title: PE-BD1

city: Louisville

first: Shirong

last: Zheng

state: KY

address: 570 S Preston St.

department: Pediatrics

institute: University of Louisville

description: diabetes with D6-/-

hyb_protocol: Probes from 3 six-month old female mice in each group were hybridized to Affymetrix mouse gene 1.0 ST arrays.

scan_protocol: scanned with a GCS 3000 7G scanner

data_processing: signals analyzed with Command Console software (Affymetrix, Santa Clara, CA)

label_protocol: A 100 ng aliquot of RNA from each mouse was used for probe preparation with The Ambion WT Expression kit. The kit generates sense-strand cDNA from total RNA for fragmentation and labeling using the Affimetrix GeneChip WT Terminal Labeling Kit (PN90067).

growth_protocol: D6−/− mice in C57BL/6 background which was original from Charles River Italia (Calco, Italy) were bred to FVB mice for at least 10 generation to transfer the D6 deletion to the FVB background (henceforth designated as D6).  These D6 mice were bred for two generations to diabetic OVE mice on the background FVB to produce OVE mice homozygous for the D6 deletion (OVE-D6). Mice were maintained up to 6 months of age.  Animals had free access to standard rodent chow and water throughout the study.

extract_protocol: RNA was extracted with RNeasy Mini Kit (Qiagen, Santa Clarita, CA, USA) from frozen kidneys.The extracted RNA was checked for quality on Agilent 2100 Bioanalyzer. The RNA samples having RNA integrity number  (RIN) above 8.8 (average 9.1) were used for probe preparation.

treatment_protocol: Mice were grouped in 4 groups (OVE, OVE-D6, FVB, D6) in this study.

value: FVB

value: 6 months

value: kidney

tag: disease state

value: diabetes

tag: genotype/variation

value: D6 knockout


title: PE-B3

status: Public on Oct 10 2013

type: RNA

country: USA

description: diabetes with D6+/+

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: OVE

tag: strain

tag: age

tag: tissue

value: D6 wild type


title: Lung8434_NMapping250K_Nsp

type: genomic

city: Tokyo

first: Hironori

last: Ninomiya

address: 3-8-31 Ariake, Koutou ward

department: pathology

country: Japan

institute: The Japanese Foundation for Cancer Research

description: Hybridized to 250K_Nsp

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing:
After appropriate normalization of mean array intensities, signal ratios between tumours and anonymous normal references were calculated in an allele-specific manner, and allele-specific copy numbers were inferred from the observed signal ratios based on the hidden Markov model using CNAG/AsCNAR 3.0 software (http://www.genome.umin.jp).
primary data description: Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

label: Biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: lung adenocarcinoma specimen

label_protocol: Affymetrix standard protocol

extract_protocol: standard DNA extraction using QIAGEN

tag: gender

value: female

tag: group

value: ALK fusion positive


title: GTB12217_NMapping250K_Nsp

description: Hybridized to 250K_Nsp

value: male


title: PE-B1

description: diabetes with D6+/+


title: PE-BD3

description: diabetes with D6-/-


title: PE-D2

description: non-diabetes with D6-/-

value: non-diabetes


title: PE-D3

description: non-diabetes with D6-/-


title: PE-D1

description: non-diabetes with D6-/-


title: Lung9034_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: PE-F3

description: non-diabetes with D6+/+

source_name: FVB


title: PE-F2

description: non-diabetes with D6+/+


title: PE-B2

description: diabetes with D6+/+


title: PE-BD2

description: diabetes with D6-/-


title: D-3

city: Silver Spring

first: BIJU

last: ISSAC

state: MD

address: 503 Robert Grant Ave, Rm 2W123

department: Military HIV Research Program

institute: Walter Reed Army Institute of Research

description:
SAMPLE 6
treated with dsDNA for 3 hours

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data was preprocessed on GeneSpring GX from Agilent. Raw data was quantile normalized and log2 transformed

source_name: Mouse embryonic fibroblast, D-3

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

growth_protocol: Mouse embryonic fibroblast was cultured in DMEM with 10% FBS.

extract_protocol: Total RNA was isolated by RNeasy RNA extraction kit.

treatment_protocol: Cells were treated with 4 ug/ml of dsDNA using lipofectamine 2000 for 3 hours.

value: 14.5 days

tag: developmental stage

value: embryo

tag: cell type

value: embryonic fibroblast

tag: treatment

value: S365D variant (D)


title: GTB4180_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: Lung2524_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: Lung 58_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: GTB3121_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: D-0

description:
SAMPLE 5
untreated

source_name: Mouse embryonic fibroblast, D-0

value: untreated


title: PE-F1

description: non-diabetes with D6+/+


title: A-3

description:
SAMPLE 4
treated with dsDNA for 3 hours

source_name: Mouse embryonic fibroblast, A-3

value: S365A variant (A)


title: GTB2075_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: A-0

description:
SAMPLE 3
untreated

source_name: Mouse embryonic fibroblast, A-0


title: W-3

description:
SAMPLE 2
treated with dsDNA for 3 hours

source_name: Mouse embryonic fibroblast, W-3

value: mSTING (W)


title: GTB2374_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: Wild type mRNA 5

city: Los Angeles

first: Vasu

last: Punj

state: CA

address: Biggy Street

institute: USC

description: Gene expression data from TET2 Wild type patient sample

hyb_protocol: Following fragmentation, 15 µg of cRNA were hybridized for 16hr on Affymetrix HuGene-1_0-st [transcript (gene version)]  as recommended by manufacturer

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000A.

data_processing: The data was analyzed with Gene Spring GX 12

source_name: lymphoma biopsies

label_protocol: Starting from 5 µg total RNA, labeled cRNA was prepared using the Roche Microarray cDNA Synthesis, Microarray RNA Target Synthesis (T7) and Microarray Target Purification Kit, according to the manufacturer's instructions

growth_protocol: Patient Samples

extract_protocol: RNA was extracted from fresh frozen lymphoma biopsies using  RNeasy mini kit (Qiagen Valenica, CA)

tag: genotype

value: Wild type

value: lymphoma biopsy


title: Wild type mRNA 4


title: W-0

description:
SAMPLE 1
untreated

source_name: Mouse embryonic fibroblast, W-0


title: Wild type mRNA 3


title: Lung Ca-5544_NMapping250K_Nsp

description: Hybridized to 250K_Nsp

value: ALK fusion negative


title: Lung Ca-5794_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: Lung Ca-4661_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: Lung 9736_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: Wild type mRNA 1


title: Wild type mRNA 2


title: Lung Ca-5574_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: Lung Ca-7969_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: TET2 Mutant mRNA 6

description: Gene expression data from TET2 mutant patient sample

value: TET2 Mutant


title: TET2 Mutant mRNA 5


title: Lung Ca-4616_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: TET2 Mutant mRNA 3


title: Lung Ca-4607_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: Lung Ca-7889_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: Lung 10118_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: Lung Ca-4585_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: Lung 10744_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: Lung Ca-4372_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: TET2 Mutant mRNA 4


title: Lung Ca-4365_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: Lung Ca-4244_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: Lung Ca-4449_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: Lung Ca-4751_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: Lung Ca-4164_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: Lung Ca-4286_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: Lung Ca-4276_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: Lung 4174_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: Lung Ca-4205_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: Lung Ca-3405_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: Lung Ca-3807_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: Lung Ca-3044_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: Lung Ca-3888_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: Lung Ca-3415_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: Lung Ca-2839_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: Lung Ca-2862_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: LungCa3152_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: Lung Ca-3088_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: Lung Ca-2803_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: Lung Ca-2145_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: Lung Ca-2787_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: Lung Ca-2914_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: Lung Ca-2766_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: Lung Ca-2727_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: Lung Ca-2751_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: Lung Ca-3042_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: Lung Ca-2784_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: Lung 7235_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: LungCa2780_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: LungCa2697_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: Lung 2668_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: Lung Ca-2267_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: Lung Ca-2308_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: Lung 2525_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: Lung Ca-2725_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: Lung Ca-2361_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: Lung Ca-2245_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: Lung Ca-2317_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: Lung Ca-2231_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: Lung Ca-2773_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: Lung Ca-2706_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: LungCa2248_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: Lung 1986_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: Lung 2022_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: Lung 1750_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: TL3 LAMC2 KO 3

city: Singapore

first: Lizhen

last: Liu

address: 14 Medical Drive

country: Singapore

institute: Cancer Science Institute

description: TL3 LAMC2 shRNA replicate 3

hyb_protocol: Bitinylated cRNA were fragmented and hybridised to an illumina whole genome expression chip, Human HT-12 v4.0 for 18 h at 58°C. Beadchips were then washed and stained and subsequently scanned to obtain fluorescence intensities.

scan_protocol: Gene Chips were scanned using an Illumina Bead Array Reader

data_processing: The data were analyzed using RMA in the bioconductor and normalized using the Cross Correlation method.  The trimmed mean target intensity of each array was set to 8.

source_name: TL3 cell lines

label_protocol: cRNA were synthesized using Illumina Total Prep RNA Amplification Kit (Illumina)

growth_protocol: Cells were grown under normal culture conditions for 3 day

extract_protocol: Total RNA was isolated from cultured cells with RNeasy mini kit (Qiagen GmbH, Hilden, Germany) according to the manufacturer’s protocol.

treatment_protocol: Three different clones from TL3 and HTH 83 cell lines stably expressing scramble shRNA and LAMC2 shRNA were used

value: Anaplastic thyroid carcinoma

tag: expression

value: TL3 LAMC2 shRNA

tag: cell line


title: Lung Ca-4412_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: Lung Ca-2178_NMapping250K_Nsp

description: Hybridized to 250K_Nsp

value: female


title: Lung 2101_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: Lung 1811_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: LungCa3141_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: Lung Ca-2088_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: Lung 2713_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: Lung 1973_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: Lung 1643_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: TL3 SCR 3

description: TL3 SCR shRNA replicate 3

value: TL3 SCR shRNA


title: TL3 LAMC2 KO 1

description: TL3 LAMC2 shRNA replicate 1


title: Lung 1625_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: Raji_DAMD

city: Seattle

first: Scott

middle: J.

last: Diede

state: WA

address: 1100 Fairview Avenue North, Mailstop c3-168

institute: Fred Hutchinson Cancer Research Center

description:
control CEL: hWBC_rep1.CEL
control CEL: hWBC_rep2.CEL
Raji DAMD, Technical Rep 1-2, Promoter Array

hyb_protocol: Approximately 7.5μg of DNA was hybridzed per array using the Affymetrix hybridization kit. Arrays were hybridized for 16 hours at 45° at 60rpm using an Affymetrix hybridization oven.

scan_protocol: Arrays were scanned on an Affymetrix Scanner 3000 7G

data_processing: Affymetrix Human or Mouse Tiling 1.0R Promoter Arrays were analyzed using Tiling Array Software (v 1.1.02, Affymetrix). Raw data were scaled to a target intensity of 100 and normalized by quantile normalization. For probe analysis, a bandwidth of 250 bp was used and perfect match (PM) probes were used in a Wilcoxon Rank Sum two-sided test.

source_name: Raji DAMD Assay

label_protocol: Samples (7.5μg of DNA) were enzymatically fragmented and labeled using the WT Labeling Kit (Affymetrix) to add biotinylated compound to the ends of the fragments.

extract_protocol: Genomic DNA was extracted from cell lines, primary human medulloblastoma, normal cerebellum, and mouse tumors using a QIAGEN Blood & Cell Culture DNA kit per manufacturer's instructions. The DAMD assay was performed as described (Mahoney SE, Yao Z, Keyes CC, Tapscott SJ, & Diede SJ (2012). Genome-wide DNA methylation studies suggest distinct DNA methylation patterns in pediatric embryonal and alveolar rhabdomyosarcomas. Epigenetics 7(4)).

value: Raji

value: Burkitt lymphoma cancer cell

source_name: WBC DAMD Assay

value: peripheral white blood cells


title: Lung 1461_NMapping250K_Nsp

description: Hybridized to 250K_Nsp

value: male


title: Lung 1336_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: TL3 LAMC2 KO 2

description: TL3 LAMC2 shRNA replicate 2


title: TL3 SCR 1

description: TL3 SCR shRNA replicate 1


title: Daudi_DAMD

description:
control CEL: hWBC_rep1.CEL
control CEL: hWBC_rep2.CEL
Daudi DAMD, Technical Rep 1-2, Promoter Array

source_name: Daudi DAMD Assay

value: Daudi


title: HTH83 LAMC2 KO 3

description: HTH83 LAMC2 shRNA replicate 3

source_name: HTH83 cell lines

value: HTH83 LAMC2 shRNA


title: HTH83 LAMC2 KO 2

description: HTH83 LAMC2 shRNA replicate 2


title: HTH83 SCR 3

description: HTH83 SCR shRNA replicate 3

value: HTH83 SCR shRNA


title: HTH83 LAMC2 KO 1

description: HTH83 LAMC2 shRNA replicate 1


title: miMF2_FvMFp4_F_DAMD

description:
control CEL: mMFp4_F_rep1.CEL
control CEL: mMFp4_F_rep2.CEL
iMF2 DAMD + 0.5% formamide, Technical Rep 1-2, Promoter Array

source_name: iMF2 DAMD Assay + 0.5% formamide

tag: background strain

value: fibroblast cell

source_name: MFp4 DAMD Assay + 0.5% formamide

value: primary fibroblasts


title: miMF1_FvMFp4_F_DAMD

description:
control CEL: mMFp4_F_rep1.CEL
control CEL: mMFp4_F_rep2.CEL
iMF1 DAMD + 0.5% formamide, Technical Rep 1-2, Promoter Array

source_name: iMF1 DAMD Assay + 0.5% formamide


title: HTH83 SCR 2

description: HTH83 SCR shRNA replicate 2


title: m248 sorted B

city: Rehovot

first: Shlomi

last: Madar

address: Hertzl

country: Israel

institute: Weizmann institute of science

description: H1299-248 co-cultivated with CAFs 2 replicates out of 2

hyb_protocol: According to manufacturer’s protocol.

scan_protocol: According to manufacturer’s protocol.

data_processing: The limma package (Smyth and Speed, 2003) was used for microarray processing. Background was corrected using the function backgroundCorrect and normalization within and between arrays was performed using the functions normalizeWithinArrays and normalizeBetweenArrays, respectively. Spots with the same probes were averaged. Analysis of variance (ANOVA) including contrasts was applied to the data set using Partek Genomic Suite 6.5 (Inc. St. Charles, MO).

source_name: m248 sorted

label_protocol: According to manufacturer’s protocol.

growth_protocol: Cells were grown alone or in co-cultivation for 24h.

extract_protocol: Total RNA was extracted using Tri-Reagent (MRC Inc.) according to manufacturer’s protocol.

value: co-cultivated for 24 hrs

value: H1299-248 co-cultivated with CAFs

source_name: Common reference

tag: sample type

value: reference


title: Lung 1462_NMapping250K_Nsp

description: Hybridized to 250K_Nsp

source_name: lung adenocarcinoma specimen

value: ALK fusion negative


title: HTH83 SCR 1

description: HTH83 SCR shRNA replicate 1

value: Anaplastic thyroid carcinoma


title: Lung 1729_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: Lung 1078_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: Lung 492_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: Lung 1354_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: Lung 464_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: Lung 321_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: Lung 514_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: m10T_FvMFp4_F_DAMD

description:
control CEL: mMFp4_F_rep1.CEL
control CEL: mMFp4_F_rep2.CEL
10T DAMD + 0.5% formamide, Technical Rep 1-2, Promoter Array

source_name: 10T DAMD Assay + 0.5% formamide


title: Lung 1452_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: Lung 204_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: miMF2vMFp4_DAMD

description:
control CEL: mMFp4_rep1.CEL
control CEL: mMFp4_rep2.CEL
iMF2 DAMD, Technical Rep 1-2, Promoter Array

source_name: iMF2 DAMD Assay

source_name: MFp4 DAMD Assay


title: m175 sorted B

description: H1299-175 co-cultivated with CAFs 2 replicates out of 2

source_name: m175 sorted

value: H1299-175 co-cultivated with CAFs


title: HK3T (m248) A

description: CAFs co-cultivated with H1299-248 1 replicate out of 2

value: CAFs co-cultivated with H1299-248


title: m248 sorted A

description: H1299-248 co-cultivated with CAFs 1 replicate out of 2


title: m175 sorted A

description: H1299-175 co-cultivated with CAFs 1 replicate out of 2


title: miMF1vMFp4_DAMD

description:
control CEL: mMFp4_rep1.CEL
control CEL: mMFp4_rep2.CEL
iMF1 DAMD, Technical Rep 1-2, Promoter Array

source_name: iMF1 DAMD Assay


title: Lung 1330_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: HK3T (m248) B

description: CAFs co-cultivated with H1299-248 2 replicates out of 2


title: m3T3_FvMFp4_F_DAMD

description:
control CEL: mMFp4_F_rep1.CEL
control CEL: mMFp4_F_rep2.CEL
3T3 DAMD + 0.5% formamide, Technical Rep 1-2, Promoter Array

source_name: 3T3 DAMD Assay + 0.5% formamide


title: Lung 194_NMapping250K_Nsp

description: Hybridized to 250K_Nsp

value: female


title: HK3T (m175) A

description: CAFs co-cultivated with H1299-175 1 replicate out of 2

value: CAFs co-cultivated with H1299-175


title: m10TvMFp4_DAMD

description:
control CEL: mMFp4_rep1.CEL
control CEL: mMFp4_rep2.CEL
10T DAMD, Technical Rep 1-2, Promoter Array

source_name: 10T DAMD Assay


title: ECOR sorted A

description: H1299 co-cultivated with CAFs 1 replicate out of 2

source_name: ECOR sorted

value: H1299 co-cultivated with CAFs


title: Cervical Cancer Tissue-25

city: Navi Mumbai

first: Rita

last: Mulherkar

state: Maharashtra

address: Kharghar

country: India

institute: Advanced Centre for Treatment, Research and Education in Cancer (ACTREC)

description: III_CT 1187

hyb_protocol: Hybridization was done in 2X Hyb buffer containing 50% formamide, 10X SSC and 0.2% SDS (adapted from Quackenbush protocol) in a 42 degrees Centigrade waterbath overnight in a Hyb chamber, with the probe under a coverslip, as described by Pat Brown Lab http://cmgm.stanford.edu/pbrown/protocols/index.html

scan_protocol: Scanned in Axon 4200A Professional according to the manufacturer's instructions. Gridding and alignment was done using GenePix Version 5.0 and the files were saved as GPR files.

data_processing: Data was analyzed using Agilent Genespring GX11.5 software. The raw intensity data was normalized by log2 transformation and Lowess normalization. Baseline correction was done to median of all samples.

source_name: Cervical Cancer Tissue

label_protocol: For generation of fluorescently labeled cDNA, post-labeling method was utilized. In the first step, the RNA is converted into cDNA in the presence of aminoallyl-dUTP and other dNTPs. The addition of Cy3 and Cy5 N- hydroxysuccinimidyl esters (NHS esters) to the prepared cDNA in the second step leads to chemical coupling (esterification reaction) at the aminoallyl-dUTP site.

extract_protocol: RNA isolation was done using the RNeasy RNA extraction kit (Qiagen) as per manufacturer’s instructions. RNA obtained was quantitated using Nanodrop and quality checked using formaldehyde-agarose gel electrophoresis.

treatment_protocol: Snap frozen in Liquid nitrogen

tag: cancer stage

value: IIIB

source_name: Universal Human Reference RNA (UHRR)

tag: sample info

value: purchased from Stratagene, Cat No. 740000

value: a pool of RNA made from 10 different human cell lines


title: Lung 864_NMapping250K_Nsp

description: Hybridized to 250K_Nsp

value: male


title: m3T3vMFp4_DAMD

description:
control CEL: mMFp4_rep1.CEL
control CEL: mMFp4_rep2.CEL
3T3 DAMD, Technical Rep 1-2, Promoter Array

source_name: 3T3 DAMD Assay


title: Lung 165_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: Lung 215_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: TL3 SCR 2

description: TL3 SCR shRNA replicate 2

source_name: TL3 cell lines

value: TL3 SCR shRNA


title: Cervical Cancer Tissue-24

description: III_CT 1179


title: ECOR sorted B

description: H1299 co-cultivated with CAFs 2 replicates out of 2


title: mSmoA2_2vWTCbl_DAMD

description:
control CEL: mWTCblSmoA2_rep1.CEL
control CEL: mWTCblSmoA2_rep2.CEL
SmoA2 Medulloblastoma Tumor 2 DAMD, Technical Rep 1-2, Promoter Array

source_name: SmoA2 medulloblastoma DAMD Assay

value: SmoA2 medulloblastoma tumor

source_name: WTCbl DAMD Assay

value: normal cerebellum


title: Cervical Cancer Tissue-23

description: III_CT 1178


title: mSmoA2_1vWTCbl_DAMD

description:
control CEL: mWTCblSmoA2_1_rep1.CEL
control CEL: mWTCblSmoA2_1_rep2.CEL
SmoA2 Medulloblastoma Tumor 1 DAMD, Technical Rep 1-2, Promoter Array


title: m248 only A

description: H1299-248 grown alone, sorted 1 replicate out of 2

source_name: m248 only

value: co-cultivated for 24 hrs


title: m175 only B

description: H1299-175 grown alone, sorted 2 replicates out of 2

source_name: m175 only

source_name: Common reference


title: Cervical Cancer Tissue-22

description: III_CT 1131


title: m248 only B

description: H1299-248 grown alone, sorted 2 replicates out of 2


title: mSmoA1vWTCbl_DAMD

description:
control CEL: mWTCblSmoA1_rep1.CEL
control CEL: mWTCblSmoA1_rep2.CEL
SmoA1 Medulloblastoma Tumor DAMD, Technical Rep 1-2, Promoter Array

source_name: SmoA1 medulloblastoma DAMD Assay

value: SmoA1 medulloblastoma tumor


title: ECOR only B

description: H1299 grown alone, sorted 2 replicates out of 2

source_name: ECOR only

value: reference


title: m175 only A

description: H1299-175 grown alone, sorted 1 replicate out of 2


title: Lung 148_NMapping250K_Nsp

description: Hybridized to 250K_Nsp

source_name: lung adenocarcinoma specimen

value: ALK fusion negative


title: Lung 111_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: Lung 120_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: ECOR only A

description: H1299 grown alone, sorted 1 replicate out of 2


title: Cervical Cancer Tissue-21

description: III_CT 1099


title: Cervical Cancer Tissue-20

description: III_CT 905


title: HK3T (ECOR) B

description: CAFs co-cultivated with H1299 2 replicates out of 2

source_name: HK3T (ECOR)

value: CAFs co-cultivated with H1299


title: Cervical Cancer Tissue-19

description: III_CT 859


title: mBrCA3_DAMD

description:
control CEL: mBrCON_rep1.CEL
control CEL: mBrCON_rep2.CEL
Chodish Breast Carcinoma Tumor 3 DAMD, Technical Rep 1-2, Promoter Array

source_name: Chodish Breast Cancer Tumor 3 DAMD Assay

value: Chodish breast carcinoma tumor

source_name: WTcon DAMD Assay

value: peripheral white blood cells


title: HK3T (m175) B

description: CAFs co-cultivated with H1299-175 2 replicates out of 2


title: HK3T only B

description: CAFs grown alone, sorted 2 replicates out of 2

source_name: HK3T only


title: mBrCA2_DAMD

description:
control CEL: mBrCON_rep1.CEL
control CEL: mBrCON_rep2.CEL
Chodish Breast Carcinoma Tumor 2 DAMD, Technical Rep 1-2, Promoter Array

source_name: Chodish Breast Cancer Tumor 2 DAMD Assay


title: mBrCA1_DAMD

description:
control CEL: mBrCON_rep1.CEL
control CEL: mBrCON_rep2.CEL
Chodish Breast Carcinoma Tumor 1 DAMD, Technical Rep 1-2, Promoter Array

source_name: Chodish Breast Cancer Tumor 1 DAMD Assay


title: mBrCA4_DAMD

description:
control CEL: mBrCON_rep1.CEL
control CEL: mBrCON_rep2.CEL
Chodish Breast Carcinoma Tumor 4 DAMD, Technical Rep 1-2, Promoter Array

source_name: Chodish Breast Cancer Tumor 4 DAMD Assay


title: Lung 198_NMapping250K_Nsp

description: Hybridized to 250K_Nsp

value: female


title: Cervical Cancer Tissue-18

description: III_CT 809

source_name: Cervical Cancer Tissue

source_name: Universal Human Reference RNA (UHRR)


title: Cervical Cancer Tissue-17

description: II_CT 1077

value: IIB


title: Cervical Cancer Tissue-16

description: II_CT 1063


title: Lung 118_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: mTumor1vWTspleen_DAMD

description:
test CEL: mTumor1_rep1.CEL
test CEL: mTumor1_rep2.CEL
control CEL: mWTspleen_rep1.CEL
control CEL: mWTspleen_rep2.CEL
Eµ-MYC Tumor 1 DAMD, Technical Rep 1-2, Promoter Array

source_name: Eµ-MYC Tumor 1 DAMD Assay

value: Eµ-MYC Burkitt lymphoma tumor

source_name: WTspleen DAMD Assay

value: normal spleen


title: mTumor4vWTmsn_DAMD

description:
test CEL: mTumor4_rep1.CEL
test CEL: mTumor4_rep2.CEL
control CEL: mWTmsn_rep1.CEL
control CEL: mWTmsn_rep2.CEL
Eµ-MYC Tumor 4 DAMD, Technical Rep 1-2, Promoter Array

source_name: Eµ-MYC Tumor 4 DAMD Assay

source_name: WTmsn DAMD Assay

value: normal mesenteric lymph node


title: Cervical Cancer Tissue-15

description: II_CT 1021

value: purchased from Stratagene, Cat No. 740000

value: a pool of RNA made from 10 different human cell lines


title: Lung 103_NMapping250K_Nsp

description: Hybridized to 250K_Nsp

value: male


title: mTumor4vWTspleen_DAMD

description:
test CEL: mTumor4_rep1.CEL
test CEL: mTumor4_rep2.CEL
control CEL: mWTspleen_rep1.CEL
control CEL: mWTspleen_rep2.CEL
Eµ-MYC Tumor 4 DAMD, Technical Rep 1-2, Promoter Array


title: mTumor3vWTspleen_DAMD

description:
test CEL: mTumor3_rep1.CEL
test CEL: mTumor3_rep2.CEL
control CEL: mWTspleen_rep1.CEL
control CEL: mWTspleen_rep2.CEL
Eµ-MYC Tumor 3 DAMD, Technical Rep 1-2, Promoter Array

source_name: Eµ-MYC Tumor 3 DAMD Assay


title: mTumor3vWTmsn_DAMD

description:
test CEL: mTumor3_rep1.CEL
test CEL: mTumor3_rep2.CEL
control CEL: mWTmsn_rep1.CEL
control CEL: mWTmsn_rep2.CEL
Eµ-MYC Tumor 3 DAMD, Technical Rep 1-2, Promoter Array


title: Cervical Cancer Tissue-14

description: II_CT 1015


title: Lung 174_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: Cervical Cancer Tissue-13

description: II_CT 935


title: Cervical Cancer Tissue-12

description: II_CT 871

value: IIA


title: Lung 62_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: mTumor1vWTmsn_DAMD

description:
test CEL: mTumor1_rep1.CEL
test CEL: mTumor1_rep2.CEL
control CEL: mWTmsn_rep1.CEL
control CEL: mWTmsn_rep2.CEL
Eµ-MYC Tumor 1 DAMD, Technical Rep 1-2, Promoter Array


title: Cervical Cancer Tissue-11

description: II_CT 805


title: Lung 192_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: 11168_treated with 4mg/L Erythromycin_replicate2

city: Ames

first: Qingqing

last: Xia

state: IA

address: 1116 VMPM Iowa State University

institute: Iowa State University

hyb_protocol: After purification, the fluorescent labeling of the DNA was quantitated, and equal amounts of labeled cDNA of the wild-type and the mutant were mixed and dried in a speed vacuum concentrator. After resuspension with hybridization buffer provided by the slide manufacturer, the mixture was denatured by heating at 95 ◦C for 10 min. The hybridization mixture was loaded onto a microarray slide and hybridized in a shaking incubator at 42 ºC for 16 h. Slides were washed as the manufacture’s recommendations and dried by centrifugation.

scan_protocol: Using a ScanArray Express laser scanner (Applied Biosystem Inc., Foster City, CA) each dye channel of each slide was scanned at a 10 μm resolution using three predetermined laser power and photomultiplier gain settings. Thus for each slide six scans were performed, three separate scans at different settings of each of the two dye channels.

data_processing: ImaGene software (BioDiscovery, El Segundo, CA) was used for spot finding and to measure the spot-specific mean signal strength of each spot. The fluorescentc intensities of all spots were log2 transformed. The median of the three log2-transformed spot signals was determined and this value was used as spot signal for all further calculations. As an additional measure against intensity dependent dye bias the data was then subjected to LOWESS normalization.

organism: Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819

source_name: NCTC 11168, treated with 4mg/ml Ery, 30min

label_protocol: cDNA was synthesized using aminoallyl-dNTP according to the manufacturer’s instruction. After purification, aminoallyl labeled cDNA was fluorescently labeled with Cy-3/cy-5 mono-Reactive Dye Pack (Amersham Biosciences, Piscataway, NJ)

growth_protocol: wild-type C. jejuni NCTC 11168 (Ery MIC: 0.25 mg/L) was grown for 5 hours in MH to OD600 of approximately 0.2 with shaking (160 rpm) at 42℃ under microaerobic condition.

extract_protocol: Total RNA was isolated using RNAprotectTM bacteria reagent (Qiagen) and an RNeasy kit (Qiagen) according to the manufacturer’s protocol with an optional step of on-column DNase treatment with RNase-Free DNase (Qiagen). RNA concentration was measured with a NanoDrop ND-1000 (NanoDrop Technologies, Wilmington, DE)

treatment_protocol: Fifteen mL aliquots of NTCT 11168 culture (in duplicates) were treated with either sham (ethanol solvent for Ery), a lethal dose of Ery (4 mg/L; 16x MIC). All cultures were thoroughly mixed and statically incubated under microaerobic conditions for 30 minutes at 42℃. After 30 minutes treatment, the cultures were immediately mixed with RNAprotect™ (Qiagen, Valencia, CA) to stabilize the total bacterial RNA.

tag: agent

value: 4mg/ml Ery

source_name: NCTC 11168 treated with sham, 30min

growth_protocol: Campylobacter strains were routinely cultured from frozen stocks (-80 ℃) on Mueller-Hinton (MH) agar or broth at 42℃ under microaerobic conditions (85% N2, 10% CO2 and 5% O2). wild-type strain NCTC 11168 was grown for 5 hours in MH to OD600 of approximately 0.2 with shaking (160 rpm) at 42oC under microaerobic condition.

value: sham


title: Lung 66_NMapping250K_Nsp

description: Hybridized to 250K_Nsp

source_name: lung adenocarcinoma specimen


title: 11168_treated with 4mg/L Erythromycin_replicate3


title: Lung 77_NMapping250K_Nsp

description: Hybridized to 250K_Nsp


title: 11168_treated with 4mg/L Erythromycin_replicate1


title: HK3T (ECOR) A

description: CAFs co-cultivated with H1299 1 replicate out of 2

source_name: HK3T (ECOR)

value: co-cultivated for 24 hrs

source_name: Common reference


title: Cervical Cancer Tissue-8

description: I_CT 1138

value: IB


title: Cervical Cancer Tissue-9

description: II_CT 503


title: Cervical Cancer Tissue-10

description: II_CT 800


title: genomic DNA from Mutant 11

description:
TET2 Mutant lymphoma biopsy
G12

hyb_protocol: Bisulphite conversion and subsequent cleanup was carried out using EZ DNA Methylation Kit ( Zymo Research); Each bisulfite-DNA samplewas whole genome amplified (WGA) followed by enzymatic fragmentation and hybrdization to Illumina Infinum Human Methylation 450 Beadchip (HumanMethylation450_15017482_v.1.1). During this hybridization, the WGA-DNA molecules anneal to methylation-specific DNA oligomers linked to individual bead types, with each bead type corresponding to a specific DNA CpG site and methylation state. There are two different bead types for each locus, one with an oligomer that anneals specifically to the methylated version of the locus, while the other oligomer anneals to the unmethylated version of the locus. The oligomer probe designs follow the Infinium I and II chemistries, in which locus-specific base extension follows hybridization to a methylation-specific oligomer as detailed by manufacturer. After labeled nucleotide incorporation, the intensities were obtained after scanning each hybridized array. BeadArrays are scanned and the raw data are extracted to calculate the beta value DNA methylation score for each probe and sample.

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
Genome Studio software 2011.1 and R statistical software
Genome Studio 2011.1 and R statistical software.   Non_normalized data matrix contains unmethylated (U) and methylated (M) signal intensities for each CpG locus. The beta value is calculated as (M/(M+U)), in which M and U refer to the mean methylated and unmethylated probe signal intensities, respectively.The data points  for the following conditions; 1) Probes containing single-nucleotide polymorphisms (SNPs), 2) those that overlap with a repetitive element that covers the targeted CpG dinucleotide, 3) those that overlap with regions of insertions and deletions in the human genome. Further,measurements in which the fluorescent intensity is not statistically significantly above background signal (detection p-value > 0.05) are removed from the data set.  .

label: Cy5 and Cy3

source_name: lymphoma biopsies

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted and purified from fresh frozen lymphoma biopsy samples obtained from cases of DLBCL and normal peripheral blood B lymphocytes. After proteinase K digestion DNA was isolated using  Purescript DNA isolation Kit (Gentra system) as recommended by manufacturer.

value: lymphoma biopsy

value: TET2 Mutant


title: HK3T only A

description: CAFs grown alone, sorted 1 replicate out of 2

source_name: HK3T only

value: reference


title: Cervical Cancer Tissue-6

description: I_CT 833


title: genomic DNA from Mutant 9

description:
TET2 Mutant lymphoma biopsy
G9


title: genomic DNA from Mutant 12

description:
TET2 Mutant lymphoma biopsy
G6


title: genomic DNA from Mutant 13

description:
TET2 Mutant lymphoma biopsy
G7


title: genomic DNA from Mutant 14

description:
TET2 Mutant lymphoma biopsy
G15


title: Cervical Cancer Tissue-7

description: I_CT 843


title: genomic DNA from Mutant 8

description:
TET2 Mutant lymphoma biopsy
G8


title: Cervical Cancer Tissue-3

description: I_CT 513


title: Cervical Cancer Tissue-5

description: I_CT 515


title: Cervical Cancer Tissue-4

description: I_CT 514


title: Normal Cervical Tissue-4

description: N_CN 322

source_name: Normal (non-malignant) Cervical Tissue

extract_protocol: RNA isolation was done using TriZol reagent (Life Technologies) as per standard protocol followed by clean up using RNeasy extraction kit (Qiagen). RNA obtained was quantitated using Nanodrop and quality checked using formaldehyde-agarose gel electrophoresis.


title: Cervical Cancer Tissue-2

description: I_CT 510


title: genomic DNA from Mutant 6

description:
TET2 Mutant lymphoma biopsy
G16


title: Normal Cervical Tissue-2

description: N_CN 314


title: Normal Cervical Tissue-3

description: N_CN 321


title: Cervical Cancer Tissue-1

description: I_CT 500


title: Normal Cervical Tissue-1

description: N_CN 310


title: JL272_treated with 4mg/L Erythromycin_replicate4

data_processing: ImaGene software (BioDiscovery, El Segundo, CA) was used for spot finding and to measure the spot-specific mean signal strength of each spot. The fluorescentc intensities of all spots were log2 transformed. The median of the log2-transformed spot signals was determined and this value was used as spot signal for all further calculations. As an additional measure against intensity dependent dye bias the data was then subjected to LOWESS normalization.

organism: Campylobacter jejuni

source_name: JL272 treated with 4mg/ml Ery, 30min

growth_protocol: Erythromycin resistant strain JL272 (Ery MIC: 1024mg/L) was grown for 5 hours in MH to OD600 of approximately 0.2 with shaking (160 rpm) at 42℃ under microaerobic condition.

treatment_protocol: Strain JL272 was treated with 4 mg/L Ery (16x MIC of wild-type strain) under the same condition as NCTC 11168

source_name: JL272 treated with sham, 30min

growth_protocol: Campylobacter strains were routinely cultured from frozen stocks (-80 ℃) on Mueller-Hinton (MH) agar or broth at 42℃ under microaerobic conditions (85% N2, 10% CO2 and 5% O2). JL272 was grown for 5 hours in MH to OD600 of approximately 0.2 with shaking (160 rpm) at 42oC under microaerobic condition.


title: JL272_treated with 4mg/L Erythromycin_replicate3


title: genomic DNA from Mutant 5

description:
TET2 Mutant lymphoma biopsy
G14


title: JL272_treated with 4mg/L Erythromycin_replicate2


title: JL272_treated with 4mg/L Erythromycin_replicate1


title: genomic DNA from Mutant 4

description:
TET2 Mutant lymphoma biopsy
G13


title: genomic DNA from WT 19

description:
TET2 wild type lymphoma biopsy
G10

value: Wild type


title: 11168_treated with 0.125mg/L Erythromycin_replicate2

scan_protocol: Using a ScanArray Express laser scanner (Applied Biosystem Inc., Foster City, CA) each dye channel of  each slides was scanned at a 10 μm resolution using two or three predetermined laser power and photomultiplier gain settings. Thus for rep1, five scan were perfprmed, and for rep2 and rep3 six scans were performed.

source_name: NCTC 11168, treated with 0.125mg/ml Ery, 30min

treatment_protocol: Fifteen mL aliquots of NTCT 11168 culture (in duplicates) were treated with either sham (ethanol solvent for Ery), a sub-lethal dose of Ery (0.125 mg/L; 0.5x MIC). All cultures were thoroughly mixed and statically incubated under microaerobic conditions for 30 minutes at 42℃. After 30 minutes treatment, the cultures were immediately mixed with RNAprotect™ (Qiagen, Valencia, CA) to stabilize the total bacterial RNA.

value: 0.125mg/ml Ery

tag: stain


title: 11168_treated with 0.125mg/L Erythromycin_replicate1


title: genomic DNA from Mutant 10

description:
TET2 Mutant lymphoma biopsy
G11


title: genomic DNA from Mutant 2

description:
TET2 Mutant lymphoma biopsy
G1


title: 11168_treated with 0.125mg/L Erythromycin_replicate3


title: Control myotubes, biological replicate 11

status: Public on Oct 09 2013

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum Muenchen

hyb_protocol: According to the Affymetrix expression protocol

data_processing: Expression console (Build 1.2.1.20, Affymetrix) was used to obtain normalized RMA gene-level data (standard settings including sketch-quantile normalisation)

source_name: Control myotubes

label_protocol: WT Expression Kit (Ambion) and the WT Terminal Labeling Kit (Affymetrix)

extract_protocol: RNeasy Mini Kit (Qiagen) including DNase treatment

tag: individual id

value: individual 11

tag: age (yrs)

value: primary human myotubes

tag: sample group

value: control


title: genomic DNA from WT 16

description:
TET2 wild type lymphoma biopsy
G33

tag: tissue


title: Control myotubes, biological replicate 7

scan_protocol: According to the Affymetrix expression protocol

value: individual 07

tag: gender


title: Control myotubes, biological replicate 8

value: individual 08


title: Control myotubes, biological replicate 10

value: individual 10


title: Control myotubes, biological replicate 12

value: individual 12

value: male


title: Control myotubes, biological replicate 9

value: individual 09

value: female


title: genomic DNA from WT 14

description:
TET2 wild type lymphoma biopsy
G31


title: Control myotubes, biological replicate 6

value: individual 06


title: genomic DNA from WT 17

description:
TET2 wild type lymphoma biopsy
G34


title: Control myotubes, biological replicate 4

value: individual 04


title: genomic DNA from WT 18

description:
TET2 wild type lymphoma biopsy
G5

value: lymphoma biopsy


title: genomic DNA from WT 12

description:
TET2 wild type lymphoma biopsy
G29


title: genomic DNA from WT 10

description:
TET2 wild type lymphoma biopsy
G27


title: Control myotubes, biological replicate 5

value: individual 05


title: genomic DNA from Mutant 7

description:
TET2 Mutant lymphoma biopsy
G3

value: TET2 Mutant


title: Control myotubes, biological replicate 3

value: individual 03


title: genomic DNA from WT 15

description:
TET2 wild type lymphoma biopsy
G32

value: Wild type


title: Control myotubes, biological replicate 2

value: individual 02


title: In vitro EPS-stimulated myotubes, biological replicate 10

source_name: In vitro EPS-stimulated myotubes

value: primary human myotubes

value: in-vitro electric pulse stimulation (EPS) for 24hr


title: In vitro EPS-stimulated myotubes, biological replicate 12


title: Control myotubes, biological replicate 1

value: individual 01

value: control


title: In vitro EPS-stimulated myotubes, biological replicate 9


title: In vitro EPS-stimulated myotubes, biological replicate 11

value: individual 11


title: In vitro EPS-stimulated myotubes, biological replicate 7

value: individual 07


title: genomic DNA from WT 5

description:
TET2 wild type lymphoma biopsy
G21


title: genomic DNA from WT 8

description:
TET2 wild type lymphoma biopsy
G25


title: In vitro EPS-stimulated myotubes, biological replicate 6

value: male


title: In vitro EPS-stimulated myotubes, biological replicate 8

value: individual 08


title: In vitro EPS-stimulated myotubes, biological replicate 5


title: genomic DNA from WT 2

description:
TET2 wild type lymphoma biopsy
G19


title: genomic DNA from WT 13

description:
TET2 wild type lymphoma biopsy
G30


title: In vitro EPS-stimulated myotubes, biological replicate 4


title: In vitro EPS-stimulated myotubes, biological replicate 1

value: female


title: genomic DNA from WT 7

description:
TET2 wild type lymphoma biopsy
G24


title: Tmprss6 KO, LPS injected 1

city: Milano

first: Michela

last: Riba

address: via Olgettina 60

department: COSR, Center for Omics Sciences

country: Italy

institute: IRCCS, Ospdale San Raffaele

description:
KO+LPS-1.AVG_Signal
experiment replicate 1

hyb_protocol: 750 ng of cRNA in 11 µl (150 ng/µl) were hybridized to the BeadChip Array at 58°C overnight. The fluorescent signal was developed through a streptavidin-Cy3 staining step.

scan_protocol: Beadchips were imaged using the Illumina BeadArray Reader; the software Illumina® GenomeStudio was used to take fluorescent hybridization signals.

data_processing: The data were normalized using the cubic spline algorith implemented in the Illumina® GenomeStudio software

source_name: mouse liver_Tmprss6 KO, LPS injected

label_protocol: Total RNA was first reverse transcribed into cDNA and then in vitro trascribed into biotin-UTP labelled cRNA using the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin, TX)

growth_protocol: 4 weeks old mice were maintained an iron replete (Tmprss6 KO mice) or an iron deficient (control littermates) diet for 3 weeks.

extract_protocol: Total liver 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: Mice were injected with LPS (from Escherichia coli O26:B6; 0.1 mg/kg) or saline solution, and sacrificed 6 hrs later.

tag: strain

value: mixed 129/Ola × C57BL/6

value: liver

tag: genotype/variation

value: Tmprss6 KO

tag: growth protocol

value: 4 week old mice maintained on iron replete diet for 3 weeks

tag: stress

value: LPS

tag: age

value: 7 weeks old


title: Wild-type H37Rv_Anaerobic

city: Hefei

first: Yuzhi

last: Hong

state: Anhui Province

address: 3 Feixi Road

department: Modern Experiment Technology Center

country: China

institute: Anhui University

description: Gene expression upon the beginning of anaerobiosis at NRP-2 stage in the dormancy model

hyb_protocol: Each Slide was hybridized with 1.65μg 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), Stabilization and Drying Solution (Cat#5185-5979, Agilent technologies, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565BA, Agilent technologies, Santa Clara, CA, US) and Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US) with default settings，Scan resolution=5μm, PMT 100%，10%.

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

organism: Mycobacterium tuberculosis

source_name: Wild-type H37Rv, Anaerobic

label_protocol: Total RNA was amplified and labeled by Low RNA Input Linear Amplification kit (Cat#5184-3523, Agilent technologies, Santa Clara, CA, US), 5-(3-aminoallyl)-UTP (Cat#AM8436, Ambion, Austin, TX,US), Cy3 NHS ester (Cat#PA13105,GE healthcare Biosciences, Pittsburgh, PA,US) followed the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

growth_protocol: Wild-type H37Rv and Δdgc strains were grown at 37oC in 7H9-OADC-Tween 80 medium under aerobic conditions or in an in vitro dormancy model with methylene blue  by rapid shaking. Bacteria were collected at OD600 =1.3 for the aerobic cultures and upon the beginning of complete decolorization of methylene blue (a oxygen sensitive indicator) for the cultures in the dormancy model.

extract_protocol: Total RNA was extracted using TRIZOL Reagent following 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: Bacteria were incubated on ice for 1 min and then centrifuged at 12,000 g for 30 s. The cell pellets were added with fresh chloroform/methanol (3:1, v/v) at a rate of 200 μl per OD, votexed for 20 s, and immediately mixed well with 5 vol Trizol (Takara, Dalian, China).

value: wild-type H37Rv

tag: Stage


title: genomic DNA from WT 6

description:
TET2 wild type lymphoma biopsy
G22

value: lymphoma biopsy

tag: genotype

value: Wild type


title: Tmprss6 KO, saline injected 2

description:
KO-2.AVG_Signal
experiment replicate 2

source_name: mouse liver_Tmprss6 KO, saline injected


title: In vitro EPS-stimulated myotubes, biological replicate 2

value: individual 02

value: primary human myotubes

value: in-vitro electric pulse stimulation (EPS) for 24hr


title: Δdgc_Anaerobic_rep2

description: Gene expression upon the beginning of anaerobiosis at NRP-2 stage in the dormancy model (but with extra 2 hour later than sampling of Δdgc_Anaerobic-1 )

source_name: Δdgc, Anaerobic, replicate 2

value: Δdgc


title: Tmprss6 KO, LPS injected 3

description:
KO+LPS-3.AVG_Signal
experiment replicate 3


title: In vitro EPS-stimulated myotubes, biological replicate 3

value: individual 03


title: genomic DNA from WT 9

description:
TET2 wild type lymphoma biopsy
G26


title: genomic DNA from WT 4

description:
TET2 wild type lymphoma biopsy
G20


title: genomic DNA from WT 1

description:
TET2 wild type lymphoma biopsy
G18


title: Tmprss6 KO, saline injected 1

description:
KO-1.AVG_Signal
experiment replicate 1

value: control


title: genomic DNA from WT 3

description:
TET2 wild type lymphoma biopsy
G2


title: Wild-type H37Rv_Aerobic_OD=1.3

description: Gene expression at OD600=1.3 for aerobic culture

source_name: Wild-type H37Rv, Aerobic, OD=1.3

value: OD600=1.3 for aerobic culture


title: RAW-Blrp-LXRb-GW3965

type: SRA

city: La Jolla

first: Nathanael

middle: Judge

last: Spann

address: 9500 Gilman Drive CMMW 219A

department: Cellular and Molecular Medicine

institute: UCSD

description: Blrp-LXRbeta ChIP-Seq, GW3965

library_source: genomic

data_processing:
Libraries were sequenced for 36 or 50 cycles on an Illumina Genome Analyzer, Illumina Genome Analyzer II or HiSeq 2000, respectively, according to the manufacturer’s instructions.
Reads were aligned to the mm9 genome (NCBI build using bowtie (v0.12.7), keeping only reads that mapped best to a single, unique location.
For ChIP-Seq, Aligned read files were analyzed with HOMER (http://biowhat.ucsd.edu/homer/) to find peaks, calculate RPKM from the gene bodies of RefSeq genes, and perform other analyses in the study. Each ChIP-Seq experiment was normalized to a total of 10^7 uniquely mapped tags by adjusting the number of tags at each position in the genome to the correct fractional amount given the total tags mapped. UCSC Genome Browser BigWig or BigWig hub text files were created by calculating ChIP-Fragment pileups given a fragment size of ~150 bp.
Genome_build: mm9

source_name: BirA/BLRP-LXRb RAW264.7 cells

growth_protocol: The Indicated RAW264.7 stable cell lines were plated in RPMI medium 1640 and 10% fetal bovine serum, washed after adherence and again fed with fresh medium. The following day fresh medium containing 0.5% fetal bovine serum was added to the cells and serum starvation was carried overnight. After serum starvation the cells were treated with 1uM GW3965 for 2 hours.

extract_protocol: Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody. Alternatively, lysates clarified from isolated nuclei were treated with MNase and protein-DNA complexes were isolated with antibody. Libraries were prepared according to Illumina's instructions. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (minus exo) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation, ChIP DNA was PCR-amplified with Illumina Genomic adaptors or with NEXTflex DNA barcodes adaptors for 18 cycles and library fragments (ChIP) (insert plus adaptor and PCR primer sequences) were size-selected (150-250bp) from a 2% agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on Illumina Genome Analyzer II or Illumina HiSeq 2000 according to the manuactuere’s instructions.

tag: cell type

value: Macrophage Cell line RAW264.7

tag: treatment

tag: chip ab

value: Biotin-tagged LXRb bound to NanoLink Streptavidin Magnetic Microspheres (Solulink M1002-010)


title: genomic DNA from WT 11

description:
TET2 wild type lymphoma biopsy
G28


title: Δdgc_Aerobic_OD=1.3

source_name: Δdgc, Aerobic, OD=1.3


title: Δdgc_Anaerobic_rep1

source_name: Δdgc, Anaerobic, replicate 1

value: anaerobiosis at NRP-2 stage in the dormancy model


title: Tmprss6 KO, saline injected 3

description:
KO-3.AVG_Signal
experiment replicate 3

value: mixed 129/Ola × C57BL/6

value: liver

value: Tmprss6 KO


title: iron deficient control littermates, LPS injected 2

description:
ID+LPS-2.AVG_Signal
experiment replicate 2

source_name: mouse liver_iron deficient control littermates, LPS injected

value: wild type

value: 4 week old mice maintained on iron deficient diet for 3 weeks

value: LPS

value: 7 weeks old


title: iron deficient control littermates, LPS injected 3

description:
ID+LPS-3.AVG_Signal
experiment replicate 3


title: iron deficient control littermates, saline injected 3

description:
ID-3.AVG_Signal
experiment replicate 3

source_name: mouse liver_iron deficient control littermates, saline injected


title: iron deficient control littermates, saline injected 1

description:
ID-1.AVG_Signal
experiment replicate 1


title: Normoxia, low dietary lipid content_Ss92

status: Public on Oct 07 2013

city: Legnaro (PD)

first: Serena

last: Ferraresso

state: Padova

address: Viale dell'Università

department: Dept of Comparative Biomedicine and Food Science

institute: University of Padova

description: S. solea individual fed with commercial diet containing 11% lipids and kept in normoxic conditions

hyb_protocol: Hybridized according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol

scan_protocol: Array was scanned according to standard Agilent protocol at a resolution of 5 microns modifying default setting to scan the slide twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%)

data_processing: Data processed with FeatureExtraction v9.5 and quantile normalized using R2.6.1 statistical software

organism: Solea solea

source_name: liver

label_protocol: Amplified and labeled according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol

extract_protocol: Extracted according to QiAgen RNeasy MiniKit protocol for tissue samples

value: normoxic conditions

tag: diet

value: 11% lipids


title: Normoxia, low dietary lipid content_Ss96


title: iron deficient control littermates, LPS injected 1

description:
ID+LPS-1.AVG_Signal
experiment replicate 1


title: Normoxia, low dietary lipid content_Ss98


title: Normoxia, low dietary lipid content_Ss94


title: [-/-]-ALP-Apr2012-rep1

status: Public on Oct 08 2013

city: Barcelona

first: Victoria

last: Core

address: Baldiri Reixac, 10

department: Functional Genomics Core

country: Spain

institute: Institute for Research in Biomedicine

hyb_protocol: 8 µg of cDNA was hybridized per microarray for 16 hours of hybridization at 45ºC, washing and staining of microarrays was performed using a GeneAtlas Fluidics Station (Affymetrix, Santa Clara, CA)

scan_protocol: GeneChips were scanned in a GeneAtlas Imaging Station (Affymetrix, Santa Clara, CA)

data_processing: CEL files were generated from images (DAT files) using Command Console (Affymetrix, Santa Clara, CA), log2 RMA expression estimates were calculated using Partek Genomics Suite

source_name: knockout ALP

label_protocol: RNA was amplified for 23 cycles using the TransPlex Complete Whole Transcriptome Amplification Kit (Sigma; reference WTA2) and subsequently labeled using GeneChip Mapping 250K Nsp Assay Kit (Affymetrix; catalog # 900766), as described in Gonzalez Roca et al. 2012.

growth_protocol: freshly isolated progenitor cells from lineage depleted bone marrow of ID2-GFP reporter were analysed. Cells were not cultivated prior RNA isolation.

extract_protocol: RNA was extracted using Agencourt RNAClean XP magnetic beads (Beckman Coulter) as described (Gonzalez Roca et al. 2010)

treatment_protocol: cells were flow cytometrically isolated from lineage depleted bone marrow derived from ID2-GFP reporter mice and immediately lysed for RNA purification.

value: ALP cells (all lymphoid progenitors)

value: Nfil3 knockout

tag: date

value: April 2012


title: wt-prepro-May2012-rep2

source_name: wild type prepro

value: prepro NK cells


title: [-/-]-ALP-May2012-rep2


title: Normoxia, low dietary lipid content_Ss90


title: iron deficient control littermates, saline injected 2

description:
ID-2.AVG_Signal
experiment replicate 2

value: control


title: [-/-]-prepro-May2012-rep2

source_name: knockout prepro


title: [-/-]-prepro-Apr2012-rep1


title: wt-ALP-Apr2012-rep1

source_name: wild type ALP


title: Normoxia, low dietary lipid content_Ss86


title: Normoxia, low dietary lipid content_Ss82


title: Normoxia, low dietary lipid content_Ss84


title: Normoxia, low dietary lipid content_Ss100


title: Normoxia, low dietary lipid content_Ss80


title: Normoxia, low dietary lipid content_Ss70


title: Normoxia, low dietary lipid content_Ss74


title: Normoxia, low dietary lipid content_Ss78


title: Normoxia, low dietary lipid content_Ss66


title: Normoxia, low dietary lipid content_Ss76


title: Normoxia, low dietary lipid content_Ss88


title: wt-ALP-May2012-rep2


title: Normoxia, low dietary lipid content_Ss68


title: wt-prepro-Apr2012-rep1


title: Normoxia, high dietary lipid content_Ss87

description: S. solea individual fed with commercial diet containing 20% lipids and kept in normoxic conditions

value: 20% lipids


title: Normoxia, low dietary lipid content_Ss64


title: Normoxia, high dietary lipid content_Ss81


title: Normoxia, high dietary lipid content_Ss89


title: Normoxia, high dietary lipid content_Ss93


title: Normoxia, high dietary lipid content_Ss95


title: Normoxia, high dietary lipid content_Ss97


title: Normoxia, high dietary lipid content_Ss99


title: Normoxia, high dietary lipid content_Ss85


title: Normoxia, high dietary lipid content_Ss91


title: Normoxia, high dietary lipid content_Ss79


title: Normoxia, high dietary lipid content_Ss75


title: Normoxia, high dietary lipid content_Ss77


title: Tmprss6 KO, LPS injected 2

description:
KO+LPS-2.AVG_Signal
experiment replicate 2

value: 4 week old mice maintained on iron replete diet for 3 weeks


title: Normoxia, high dietary lipid content_Ss73


title: Normoxia, high dietary lipid content_Ss69


title: Normoxia, high dietary lipid content_Ss61


title: Normoxia, high dietary lipid content_Ss63


title: Hypoxia, low dietary lipid content_Ss28

description: S. solea individual fed with commercial diet containing 11% lipids and exposed to severe hypoxia

value: severe hypoxia


title: Hypoxia, low dietary lipid content_Ss32


title: Normoxia, high dietary lipid content_Ss83


title: Hypoxia, low dietary lipid content_Ss38


title: Hypoxia, low dietary lipid content_Ss34


title: Hypoxia, low dietary lipid content_Ss36


title: Hypoxia, low dietary lipid content_Ss18


title: Hypoxia, low dietary lipid content_Ss16


title: Normoxia, high dietary lipid content_Ss71


title: Hypoxia, low dietary lipid content_Ss26


title: Hypoxia, low dietary lipid content_Ss06


title: Hypoxia, low dietary lipid content_Ss40


title: Hypoxia, low dietary lipid content_Ss14


title: Hypoxia, high dietary lipid content_Ss39

description: S. solea individual fed with commercial diet containing 20% lipids and exposed to severe hypoxia


title: Hypoxia, low dietary lipid content_Ss10


title: Hypoxia, low dietary lipid content_Ss02


title: Hypoxia, high dietary lipid content_Ss37


title: Hypoxia, high dietary lipid content_Ss35


title: Hypoxia, low dietary lipid content_Ss22


title: Hypoxia, high dietary lipid content_Ss33


title: Hypoxia, high dietary lipid content_Ss31


title: Hypoxia, high dietary lipid content_Ss27


title: Hypoxia, high dietary lipid content_Ss29


title: Hypoxia, high dietary lipid content_Ss25


title: Hypoxia, high dietary lipid content_Ss23


title: Hypoxia, high dietary lipid content_Ss15


title: Hypoxia, high dietary lipid content_Ss19


title: Hypoxia, high dietary lipid content_Ss05


title: Hypoxia, high dietary lipid content_Ss03


title: Hypoxia, low dietary lipid content_Ss08


title: Hypoxia, high dietary lipid content_Ss09


title: Hypoxia, high dietary lipid content_Ss07


title: Hypoxia, high dietary lipid content_Ss01


title: Hypoxia, high dietary lipid content_Ss21


title: Hypoxia, high dietary lipid content_Ss11


title: Hypoxia, high dietary lipid content_Ss13


title: H2170 miR-4423 overexpression 3

city: Boston

first: Avrum

last: Spira

state: MA

address: 72 East Concord Street, E631

department: Computational Biomedicine

institute: Boston University

hyb_protocol: cDNA was fragmented end-labeled with a biotinylated dideoxynucleotide using terminal transferase and added to a hybridization cocktail, loaded on a Human Gene1.0 ST GeneChip and hybridized for 16 hours at 45 ºC under rotation  (60 rpm). Following hybridization, the array was washed and stained according to the standard Affymetrix protocol.

scan_protocol: Arrays were scanned using an Affymetrix GeneChip Scanner 3000. These scans were used to generate CEL files for each array.

data_processing: Transcript-level gene expression estimates were generated via the robust multichip average (RMA) algorithm within each batch using the Entrez Gene CDF v11 (http://brainarray.mbni.med.umich.edu) in R v2.9.2.

source_name: H2170 cancer cell line

label_protocol: The total RNA was converted to cDNA and subsequently amplified and biotin-labeled.

growth_protocol: H2170 cells were plated in 24-well plates and culture in RPMI-1640 Medium (ATCC) until they reached 40% confluency.

extract_protocol: Total RNA was isolated using the miRNeasy mini kit (Qiagen) as per manufacturer’s instructions.

treatment_protocol: H2170 cells were  transduced with a lentivirus overexpressing an empty vector as a control using polybrene at a concentration of 1ug/ml.

tag: condition

value: miR-4423 overexpression

tag: batch


title: H2170 Empty Vector 3

treatment_protocol: H2170 cells were  transduced with a lentivirus overexpressing miR-4423 using polybrene at a concentration of 1ug/ml.

value: Empty vector control


title: SW900 miR-4423 overexpression 3

source_name: SW900 cancer cell line

growth_protocol: SW900 cells were plated in 24-well plates and culture in RPMI-1640 Medium (ATCC) until they reached 40% confluency.

treatment_protocol: SW900 cells were  transduced with a lentivirus overexpressing an empty vector as a control using polybrene at a concentration of 1ug/ml.


title: H2170 Empty Vector 1


title: H2170 miR-4423 overexpression 2


title: SW900 miR-4423 overexpression 2


title: SW900 Empty Vector 3

treatment_protocol: SW900 cells were  transduced with a lentivirus overexpressing miR-4423 using polybrene at a concentration of 1ug/ml.


title: Pt#30-3T40L+IL-21

city: Amsterdam

first: Richard

last: Volckmann

state: Noord-Holland

address: van der Boechorststraat 6a

department: Laboratory of Experimental Oncology and Radiobiology

country: Netherlands

institute: msterdam UMC and University of Amsterdam

hyb_protocol: 10 µg of labeled cRNA was hybridized to Affymetrix Human genome U133 Plus 2.0 arrays according to manufacturer’s protocol (Affymetrix).

scan_protocol: Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer’s protoco

data_processing: Expression data (cel files) were normalized with the MAS5.0 algorithm (target signal = 100) using GCOS software (Affymetrix)

source_name: Tumor

label_protocol: RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 4 µg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with One-Cycle cDNA synthesis Kit (Affymetrix) according to manufacturer’s protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation.

growth_protocol: primary material

extract_protocol: Total RNA was isolated using Trizol (Invitrogen) and purified with RNeasy (Qiagen) according to manufacturer’s protocol,

treatment_protocol: CLL cells were cultured with CD40L-expressing fibroblasts, autologous activated T cells (anti-CD3/anti-CD28), or CD40L-expressing fibroblasts + IL-21 (25 ng/ml) for 16 hours. CLL cells were then sorted to purity as CD20+ CD5+ cells.

value: tumor

value: CD20+ CD5+ cells from CLL cell culture

value: IL-21 + cocultured with CD40L- cells


title: SW900 miR-4423 overexpression 1


title: H2170 Empty Vector 2


title: Pt#27-PB


title: H2170 miR-4423 overexpression 1


title: PT#2-3T40L+IL-21


title: SW900 Empty Vector 2


title: Calu6 miR-4423 overexpression 3

source_name: Calu6 cancer cell line

growth_protocol: Calu6 cells were plated in 24-well plates and culture in RPMI-1640 Medium (ATCC) until they reached 40% confluency.

treatment_protocol: Calu6 cells were  transduced with a lentivirus overexpressing an empty vector as a control using polybrene at a concentration of 1ug/ml.


title: SW900 Empty Vector 1


title: Pt#11-3T40L+IL-21


title: Pt#5B-3T40L+IL-21


title: Calu6 miR-4423 overexpression 2


title: Calu6 Empty Vector 2

treatment_protocol: Calu6 cells were  transduced with a lentivirus overexpressing miR-4423 using polybrene at a concentration of 1ug/ml.


title: Calu6 Empty Vector 3


title: Pt#5B-3T40

value: cocultured with CD40L- cells


title: PT#2-Tact

value: cocultured with activated T cells


title: Calu6 miR-4423 overexpression 1


title: Pt#19-PB


title: PT#2-PB


title: Pt#19-3T40


title: PT#2-3T40


title: H1299 Empty Vector 3

source_name: H1299 cancer cell line

growth_protocol: H1299 cells were cultured in RPMI 1640 growth medium (ATCC) and plated at a 50% confluence in 60mm plates 24h before transfection.

treatment_protocol: Plasmids containing miR-4423 were transfected using Lipofectamine 2000 (Invitrogen) as per manufacturer’s protocol.


title: Pt#19-Tact


title: Pt#27-3T40


title: H1299 miR-4423 overexpression 1

treatment_protocol: Plasmids containing empty vector as a control were transfected using Lipofectamine 2000 (Invitrogen) as per manufacturer’s protocol.


title: Pt#24-Tact


title: Pt#27-Tact


title: H1299 Empty Vector 1


title: H1299 miR-4423 overexpression 3


title: Calu6 Empty Vector 1


title: Pt#24-PB


title: Pt#24-3T40


title: H1299 miR-4423 overexpression 2


title: case 190

status: Public on Oct 06 2013

city: Oklahoma City

first: Kathy

middle: L

last: Sivils

state: OK

address: 825 NE 13th St.

department: Arthritis and Clinical Immunology

institute: Oklahoma Medical Research Fondation

hyb_protocol: Samples were hybridized to Human WG-6 BeadChip microarrays (Illumina, San Diego), which were then washed under high stringency and labeled with streptavidin-Cy3.

scan_protocol: Fluorescent intensity-based gene expression data was collected using an Illumina BeadStation 500 scanner.

data_processing: The GEP data were obtained from two separate microarray experiments. Quality control was applied in each dataset to filter out transcripts that were expressed in less than 10% of the subjects (detection call threshold: P<0.05) and probes with differential missing rates (P<0.001 by Fisher’s exact test) between the two datasets.  Re-annotation and Mapping of Oligonucleotide Array Technologies (ReMOAT) was used to determine the quality of Illumina BeadArray probes.  Each dataset was then normalized independently using Robust Multiarray Average (RMA) followed by log2 transformation and quantile normalization.  ComBat was subsequently applied to the combined dataset to adjust for non-biological experimental variation (batch effect).  After QC and normalization, 15,063 probes (in 12,248 genes) were kept for further statistical analysis.

source_name: whole peripheral blood

label_protocol: Double-stranded cDNA was synthesized using a T7 promoter, and biotin-labeled cRNA was transcribed using the Illumina TotalPrep RNA Amplification System (Ambion).

extract_protocol: Total RNA was obtained by blood collection into PaxGene tubes (BD company) and extracted following manufacturer’s protocols (Qiagen). Excess globin transcripts were removed using GLOBINclearTM (Ambion). RNA concentrations were determined using a Nanodrop spectrophotometer, and RNA quality was assessed with an Agilent 2100 Bioanalyzer (quality threshold 28s:18srRNA ratios above 1.0).

tag: disease state

value: Sjögrens syndrome


title: case 188


title: case 184


title: case 182


title: case 185


title: case 183


title: case 189


title: case 186


title: case 187


title: case 179


title: case 172


title: case 180


title: case 178


title: case 173


title: case 167


title: case 176


title: case 170


title: case 166


title: case 171


title: case 174


title: case 181


title: case 175


title: case 177


title: case 168


title: case 169


title: Hypoxia, low dietary lipid content_Ss30

value: 11% lipids


title: case 162


title: case 165


title: case 161


title: case 159


title: case 164


title: case 156


title: case 160


title: case 158


title: case 163


title: case 155


title: case 154


title: case 153


title: case 157


title: case 148


title: case 152


title: case 151


title: case 145


title: case 147


title: case 149


title: case 146


title: case 140


title: case 143


title: case 141


title: case 144


title: case 150


title: case 138


title: case 142


title: case 139


title: case 137


title: case 132


title: case 136


title: case 135


title: case 134


title: case 133


title: case 127


title: case 131


title: case 119


title: case 118


title: case 129


title: case 130


title: case 110


title: case 117


title: case 125


title: case 123


title: case 128


title: case 111


title: case 124


title: case 126


title: case 121


title: case 112


title: case 120


title: case 113


title: case 114


title: case 108


title: case 122


title: case 109


title: H1299 Empty Vector 2


title: case 116


title: case 107


title: case 101


title: case 104


title: case 105


title: case 106


title: case 102


title: case 97


title: case 99


title: case 96


title: case 94


title: case 98


title: case 89


title: case 91


title: case 90


title: case 92


title: case 87


title: case 88


title: case 95


title: case 86


title: case 84


title: case 115


title: case 93


title: case 85


title: case 82


title: case 81


title: case 83


title: case 74


title: case 76


title: case 75


title: case 79


title: case 80


title: case 73


title: case 71


title: case 78


title: case 72


title: case 65


title: case 67


title: case 69


title: case 70


title: case 103


title: case 66


title: case 68


title: case 61


title: case 63


title: case 77


title: case 62


title: case 55


title: case 60


title: case 59


title: case 57


title: case 54


title: case 49


title: case 53


title: case 50


title: case 64


title: case 52


title: case 44


title: case 48


title: case 47


title: case 58


title: case 46


title: case 45


title: case 56


title: case 51


title: case 41


title: case 42


title: case 40


title: case 36


title: case 43


title: case 30


title: case 35


title: case 37


title: case 38


title: case 31


title: case 24


title: case 21


title: case 28


title: case 29


title: case 23


title: case 22


title: case 18


title: case 33


title: case 39


title: case 34


title: case 32


title: case 17


title: case 25


title: case 19


title: case 27


title: case 26


title: case 15


title: case 13


title: case 10


title: case 16


title: case 6


title: case 11


title: case 12


title: case 20


title: case 7


title: case 100


title: case 4


title: case 9


title: control 32


title: case 3


title: control 31


title: case 8


title: case 14


title: control 28


title: case 1


title: control 30


title: control 29


title: case 2


title: control 24


title: control 26


title: control 25


title: case 5


title: control 27


title: Complete clinical responder 219

city: Paris

first: Martine

middle: S

last: Aggerbeck

address: 45 rue des Saints Pères

country: France

institute: INSERM

description: Clontech universal RNA reference comprising RNA from 10 human tissues

hyb_protocol: The probes (1 µg each of a biopsy sample and of the reference, direct design) were hybridized to a “pan-genomic human 44K” microarray (Agilent) containing 41,000 probes corresponding to genes or expressed sequence tags using the Agilent 60-mer oligo microarray processing protocol (Agilent). Hybridization was performed for 17 hours at 60°C with rotation in a hybridization oven (Agilent) as described by the manufacturer. The microarrays were washed as described in the manufacturer’s protocol and dried immediately in a speed-vac centrifuge for 2 minutes.

scan_protocol: The microarrays were scanned using an Axon 4000B scanner (Molecular Devices, Sunnyvale, CA, USA) equipped with 532 and 635 nm excitation lasers for Cy3 and Cy5, at 100% laser power at 5µm resolution. PMT voltages were automatically adjusted to balance the distributions of the red and green intensities and to optimize the dynamics of image quantification. The rate of saturated pixels was limited to 0.01%.

data_processing: The resulting 16 bit images were analyzed and the quantification of signal values of the arrays was performed  using GenePix Pro 6.0 software (Axon Instruments, Union City, CA) Segmentation was computed with the “adaptive circle” method of processing. Backgrounds were not subtracted and not found, saturated and bad spots were discarded. Intra-array normalisation (excluding control spots, 2,615 probes) was performed using the loess method (Smyth and Speed 2003) with a 0.5 span parameter.

source_name: Biopsy Complete clinical responder 219

label_protocol: Briefly, 200-300ng total RNA extracted from the biopsies or from the RNA reference were labelled using cyanine3-CTP or cyanine5-CTP and the “Low RNA Input Fluorescent Linear Amplification Kit” (Agilent), according to the manufacturer’s instructions. The fluorescent probes were purified (Purification RNeasy Mini Kit, Qiagen) and the concentration of the probes and the level of incorporation of the dyes into the probes was measured (Nanodrop D-1000 spectrophotometer). Agarose electrophoresis of the labelled probes (1.2% agarose gel in 0.5 X TBE) performed on a microscope slide together with DNA markers (100 bp, Biolabs) was performed and the fluorescence of the gel was assessed in a Genetac IV scanner (Perkin-Elmer). Both the intensity of the signal and the profile of the samples indicated the quality of the labelling.

extract_protocol: Tumour samples were obtained during endoscopy under general anesthesia before any treatment. Each tumour biopsy was immediately put into RNAlater (Ambion) to avoid degradation of RNA. The biopsy was cut into 2 pieces, one for pathological examination and the other one was immediately frozen at -80°C until further processing for RNA extraction. Preparation and assessment of RNA quality. “Tripure isolation reagent” (Roche) was used to extract RNA from the same biopsy. Briefly, the biopsy (less than 100mg) was homogenized in 1 mL Tripure with 3 sterile tungsten beads in a Retsch MM20 Mixer Mill (3 min grinding at speed 29, 3 times). After addition of two hundred µL of chloroform, the tube was shaken vigorously at room temperature for at least 5 min and allowed to sit for another 5 min before centrifugation (15 min, 12,500 rpm, 4°C). The aqueous upper layer, containing RNA was collected.  After the addition of 500 µL isopropanol and incubation at -20°C for 10 min, the RNA was pelleted by centrifugation (15 min, 12,500 rpm, 4°C. The pellet was washed with 1 mL of 75% ethanol, centrifuged as described above and dried at room temperature for 10 min. Total RNA were resuspended into 40 µL of RNase-free water. RNA was further purified with the RNase-free DNase Set (Qiagen) and RNeasy minielute cleanup (Qiagen), according to the manufacturer’s protocol. RNAs were quantified using a Nanodrop ND-1000 spectrophotometer and their quality was assessed by electrophoresis using a BioAnalyzer (Agilent).

treatment_protocol: The patients received PF (25 mg/m2/day cispaltin and 1g/m2/day 5FU) induction chemotherapy delivered as daily continuous i.v. infusions in 4-day courses. Usually 3 courses (range 2-5) were given with 14-21 day intervals between the courses and the dosages were adjusted to take into account individual tolerance and response

tag: response

value: Complete clinical responder to chemotherapy

tag: tissue

value: head and neck squamous cell carcinoma tumor

source_name: Clontech universal RNA reference from 10 human tissues

tag: sample type


title: Complete clinical responder 195

source_name: Biopsy Complete clinical responder 195

value: Clontech universal RNA reference from 10 human tissues


title: control 21


title: Complete clinical responder 169

source_name: Biopsy Complete clinical responder 169


title: control 22


title: Complete clinical responder 164

source_name: Biopsy Complete clinical responder 164


title: Complete clinical responder 156

source_name: Biopsy Complete clinical responder 156


title: control 18


title: Complete clinical responder 130

source_name: Biopsy Complete clinical responder 130


title: control 17


title: control 23


title: control 20


title: Complete clinical responder 121

source_name: Biopsy Complete clinical responder 121


title: Complete clinical responder 157

source_name: Biopsy Complete clinical responder 157


title: control 14


title: control 19


title: control 15


title: control 16


title: Complete clinical responder 23

source_name: Biopsy Complete clinical responder 23


title: Complete clinical responder 109

source_name: Biopsy Complete clinical responder 109


title: Complete clinical responder 110

source_name: Biopsy Complete clinical responder 110


title: Complete clinical responder 57

source_name: Biopsy Complete clinical responder 57


title: Complete clinical responder 40

source_name: Biopsy Complete clinical responder 40


title: control 12


title: control 10


title: control 11


title: Nonresponder 302

source_name: Biopsy Nonresponder 56

value: Nonresponder to chemotherapy


title: Nonresponder 223

source_name: Biopsy Nonresponder 54


title: control 13

source_name: whole peripheral blood


title: Nonresponder 246

source_name: Biopsy Nonresponder 55


title: control 9


title: control 6


title: Nonresponder 303

source_name: Biopsy Nonresponder 57

source_name: Clontech universal RNA reference from 10 human tissues


title: control 7


title: control 8


title: control 4


title: Nonresponder 48

source_name: Biopsy Nonresponder 48


title: Nonresponder 143

source_name: Biopsy Nonresponder 50


title: control 5


title: Nonresponder 140

source_name: Biopsy Nonresponder 49


title: M-BE_TGF-β1_6days_rep3

city: Beijing

first: Bangrong

last: Cao

address: NO.17 Panjiayuannanli, Chaoyang District, Beijing, P.R.China

institute: Cancer Institute & Hospital, Chinese Academy of Medical Sciences

description:
Day6_3
Gene expression in TGF-β1-treated M-BE cells.

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 μl containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 55 μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100% and 10%, dynamic range is extended).

data_processing: The scanned images were analyzed with Feature Extraction Software v9.1 (Agilent) using default parameters (protocol GE1_105_Dec08 and Grid: 014850_D_20070207) to obtain background subtracted and spatially detrended Processed Signal intensities. Log2-transformed raw intensities were normalized across a series of arrays with the median-absolute scaling method using the limma package of R software.

source_name: M-BE cells, TGF-β1 treated, 6 days

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: The immortalized human bronchial epithelium cell line M-BE was cultured in serum-free LHC-9 medium, and incubated at 37 ℃ with 3.5% CO2.

extract_protocol: RNA was prepared using TRIzol reagent (Invitrogen, Carlsbad, CA), and then purified using the RNeasy Mini Kit (Qiagen, Germantown, MD), according to the manufacturer's instructions. RNA was quantitated using a ND-1000 UV-VIS Spectrophotometer (NanoDrop Technologies, Wilmington, DE), and the integrity of the RNA was assessed with the RNA 6000 LabChip kit in combination with the Agilent 2100 Bioanalyzer (Agilent, Pal Alto, CA).

treatment_protocol: M-BE cells in cultures were treated with human recombinant TGF-β1 (R&D system, Minneapolis, MN, USA) at a final concentration of 5 ng/ml for six days (changing fresh medium with the same concentration of TGF-β1 every three days). M-BE cultured without TGF-β1 were considered as controls.

tag: cell line

value: M-BE

value: immortalized human bronchial epithelial cells

tag: treatment duration

value: 6 days


title: Nonresponder 210

source_name: Biopsy Nonresponder 53


title: M-BE_TGF-β1_6days_rep2

description:
Day6_2
Gene expression in TGF-β1-treated M-BE cells.


title: control 3


title: Nonresponder 198

source_name: Biopsy Nonresponder 52


title: control 1


title: M-BE_TGF-β1_6days_rep1

description:
Day6_1
Gene expression in TGF-β1-treated M-BE cells.


title: IMR32 (kl1), t = 72 hrs_AMC NB 496

growth_protocol: Cells were cultured in MEM (Invitrogen) containing 10% fetal calf serum at 37 degrees Celsius.

extract_protocol: Total RNA was isolated using Trizol (Invitrogen) and purified with RNeasy (Qiagen) according to manufacturer’s protocol.

treatment_protocol: Cells were plated 24 hours before transduction with lentivirus containing shRNA. RNA was harvested at 0 or 76 hours after transduction.

value: Neuroblastoma cell

tag: treatment condition

tag: shrna

value: Sigma MISSION TRCN0000040074 (EZH2)

tag: sequence

value: GCTAGGTTAATTGGGACCAAA


title: IMR32 (kl1), t = 0hrs_AMC NB 490

value: no lenti


title: IMR32 (kl1), t = 72 hrs_AMC NB 592

value: Sigma MISSION SHC002 (control)

value: CAACAAGATGAAGAGCACCAA


title: M-BE_control_rep2

description:
Con2
Gene expression in control M-BE cells.

source_name: M-BE cells, control


title: Nonresponder 159

source_name: Biopsy Nonresponder 51


title: IMR32 (kl1), t = 0  hrs_AMC NB 590


title: control-continuous_expose-26h_harvest-rep4

status: Public on Oct 05 2013

city: Ft. Detrick

first: John

middle: A.

last: Lewis

address: 568 Doughten Drive

department: Biomarkers Program

institute: U.S. Army Center for Environmental Health Research

description: gene expression data from L4 larvae

hyb_protocol: Biotin labeled cRNA was fragmented and hybridized to Affymetrix C. elegans whole genome GeneChips as recommended by Affymetrix.

scan_protocol: Hybridized  Affymetrix C. elegans whole genome GeneChips were then scanned as recommended by Affymetrix.

data_processing: Probe set expression levels were calculated using RMA processing of raw data within Partek Genomics Suite (Partek, Inc.).

organism: Caenorhabditis elegans

source_name: whole organism

label_protocol: cDNA was synthesized using SuperScript Choice kit and a T24T7 primer following the manufacturer's protocol. Biotin labeled cRNA was synthesized using the Enzo BioArray High Yield Kit following the manufacturer's protocol.

growth_protocol: C. elegans cultures were grown in CeHR medium at 22.5 °C in T-75 tissue culture flasks with shaking at 70 rpm.

extract_protocol: Flash frozen worms were pulverized under liquid nitrogen in a Spex 6750 Freezer Mill. RNA was extracted from pulverized worms with Trizol followed by an additional purification step using RNeasy Midi columns. PolyA RNA was then isolated using OligoTex. All steps were performed following manufacturers recommendations.

treatment_protocol: Cultures of 250,000 synchronized L1 worms were grown in 30 mL CeHR medium. A separate T-75 culture flask was set up for each condition. After ~41 h, when 50% of the worms had passed the L3/L4 molt,  the exposures were initiated. Four flasks of worms were harvested prior to beginning the exposure as the 0 h controls. Equal volumes of water or dichlorvos stock (diluted for 0.6 µM or 15 µM final concentration as appropriate) were added to the remaining flasks, which were then returned to the incubator. The flasks were treated according to one of three protocols. In the first protocol, the set of flasks was incubated without interruption for the duration of the experiment (continuous) with flasks being harvested at 2, 8, 14, 20, and 26 h. The other two sets were incubated for 2 or 8 h, at which time the worms were centrifuged out of the exposure medium, washed 3 times with a modified CeHR medium (Washout Buffer), resuspended in fresh CeHR medium without dichlorvos, and returned to the incubator. Flasks were harvested at 6 h intervals following the washout through 26 h. Untreated controls (or shams) and low and high concentrations flasks were prepared for each harvest time of each of the three protocols.

tag: developmental stage

value: L4 larvae

tag: exposure concentration

value: 0 µM DDVP (control)

tag: exposure protocol duration

value: continuous

tag: harvest time


title: control 2


title: M-BE_control_rep1

description:
Con1
Gene expression in control M-BE cells.

tag: cell type

tag: treatment


title: IMR32 (kl1), t = 72 hrs_AMC NB 591


title: SJ8pTr6 (kl3) clone 1D, t = 72 hrs_AMC NB 248

treatment_protocol: Cells were plated 24 hours before addition of doxycycline. RNA was harvested at 0 or 76 hours after addition of doxycycline.

value: EZH2 siRNA dox


title: M-BE_control_rep3

description:
Con3
Gene expression in control M-BE cells.


title: high_DDVP-continuous_expose-20h_harvest-rep4

description: gene expression data from L4 larvae

value: 15 µM DDVP (high)


title: high_DDVP-continuous_expose-26h_harvest-rep4

description: gene expression data from L4 larvae


title: low_DDVP-continuous_expose-20h_harvest-rep4

description: gene expression data from L4 larvae

value: 0.6 µM DDVP (low)


title: IMR32pTr6 (kl43) clone 2E, t = 72 hrs_AMC NB 246


title: control-continuous_expose-20h_harvest-rep4

description: gene expression data from L4 larvae


title: SJ8pTr6 (kl3) clone 1D, t = 0hrs_AMC NB 247


title: IMR32pTr6 (kl43) clone 2E, t = 0 hrs_AMC NB 245


title: high_DDVP-continuous_expose-14h_harvest-rep4

description: gene expression data from L4 larvae


title: low_DDVP-continuous_expose-14h_harvest-rep4

description: gene expression data from L4 larvae


title: low_DDVP-continuous_expose-26h_harvest-rep4

description: gene expression data from L4 larvae


title: control-continuous_expose-14h_harvest-rep4

description: gene expression data from L4 larvae


title: high_DDVP-8h_expose-14h_harvest-rep4

description: gene expression data from L4 larvae

value: 8 hr


title: low_DDVP-8h_expose-14h_harvest-rep4

description: gene expression data from L4 larvae


title: high_DDVP-8h_expose-26h_harvest-rep4

description: gene expression data from L4 larvae


title: control-8h_expose-26h_harvest-rep4

description: gene expression data from L4 larvae


title: low_DDVP-8h_expose-20h_harvest-rep4

description: gene expression data from L4 larvae


title: control-8h_expose-20h_harvest-rep4

description: gene expression data from L4 larvae


title: low_DDVP-2h_expose-26h_harvest-rep4

description: gene expression data from L4 larvae

value: 2 hr


title: high_DDVP-continuous_expose-8h_harvest-rep4

description: gene expression data from L4 larvae


title: control-2h_expose-26h_harvest-rep4

description: gene expression data from L4 larvae


title: low_DDVP-8h_expose-26h_harvest-rep4

description: gene expression data from L4 larvae


title: control-continuous_expose-8h_harvest-rep4

description: gene expression data from L4 larvae


title: control-8h_expose-14h_harvest-rep4

description: gene expression data from L4 larvae


title: high_DDVP-8h_expose-20h_harvest-rep4

description: gene expression data from L4 larvae


title: high_DDVP-2h_expose-20h_harvest-rep4

description: gene expression data from L4 larvae


title: low_DDVP-continuous_expose-8h_harvest-rep4

description: gene expression data from L4 larvae


title: control-2h_expose-20h_harvest-rep4

description: gene expression data from L4 larvae


title: control-2h_expose-14h_harvest-rep4

description: gene expression data from L4 larvae


title: high_DDVP-2h_expose-26h_harvest-rep4

description: gene expression data from L4 larvae


title: low_DDVP-2h_expose-20h_harvest-rep4

description: gene expression data from L4 larvae


title: high_DDVP-continuous_expose-2h_harvest-rep4

description: gene expression data from L4 larvae


title: control-2h_expose-8h_harvest-rep4

description: gene expression data from L4 larvae


title: low_DDVP-continuous_expose-2h_harvest-rep4

description: gene expression data from L4 larvae


title: low_DDVP-2h_expose-14h_harvest-rep4

description: gene expression data from L4 larvae


title: low_DDVP-2h_expose-8h_harvest-rep4

description: gene expression data from L4 larvae


title: high_DDVP-2h_expose-8h_harvest-rep4

description: gene expression data from L4 larvae


title: high_DDVP-continuous_expose-26h_harvest-rep3

description: gene expression data from L4 larvae


title: high_DDVP-2h_expose-14h_harvest-rep4

description: gene expression data from L4 larvae


title: low_DDVP-continuous_expose-26h_harvest-rep3

description: gene expression data from L4 larvae


title: control-continuous_expose-26h_harvest-rep3

description: gene expression data from L4 larvae


title: high_DDVP-8h_expose-26h_harvest-rep3

description: gene expression data from L4 larvae


title: high_DDVP-continuous_expose-20h_harvest-rep3

description: gene expression data from L4 larvae


title: control-continuous_expose-2h_harvest-rep4

description: gene expression data from L4 larvae


title: low_DDVP-8h_expose-26h_harvest-rep3

description: gene expression data from L4 larvae


title: control-continuous_expose-0h_harvest-rep4

description: gene expression data from L4 larvae


title: high_DDVP-continuous_expose-14h_harvest-rep3

description: gene expression data from L4 larvae


title: low_DDVP-continuous_expose-20h_harvest-rep3

description: gene expression data from L4 larvae


title: high_DDVP-8h_expose-20h_harvest-rep3

description: gene expression data from L4 larvae


title: low_DDVP-continuous_expose-14h_harvest-rep3

description: gene expression data from L4 larvae


title: control-8h_expose-26h_harvest-rep3

description: gene expression data from L4 larvae


title: low_DDVP-8h_expose-14h_harvest-rep3

description: gene expression data from L4 larvae


title: low_DDVP-8h_expose-20h_harvest-rep3

description: gene expression data from L4 larvae


title: high_DDVP-8h_expose-14h_harvest-rep3

description: gene expression data from L4 larvae


title: control-continuous_expose-14h_harvest-rep3

description: gene expression data from L4 larvae


title: control-8h_expose-20h_harvest-rep3

description: gene expression data from L4 larvae


title: high_DDVP-2h_expose-26h_harvest-rep3

description: gene expression data from L4 larvae


title: control-continuous_expose-8h_harvest-rep3

description: gene expression data from L4 larvae


title: low_DDVP-2h_expose-26h_harvest-rep3

description: gene expression data from L4 larvae


title: control-2h_expose-26h_harvest-rep3

description: gene expression data from L4 larvae


title: low_DDVP-2h_expose-20h_harvest-rep3

description: gene expression data from L4 larvae


title: high_DDVP-2h_expose-20h_harvest-rep3

description: gene expression data from L4 larvae


title: control-8h_expose-14h_harvest-rep3

description: gene expression data from L4 larvae


title: control-2h_expose-20h_harvest-rep3

description: gene expression data from L4 larvae


title: high_DDVP-2h_expose-14h_harvest-rep3

description: gene expression data from L4 larvae


title: high_DDVP-2h_expose-8h_harvest-rep3

description: gene expression data from L4 larvae


title: low_DDVP-continuous_expose-8h_harvest-rep3

description: gene expression data from L4 larvae


title: control-2h_expose-14h_harvest-rep3

description: gene expression data from L4 larvae


title: control-continuous_expose-20h_harvest-rep3

description: gene expression data from L4 larvae


title: low_DDVP-2h_expose-8h_harvest-rep3

description: gene expression data from L4 larvae


title: low_DDVP-continuous_expose-20h_harvest-rep2

description: gene expression data from L4 larvae


title: low_DDVP-2h_expose-14h_harvest-rep3

description: gene expression data from L4 larvae


title: high_DDVP-8h_expose-26h_harvest-rep2

description: gene expression data from L4 larvae


title: control-continuous_expose-26h_harvest-rep2

description: gene expression data from L4 larvae


title: control-continuous_expose-20h_harvest-rep2

description: gene expression data from L4 larvae


title: control-2h_expose-8h_harvest-rep3

description: gene expression data from L4 larvae


title: low_DDVP-continuous_expose-2h_harvest-rep3

description: gene expression data from L4 larvae


title: high_DDVP-continuous_expose-20h_harvest-rep2

description: gene expression data from L4 larvae


title: high_DDVP-continuous_expose-26h_harvest-rep2

description: gene expression data from L4 larvae


title: control-continuous_expose-0h_harvest-rep3

description: gene expression data from L4 larvae


title: high_DDVP-continuous_expose-14h_harvest-rep2

description: gene expression data from L4 larvae


title: low_DDVP-continuous_expose-26h_harvest-rep2

description: gene expression data from L4 larvae


title: control-continuous_expose-2h_harvest-rep3

description: gene expression data from L4 larvae


title: high_DDVP-continuous_expose-2h_harvest-rep3

description: gene expression data from L4 larvae


title: control-continuous_expose-14h_harvest-rep2

description: gene expression data from L4 larvae


title: low_DDVP-continuous_expose-14h_harvest-rep2

description: gene expression data from L4 larvae


title: low_DDVP-8h_expose-26h_harvest-rep2

description: gene expression data from L4 larvae


title: high_DDVP-8h_expose-20h_harvest-rep2

description: gene expression data from L4 larvae


title: low_DDVP-continuous_expose-8h_harvest-rep2

description: gene expression data from L4 larvae


title: control-8h_expose-26h_harvest-rep2

description: gene expression data from L4 larvae


title: high_DDVP-continuous_expose-8h_harvest-rep2

description: gene expression data from L4 larvae


title: control-8h_expose-14h_harvest-rep2

description: gene expression data from L4 larvae


title: low_DDVP-8h_expose-14h_harvest-rep2

description: gene expression data from L4 larvae


title: control-8h_expose-20h_harvest-rep2

description: gene expression data from L4 larvae


title: low_DDVP-8h_expose-20h_harvest-rep2

description: gene expression data from L4 larvae


title: high_DDVP-2h_expose-26h_harvest-rep2

description: gene expression data from L4 larvae


title: control-continuous_expose-8h_harvest-rep2

description: gene expression data from L4 larvae


title: high_DDVP-8h_expose-14h_harvest-rep2

description: gene expression data from L4 larvae


title: low_DDVP-2h_expose-20h_harvest-rep2

description: gene expression data from L4 larvae


title: low_DDVP-2h_expose-26h_harvest-rep2

description: gene expression data from L4 larvae


title: control-2h_expose-8h_harvest-rep2

description: gene expression data from L4 larvae


title: high_DDVP-2h_expose-14h_harvest-rep2

description: gene expression data from L4 larvae


title: control-continuous_expose-0h_harvest-rep2

description: gene expression data from L4 larvae


title: low_DDVP-continuous_expose-2h_harvest-rep2

description: gene expression data from L4 larvae


title: high_DDVP-2h_expose-20h_harvest-rep2

description: gene expression data from L4 larvae


title: low_DDVP-2h_expose-14h_harvest-rep2

description: gene expression data from L4 larvae


title: high_DDVP-2h_expose-8h_harvest-rep2

description: gene expression data from L4 larvae


title: low_DDVP-2h_expose-8h_harvest-rep2

description: gene expression data from L4 larvae


title: high_DDVP-continuous_expose-2h_harvest-rep2

description: gene expression data from L4 larvae


title: high_DDVP-continuous_expose-26h_harvest-rep1

description: gene expression data from L4 larvae


title: control-continuous_expose-2h_harvest-rep2

description: gene expression data from L4 larvae


title: control-2h_expose-20h_harvest-rep2

description: gene expression data from L4 larvae


title: control-2h_expose-14h_harvest-rep2

description: gene expression data from L4 larvae


title: low_DDVP-continuous_expose-20h_harvest-rep1

description: gene expression data from L4 larvae


title: high_DDVP-continuous_expose-20h_harvest-rep1

description: gene expression data from L4 larvae


title: control-continuous_expose-20h_harvest-rep1

description: gene expression data from L4 larvae


title: control-continuous_expose-26h_harvest-rep1

description: gene expression data from L4 larvae