phenotype


title: TiO2 treated germinant, biological rep2

description: Gene expression data from 12 days old seedlings exposed to 500mg/L TiO2


title: TiO2 treated germinant, biological rep3


title: Millipore Water treated germinant rep1


title: Streptomyces_36h_Adp36D

description: Gene expression at 36h in the ∆adpAch

value: ∆adpAch


title: Cell line OCI-M1

description: Gene expression data from AML cell line

source_name: Cell line OCI-M1


title: Streptomyces_36h_Adp36h

description: Gene expression at 36h in the ∆adpAch


title: Cell line THP-1

description: Gene expression data from AML cell line

source_name: Cell line THP-1


title: Streptomyces_24h_A424h

description: Gene expression at 24h in the ∆adpAch


title: Cell line NB-4

description: Gene expression data from AML cell line

source_name: Cell line NB-4


title: TiO2 treated germinant, biological rep1


title: Streptomyces_24h_A224h

description: Gene expression at 24h in the ∆adpAch

source_name: Mycelium


title: Streptomyces_36h_A36B

description: Gene expression at 36h in the ∆adpAch


title: Cell line MO7E

description: Gene expression data from AML cell line

source_name: Cell line MO7E


title: Streptomyces_24h_A124h

description: Gene expression at 24h in the ∆adpAch


title: Streptomyces_16h_A16B2

description: Gene expression at 16h in the ∆adpAch


title: KCl treated germinant, biological rep3

description: Gene expression data from 12 days old seedlings exposed to 0.1mM KCl

value: KCl


title: KCl treated germinant, biological rep1


title: Cell line MOLM-16

description: Gene expression data from AML cell line

source_name: Cell line MOLM-16


title: Cell line SKM-1

description: Gene expression data from AML cell line

source_name: Cell line SKM-1


title: Cell line ML-2

description: Gene expression data from AML cell line

source_name: Cell line ML-2


title: KCl treated germinant, biological rep2


title: Cell line MOLM-13

description: Gene expression data from AML cell line

source_name: Cell line MOLM-13


title: Streptomyces_16h_A16C

description: Gene expression at 16h in the ∆adpAch


title: Cell line HL-60

description: Gene expression data from AML cell line

source_name: Cell line HL-60


title: Cell line F-36P

description: Gene expression data from AML cell line

source_name: Cell line F-36P


title: Human SZ95 sebocytes_control vs 10 μM CBD-treated (24hrs)_CONTROL_rep3

city: Debrecen

first: Attila

last: Oláh

address: Nagyerdei krt. 98.

department: Department of Physiology

country: Hungary

institute: University of Debrecen

description: Sample biological set 3

hyb_protocol: Gene Expression Hybridization Kit Agilent according to the manufacturer protocol

scan_protocol: Agilent scanner, FE SW 9.5

data_processing: To read out and process the microarray image files the Agilent Feature Extraction Software was used. R/BioConductor software (R version: 2.15.1, limma package) was used for background subtraction and quantile normalization. Weights of features were set according to Agilent's recommendations.

source_name: SZ95 sebocytes_vehicle

label_protocol: Low Input QuickAmp 6.5

growth_protocol: Human immortalized SZ95 sebocytes, originated from human facial sebaceous glands (Zouboulis et al, J Invest Dermatol, 1999), were cultured in Sebomed® Basal Medium (Biochrom) supplemented with 10% fetal bovine serum (LifeTechnologies), 1 mM CaCl2, 5 ng/ml human epidermal growth factor (Sigma-Aldrich), 50 IU/ml penicillin and 50 μg/ml streptomycin (both from Teva).

extract_protocol: Total RNA was extracted by using Trizol following manufacturer's instructions

treatment_protocol: Cells were seeded to Petri-dishes. At cca. 60% confluence, cells were treated by CBD (10 μM) or by vehicle (ethanol) for 24 hrs.

value: immortalized human sebaceous gland cells

tag: treated with

value: ethanol for 24hr (vehicle control)


title: L_arcana_CGH_rep4

type: genomic

city: Strömstad

first: Marina

last: Panova

address: Tjärnö

department: Biol and Env Sciences

country: Sweden

institute: Gothenburg University

description:
This sample is of Littorina arcana. It is the fourth of four biological replicates used in this experiment.
LA_4

hyb_protocol: Hybridization was performed using 20 ug of labeled DNA for 48 hours at 42°C in NimbleGen Hybridization System followed by with NimbleGen Washing Kit according to the manufacturer's protocol.

scan_protocol: Scanning was performed using Agilnet G2565AA microarray scanner (Agilent Technologies, Santa Clara, CA) at 2 um-resolution.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.5 (Roche NimbleGen, Inc.).

molecule: genomic DNA

organism: Littorina arcana

source_name: Littorina arcana

label_protocol: Labeling was performed with a starting amount of 1 ug genomic DNA, NimbleGen Dual label kit and following the manufacturer's protocol.

growth_protocol: Snails were collected in the field.

extract_protocol: Total DNA was extracted from foot muscle tissue using the CTAB digestion (including RNase treatment) followed by chloroform precipitation.  DNA quality and concentration was determined using NanoDrop spectrophotometer (Thermo Scientific) and agarose-gel electrophoresis.

tag: geogr. region

value: East coast of Britain


title: MCF-7-control, biological replicate 3

city: Atlanta

first: Roman

middle: F. N.

last: Mezencev

state: GA

address: 310 Ferst Dr

department: School of Biology

institute: Georgia Institute of Technology

description: gene expression data from breast cancer cell line MCF-7 transfected with control  plasmid

hyb_protocol: 5 ug of labelled cDNA were hybridized for 16 hr at 45C (rotation 60 rpm) on Human Genome U133 Plus 2.0 Array. Chips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G

data_processing: The data were analyzed with Expression Console software Build 1.2.1.20 (Affymetrix, Santa Clara, CA, USA) using the Affymetrix default analysis setting for PLIER algorithm

source_name: MCF-7 with control plasmid

label_protocol: RNA was processed to cDNA and amplified using the Applause 3'-Amp System (NuGEN, San Carlos, CA, USA), and the cDNA was fragmented and labeled using the Encore Biotin Module (NuGEN) according to the manufacturer’s instructions

growth_protocol: cells were maintained in RPMI 1640 medium supplemented with 10% FBS (Atlanta Biologicals, Lawrenceville, GA), 1% antibiotic-antimycotic solution (Mediatech-Cellgro, Manassas, VA) and 400 ug/mL G418 (Geneticin, GIBCO)

extract_protocol: total RNA was isolated using the RNeasy Mini Kit (Quiagen, Valencia, CA, USA) according to the manufacturer’s instructions

value: epithelial-like


title: MCF-7-control, biological replicate 2


title: Cell line GDM-1

description: Gene expression data from AML cell line

source_name: Cell line GDM-1


title: L_compressa_CGH_rep4

description:
This sample is of Littorina compressa. It is the fourth of four biological replicates used in this experiment.
LC_4

organism: Littorina compressa

source_name: Littorina compressa


title: Streptomyces_16h_A16A

description: Gene expression at 16h in the ∆adpAch


title: Cell line EOL-1

description: Gene expression data from AML cell line

source_name: Cell line EOL-1


title: MCF-7-Snail, biological replicate 3

description: gene expression data from breast cancer cell line MCF-7 transfected to express the transcription factor Snail

source_name: MCF-7 with ectopic Snail expression

value: mesenchymal-like


title: L_saxatilis_Sweden_Wave_CGH_rep4

description:
This sample is of Littorina arcana. It is the third of four biological replicates used in this experiment.
LS_Sw_Wave_4

organism: Littorina saxatilis

source_name: Littorina saxatilis Swedish Wave ecotype

value: West coast of Sweden

value: Wave


title: Human SZ95 sebocytes_control vs 10 μM CBD-treated (24hrs)_rep2-1 (technical repeat of rep2)

description: Second microarray of Sample set 2

hyb_protocol: The hybridization procedure was performed according to the Two-color Microarray-Based Gene Expression Analysis (Qick Amp Labeling) protocol using the Agilent Gene Expression Hybridization Kit. Briefly, 825 ng of the corresponding Cy3- and Cy5-labeled cRNA were combined and hybridized overnight (17 hours, 65 °C) to Agilent Whole Human Genome 4x44K Oligo Microarrays using Agilent’s recommended hybridization chamber and oven.

scan_protocol: Fluorescence signals of Microarrays were detected by Agilent’s Microarray Scanner.

data_processing: To read out and process the microarray image files the Agilent Feature Extraction Software was used.  R/BioConductor software (R version: 2.15.1, limma package) was used for background subtraction and LOWESS normalization. Extracted channels were quantile normalized. Weights of features were set according to Agilent's recommendations.

label_protocol: RNA samples (200 ng of each) were amplified and labeled using the Agilent Low Input  Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer’s protocol, with Spike-In controls

source_name: SZ95 sebocytes_CBD

value: 10 μM (-)-cannabidiol (CBD) for 24hrs


title: L_saxatilis_Sweden_Crab_CGH_rep4

description:
This sample is of Littorina saxatilis Swedish Crab ecotype. It is the fourth of four biological replicates used in this experiment.
LS_Sw_Crab_4

value: Crab


title: L_arcana_CGH_rep3

description:
This sample is of Littorina saxatilis Swedish Wave ecotype. It is the fourth of four biological replicates used in this experiment.
LA_3


title: MCF-7-Snail, biological replicate 2


title: L_saxatilis_Spain_Crab_CGH_rep4

description:
This sample is of Littorina saxatilis Spanish Crab ecotype. It is the fourth of four biological replicates used in this experiment.
LS_Sp_Crab_4

source_name: Littorina saxatilis Swedish Crab ecotype

value: Galician coast, Spain


title: L_arcana_CGH_rep1

description:
This sample is of Littorina arcana. It is the first of four biological replicates used in this experiment.
LA_1


title: Human SZ95 sebocytes_control vs 10 μM CBD-treated (24hrs)_rep1

description: Sample biological set 1


title: Human SZ95 sebocytes_control vs 10 μM CBD-treated (24hrs)_rep2

description: Sample biological set 2


title: L_saxatilis_Spain_Wave_CGH_rep4

description:
This sample is of Littorina saxatilis Spanish Wave ecotype. It is the fourth of four biological replicates used in this experiment.
LS_Sp_Wave_4


title: L_arcana_CGH_rep2

description:
This sample is of Littorina arcana. It is the second of four biological replicates used in this experiment.
LA_2


title: MCF-7-control, biological replicate 1


title: L_saxatilis_Spain_Crab_CGH_rep3

description:
This sample is of Littorina saxatilis Spanish Crab ecotype. It is the third of four biological replicates used in this experiment.
LS_Sp_Crab_3


title: GSK3 CTRL 4

city: Chapel Hill

first: William

middle: D

last: Snider

state: NC

address: Mason Farm Road

department: Neuroscience Center

institute: UNC Chapel Hill

description: gene expression from embryonic cortex at E18

hyb_protocol: Protocol conducted at Microarray Core UNC

data_processing: These data were analyzed using the Affymetrix Mouse Gene 2.0 St array and Partek Genomics Suite Version 6.12.0712

source_name: mouse embryo at E18

growth_protocol: Embryonic day 18

extract_protocol: RNA was extracted using the MiRNAeasy kit (Qiagen)

treatment_protocol: no treatment, comparison of knockout versus control

tag: tissue type

value: embryonic cortex

value: GSK-3 alpha -/- beta loxp/loxp


title: L_saxatilis_Britain_Wave_CGH_rep4

description:
This sample is of Littorina saxatilis British Wave ecotype. It is the fourth of four biological replicates used in this experiment.
LS_Br_Wave_4


title: GSK3 CKO 6

scan_protocol: Protocol conducted at Microarray Core UNC

value: GSK-3:Nex conditional mutant


title: Cell line OCI-AML3

description: Gene expression data from AML cell line

source_name: Cell line OCI-AML3


title: GSK3 CTRL 3

label_protocol: Protocol conducted at Microarray Core UNC


title: GSK3 CKO 7


title: MCF-7-Snail, biological replicate 1


title: L_saxatilis_Britain_Crab_CGH_rep4

description:
This sample is of Littorina saxatilis British Crab ecotype. It is the fourt of four biological replicates used in this experiment.
LS_Br_Crab_4


title: L_saxatilis_Britain_Wave_CGH_rep3

description:
This sample is of Littorina saxatilis British Wave ecotype. It is the third of four biological replicates used in this experiment.
LS_Br_Wave_3


title: GSK3 CTRL 2


title: GSK3 CKO 5


title: L_saxatilis_Sweden_Wave_CGH_rep3

description:
This sample is of Littorina saxatilis Swedish Wave ecotype. It is the third of four biological replicates used in this experiment.
LS_Sw_Wave_3


title: Fzd2 mutant lung -biological rep 3

city: Philadelphia

first: Rachel

middle: S

last: Kadzik

state: PA

address: Translational Research Center, 11th Flr.; Room 179, 3400 Civic Center Boulevard, Bldg 421

department: Molecular Cardiology

institute: University of Pennsylvania

hyb_protocol: cDNAs were added to Affymetrix hybridization cocktails, heated at 99ºC for 2 min and hybridized for 16 h at 45ºC to GeneChips (Affymetrix Inc., Santa Clara CA). The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.

scan_protocol: A confocal scanner was used to collect fluorescence signal after excitation at 570 nm.

data_processing: The data were analyzed using scripts written in the R languge using the Bioconductor package Oligo using the default settings for RMA.

source_name: E12.5 Lung, Fzd2 CKO

label_protocol: 100ng of total RNA was converted to first-strand cDNA using reverse transcriptase primed by a poly(T) oligomer that incorporated the T7 RNA polymerase promoter. Second-strand cDNA synthesis was followed by in vitro transcription (Affymetrix One-Cycle Target Labeling Kit) for linear amplification and biotinylation of each transcript.

growth_protocol: Timely matings were set up to obtain E12.5 embryos

extract_protocol: RNA was extracted using Rneasy mini kit (Qiagene)

treatment_protocol: Lung buds were disected from E12.5 embryos with appropriate genotypes and stored in Trizol for future RNA extraction

tag: genotype

value: Fzd2Flox/Flox; Shh cre/+

value: embryonic lung


title: L_fabalis_CGH_rep4

description:
This sample is of Littorina fabalis. It is the fourth of four biological replicates used in this experiment.
LF_4

organism: Littorina fabalis

source_name: Littorina fabalis


title: ShhCre control lung -biological rep 3

source_name: E12.5 Lung, Shhcre control

value: Shh cre/+


title: Fzd2 mutant lung -biological rep 2


title: L_saxatilis_Britain_Crab_CGH_rep3

description:
This sample is of Littorina saxatilis British Crab ecotype. It is the third of four biological replicates used in this experiment.
LS_Br_Crab_3


title: ShhCre control lung -biological rep 2


title: L_saxatilis_Spain_Crab_CGH_rep2

description:
This sample is of Littorina saxatilis Spanish Crab ecotype. It is the second of four biological replicates used in this experiment.
LS_Sp_Crab_2


title: L_saxatilis_Sweden_Crab_CGH_rep3

description:
This sample is of Littorina saxatilis Swedish Crab ecotype. It is the third of four biological replicates used in this experiment.
LS_Sw_Crab_3


title: L_saxatilis_Spain_Crab_CGH_rep1

description:
This sample is of Littorina saxatilis Spanish Crab ecotype. It is the first of four biological replicates used in this experiment.
LS_Sp_Crab_1


title: L_compressa_CGH_rep3

description:
This sample is of Littorina compressa. It is the third of four biological replicates used in this experiment.
LC_3


title: L_saxatilis_Britain_Wave_CGH_rep1

description:
This sample is of Littorina saxatilis British Wave ecotype. It is the first of four biological replicates used in this experiment.
LS_Br_Wave_1


title: L_compressa_CGH_rep2

description:
This sample is of Littorina compressa. It is the second of four biological replicates used in this experiment.
LC_2


title: L_saxatilis_Britain_Crab_CGH_rep2

description:
This sample is of Littorina saxatilis British Crab ecotype. It is the second of four biological replicates used in this experiment.
LS_Br_Crab_2


title: L_saxatilis_Sweden_Crab_CGH_rep2

description:
This sample is of Littorina saxatilis Swedish Crab ecotype. It is the second of four biological replicates used in this experiment.
LS_Sw_Crab_2


title: L_saxatilis_Spain_Wave_CGH_rep2

description:
This sample is of Littorina saxatilis Spanish Wave ecotype. It is the second of four biological replicates used in this experiment.
LS_Sp_Wave_2


title: Fzd2 mutant lung -biological rep 1


title: ShhCre control lung -biological rep 1


title: L_saxatilis_Sweden_Wave_CGH_rep2

description:
This sample is of Littorina saxatilis Swedish Wave ecotype. It is the second of four biological replicates used in this experiment.
LS_Sw_Wave_2


title: L_saxatilis_Spain_Wave_CGH_rep3

description:
This sample is of Littorina saxatilis Spanish Wave ecotype. It is the third of four biological replicates used in this experiment.
LS_Sp_Wave_3


title: L_fabalis_CGH_rep3

description:
This sample is of Littorina fabalis. It is the third of four biological replicates used in this experiment.
LF_3


title: L_compressa_CGH_rep1

description:
This sample is of Littorina compressa. It is the first of four biological replicates used in this experiment.
LC_1


title: L_saxatilis_Sweden_Wave_CGH_rep1

description:
This sample is of Littorina saxatilis Swedish Wave ecotype. It is the first of four biological replicates used in this experiment.
LS_Sw_Wave_1


title: Col_D_r3

city: Wuhan

first: Kenichi

last: Tsuda

address: No.1 Shizishan Road

institute: Huazhong Agricultural University

hyb_protocol: Hybridization was performed by NimbleGen standard operating protocol.

scan_protocol: Scanning was performed by NimbleGen standard operating protocol.

data_processing:
The raw data (.pair file) was subjected to RMA using NimbleGen software.
Among transcripts, ones which have higher expression values were selected as representative transcripts for the genes.

label_protocol: Labeling was performed by NimbleGen standard operating protocol.

growth_protocol: Arabidopsis plants were grown in a controlled environment at 22°C with a 12 h photoperiod and 75% relative humidity.

extract_protocol: Total RNA from leaves was isolated using the Trizol Reagent method according to the manufacturer’s recommendations (Invitrogen)

treatment_protocol: Leaves of four-week-old Arabidopsis plants were infiltrated with 0.1% ethanol(control) or 2 µM DEX.

value: Wild-type

tag: treatment

value: 2 µM DEX

value: 24 hpi

value: leaf


title: sid2_D_r3

tag: tissue


title: L_fabalis_CGH_rep2

description:
This sample is of Littorina fabalis. It is the second of four biological replicates used in this experiment.
LF_2


title: L_saxatilis_Sweden_Crab_CGH_rep1

description:
This sample is of Littorina saxatilis Swedish Crab ecotype. It is the first of four biological replicates used in this experiment.
LS_Sw_Crab_1


title: L_saxatilis_Spain_Wave_CGH_rep1

description:
This sample is of Littorina saxatilis Spanish Wave ecotype. It is the first of four biological replicates used in this experiment.
LS_Sp_Wave_1


title: L_fabalis_CGH_rep1

description:
This sample is of Littorina fabalis. It is the first of four biological replicates used in this experiment.
LF_1


title: L_saxatilis_Britain_Crab_CGH_rep1

description:
This sample is of Littorina saxatilis British Crab ecotype. It is the first of four biological replicates used in this experiment.
LS_Br_Crab_1

value: East coast of Britain


title: nitrogen starvation and osmotic stress - ACY044 SD -N2+0.375M KCl / ACY044 SD

city: Tucson

first: James

middle: E

last: Hughes Hallett

state: AZ

address: 1007 E. Lowell Street

department: Molecular and Cellular Biology

institute: University of Arizona

hyb_protocol: as described in Capaldi et al (2008). Nature Genetics 40, 1300 - 1306 (2008). doi:10.1038/ng.235

scan_protocol: Microarrays scanned on Genepix 4000b. Images were quantified with Genepix Pro software version 6.1.

data_processing: Background subtraction and filtering (regression correlation >0.6 AND mean intensity/median background intensity is >1.5-fold in EITHER channel) performed by Stanford Microarray Database version 2.14 (Nucl. Acids Res. (2007) 35 (suppl 1): D766-D770. doi: 10.1093/nar/gkl1019).

molecule: polyA RNA

organism: Saccharomyces cerevisiae

source_name: Nitrogen starvation and KCl stress, 0.375M, 20min

tag: strain

source_name: mid-log

value: mid-log


title: total carbon stavation and rapamycin treatment - ACY044 SD -G+Rap / ACY044 SD

source_name: Glucose starvation and Rapamyin treatment, 200nM, 20min

label_protocol: as described in Capaldi et al (2008). Nature Genetics 40, 1300 - 1306 (2008). doi:10.1038/ng.235


title: total nitrogen and carbon starvation (20min) - ACY044 SD -N2-G / ACY044 SD

source_name: Nitrogen and Glucose starvation, 20min

extract_protocol: as described in Capaldi et al (2008). Nature Genetics 40, 1300 - 1306 (2008). doi:10.1038/ng.235

value: Nitrogen and Glucose starvation, 20min


title: Snf1 knockout - ACY509 / ACY044

source_name: Snf1 delete

value: Snf1 delete


title: nmpp1 treatment (20 min) - ACY142 +nmpp1 / ACY142

source_name: TPK1-3 inhibition by nmpp1, 100nM, 20min


title: Snf1 total nitrogen starvation (20min) - ACY509 SD -N2 / ACY509 SD

source_name: Nitrogen starvation, 20min

value: Nitrogen starvation, 20min


title: sid2_D_r2

tag: genotype/variation


title: Snf1 osmotic stress (20min) - ACY509 SD +0.375M KCl/ ACY509 SD

source_name: KCl stress, 0.375M, 20min

value: KCl stress, 0.375M, 20min


title: Col_m_r3

value: 0.1% ethanol


title: Snf1 0.02% glucose starvation (20min) - ACY509 SD 0.02% glucose starvation / ACY509 SD

source_name: Glucose starvation, 20min

value: Glucose starvation, 20min


title: Snf1 0.1% glucose starvation (20min) - ACY509 SD 0.1% glucose starvation / ACY509 SD


title: sid2_m_r2


title: Col_m_r2


title: Col_D_r2


title: sid2_m_r3


title: Col_D_r1


title: sid2_AvrRpt2_r3

source_name: Arabidopsis_sid2_Pto AvrRpt2

treatment_protocol: Four-week-old Arabidopsis Col-0 and sid2 leaves were infiltrated with Pto DC3000 hrcC, Pto DC3000 carrying an empty vector, Pto DC3000 carrying AvrRpt2 or water (mock) and samples were collected at 24 hpi.

value: Pto AvrRpt2


title: Human SZ95 sebocytes_control vs 10 μM CBD-treated (24hrs)_CBD_rep3

description: Sample biological set 3

source_name: SZ95 sebocytes_CBD

tag: cell line

value: immortalized human sebaceous gland cells

value: 10 μM (-)-cannabidiol (CBD) for 24hrs


title: oxidative stress (20min) - WT / WT+0.4mM H2O2

description: 251632210313-1 is a dye swap

source_name: Oxidative stress, 0.4mM H2O2, 20min

value: Oxidative stress, 0.4mM H2O2, 20min


title: Col_m_r1


title: heatshock (20min) - WT 42C / WT

source_name: Heatshock, 42C, 20min

value: Heatshock, 42C, 20min


title: sid2_D_r1


title: 0.1% glucose starvation (20min) - WT SD 0.1% glucose / WT SD


title: sid2_m_r1


title: sid2_AvrRpt2_r2


title: amino acid starvation (20min) - WT SD -AA / WT SD

source_name: Amino acid starvation, 20min

value: Amino acid starvation, 20min


title: sid2_AvrRpt2_r1


title: total nitrogen starvation (20min) - WT SD -N2 / WT SD


title: rapamycin treatment (20min) - WT SD +RAP / WT SD

source_name: Rapamycin, 200nM, 20min

value: Rapamycin, 200nM, 20min


title: osmotic stress (20min) - WT SD +KCL / WT SD


title: sid2_pLAFR_r2

value: Pto EV

value: 24 hpi


title: sid2_pLAFR_r3

value: leaf


title: Col_AvrRpt2_r3

source_name: Arabidopsis_WT_Pto AvrRpt2

value: Wild-type


title: Col_AvrRpt2_r1


title: sid2_hrcC_r3

value: Pto hrcC-


title: Col_pLAFR_r2


title: MSC donor3_1.5 kPa

city: Aachen

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

institute: RWTH Aachen University

description: gene expression data of MSC donor3 cultivated for 4 passages on 1.5 kPa PDMS

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Arrays were scanned using Affymetrix GeneChip Scanner 3000.

data_processing: CEL files were processed using the Affymetrix Power Tools (APT) Software Package. Normalization was done employing RMA (Irizarry et al., Biostatistics 4, 249-264, 2003).

source_name: mesenchymal stromal cells (MSC)

label_protocol: Standard Affymetrix protocol.

growth_protocol: MSCs were cultivated in 10% hPL-Medium at 37°C at humified atmosphere containing 5% carbon dioxide with medium changes twice per week. Passaging was carried out upon 80% confluent growth. MSCs were isolated from lipoaspirates after patient’s written consent using guidelines approved by the Ethic committee of the RWTH Aachen University Medical School (Permit Number EK163/07).

extract_protocol: RNA was isolated from 106 cells using the NucleoSpin RNA Isolation Kit.

treatment_protocol: MSCs were cultivated for 4 passages in parrallel on TCP, 50 kPa PDMS and 1.5 kPa PDMS.

value: MSC

tag: substrate

value: 1.5 kPa PDMS

tag: donor


title: sid2_pLAFR_r1


title: Col_pLAFR_r1


title: MSC donor3_50 kPa

description: gene expression data of MSC donor3 cultivated for 4 passages on 50 kPa PDMS

tag: cell type

value: 50 kPa PDMS


title: sid2_hrcC_r2


title: Col_AvrRpt2_r2


title: MSC donor2_1.5 kPa

description: gene expression data of MSC donor2 cultivated for 4 passages on 1.5 kPa PDMS


title: MSC donor2_50 kPa

description: gene expression data of MSC donor2 cultivated for 4 passages on 50 kPa PDMS


title: L_saxatilis_Britain_Wave_CGH_rep2

description:
This sample is of Littorina saxatilis British Wave ecotype. It is the second of four biological replicates used in this experiment.
LS_Br_Wave_2

value: East coast of Britain

tag: ecotype

value: Wave


title: MSC donor3_TCP

description: gene expression data of MSC donor3 cultivated for 4 passages on TCP

value: tissue culture plastic (TCP)


title: CD19-enriched CLL patient sample, patient #9701

city: South San Francisco

first: Ru-Fang

last: Yeh

address: 1 DNA Way

institute: Genentech

description:
CD19-enriched CLL clinical sample
A0018413

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials per manufacturers recommendation. Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 (fluidics protocol FS450_0001).

scan_protocol: Arrays were scanned using the Affymetrix GCS 3000 7G and Gene-Chip Operating Software v.1.3.0 to produce .CEL intensity files.

data_processing:
.CEL files were background adjusted, quantile normalized and summarized at the transcript level using only core probesets that mapped to RefSeq transcripts, by apt (Affymetrix Power Tool version 1.12.0) software that used the RMA algorithm.
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.na29.hg18.probeset.csv

source_name: CLL clinical sample, CD19-enriched

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: Pretreatment specimens from relapsed chronic lymphocytic leukemia patients

extract_protocol: CLL samples were positively enriched by magnetic cell sorting using CD19 microbeads and MACS columns (Miltenyi Biotec Ltd, Surrey, UK). Total RNA was isolated using Trizol (Invitrogen) and RNeasy kit (QIAGEN).

treatment_protocol: not applicable

tag: subject status

value: relapsed chronic lymphocytic leukemia (CLL) patient

tag: patient id

value: patient #9701

tag: binet stage

value: B

value: CD19-enriched CLL patient sample


title: Col_hrcC_r3

tag: time


title: MSC donor1_1.5 kPa

description: gene expression data of MSC donor1 cultivated for 4 passages on 1.5 kPa PDMS


title: Ring1b in KAP1 fl/fl + OHT

type: SRA

city: Ann Arbor

first: Tom

middle: Klaus

last: Kerppola

state: Michigan

address: 1150 West Medical Center Drive

department: Biological Chemistry

institute: University of Michigan

library_source: genomic

data_processing:
Basecalling was performed using Illumina Casava-1.8.2 software
The ChIP-seq tags from all samples were mapped to the mouse reference genome (mm10) using Bowtie2 with default parameters
The coverage of ChIP-seq tags in each dataset within promoters and genes was quantified using ngs.plot.r version 1.64
The KAP1 and Ring1b binding regions were mapped by using the ChIP-seq tags from the untreated cells as the data file and the ChIP-seq tags from the same cells treated with OHT as the control file using MACS version 1.4.2 with default parameters
The KAP1 and Ring1b binding regions that were located within promoters and genes were identified using bedtools v2.16.2 and the mouse refSeq gene table for the mm10 genome assembly from the UCSC DAS server
The regions where KAP1 and Ring1b binding overlapped within genes and promoter were identified using bedtools v2.16.2
Genome_build: mouse GRCm38/mm10
Supplementary_files_format_and_content: Processed data files are provided in .bed format for  KAP1 binding regions in KAP1 fl/fl wild type cells (anti-KAP1 ChIP-seq tag enrichment in untreated versus tamoxifen treated cells); Ring1b binding regions in Ring1b fl/fl wild type cells (anti-Ring1b ChIP-seq tag enrichment in untreated versus tamoxifen treated cells); Ring1b binding regions in KAP1 fl/fl mutant cells (anti-Ring1b ChIP-seq tag enrichment in tamoxifen treated KAP1 fl/fl cells versus tamoxifen treated Ring1b fl/fl cells);
Supplementary_files_format_and_content: Processed data files are provided in .xls format for overlapping and non-overlapping KAP1 and; Ring1b binding regions within promoters and genes.

source_name: Mouse ES cells KAP1 fl/fl knockout

growth_protocol: All cells were cultured on irradiated MEFs under the conditions described

extract_protocol:
Equal numbers of cells were fixed using formaldehyde at a final concentration of 1.2% for 10 min at room temperature. Formaldehyde fixation was terminated by adding glycine to a final concentration of 125 mM for 10 min. The fixed cells were washed with cold PBS, collected by scraping and harvested by centrifugation at 2,000g for 5 min at 4°C.  3 X107 cells were suspended in 1 ml LB1 (50 mM Hepes-KOH, pH 7.9, 140mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100) and were rocked at 4°C for 10 min. Cells were pelleted by centrifugation at 1,350g at 4°C for 5 min. The pellets were suspended in 1 ml LB2 (10 mM Tris-HCl, pH 8.0, 200 mM NaCl, 1.5 mM EDTA) and rocked at room temperature for 10 min. After centrifugation, the pellets were suspended in 1 ml of LB3 (10 mM Tris-HCl, pH 8.0, 100 mM NaCl, 1.5 mM EDTA, 0.1% Na-Deoxycholate, 0.5% Na-Lauroylsarcosine). The chromatin was sonicated until a size distribution with a mode of approximately 200 bp was reached using a Bioruptor (Diagenode). After sonication, Triton X-100 was added to a concentration of 1%.  The mixture was centrifuged at 20,000g for 10 min at 4°C. To the lysates, BSA and tRNA were added to obtain the final concentrations of 1 mg/ml and 0.25 mg/ml, respectively. After pre-clearing with agarose beads, the indicated antibodies (anti-KAP1, 5 µg; anti-Ring1b, 3 µg; anti-H3, 5 µg [served as a control to test for any variability in preparation of ChIP samples and construction of sequencing libraries]) were added to 1 ml of fragmented chromatin and the mixtures were rotated at 4 °C for overnight. Agarose beads were added to the mixture and the mixtures were rotated at 4 °C for an additional 3 h. The beads were washed 5 times with 1 ml of RIPA buffer (50 mM Hepes-KOH, pH 7.9, 0.5 M LiCl, 0.5 M EDTA, 1.0% NP-40, 0.7% Na-Deoxycholate). After transferring the beads to new tubes, they were washed once with 1 ml of TE buffer containing 50 mM NaCl. The immunoprecipitated chromatin was eluted with elution buffer (50 mM Tris-HCl, pH8.0, 10 mM EDTA, 1.0% SDS) and the cross-links were reversed by addition of RNase A and Proteinase K at final concentrations of 0.2 µg/ml each. After phenol: chloroform extraction, the DNAs were precipitated and dissolved in Qiagen Buffer EB (10 mM Tris•HCl, pH8.5).
Fragment libraries for sequencing were prepared using the Illumina DNA Sample Prep Kit (#IP-102-1001-CHIP-SEQ) following the instructions provided by Illumina. The DNA ends were repaired using a mixture of T4 DNA polymerase, the Klenow fragment of E. coli DNA polymerase I and T4 polynucleotide kinase. Single base dA overhangs were produced using the Klenow fragment and dATP.  Adapters provided by Illumina were ligated to the ends of the DNA fragments. The libraries were size-fractionated by gel electrophoresis and fragments of 100-300 bp in length were isolated.  The recovered DNAs were subjected to PCR amplification using primers provided by Illumina. After purification, the reproducibility of the workflow was tested by qPCR quantification of DNA precipitated by anti-H3 antibodies from different samples.  The amounts of DNA precipitated by anti-H3 antibody from  tamoxifen-treated cells and from control cells were not significantly different, indicating that sample preparation and library construction did not introduce variability into the analysis.  The DNA concentrations of the libraries were quantified using a Qubit 2.0 Fluorometer and the size distributions were determined using a Agilent 2100 Bioanalyzer.  The fragment libraries were sequenced using the Illumina HiSeq2000 with version 3 reagent chemistry at the University of Michigan Medical School DNA Sequencing Core Facility.

treatment_protocol: The cells were treated with 4-hydroxy-tamoxifen (+OHT) or with vehicle (ethanol) (−OHT) for 24 hours followed by 48 hours culture in the presence (Ring1b fl/fl) or absence (KAP1 fl/fl) of tamoxifen

tag: cells

value: Mouse ES cells KAP1 fl/fl

value: anti-Ringb (MBL, D139-3)


title: sid2_hrcC_r1


title: MSC donor1_50 kPa

description: gene expression data of MSC donor1 cultivated for 4 passages on 50 kPa PDMS


title: Ring1b in Ring1b fl/fl + OHT

source_name: Mouse ES cells Ring1b fl/fl knockout

value: Mouse ES cells Ring1b fl/fl


title: Ring1b in Ring1b fl/fl - OHT

source_name: Mouse ES cells Ring1b fl/fl wild type

value: vehicle (ethanol)


title: MSC donor2_TCP

description: gene expression data of MSC donor2 cultivated for 4 passages on TCP


title: Col_pLAFR_r3

value: Pto EV

value: 24 hpi

value: leaf


title: KAP1 in KAP1 fl/fl + OHT

value: anti-KAP1 (Abcam, ab10484)


title: KAP1 in KAP1 fl/fl - OHT

source_name: Mouse ES cells KAP1 fl/fl wild type


title: MSC donor1_TCP

description: gene expression data of MSC donor1 cultivated for 4 passages on TCP

value: MSC


title: Col_hrcC_r2

value: Wild-type

value: Pto hrcC-


title: Glycolaldehdye-treated strain  replicate 2

city: Saga

first: Lahiru

middle: Niroshan

last: Jayakody

state: Kyushu

address: Honjo-machi Honjo

department: Bioscience and Biotechnology

country: Japan

institute: Saga University

description: gene expression after 4 h in 2% glucose containing SC medium

hyb_protocol: Six hundreds nano gram of each labeled cRNA was fragmented by adding 5 μL 10 x blocking agent and 1 μL of 25 x fragmentation buffer, and then heated at 60°C for 30 min. Finally 25 μL 2 x GE hybridization buffer was added to dilute the labeled cRNA. 50 μL of hybridization solution was dispensed into the gasket slide and assembled to the Yeast (V1) Gene Expression Microarray, 4×44K (Agilent®)

scan_protocol: The slides were incubated for 17 h at 65 °C in an Agilent hybridization oven and washed at room temperature. The hybridized array was immediately scanned with an Agilent Microarray Scanner (Agilent Technologies, Inc.)

data_processing: Raw data were extracted using the software provided by Agilent Feature Extraction Software (v11.0.1.1). The raw data for same gene was then summarized automatically in Agilent feature extraction protocol to generate raw data text file, providing expression data for each gene probed on the array. Array probes that have Flag A in samples were filtered out. Selected gProcessedSignal value was transformed by logarithm and normalized by quantile method.  Statistical significance of the expression data was determined using fold change and independent T-test in which the null hypothesis was that no difference exists among groups. False discovery rate (FDR) was controlled by adjusting p value using Benjamini-Hochberg algorithm. For DEG sets, Hierarchical cluster analysis was performed using complete linkage and euclidean distance as a measure of similarity. Gene-Enrichment and Functional Annotation analysis for significant probe list was performed using DAVID (http://david.abcc.ncifcrf.gov/home.jsp).  All data analysis and visualization of differentially expressed genes was conducted using R 3.0.2 (www.r-project.org)

source_name: Yeast BY4743

label_protocol: RNA labeling and hybridization were performed by using the Agilent one-color microarray-based gene expression analysis protocol (Agilent Technology, V 6.5, 2010). Briefly, 200 ng of total RNA from each sample was linearly amplified and labeled with Cy3-dCTP. The labeled cRNAs were purified by RNAeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000 (NanoDrop, Wilmington, USA).

growth_protocol: For RNA extraction, yeast cells were grown overnight in 2% glucose cntaining synthetic minimal medium with or wothout 10 mM of glycolaldehdye. The,   OD600= 0.1 cells were added into the  10 mL of medium and grown at 30℃ for 4 h in static condition, and cells were extracted for RNA isolation.

extract_protocol: Total RNA was extracted by the hot phenol method (3). After the extraction, RNA was further purified using the RNeasy Mini Kit (Qiagen, Valencia, CA). The purified RNA was stored at -80 °C. For the quality control, RNA purity and integrity were evaluated by OD 260/280 ratio, and analyzed by Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, USA). RNA extraction and its purification experiments were performed 3 times independently from 3 respective, independent starter cultures

treatment_protocol: Yeast cells were treated with 10 mM of glycolaldehdye for 4 h in static condition

tag: ploidy

value: Haploid

tag: growth condition

value: anaerobic growth for 4h at 30 ℃

value: 10 mM of glycolaldehdye for 4 h


title: MSC donor10_hPL-gel

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to Illumina Infinium HumanMethylation450 Beadchip using standard Infinium HD Methylation Assay protocol.

scan_protocol: Standard Infinium HD Methylation Assay protocol

data_processing: Initial analysis was performed by the GenomeStudio 2010.3 (Modul M Version 1.8.5). Data were normalized with internal controls according to Illumina´s standard procedures. Methylation level at each locus was calculated with the GenomeStudio Methylation module as beta-value (ranging from 0 to 1). The number of beads per feature varies between chips and beta-values were calculated as average of at least three technical replica.

label: Cy5 and Cy3

extract_protocol: Genomic DNA was isolated using the Qiagen DNA Blood Midi Kit.

value: hPL-gel


title: Glycolaldehdye-treated strain  replicate 3


title: sid2_mock_r3

value: water


title: Glycolaldehdye-treated strain  replicate 1


title: Col_hrcC_r1


title: sid2_mock_r2


title: sid2_mock_r1


title: MSC donor10_TCP

label_protocol: Standard Infinium HD Methylation Assay protocol

value: tissue culture plastic (TCP)


title: Col_mock_r2


title: Glycolaldehdye-nontreated strain  replicate 3

description: gene expression after 4 h in 2% glucose containing SC medium in the presence of 10 mM glycolaldehdye


title: Col_mock_r1


title: Col_mock_r3


title: MSC donor9_hPL-gel


title: MSC donor9_TCP


title: MSC donor11_TCP


title: MSC donor8_hPL-gel


title: MSC donor8_TCP


title: Glycolaldehdye-nontreated strain  replicate 2


title: MSC donor11_hPL-gel


title: SG13X-C4

status: Public on Jul 28 2014

city: Grand Rapids

first: Karl

last: Dykema

state: MI

address: 333 Bostwick Ave. NE

institute: Van Andel Institute

description: Gene expression ratios were obtained by comparing tumor and normal kidney tissues.

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: The data were analyzed with custom CDF environments created by the MBNI - CDF: Mm_ENTREZG_11.0.1 was used.

label: R-Phycoerythrin Streptavidin (SAPE), from Molecular Probes, 1 mg/ml  ( we use 6 ul per reaction )

source_name: Mus musculus

label_protocol: 10 ug of Qiagen-purified total RNA

value: xenograft tumor from knockout mice form FLCN-deficient mouse cells

tag: genotype

value: FLCN deficient


title: WT

value: normal mouse kidney tissue

value: wild type


title: SG120

value: tumor from knockout mice


title: SG118


title: SG069N


title: KSP

value: natural cysts from knockout


title: MSC donor7_TCP


title: SG068N


title: SG121


title: JDK54X-23


title: SG104


title: cartilage_RAAK_35_Preserved

city: Leiden

first: Yolande

middle: F. M.

last: Ramos

address: Einthovenweg 20

department: Molecular Epidemiology

institute: Leiden University Medical Center

hyb_protocol: Standard Illumina hybridization protocol with Ambion TotalPrep-96 RNA amplification kit

scan_protocol: Slides were scanned with the Illumina Beadscanner 500GX

data_processing: Raw data were prepared with GenomeStudio Software (Gene Expression module v1.0), without normalization or background substraction and with imputation of missing data. Subsequently, quality control was performed in R statistical programming language using the lumi-package, and data were prepared for analysis by applying robust spline normalization (RSN) and variance-stabilizing transformation (vst)

source_name: articular cartilage

label_protocol: To perform cDNA synthesis, amplification, biotin labeling, and hybridization onto the microarrays the Ambion TotalPrep-96 RNA amplification kit was used according to the manufacturer's protocol.

extract_protocol: RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with the QIAGEN RNeasy mini kit following the manufacturer's recommendations. Quality control was performed with the 2100 Bioanalyser (Agilent).

tag: Sex

value: Female

tag: age (yrs)

value: cartilage

tag: disease state

value: Preserved


title: cartilage_RAAK_34_OA

tag: tissue

value: OA


title: MSC donor7_1.5 kPa

value: MSC

value: 1.5 kPa PDMS


title: cartilage_RAAK_36_OA


title: cartilage_RAAK_34_Preserved


title: cartilage_RAAK_35_OA


title: MSC donor5_1.5 kPa


title: MSC donor6_50 kPa

value: 50 kPa PDMS


title: MSC donor6_TCP


title: MSC donor5_TCP


title: cartilage_RAAK_33_Preserved

value: Male


title: cartilage_RAAK_33_OA


title: MSC donor7_50 kPa


title: cartilage_RAAK_32_Preserved


title: MSC donor6_1.5 kPa


title: MSC donor4_TCP


title: MSC donor4_1.5 kPa


title: cartilage_RAAK_36_Preserved


title: cartilage_RAAK_32_OA


title: MSC donor4_50 kPa


title: cartilage_RAAK_31_Preserved


title: cartilage_RAAK_29_OA


title: cartilage_RAAK_30_Preserved


title: MSC donor5_50 kPa


title: cartilage_RAAK_28_OA


title: cartilage_RAAK_30_OA


title: cartilage_RAAK_27_OA


title: cartilage_RAAK_26_Preserved


title: cartilage_RAAK_31_OA


title: cartilage_RAAK_29_Preserved


title: cartilage_RAAK_26_OA


title: cartilage_RAAK_25_Preserved


title: cartilage_RAAK_28_Preserved


title: PIP1_B

city: Kyoto

first: Junetha

last: Syed

state: Kyoto

address: Kitashirakawa-Oiwakecho,Sakyo-Ku

department: Chemistry, Graduate School of Science

institute: Kyoto University

description: Gene expression in MDA-MB-231 cells after 48hr treatment with 10 μM of PIP1, replicate 2

hyb_protocol: 3.5 ug of fragmented and labelled cDNA were hybridized for 20 hr at 48°C to Human Gene 2.1 ST Array Strip (Affymetrix,USA) . Strip was washed and stained in the Fluidics Station of GeneAtlas System.

scan_protocol: Strip was scanned using the Imaging Station of GeneAtlas® Personal Microarray System (Affymetix, USA) .

data_processing: The hybridized probeset values were normalized using iterPLIER algorithm in the Affymetrix gene Expression Console 1.3.1 sofware core probeset analysis

source_name: MDA-MB-231 Cells, PIP1, replicate 2

label_protocol: 5.5 µg of single stranded DNA is fragmented and labelled with biotin according to the standard Affymetrix protocol from 100 ng total RNA as starting material (WT PLUS Reagent Kit User Manual, 2013, Affymetrix).

growth_protocol: MDA-MB-231 cells (ECACC) were grown in DMEM (Dulbecco's modified Eagle's medium supplemted with 10% fetal bovine serum (FBS), 100 U/mL penicillin, 100 µg/mL streptomycin in 5% CO2

extract_protocol: Total RNA was prepared using  RNeasy mini kit (Qiagen, Valencia, CA) following the manufacturer's recommendations. The integrity of RNA was checked using Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA) and quantified using a Nanodrop ND1000 v3.5.2 spectrophotometer.

treatment_protocol: MDA-MB-231 cells were suspended in fresh medium and were seeded to grow in 6 well-plates at  2 × 10^5 cells/well for 24 hours. The medium was then removed and replaced with 2 ml of fresh medium supplemented with DMSO (0.005% Control) and 10 µM final concentration of PIP1. The cells were incubated for 48 hours.

tag: cell line

value: breast cancer

tag: cell line origin

value: human caucasian breast adenocarcinoma

tag: morphology

value: epithelial


title: cartilage_RAAK_27_Preserved


title: cartilage_RAAK_24_Preserved


title: PIP1_A

description: Gene expression in MDA-MB-231 cells after 48hr treatment with 10 μM of PIP1, replicate 1

source_name: MDA-MB-231 Cells, PIP1, replicate 1

tag: cell type


title: cartilage_RAAK_25_OA


title: Glycolaldehdye-nontreated strain  replicate 1

value: Haploid

value: anaerobic growth for 4h at 30 ℃

tag: strain

tag: treatment


title: DMSO_A

description: Gene expression in MDA-MB-231 cells after 48hr treatment with DMSO, replicate 1

source_name: MDA-MB-231 Cells, DMSO, replicate 1


title: cartilage_RAAK_23_Preserved


title: cartilage_RAAK_21_Preserved


title: DMSO_B

description: Gene expression in MDA-MB-231 cells after 48hr treatment with DMSO, replicate 2

source_name: MDA-MB-231 Cells, DMSO, replicate 2


title: cartilage_RAAK_22_OA


title: cartilage_RAAK_24_OA


title: cartilage_RAAK_20_Preserved


title: cartilage_RAAK_23_OA


title: cartilage_RAAK_19_Preserved


title: cartilage_RAAK_21_OA


title: cartilage_RAAK_20_OA