title: CTC from 4D model on day 25, biological replicate #3

source_name: H1299 cells

tag: cell type

value: CTC

value: day 25


title: FC-28 Lungs

status: Public on Mar 12 2015

type: RNA

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

country: USA

institute: Baylor College of Medicine

hyb_protocol: According to Illumina protocol.

scan_protocol: According to Illumina protocol.

data_processing: The image data were compiled into a project using  Beadstudio software gene expression module version 3.2.7.  No normalization was used. The data was exported as txt files using the build-in function of export to GeneSpring GX format (please note that the ID_REF column in raw data files contains 'Array_Address_Id'). The option of sample probe profile was chosen. Data were subsequently quantile normalized for the analysis.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: OS lung metastasis_FC-28 specimen

label_protocol: According to Illumina protocol.

growth_protocol: Three genetically engineered mouse lines were used in this study.  Col2.3-Cre mice contain a rat Col1a1 2.3 kb rat promoter driving a Cre transgene (Liu et al., 2004) These mice express Cre  in osteoblast lineages.  These mice were backcrossed into a C57BL/6 background and further crossed to either floxed p53 mice or LSL-p53R172H mice.  Floxed p53 mice were generated by the Berns laboratory (Marino et al., 2000) and obtained from the NCI Mouse Repository. These mice were also backcrossed into a C57BL/6 background and contain a wildtype p53 allele that can be excised by Cre recombinase binding to LoxP sites located in introns 1 and 10 of the p53 gene.  The LSL-p53R172H mice were made by the Jacks laboratory (Olive et al., 2004), obtained from the NCI Mouse Repository and backcrossed into a C57BL/6 background. These mice contain a “hot spot” point-mutant allele of Trp53 frequently observed in human tumors that can be activated by Cre-mediated deletion of the lox-stop-lox (LSL) cassette located in the altered p53 promoter.  All mice were bred and maintained in a specific pathogen-free animal facility at Baylor College of Medicine. All research with mice was conducted in compliance with the Baylor Animal Protocol Committee (Baylor College of Medicine Animal Protocol AN336) and AAALAC recommendations as published in The Guide for the Care and Use of Laboratory Animals (NRC1996).

extract_protocol: Total RNA was extracted from tissue samples, using Trizol. RNA quality were inspected on a 2100 Bioanalyzer (Agilent).

tag: sample group

value: OS lung metastasis

tag: specimen id

value: FC-28 specimen


title: FC-279 primary

source_name: primary OS that produced metastatic lesion_FC-279 specimen

value: FC-279 specimen


title: FC-28 primary

source_name: primary OS that produced metastatic lesion_FC-28 specimen


title: RF-212 primary

source_name: primary OS that produced metastatic lesion_RF-212 specimen

value: RF-212 specimen


title: RF-89 primary

source_name: primary OS that produced metastatic lesion_RF-89 specimen

value: RF-89 specimen


title: RF-379 primary

source_name: primary OS that produced metastatic lesion_RF-379 specimen

value: RF-379 specimen


title: CB_R306C_4

city: brookline

first: Harrison

middle: Wren

last: Gabel

state: Massachusetts

address: 220 longwood avenue

department: Neurbiology

institute: Harvard Medical School

hyb_protocol: Hybridization was carried out as described in the GeneChip® Whole Transcript (WT) Sense Target  Labeling Assay Manual v4 Chapter 5

scan_protocol: Arrays were scanned with the Affymetrix GeneChip Scanner 3000

data_processing:
Data were processed using Genespring software (Agilent). Gene level expression were summarized use RMA16.
probe group file: MoEx-1_0-st-v1.r2.pgf
meta-probeset file: MoEx-1_0-st-v1.r2.dt1.mm9.core.mps

source_name: cerebellum

label_protocol: Fragmentation and labeling were carried out using the The Ambion® WT Expression Kit

growth_protocol: Mice were housed under standard conditions in the animal facility

extract_protocol: Cerebellum was dissected from 8-10 week old MeCP2 R306C or wild-type littermate controls. RNA was trizol and extracted using Qiagen Rneasy purification with on column DNase steps.

tag: age

value: 8-10 weeks

tag: brain region

value: cerebellum

tag: genotype

value: Mecp2 R306C/y


title: CR-113A primary

source_name: primary OS that produced metastatic lesion_CR-113A specimen

value: CR-113A specimen


title: CR-147 primary

source_name: primary OS that produced metastatic lesion_CR-147 specimen

value: CR-147 specimen


title: CB_R306C_2


title: CB_R306C_1


title: CB_WT_3

value: Mecp2 +/y


title: CB_WT_4


title: CB_WT_2


title: CB_WT_1


title: RF-43

source_name: localized and non-metastatic OS_RF-43 specimen

value: localized and non-metastatic OS

value: RF-43 specimen


title: CR-65

source_name: localized and non-metastatic OS_CR-65 specimen

value: CR-65 specimen


title: CRE-155 primary

source_name: primary OS that produced metastatic lesion_CRE-155 specimen

value: CRE-155 specimen


title: M2c macrophage 24h Replicate 3

city: Parma

first: Eleonora

last: Derlindati

address: via gramsci, 14

country: Italy

institute: University of Parma

description: M2c 24h Rep3

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software (version A.9.5.1.1), LOWESS normalization was applied. Probes detectable in at least one condition (two out of three biological replicates) were kept for further data analysis.

organism: Homo sapiens

source_name: Human macrophage

label_protocol: 500ng of total RNA were primed with an oligo (d)T-T7 primer and retrotranscribed into dsDNA with MMLV-RT. Then cDNA sample was amplified using T7 RNA Polymerase and labelled with cy5 (Quick Amp Labeling Kit, Agilent) following manifacture instructions

extract_protocol:
cell isolation protocol: Peripheral blood mononuclear cells (PBMC) were isolated from 20ml of peripheral blood using Ficoll stratification
Total RNA extracted using Rneasy Mini Kit (Qiagen) purification following manifacture instructions

tag: polarization

value: deactivated macrophage (IL10)

tag: time lysis after stimuli addition

source_name: Leucocyte

tag: reference

value: commercial RNA, pool from human leucocyte


title: CB_cKO_d3a_3

value: 10-11 weeks of age

value: Dnmt3a flx/flx Tg(Nes-cre)1Kln/J


title: RF-56

source_name: localized and non-metastatic OS_RF-56 specimen

value: RF-56 specimen


title: circulating tumor cells - C2c

description: circulating tumor cells - C2c (A549)

hyb_protocol: Ten microgram of dye labeled RNA was further hybridized with OneArray slide in a humidified oven with 2X SSPE buffer at 50C for 14-16 hours.

scan_protocol: The slides were scanned using Axon GenePix 4100 from Molecular Devices at wavelength 635 to 532 nm.

data_processing: The filtered data were log2 transformed and corrected using quantile normalization before their average ratios and significance values were calculated.

source_name: A549 circulating tumor cells

label_protocol: Target RNA was labeled with Cye5 dye and OneArray slide is pre-hybridized to reduce the background signals and increase the performance of microarray.

growth_protocol: We created the 4D model (previously described as ex vivo 3D model) as previously described. Briefly, we used decellularized lung matrices from 6-week-old rats using 0.1% SDS and 1% Triton-X100. The acellular matrices were thoroughly washed with PBS supplemented with antibiotics (100 IU/mL penicillin, 100 ug/mL streptomycin, and 0.25 ug/mL amphotericin; MP Biomedicals, Solon, OH, USA). Next, we cannulated the trachea and placed 25 million A549 cells diluted in 50 ml of complete media through the trachea of the 4D model (n=3). We collected the cells with media that passively came out of the model into a 500-mL container, we passed the media again through the trachea three times, and incubated it at 37degC for 2 hours to allow for cell attachment. We then counted the cells in the container and determined the percentage of tumor cells that were seeded on the 4D model. We placed an additional 200 mL of complete media in the bioreactor previously described and allowed the media to go through the pump at 6 ml per minute and then through the oxygenator and the pulmonary artery of the acellular lung matrix. Media in bioreactor was replaced with fresh media every day for 15 days. After 15 days, we removed the tissue of the 4D lung model.

extract_protocol: According to Human OneArray protocol.

tag: cell line

tag: circulating tumor cells


title: circulating tumor cells - C3a

description: circulating tumor cells - C3a (A549)


title: RF-44

source_name: localized and non-metastatic OS_RF-44 specimen

value: RF-44 specimen


title: circulating tumor cells - C3b

description: circulating tumor cells - C3b (A549)


title: M2c macrophage 24h Replicate 2

description: M2c 24h Rep2


title: CB_cKO_d3a_1


title: circulating tumor cells - C2a

description: circulating tumor cells - C2a (A549)


title: circulating tumor cells - C2b

description: circulating tumor cells - C2b (A549)


title: RF-191

source_name: localized and non-metastatic OS_RF-191 specimen

value: RF-191 specimen


title: H1299 cell grown on 4D model - primary tumor on day 25, biological replicate #2

data_processing: The filtered data were log2 transformed and corrected using quantile normalization before their average ratios and significance values were calculated. Technical replicates (there being three technical replicates per biological replicate) were averaged together.

source_name: H1299 cells

growth_protocol: We created the 4D model as previously described (PMID:23934967).  Briefly, we used decellularized lung matrices from 6-week-old rats using 0.1% SDS and 1% Triton-X100.  The acellular matrices were thoroughly washed with PBS supplemented with antibiotics (100 IU/mL penicillin, 100 ug/mL streptomycin, and 0.25 ug/mL amphotericin; MP Biomedicals, Solon, OH, USA).  Next, we cannulated the trachea and placed 25 million H1299 cells diluted in 50 ml of complete media through the trachea of the 4D model (n=3). We collected the cells with media that passively came out of the model into a 500-mL container, we passed the media again through the trachea three times, and incubated it at 37degC for 2 hours to allow for cell attachment. We then counted the cells in the container and determined the percentage of tumor cells that were seeded on the 4D model.  We placed an additional 200 mL of complete media in the bioreactor previously described and allowed the media to go through the pump at 6 ml per minute and then through the oxygenator and the pulmonary artery of the acellular lung matrix.  Media in bioreactor was replaced with fresh media every day for 25 days. There were live CTC in the media which were counted and stored in Trizol (Iso-RNA Lysis reagent) at -80°C. The primary tumor was isolated on day 2 and day 25. The metastatic lesion was isolated by performing a lobectomy of the right upper lobe on day 10, the right middle lobe on day 20, and the right lower lobe on day 25.

value: H1299 cell - primary tumor

tag: time point

value: day 25


title: circulating tumor cells - C1c

description: circulating tumor cells - C1c (A549)


title: M2c macrophage 12h Replicate 3

description: M2c 12h Rep3


title: circulating tumor cells - C3c

description: circulating tumor cells - C3c (A549)


title: CB_cKO_d3a_2

value: cerebellum


title: H1299 cell grown on 4D model - primary tumor on day 25, biological replicate #1


title: CB_WT_d3a_3

value: Dnmt3a flx/flx


title: Normal_A419_ChipE_5mC_Expt2

type: genomic

city: CUHK, Shatin

first: Hoi-Hung

last: Cheung

address: Rm.708A, LKS Integrated Biomedical Sciences Bldg.

department: School of Biomedical Sciences

country: Hong Kong

institute: The Chinese University of Hong Kong

description:
A419 E_pvalue_Hs_NCBIv36.BED
Normal

hyb_protocol: Samples were prepared and hybridized to GeneChip Human Tiling 2.0R Array according to Affymetrix specifications.

scan_protocol: The tiling arrays were scanned using an Affymetrix GeneChip Scanner GCS3000 according to manufacturer's instruction.

data_processing:
The signal intensity data was analyzed with the Affymetrix Tiling Analysis Software (version 1.1) using parameters: two-sided test, 250 bp bandwidth and perfect match only.
The resulting BED files are generated by the Affymetrix Tiling Analysis Software (version 1.1) using parameters: Threshold = 20 (p < 0.01), Gap = 100.

label: Biotin

molecule: genomic DNA

source_name: Genomic DNA, sonicated, anti-5mC

growth_protocol: Primary tumors and normal tissues without any culture

extract_protocol: Genomic DNA was directly extracted from tissues using column-based purification method

treatment_protocol: Untreated and frozen before DNA extraction

tag: treatment

value: IP

tag: tissue

value: normal testicular tissue

tag: source tissue

value: testis

tag: antibody


title: Normal_A419_ChipB_5mC_Expt2

description:
A419 B_pvalue_Hs_NCBIv36.BED
Normal

label_protocol: Samples were prepared and hybridized to GeneChip Human Tiling 2.0R Array according to Affymetrix specifications.


title: Normal_A419_ChipE_5mC_Expt1

description:
A419 E_pvalue_Hs_NCBIv36.BED
Normal


title: Normal_A090_ChipE_5mC_Expt2

description:
A090 E_pvalue_Hs_NCBIv36.BED
Normal


title: Normal_A419_ChipB_5mC_Expt1

description:
A419 B_pvalue_Hs_NCBIv36.BED
Normal


title: circulating tumor cells - C1b

description: circulating tumor cells - C1b (A549)


title: Normal_A090_ChipE_5mC_Expt1

description:
A090 E_pvalue_Hs_NCBIv36.BED
Normal


title: Normal_A090_ChipB_5mC_Expt2

description:
A090 B_pvalue_Hs_NCBIv36.BED
Normal


title: circulating tumor cells - C1a

description: circulating tumor cells - C1a (A549)


title: CB_WT_d3a_1


title: CR-93

source_name: localized and non-metastatic OS_CR-93 specimen

value: localized and non-metastatic OS

value: CR-93 specimen


title: EC_3256_ChipE_5mC_Expt2

description:
3256 E_pvalue_Hs_NCBIv36.BED
embryonal carcinoma

value: testicular embryonic carcinoma


title: CB_WT_d3a_2


title: Normal_A090_ChipB_5mC_Expt1

description:
A090 B_pvalue_Hs_NCBIv36.BED
Normal


title: EC_3256_ChipE_5mC_Expt1


title: Patient B30, IBD, Before Intervention

city: Boston

first: Manoj

last: Bhasin

state: MA

address: 330 Brookline Avenue  RN 380E

institute: Beth Israel Deaconess Medical Center

description: Patient B30

hyb_protocol: Samples were hybridized to Affymetrix HT HG-133+PM  Array Plate GeneChips using the Affymetrix standard hybridization protocol.

scan_protocol: Gene Titan System.

data_processing: The data was normalised using Robust Multichip Average (RMA) method that include background adjustment, quantile normalization and final summarization of  oligonucleotides per transcript using the median polish algorithm

source_name: Peripheral blood

label_protocol: GeneChip 3’ IVT Express kit.

extract_protocol: Total RNA was isolated from blood paxgene tubes using standard qiagen protocol.

treatment_protocol: Relaxation Response based mind-body group intervention (RR-MBI), focusing on elicitation of the RR and cognitive skill building.

tag: patient

tag: disease state

value: IBD

value: before intervention

value: peripheral blood


title: EC_3256_ChipB_5mC_Expt2

description:
3256 B_pvalue_Hs_NCBIv36.BED
embryonal carcinoma


title: M2a macrophage 24h Replicate 3

description: M2a 24h Rep3

value: alternative activated macrophage (IL4)

value: commercial RNA, pool from human leucocyte


title: M2c macrophage 12h Replicate 2

description: M2c 12h Rep2

value: deactivated macrophage (IL10)


title: M2a macrophage 24h Replicate 2

description: M2a 24h Rep2


title: Patient B25, IBD, After 9 weeks of Intervention

description: Patient B25

value: after 9 weeks of intervention


title: Patient B30, IBD, After 9 weeks of Intervention

description: Patient B30


title: M2a macrophage 12h Replicate 2

description: M2a 12h Rep2


title: M2c macrophage 6h Replicate 3

description: M2c 6h Rep3


title: Patient B29, IBD, After 9 weeks of Intervention

description: Patient B29


title: EC_3256_ChipB_5mC_Expt1


title: Patient B29, IBD, Before Intervention

description: Patient B29


title: EC_2761_ChipE_5mC_Expt1

description:
2761 E_pvalue_Hs_NCBIv36.BED
embryonal carcinoma


title: M2c macrophage 6h Replicate 2

description: M2c 6h Rep2


title: M2a macrophage 6h Replicate 3

description: M2a 6h Rep3


title: EC_2701_ChipE_5mC_Expt2

description:
2701 E_pvalue_Hs_NCBIv36.BED
embryonal carcinoma


title: Patient B24, IBD, After 9 weeks of Intervention

description: Patient B24


title: EC_2761_ChipB_5mC_Expt1

description:
2761 B_pvalue_Hs_NCBIv36.BED
embryonal carcinoma


title: EC_2701_ChipB_5mC_Expt2

description:
2701 B_pvalue_Hs_NCBIv36.BED
embryonal carcinoma


title: EC_2701_ChipE_5mC_Expt1


title: EC_2761_ChipE_5mC_Expt2


title: EC_2080_ChipE_5mC_Expt2

description:
2080 E_pvalue_Hs_NCBIv36.BED
embryonal carcinoma


title: EC_2701_ChipB_5mC_Expt1


title: EC_2080_ChipE_5mC_Expt1


title: M2a macrophage 6h Replicate 2

description: M2a 6h Rep2


title: EC_1703_ChipE_5mC_Expt2

description:
1703 E_pvalue_Hs_NCBIv36.BED
embryonal carcinoma


title: M1 macrophage 24h Replicate 3

description: M1 24h Rep3

value: classical activated macrophage (LPS+IFNγ)


title: Patient B25, IBD, Before Intervention

description: Patient B25


title: M2a macrophage 12h Replicate 3

description: M2a 12h Rep3


title: Patient B23, IBD, Before Intervention

description: Patient B23


title: Patient B22, IBD, After 9 weeks of Intervention

description: Patient B22


title: M1 macrophage 24h Replicate 2

description: M1 24h Rep2


title: Patient B23, IBD, After 9 weeks of Intervention

description: Patient B23


title: Patient B24, IBD, Before Intervention

description: Patient B24


title: M1 macrophage 12h Replicate 3

description: M1 12h Rep3


title: EC_2080_ChipB_5mC_Expt1

description:
2080 B_pvalue_Hs_NCBIv36.BED
embryonal carcinoma


title: M1 macrophage 12h Replicate 2

description: M1 12h Rep2


title: Patient B22, IBD, Before Intervention

description: Patient B22


title: EC_1703_ChipE_5mC_Expt1


title: EC_1703_ChipB_5mC_Expt2

description:
1703 B_pvalue_Hs_NCBIv36.BED
embryonal carcinoma


title: Patient B20, IBD, After 9 weeks of Intervention

description: Patient B20


title: EC_1458_ChipE_5mC_Expt2

description:
1458 E_pvalue_Hs_NCBIv36.BED
embryonal carcinoma


title: EC_1703_ChipB_5mC_Expt1


title: EC_2080_ChipB_5mC_Expt2


title: M1 macrophage 6h Replicate 2

description: M1 6h Rep2


title: RF-364 primary

source_name: primary OS that produced metastatic lesion_RF-364 specimen

tag: sample group

value: RF-364 specimen


title: EC_1458_ChipE_5mC_Expt1


title: EC_2761_ChipB_5mC_Expt2


title: EC_1458_ChipB_5mC_Expt2

description:
1458 B_pvalue_Hs_NCBIv36.BED
embryonal carcinoma


title: Normal_A419_ChipE_Input_Expt2

description: Normal

source_name: Genomic DNA, sonicated, input control

value: untreat


title: Patient B20, IBD, Before Intervention

description: Patient B20


title: M1 macrophage 6h Replicate 3

description: M1 6h Rep3


title: Patient B16, IBD, After 9 weeks of Intervention

description: Patient B16


title: Normal_A419_ChipB_Input_Expt2

description: Normal


title: Normal_A090_ChipE_Input_Expt2

description: Normal


title: Resting Macrophage 24h Replicate 2

description: RM 24h Rep2

value: differentiated macrophages


title: Patient B14, IBD, After 9 weeks of Intervention

description: Patient B14


title: Normal_A419_ChipB_Input_Expt1

description: Normal


title: Resting Macrophage 12h Replicate 3

description: RM 12h Rep3


title: Normal_A090_ChipB_Input_Expt2

description: Normal


title: Normal_A090_ChipB_Input_Expt1

description: Normal


title: EC_3256_ChipE_Input_Expt2

description: embryonal carcinoma


title: EC_3256_ChipE_Input_Expt1

description: embryonal carcinoma


title: Normal_A419_ChipE_Input_Expt1

description: Normal


title: EC_1458_ChipB_5mC_Expt1

value: IP


title: EC_3256_ChipB_Input_Expt2

description: embryonal carcinoma


title: CB_R306C_3

source_name: cerebellum

value: 8-10 weeks

value: cerebellum

value: Mecp2 R306C/y


title: Patient B13, IBD, After 9 weeks of Intervention

description: Patient B13


title: EC_3256_ChipB_Input_Expt1

description: embryonal carcinoma

value: testis


title: Resting Macrophage 12h Replicate 2

description: RM 12h Rep2


title: Normal_A090_ChipE_Input_Expt1

description: Normal

value: normal testicular tissue


title: Resting Macrophage 24h Replicate 3

description: RM 24h Rep3


title: Resting Macrophage 6h Replicate 2

description: RM 6h Rep2


title: EC_2761_ChipE_Input_Expt1

description: embryonal carcinoma

value: testicular embryonic carcinoma


title: Resting Macrophage 6h Replicate 3

description: RM 6h Rep3


title: M2c macrophage 24h Replicate 1

extract_protocol:
cell isolation protocol: Peripheral blood mononuclear cells (PBMC) were isolated from 20ml of peripheral blood using Ficoll stratification
Total RNA extracted using Rneasy Mini Kit (Qiagen) purification following manifacture instructions.
Total RNA extracted using Rneasy Mini Kit (Qiagen) purification following manifacture instructions.

tag: time lysis after stimuli addiction


title: Patient B12, IBD, After 9 weeks of Intervention

description: Patient B12

value: IBD


title: Patient B16, IBD, Before Intervention

description: Patient B16

value: before intervention

value: peripheral blood


title: Patient B14, IBD, Before Intervention

description: Patient B14


title: M2c macrophage 12h Replicate 1

extract_protocol: cell isolation protocol: Peripheral blood mononuclear cells (PBMC) were isolated from 20ml of peripheral blood using Ficoll stratification

value: commercial RNA, pool from human leucocyte


title: M2c macrophage 6h Replicate 1

value: deactivated macrophage (IL10)


title: Patient B13, IBD, Before Intervention

description: Patient B13


title: Patient B12, IBD, Before Intervention

description: Patient B12


title: Patient B11, IBD, After 9 weeks of Intervention

description: Patient B11

value: after 9 weeks of intervention


title: EC_2701_ChipE_Input_Expt2

description: embryonal carcinoma


title: EC_2761_ChipB_Input_Expt2

description: embryonal carcinoma


title: EC_2701_ChipE_Input_Expt1

description: embryonal carcinoma


title: EC_2761_ChipE_Input_Expt2

description: embryonal carcinoma


title: EC_2701_ChipB_Input_Expt2

description: embryonal carcinoma


title: M2a macrophage 24h Replicate 1

value: alternative activated macrophage (IL4)


title: Patient B11, IBD, Before Intervention

description: Patient B11


title: Patient B09, IBD, After 9 weeks of Intervention

description: Patient B09


title: M2a macrophage 12h Replicate 1


title: EC_2080_ChipE_Input_Expt2

description: embryonal carcinoma


title: EC_2701_ChipB_Input_Expt1

description: embryonal carcinoma


title: M2a macrophage 6h Replicate 1


title: EC_2080_ChipE_Input_Expt1

description: embryonal carcinoma


title: EC_2080_ChipB_Input_Expt2

description: embryonal carcinoma


title: EC_2080_ChipB_Input_Expt1

description: embryonal carcinoma


title: EC_1703_ChipE_Input_Expt2

description: embryonal carcinoma


title: EC_1703_ChipE_Input_Expt1

description: embryonal carcinoma


title: EC_1703_ChipB_Input_Expt2

description: embryonal carcinoma


title: M1 macrophage 12h Replicate 1

value: classical activated macrophage (LPS+IFNγ)


title: M1 macrophage 24h Replicate 1


title: Patient B08, IBD, After 9 weeks of Intervention

description: Patient B08


title: Patient B08, IBD, Before Intervention

description: Patient B08


title: Patient B09, IBD, Before Intervention

description: Patient B09


title: EC_2761_ChipB_Input_Expt1

description: embryonal carcinoma

value: untreat


title: EC_1703_ChipB_Input_Expt1

description: embryonal carcinoma


title: M1 macrophage 6h Replicate 1


title: EC_1458_ChipE_Input_Expt1

description: embryonal carcinoma


title: Resting Macrophage 24h Replicate 1

value: differentiated macrophages


title: EC_1458_ChipB_Input_Expt2

description: embryonal carcinoma


title: Patient B07, IBD, After 9 weeks of Intervention

description: Patient B07


title: Normal_A419_ChipG_5mC_Expt2

description:
A419 G_pvalue_Hs_NCBIv36.BED
Normal

value: IP


title: EC_1458_ChipB_Input_Expt1

description: embryonal carcinoma


title: Normal_A419_ChipF_5mC_Expt2

description:
A419 F_pvalue_Hs_NCBIv36.BED
Normal


title: Normal_A419_ChipF_5mC_Expt1

description:
A419 F_pvalue_Hs_NCBIv36.BED
Normal


title: Normal_A419_ChipG_5mC_Expt1

description:
A419 G_pvalue_Hs_NCBIv36.BED
Normal


title: Patient B06, IBD, After 9 weeks of Intervention

description: Patient B06


title: Resting Macrophage 6h Replicate 1


title: Patient B07, IBD, Before Intervention

description: Patient B07


title: Normal_A419_ChipA_5mC_Expt2

description:
A419 A_pvalue_Hs_NCBIv36.BED
Normal


title: Patient B06, IBD, Before Intervention

description: Patient B06


title: Normal_A090_ChipF_5mC_Expt2

description:
A090 F_pvalue_Hs_NCBIv36.BED
Normal


title: Normal_A090_ChipG_5mC_Expt2

description:
A090 G_pvalue_Hs_NCBIv36.BED
Normal


title: EC_1458_ChipE_Input_Expt2

description: embryonal carcinoma


title: Normal_A090_ChipF_5mC_Expt1

description:
A090 F_pvalue_Hs_NCBIv36.BED
Normal


title: Normal_A419_ChipA_5mC_Expt1

description:
A419 A_pvalue_Hs_NCBIv36.BED
Normal


title: Patient B04, IBD, After 9 weeks of Intervention

description: Patient B04


title: Normal_A090_ChipA_5mC_Expt2

description:
A090 A_pvalue_Hs_NCBIv36.BED
Normal


title: EC_3256_ChipG_5mC_Expt2

description:
3256 G_pvalue_Hs_NCBIv36.BED
embryonal carcinoma


title: EC_3256_ChipF_5mC_Expt2

description:
3256 F_pvalue_Hs_NCBIv36.BED
embryonal carcinoma


title: Normal_A090_ChipG_5mC_Expt1

description:
A090 G_pvalue_Hs_NCBIv36.BED
Normal


title: EC_3256_ChipF_5mC_Expt1


title: EC_3256_ChipA_5mC_Expt2

description:
3256 A_pvalue_Hs_NCBIv36.BED
embryonal carcinoma


title: EC_3256_ChipG_5mC_Expt1


title: EC_3256_ChipA_5mC_Expt1


title: Normal_A090_ChipA_5mC_Expt1

description:
A090 A_pvalue_Hs_NCBIv36.BED
Normal


title: EC_2761_ChipF_5mC_Expt2

description:
2761 F_pvalue_Hs_NCBIv36.BED
embryonal carcinoma


title: EC_2761_ChipF_5mC_Expt1


title: EC_2761_ChipG_5mC_Expt1

description:
2761 G_pvalue_Hs_NCBIv36.BED
embryonal carcinoma


title: EC_2761_ChipG_5mC_Expt2


title: EC_2701_ChipF_5mC_Expt2

description:
2701 F_pvalue_Hs_NCBIv36.BED
embryonal carcinoma


title: Patient B03, IBD, After 9 weeks of Intervention

description: Patient B03


title: Patient B01, IBD, After 9 weeks of Intervention

description: Patient B01


title: Patient B01, IBD, Before Intervention

description: Patient B01


title: EC_2761_ChipA_5mC_Expt2

description:
2761 A_pvalue_Hs_NCBIv36.BED
embryonal carcinoma


title: EC_2701_ChipG_5mC_Expt2

description:
2701 G_pvalue_Hs_NCBIv36.BED
embryonal carcinoma


title: Patient B04, IBD, Before Intervention

description: Patient B04


title: Patient B03, IBD, Before Intervention

description: Patient B03


title: Resting Macrophage 12h Replicate 1


title: Patient A25, IBS, After 9 weeks of Intervention

description: Patient A25

value: IBS


title: Patient A25, IBS, Baseline Before Intervention

description: Patient A25

value: baseline before intervention


title: EC_2761_ChipA_5mC_Expt1


title: EC_2701_ChipF_5mC_Expt1


title: EC_2701_ChipA_5mC_Expt2

description:
2701 A_pvalue_Hs_NCBIv36.BED
embryonal carcinoma


title: EC_2080_ChipF_5mC_Expt1

description:
2080 F_pvalue_Hs_NCBIv36.BED
embryonal carcinoma


title: EC_2080_ChipF_5mC_Expt2


title: EC_2701_ChipA_5mC_Expt1


title: EC_2080_ChipA_5mC_Expt2

description:
2080 A_pvalue_Hs_NCBIv36.BED
embryonal carcinoma


title: EC_2080_ChipG_5mC_Expt1

description:
2080 G_pvalue_Hs_NCBIv36.BED
embryonal carcinoma


title: Patient A23, IBS, After 9 weeks of Intervention

description: Patient A23


title: Patient A23, IBS, Baseline Before Intervention

description: Patient A23


title: EC_1703_ChipF_5mC_Expt1

description:
1703 F_pvalue_Hs_NCBIv36.BED
embryonal carcinoma


title: EC_2080_ChipA_5mC_Expt1


title: EC_1703_ChipG_5mC_Expt1

description:
1703 G_pvalue_Hs_NCBIv36.BED
embryonal carcinoma


title: EC_1703_ChipA_5mC_Expt2

description:
1703 A_pvalue_Hs_NCBIv36.BED
embryonal carcinoma


title: EC_2701_ChipG_5mC_Expt1


title: Patient A18, IBS, After 9 weeks of Intervention

description: Patient A18


title: EC_1458_ChipG_5mC_Expt2

description:
1458 G_pvalue_Hs_NCBIv36.BED
embryonal carcinoma


title: EC_1703_ChipA_5mC_Expt1


title: EC_1458_ChipF_5mC_Expt2

description:
1458 F_pvalue_Hs_NCBIv36.BED
embryonal carcinoma


title: EC_1458_ChipG_5mC_Expt1


title: EC_2080_ChipG_5mC_Expt2


title: EC_1458_ChipF_5mC_Expt1


title: EC_1458_ChipA_5mC_Expt2

description:
1458 A_pvalue_Hs_NCBIv36.BED
embryonal carcinoma


title: Normal_A419_ChipG_Input_Expt2

description: Normal


title: EC_1703_ChipF_5mC_Expt2


title: EC_1703_ChipG_5mC_Expt2


title: Normal_A419_ChipF_Input_Expt2

description: Normal


title: Normal_A419_ChipG_Input_Expt1

description: Normal


title: EC_1458_ChipA_5mC_Expt1


title: Normal_A419_ChipA_Input_Expt2

description: Normal


title: Normal_A090_ChipG_Input_Expt2

description: Normal


title: Normal_A090_ChipF_Input_Expt2

description: Normal


title: Patient A18, IBS, Baseline Before Intervention

description: Patient A18


title: Patient A16, IBS, After 9 weeks of Intervention

description: Patient A16


title: Patient A15, IBS, Baseline Before Intervention

description: Patient A15


title: Normal_A419_ChipA_Input_Expt1

description: Normal


title: Patient A16, IBS, Baseline Before Intervention

description: Patient A16


title: Patient A20, IBS, Baseline Before Intervention

description: Patient A20


title: Patient A15, IBS, After 9 weeks of Intervention

description: Patient A15


title: Patient A20, IBS, After 9 weeks of Intervention

description: Patient A20


title: Normal_A090_ChipF_Input_Expt1

description: Normal


title: Normal_A090_ChipA_Input_Expt2

description: Normal


title: Patient A14, IBS, After 9 weeks of Intervention

description: Patient A14


title: Normal_A090_ChipG_Input_Expt1

description: Normal


title: EC_3256_ChipF_Input_Expt2

description: embryonal carcinoma


title: Normal_A090_ChipA_Input_Expt1

description: Normal


title: EC_3256_ChipG_Input_Expt2

description: embryonal carcinoma


title: EC_2761_ChipG_Input_Expt2

description: embryonal carcinoma


title: EC_2761_ChipF_Input_Expt2

description: embryonal carcinoma


title: EC_3256_ChipA_Input_Expt2

description: embryonal carcinoma


title: EC_3256_ChipA_Input_Expt1

description: embryonal carcinoma


title: EC_3256_ChipF_Input_Expt1

description: embryonal carcinoma


title: EC_2761_ChipG_Input_Expt1

description: embryonal carcinoma


title: EC_2761_ChipF_Input_Expt1

description: embryonal carcinoma


title: EC_2761_ChipA_Input_Expt2

description: embryonal carcinoma


title: Patient A14, IBS, Baseline Before Intervention

description: Patient A14


title: Patient A13, IBS, Baseline Before Intervention

description: Patient A13


title: Patient A10, IBS, After 9 weeks of Intervention

description: Patient A10


title: Patient A10, IBS, Baseline Before Intervention

description: Patient A10


title: EC_2701_ChipG_Input_Expt2

description: embryonal carcinoma


title: EC_2701_ChipF_Input_Expt2

description: embryonal carcinoma


title: EC_2761_ChipA_Input_Expt1

description: embryonal carcinoma


title: EC_2701_ChipF_Input_Expt1

description: embryonal carcinoma


title: EC_2701_ChipG_Input_Expt1

description: embryonal carcinoma


title: EC_2080_ChipG_Input_Expt2

description: embryonal carcinoma


title: EC_2080_ChipF_Input_Expt2

description: embryonal carcinoma


title: EC_2701_ChipA_Input_Expt2

description: embryonal carcinoma


title: EC_2080_ChipG_Input_Expt1

description: embryonal carcinoma


title: EC_2080_ChipF_Input_Expt1

description: embryonal carcinoma


title: Patient A07, IBS, After 9 weeks of Intervention

description: Patient A07


title: EC_3256_ChipG_Input_Expt1

description: embryonal carcinoma


title: Patient A13, IBS, After 9 weeks of Intervention

description: Patient A13


title: EC_2080_ChipA_Input_Expt2

description: embryonal carcinoma


title: EC_1703_ChipG_Input_Expt1

description: embryonal carcinoma


title: EC_1458_ChipF_Input_Expt2

description: embryonal carcinoma


title: Patient A07, IBS, Baseline Before Intervention

description: Patient A07


title: EC_2701_ChipA_Input_Expt1

description: embryonal carcinoma


title: EC_2080_ChipA_Input_Expt1

description: embryonal carcinoma


title: Patient A06, IBS, After 9 weeks of Intervention

description: Patient A06


title: Patient A06, IBS, Baseline Before Intervention

description: Patient A06


title: Patient A03, IBS, After 9 weeks of Intervention

description: Patient A03


title: EC_1458_ChipF_Input_Expt1

description: embryonal carcinoma


title: Patient A03, IBS, Baseline Before Intervention

description: Patient A03


title: EC_1458_ChipG_Input_Expt2

description: embryonal carcinoma


title: EC_1458_ChipA_Input_Expt2

description: embryonal carcinoma


title: EC_1458_ChipG_Input_Expt1

description: embryonal carcinoma


title: EC_1703_ChipF_Input_Expt1

description: embryonal carcinoma


title: Patient A02, IBS, After 9 weeks of Intervention

description: Patient A02


title: EC_1458_ChipA_Input_Expt1

description: embryonal carcinoma


title: Patient A01, IBS, After 9 weeks of Intervention

description: Patient A01


title: Patient A02, IBS, Baseline Before Intervention

description: Patient A02


title: Patient A01, IBS, Baseline Before Intervention

description: Patient A01


title: EC_1703_ChipA_Input_Expt1

description: embryonal carcinoma


title: Long day photorefractory rep 1

status: Public on Mar 11 2015

city: Saint Paul

first: Sunantha

last: Kosonsiriluk

state: Minnesota

address: 495 AnSci/VetMed 1988 Fitch Ave

department: Animal Science

institute: University of Minnesota

hyb_protocol: Hybridisation was performed at 42°C for 16 hr using SlideHyb Buffer (Applied Biosystems) in hybridization chambers. The arrays were washed with increasing stringency using salt sodium citrate and immediately scanned

scan_protocol: The arrays were scanned on a ScanArray 5000 (Packard BioScience)

data_processing: The fluorescence intensity of each spot from the images was extracted and graded using BlueFuse software (BlueGnome Ltd.). We filtered the data at the quality=1 and confidence>0.1 and exported to JMP Genomics (SAS Institute Inc.). The raw intensity was first transformed to log-base 2 and performed within-array Loess normalization and then standardized to a mean of 0 and standard deviation of 1 across arrays.

label: Alexa Fluor 647

organism: Meleagris gallopavo

source_name: Pooled PMM tissues of 6 long day photorefractory turkey hens

label_protocol: cDNA was synthesized and fluorescently labelled using SuperScript Plus Indirect cDNA Labeling System (Invitrogen) following manufacturer’s instructions

extract_protocol: Total RNA was extracted using RNeasy Lipid Tissue Mini Kit (Qiagen) following manufacturer’s instructions

treatment_protocol: 1) Short day photosensitive birds - kept under short day light schedule (6 Light:18 Dark; 6L:18D), 2) long day photosensitive birds - subjected to long day light regimen (16L:8D) for 10 days before the study, and 3) long day photorefractory birds - subjected to long day light schedule and maintained through a complete reproductive cycle and molt.

tag: gender

value: Female

tag: developmental stage

value: Adult

tag: phenotype

value: long day photorefractory


title: EC_1703_ChipG_Input_Expt2

description: embryonal carcinoma

value: testicular embryonic carcinoma

value: testis


title: Long day photorefractory rep 4

label: Alexa Fluor 555


title: Long day photosensitive rep 2

source_name: Pooled PMM tissues of 6 long day photosensitive turkey hens

value: long day photosensitive


title: Long day photosensitive rep 3


title: Long day photosensitive rep 1


title: reproductively active turkey rep 3

data_processing: The fluorescence intensity of each spot from the images was extracted using BlueFuse software (BlueGnome Ltd.) and exported to JMP Genomics (SAS Institute Inc.). The raw intensity was first transformed to log-base 2 and performed within-array Loess normalization and then standardized to a mean of 0 and standard deviation of 1 across arrays.

label: Alexa fluor 555, Alexa fluor 647

source_name: Pituitary gland of reproductively active turkey

tag: reproductive stage

value: Laying


title: reproductively inactive turkey rep 3

source_name: Pituitary gland of reproductively inactive turkey

value: Photorefractory


title: reproductively inactive turkey rep 1


title: ALDEFLUOR of UM-UC3 (Cy5/Cy3)

city: Sapporo

first: Ryuta

last: Inoue

state: Hokkaido

address: South1 West16

department: pathology

country: Japan

institute: Sapporo medical university

hyb_protocol: Then cRNA was synthesized using T7 RNA polymerase, which simultaneously incorporated Cy3- or Cy5-labeled cytidine triphosphate.  During this process, the samples of ALDH+ cells were labeled with Cy5, whereas the ALDH- cells were labeled with Cy3 as control cells.  Quality of the cRNA was again checked using the Nano Drop.  Cy3-labeled cRNA and Cy5-labeled cRNA were combined and then fragmented using a gene expression hybridization kit (Agilent Technologies).  Then the labeled cRNAs were hybridized to a 60-mer probe oligonucleotide microarray (G4845A human GE 4x44K V2 Microarray kit) and incubated for 20 hours at 50 °C.

scan_protocol: The fluorescent intensities were determined by an Agilent Technologies Scanner G2505C.

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.

source_name: UM-UC3 ALDH1 high activity cells

label_protocol: We used the commercially available Low Input Quick Amp Labeling Kit (Agilent Technologies). Purified total RNA (3 µg) was reverse-transcribed to generate double-stranded cDNA using an oligo dT T7 promoter primer and reverse transcriptase.

growth_protocol: Human urothelial carcinoma cell lines UM-UC3(American Type Culture Collection (ATCC), Manassas, VA, USA) was cultured in Dulbecco’s modified Eagle’s medium (DMEM) (Sigma-Aldrich, St Louis, MO, USA) supplemented with 10% fetal bovine serum (FBS).

extract_protocol: Total RNA was isolated from collected cells using an RNeasy Mini Kit (QIAGEN, Valencia, CA) following the manufacturer’s protocol.

treatment_protocol: Cells were suspended in ALDEFLUOR assay buffer containing the ALDH1 substrate boron-dipyrromethene-aminoacetaldehyde (1 μmol/l/1×106 cells) and incubated for 30 minutes at 37 °C.

value: urothelial carcinoma

source_name: UM-UC3 ALDH1 low activity cells


title: Long day photorefractory rep 3


title: ALDEFLUOR of UM-UC3 (Cy3/Cy5)


title: Long day photosensitive rep 4


title: reproductively active turkey rep 4


title: Short day photosensitive rep 4

source_name: Pooled PMM tissues of 6 short day photosensitive turkey hens

value: short day photosensitive


title: Long day photorefractory rep 2


title: Short day photosensitive rep 1


title: Short day photosensitive rep 3


title: reproductively inactive turkey rep 4


title: reproductively active turkey rep 1


title: reproductively inactive turkey rep 2


title: reproductively active turkey rep 2


title: Short day photosensitive rep 2


title: reproductively inactive chicken rep 3

organism: Gallus gallus

source_name: Pooled pituitary glands of 5 reproductively inactive chickens

value: Pullet

value: non-laying


title: reproductively inactive chicken rep 1


title: reproductively inactive chicken rep 4


title: reproductively inactive chicken rep 2


title: reproductively active chicken rep 4

source_name: Pooled pituitary glands of 5 reproductively active chickens


title: reproductively active chicken rep 3


title: Patient  neurofibroma [NF_114]

city: Oslo

first: Maren

last: Høland

address: Ullernchausséen 70

department: Institute for Cancer Research

country: Norway

institute: Oslo University Hospital

description:
benign tumour
NF_114

hyb_protocol: Chemilunimescent Detection Kit from Applied Biosystems

scan_protocol: Scanned using AB1700 Chemilunimescent Microarray Analyzer

data_processing: The ABarray software package (http://bioconductor.org/packages/1.9/bioc/html/ ABarray.html) were used to run quality check and basic statistical analysis. Quantile normalized and log2 transformed expression data were used in our downstream statistical analysis. Flag values were replaced by using the Significance Analysis of Microarrays Excel Add-in application (version 3.02; http://www-stat.stanford.edu/~tibs/SAM/) and the k nearest neighbours algorithm (k=10). Probes with signal-to-noise ratios less than three in half of the samples and probes with flagged intensity values in more than 20% of the samples were removed, leaving us with a dataset containing measurements from 18,796 probes. Gene expression intensity values were centred over the median value across all samples.

label: digoxigenein (DIG)-labeled

source_name: neurofibroma

label_protocol: NanoAmp RT-IVT Labeling Kit from Applied Biosystems and DIG-UTP from Roche

extract_protocol: RNA isolated by standard Trizol methodology

tag: patient id

value: patient 114

value: male

tag: hereditary status

value: Neurofibromatosis type 1

tag: tissue type analyzed

value: dermal neurofibroma


title: Patient  neurofibroma [NF_111]

description:
benign tumour
NF_111

value: patient 111

value: female

value: plexiform neurofibroma


title: reproductively active chicken rep 2

value: Female

value: Adult


title: reproductively active chicken rep 1


title: Normal_A419_ChipF_Input_Expt1

description: Normal

value: untreat

value: normal testicular tissue

value: testis


title: Patient  neurofibroma [NF_043]

description:
benign tumour
NF_043

value: patient 043


title: Patient  neurofibroma [NF_029]

description:
benign tumour
NF_029

value: patient 029


title: Patient  neurofibroma [NF_020]

description:
benign tumour
NF_020

value: patient 020


title: Patient 120 MPNST

description:
malignant tumour
M_120

source_name: malignant peripheral nerve sheat tumour

value: Patient 120

tag: age at diagnosis

value: 32 years

tag: status of disease 5 years

value: Dead of disease 53 months

value: Sporadic

value: metastasis


title: Patient  neurofibroma [NF_044]

description:
benign tumour
NF_044

value: patient 044

value: male

value: Neurofibromatosis type 1

value: dermal neurofibroma


title: Patient 116 MPNST

description:
malignant tumour
M_116

value: Patient 116

value: female

value: 30 years

value: Alive

value: primary tumor


title: Patient 117 MPNST

description:
malignant tumour
M_117

value: Patient 117

value: 79 years

value: Dead other cause 6 months


title: Patient  neurofibroma [NF_037]

description:
benign tumour
NF_037

value: patient 037


title: Patient 119 MPNST

description:
malignant tumour
M_119

value: Patient 119

value: 54 years


title: Patient  neurofibroma [NF_100]

description:
benign tumour
NF_100

value: patient 100


title: Patient 61 MPNST

description:
malignant tumour
M_061

value: Patient 61

value: 59 years

value: Sporadic


title: Patient 91 MPNST

description:
malignant tumour
M_091

value: Patient 91

value: 45 years


title: Patient 96 MPNST

description:
malignant tumour
M_096

value: Patient 96

value: 14 years

value: ND

value: Neurofibromatosis type 1


title: EC_1703_ChipA_Input_Expt2

description: embryonal carcinoma

tag: treatment

value: untreat

value: testicular embryonic carcinoma

value: testis


title: Patient 60 MPNST

description:
malignant tumour
M_060

value: Patient 60

value: male

value: 20 years

value: Alive

value: recurrence


title: Patient 58 MPNST

description:
malignant tumour
M_058

value: Patient 58

value: female

value: 26 years

value: Alive with disease 10 months

value: primary tumor


title: Patient 51 MPNST

description:
malignant tumour
M_051

value: Patient 51

value: 73 years

value: Dead of disease 8 months

value: Sporadic


title: Patient 53 MPNST

description:
malignant tumour
M_053

value: Patient 53

value: 15 years

value: Dead of disease 19 months

value: Neurofibromatosis type 1


title: Patient 57 MPNST

description:
malignant tumour
M_057

value: Patient 57

value: 24 years

value: Dead of disease 32 months


title: Patient 52 MPNST

description:
malignant tumour
M_052

value: Patient 52

value: 36 years

value: Alive


title: Patient 56 MPNST

description:
malignant tumour
M_056

value: Patient 56

value: male


title: 99-523-T

city: Detroit

first: Maria

last: Worsham

state: MI

address: 1 Ford Place

department: Otolaryngology

institute: Henry Ford Health System

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450k Beadchip using standard Illumina protocol

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

data_processing:
GenomeStudio V2011.1
Unmethylated and methylated signal intensities

label: Cy5 and Cy3

source_name: Tumor

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from breast cancer samples using Qiagen DNeasy Kit according to standard instructions

value: Female

tag: sample type

value: ER Positive

value: Tumor


title: Patient 50 MPNST

description:
malignant tumour
M_050

value: Patient 50

value: 30 years

value: primary tumor


title: 99-468-N

source_name: Normal

value: Normal


title: Patient 44 MPNST

description:
malignant tumour
M_044

value: Patient 44

value: 17 years

value: Dead of disease 5 months


title: Patient 49 MPNST

description:
malignant tumour
M_049

value: Patient 49

value: 27 years

value: Sporadic


title: Patient 48 MPNST

description:
malignant tumour
M_048

value: Patient 48

value: female

value: 35 years

value: Dead of disease 11 months

value: Neurofibromatosis type 1


title: 99-468-T

value: Female

value: ER Positive


title: Patient 46 MPNST

description:
malignant tumour
M_046

value: Patient 46

value: male

value: 45 years

value: Alive

value: recurrence


title: 01-083-T

value: Tumor


title: 99-523-N

value: Normal


title: 99-536-N


title: 99-506-T


title: 99-217-T


title: 99-403-T


title: 99-388-T


title: Patient 43 MPNST

description:
malignant tumour
M_043

value: Patient 43

value: 14 years

value: primary tumor


title: 99-403-N


title: Patient 35 MPNST

description:
malignant tumour
M_035

value: Patient 35

value: 42 years

value: Dead of disease 12 months

value: Sporadic


title: 99-217-N


title: 99-387-T


title: Patient 40 MPNST

description:
malignant tumour
M_040

value: Patient 40

value: female

value: 50 years


title: 99-369-N

value: Female


title: Patient 38 MPNST

description:
malignant tumour
M_038

value: Patient 38

value: 70 years

value: Neurofibromatosis type 1


title: 99-359-N


title: 01-083-N


title: Patient 34 MPNST

description:
malignant tumour
M_034

value: Patient 34

value: male

value: 15 years

value: Alive


title: 99-073-T

value: ER Positive

value: Tumor


title: Patient 32 MPNST

description:
malignant tumour
M_032

value: Patient 32

value: 77 years

value: primary tumor


title: 99-312-T


title: Patient 29 MPNST

description:
malignant tumour
M_029

value: Patient 29

value: 33 years

value: Dead of disease 14 months


title: Patient 20 MPNST

description:
malignant tumour
M_020

value: Patient 20

value: female

value: 19 years


title: Patient 26 MPNST

description:
malignant tumour
M_026

value: Patient 26

value: 22 years

value: Dead of disease 20 months

value: Sporadic


title: Patient 24 MPNST

description:
malignant tumour
M_024

value: Patient 24

value: male

value: 41 years

value: Neurofibromatosis type 1


title: 99-013-T

value: Female

value: ER Positive

value: Tumor


title: squamous cell carcinoma sample 43

city: Nashville

first: Pierre

last: Massion

state: TN

address: 2220 Pierce Ave

department: Vanderbilt Ingram Cancer Center

institute: Vanderbilt University

description: gene expression

hyb_protocol: Cy3-labeled RNA was hybridized at 65°C for 24 hr. The array was scanned and then analyzed using Agilent Feature Extraction Software (version 10.7.1.1).

scan_protocol: Scanned on an Agilent G2505C scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.1.1).

data_processing: Agilent Feature Extraction Software (v 10.7.1.1) was used for background subtraction.

source_name: squamous carcinoma cell

label_protocol: Briefly, 500 ng of total RNA with control RNA Spike-In were amplified and labeled with Cy3-CTP (Agilent Technologies, Santa Clara, California).

extract_protocol: Total RNA was extracted using Rneasy Tissue Kit (Qiagen) following manufacturer's instructions

tag: tissue

value: lung

tag: cell type

value: squamous carcinoma


title: squamous cell carcinoma sample 30

description: gene expression


title: 99-344-T


title: squamous cell carcinoma sample 29

description: gene expression


title: 01-199-N

value: Normal


title: squamous cell carcinoma sample 26

description: gene expression


title: squamous cell carcinoma sample 27

description: gene expression


title: 99-273-N


title: 01-168-N


title: 01-199-T

value: ER Negative


title: 99-312-T-2


title: 01-186-T


title: squamous cell carcinoma sample 25

description: gene expression


title: squamous cell carcinoma sample 35

description: gene expression


title: 01-148-T


title: squamous cell carcinoma sample 33

description: gene expression


title: 01-168-T


title: squamous cell carcinoma sample 28

description: gene expression


title: Patient 37 MPNST

description:
malignant tumour
M_037

value: Patient 37

value: female

value: 33 years

value: Dead of disease 16 months

value: primary tumor


title: 01-144-T


title: N1N2 and Lrp6 treated crypts 3

city: South San Francisco

first: Brian

last: Biehs

address: 1 DNA Way

institute: Genentech

hyb_protocol: Agilent In Situ Hybridization Kit Plus was used where Cy-dye labeled control and test samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, the arrays were washed twice, dried and then scanned.

scan_protocol: Scanned on an Agilent scanner, images were processed using Agilent Feature Extraction software version 10.7.

data_processing: Data were processed with ExpressionPlot version 3.5 standard Agilent pipeline, which uses R 3.0.0, and limma 3.6.7. Briefly, (1) background outliers (> 50 intensity) were reset to median background intensity in both channels, (2) background correction was performed using the background Correct function with the normexp method with an offset of 50, (3) within-array normalization was performed using the normalize WithinArraysfunction with the loess method, (4) replicate probes were averaged using theaveReps function, (5) between-array normalization was performed using the normalizeBetweenArrays function with the Aquantile method, (6) control probes (those not beginning with A_ followed by a digit) were discarded, (7) probe expression levels were summarized as log2 of expression ratio, (8) to obtain gene levels, one probe was seleted per gene using by maximizing the inter-quartile range, (9) limma was used for differential expression analysis.

source_name: Smal intestine crypts extracted from mice treated with Notch 1, Notch 2, and Lrp6 blocking antibodies for 24 hours

label_protocol: Total RNA was converted to double-stranded cDNA and then into Cy-dye labeled cRNA using Agilent’s Quick Amp Labeling Kit. For all samples, 750 ng of the labeled cRNA was fragmented and hybridized against Cy3-labeled Universal mouse reference (Stratagene, La Jolla, CA).

extract_protocol: Isolated small intestines were opened longitudinally, and washed with cold PBS. The tissue was then chopped into 5 mm pieces and incubated in cold chelation buffer (2 mM EDTA, 0.5 mM DL-Dithiothreitol in PBS) for 30 min on ice. Chelation buffer was then removed and tissue fragments were vigorously resuspended in cold PBS using a 10 mL pipette. The process was repeated until individual crypts were released from the tissue chunks. The crypt suspension fractions were pooled and strained through a 70 micron filter. Crypts were pelleted and RNA was extracted using the Qiagen RNeasy mini kit.

treatment_protocol: Mice between the ages of 6-8weeks were given a single dose of 1mg/mL Notch 1 and Notch 2 antibodies or 1mg/mL Notch 1 and Notch 2 plus 30mg/kg anti-Lrp6.

value: small intestinal crypts

tag: antibody

value: Notch 1 and Notch 2 and Lrp6

tag: treatment time

value: 24 hrs.

value: common reference


title: N1N2 and Lrp6 treated crypts 5

source_name: Universal mouse reference (Stratagene, La Jolla, CA)


title: N1N2 and Lrp6 treated crypts 4


title: 01-116-T

tag: disease state


title: N1N2 and Lrp6 treated crypts 2


title: 01-066-T


title: N1N2 and Lrp6 treated crypts 1


title: 01-186-N


title: N1N2 treated crypts 5

source_name: Smal intestine crypts extracted from mice treated with Notch 1 and Notch 2 blocking antibodies for 24 hours

value: Notch 1 and Notch 2


title: squamous cell carcinoma sample 22

description: gene expression


title: N1N2 treated crypts 4


title: 01-169-T

value: Female


title: N1N2 treated crypts 3


title: 01-177-T


title: squamous cell carcinoma sample 21

description: gene expression


title: 01-144-N


title: 00-360-T


title: 01-177-N


title: 01-061-T


title: N1N2 treated crypts 1


title: squamous cell carcinoma sample 31

description: gene expression


title: Control crypts 5

source_name: Smal intestine crypts extracted from mice treated with control antibody

value: IgG control antibody


title: 01-123-T

value: ER Positive

value: Tumor


title: 00-359-T


title: Control crypts 4


title: N1N2 treated crypts 2


title: Control crypts 3


title: 01-045-T


title: 01-015-N


title: 00-218-N


title: 01-015-T


title: 01-061-N


title: 00-164-N


title: squamous cell carcinoma sample 5

description: gene expression

value: lung

value: squamous carcinoma


title: squamous cell carcinoma sample 32

description: gene expression


title: Hyphal 6A mutant Rep 2

city: Sheffield

first: Ian

last: Sudbery

address: Firth Court, Western Bank

department: Molecular Biology and Biotechnology

country: United Kingdom

institute: University of Sheffield

hyb_protocol: Not provided

scan_protocol: Arrays were  scanned with an Axon GenePix 4000B scanner

data_processing:
Microarray data was analysed using the limma package. Arrays were background normalised using the “normexp” method and spots with an intensity of less than 50 over background in both channels were removed. Arrays were then normalized using the “print-tip loess” method. Within array replicate spots were averaged. Differentially expressed genes between wild type, fkh2(6A) and  fkh2ΔΔ  yeast samples were assessed using empirical Bayes moderated t-tests. For hyphal samples we fitted a linear model with indicator variables for genotype and used moderated t-statistics to test the significance of the coefficients for kinase mutant and deletion genotype, as well as the significance of the difference between these coefficients.  False discovery rate was assessed across all tests simultaneously using the method of Benjamini and Hochberg [71]. Where multiple probes targeted the same gene, the least significant was selected.
The results presented in the Matrix table are the last stage at which the results can easily be presented in matrix table format. The whole oligo set is printed twice on the chip, and these duplicates have been averaged. Some genes are represented by multiple spots (either as independent or repeated oligos), handling of these replicates is handled on a test-by-test basis in the p-value summarisation of the data, and is different for different models tested.

organism: Candida albicans

label_protocol: 10 µg of total RNA was reverse-transcribed with either Cy3 (control) or Cy5 (experimental) dyes

growth_protocol: C. albicans cells were routinely grown in 1% yeast extract, 2% peptone and either 2% glucose (YEPD) or galactose (YEPG), or in 0.67% yeast nitrogen base without amino acids and 2% glucose (GMM) with appropriate amino acids for auxotrophic mutants.

extract_protocol: RNeasy minikit (QIAGEN) following the manufacturer’s instructions for yeast mechanical disruption, using a TOMY Microsmash (TOMY Digital Biology, Tokyo JP). Total RNA was treated with DNase I (Roche) before RNA-cleanup using the Rneasy kit

treatment_protocol: For hyphal induction, cells were washed in sterile water and diluted to OD600 = 0.6 in pH 7.0 media supplemented with 10-20% fetal calf serum (FCS) and incubated at 37°C.

tag: morph

value: hyphal

tag: genotype


title: squamous cell carcinoma sample 8

description: gene expression


title: Over-expression Rep 2

value: yeast

value: BWP17 FKH2/FKH2-HA:URA3

value: BWP17 FKH2/FKH2/PGAL1-FKH2-GFP:URA3


title: squamous cell carcinoma sample 2

description: gene expression


title: Control crypts 1


title: squamous cell carcinoma sample 19

description: gene expression


title: Yeast 6A mutant Rep 2


title: squamous cell carcinoma sample 7

description: gene expression


title: squamous cell carcinoma sample 6

description: gene expression


title: squamous cell carcinoma sample 20

description: gene expression


title: Control crypts 2


title: Mesodinium rubrum (starved for 8 weeks)

city: Kongju

first: Jong Won

last: Han

state: Chungnam

address: Sinkwandong

department: Biology

country: South Korea

institute: Kongju National University

description: Starved for 8 weeks

hyb_protocol: After checking labeling efficiency, fragmentation of cRNA was performed by adding 10X blocking agent and 25X fragmentation buffer and incubating at 60oC for 30 min. The fragmented cRNA was resuspended with 2X hybridization buffer and directly pipetted onto assembled Agilent’s Agilent E-array (Teleaulax) (44K). The arrays hybridized at 65oC for 17 hours using Agilent Hybridization oven (Agilent Technology, USA). The hybridized microarrays were washed as the manufacturer’s washing protocol (Agilent Technology, USA).

scan_protocol: The hybridized images were scanned using Agilent’s DNA microarray scanner and quantified with Feature Extraction Software (Agilent Technology, Palo Alto, CA).

data_processing: All data normalization and further analysis were performed using GeneSpringGX 7.3 (Agilent Technology, USA).

organism:
Teleaulax amphioxeia
Mesodinium rubrum

source_name: Mesodinium rubrum

label_protocol: Amplified and labeled cRNA was purified on cRNA Cleanup Module (Agilent Technology) according to the manufacturer’s protocol. Labeled cRNA target was quantified using ND-1000 spectrophotometer (NanoDrop Technologies, Inc., Wilmington, DE).

growth_protocol: M. rubrum strain (MR-MAL01) was established by single cell isolation and maintained mixotrophically with T. amphioxeia strain (CR-MAL01).

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

treatment_protocol: A stock culture of M. rubrum was serially spiked with prey cells of T. amphioxeia. Culture was maintained phototrophically for 13 weeks (starved for 13 weeks). Total RNA was isolated from M. rubrum at 1, 8, 13 weeks after starvation and from prey, T. amphioxeia.

tag: growth condition

value: M. rubrum culture was spiked with T. amphioxeia prey cells. Culture was maintained phototrophically (starved).

tag: time

value: 8 weeks starvation


title: squamous cell carcinoma sample 3

description: gene expression


title: squamous cell carcinoma sample 4

description: gene expression


title: 00-391-T

tag: gender

value: ER Negative


title: Mesodinium rubrum (starved for 1 week)

description: Starved for 1 week

value: 1 week starvation


title: Teleaulax amphioxeia

description: Food for Mesodinium rubrum

organism: Teleaulax amphioxeia

source_name: Teleaulax amphioxeia

value: free-living T. amphioxeia cryptophyte

value: control


title: Hyphal Deletion Rep 2

value: ura3::λimm434/ ura3::λimm434 his1::hisG/ his1::hisG arg4::hisG/arg4::hisG

source_name: fkh2 ∆/∆ (URA3+)

value: BWP17 URAF::fkh2/fkh2::ARG4


title: Mesodinium rubrum (starved for 13 weeks)

description: Starved for 13 weeks

value: 13 weeks starvation


title: Yeast Deletion Rep 2


title: squamous cell carcinoma sample 1

description: gene expression


title: Yeast 6A mutant Rep 1


title: Over-expression Rep 1


title: Hyphal 6A mutant Rep 1


title: Hyphal Deletion Rep 1


title: Yeast Deletion Rep 1


title: DUSP3-KO2-LPS

city: Liège

first: Souad

last: Rahmouni

state: Liège

address: 1, Avenue de l'hopital. B34

department: GIGA-Signal Transduction

country: Belgium

institute: University of Liège

description:
SAMPLE 11
DUSP3-KO-LPS replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization method according to the manufacturer's recommendation.

source_name: Mouse macrophages

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

growth_protocol: Total RNA was isolated from mouse macrophages using high pure RNA isolation kit in accordance with the prescribed protocol provided with the kit (Roche).The yield of the extracted RNA was determined spectrophotometrically by measuring the optical density at 260nm. The purity and quality of extracted RNA were evaluated using the Experion RNA StdSens Analysis kit (Bio-Rad Laboratories).

extract_protocol: Total RNA was isolated using high pure RNA isolation kit in accordance with the prescribed protocol provided with the kit (Roche).The yield of the extracted RNA was determined spectrophotometrically by measuring the optical density at 260nm. The purity and quality of extracted RNA were evaluated using the Experion RNA StdSens Analysis kit (Bio-Rad Laboratories).

tag: strain

value: female

tag: age

value: 13 weeks old

tag: genotype/variation

tag: agent

value: LPS

value: peritoneal macrophage


title: DUSP3-KO3-PBS

description:
SAMPLE 9
DUSP3-KO-PBS replicate 3

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

value: PBS


title: DUSP3-KO3-LPS

description:
SAMPLE 12
DUSP3-KO-LPS replicate 3


title: DUSP3-KO2-PBS

description:
SAMPLE 8
DUSP3-KO-PBS replicate 2


title: squamous cell carcinoma sample 9

description: gene expression

value: lung

value: squamous carcinoma


title: 67777-N

value: Female

value: Normal


title: WT3-LPS

description:
SAMPLE 6
WT-LPS replicate 3

value: WT


title: 67777-T

value: ER Positive

value: Tumor


title: DUSP3-KO1-LPS

description:
SAMPLE 10
DUSP3-KO-LPS replicate 1


title: WT2-LPS

description:
SAMPLE 5
WT-LPS replicate 2


title: BS66459-T


title: BS66755-T


title: BS66770-T


title: BS66172-N


title: 00-012-T

value: ER Negative


title: BS66689-T


title: BS66352-T


title: 67763-T


title: WT1-LPS

description:
SAMPLE 4
WT-LPS replicate 1


title: WT1-PBS

description:
SAMPLE 1
WT-PBS replicate 1


title: WT2-PBS

description:
SAMPLE 2
WT-PBS replicate 2


title: DUSP3-KO1-PBS

description:
SAMPLE 7
DUSP3-KO-PBS replicate 1


title: WT3-PBS

description:
SAMPLE 3
WT-PBS replicate 3


title: 01-060-T


title: 00-144-N


title: BS66755-N


title: BS66352-N


title: BS66498-N


title: 00-012-N


title: BS66689-N


title: 00-291-T


title: 00-218-T


title: 01-298-N


title: 00-291-N


title: mock_D7 (sample 55)

city: Jena

first: Andreas

last: Dix

address: Beutenbergstraße 11a

country: Germany

institute: Hans-Knöll-Institut

description:
SAMPLE 55
donor 7, mock-infected blood, 8h post infection

data_processing: The data was read in, background corrected, and log2-transformed using the “lumi” package in R

source_name: Whole blood

label_protocol: A total of 500 ng isolated RNA was immediately further processed to synthesize biotin-labeled complementary RNA (cRNA) using the Illumina® TotalPrep™ RNA Amplification Kit (Ambion). All procedures were carried out as proposed in the manufacturer’s protocol. Concentration as well as quality of cRNA were verified via the NanoDrop™ 1000 Spectrophotometer system (Thermo Scientific).

extract_protocol: Blood was collected and stored in PAXgene Blood RNA Tubes (PreAnalytiX) to stabilize intracellular RNA until further use. RNA isolation was performed using the PAXgene Blood RNA Kit (PreAnalytiX) corresponding to the manufacturer’s instruction. High quality of isolated RNA was proven by RNA integrity numbers (RIN) ranging from 8.2 to 9.5.

tag: individual

value: donor 7

tag: infection

value: mock

value: 8h post infection

value: male

value: blood


title: Af_4h_D7 (sample 56)

description:
SAMPLE 56
donor 7, Aspergillus fumigatus-infected blood, 4h post infection

value: Aspergillus fumigatus

value: 4h post infection


title: Af_8h_D7 (sample 57)

description:
SAMPLE 57
donor 7, Aspergillus fumigatus-infected blood, 8h post infection


title: Af_4h_D6 (sample 52)

description:
SAMPLE 52
donor 6, Aspergillus fumigatus-infected blood, 4h post infection

value: donor 6


title: kidney_ciplatin_CELL_rep3

city: Zhenjiang

first: Yuan

last: Zhu

state: Jiangsu

address: xuefu road

country: China

institute: Jiangsu Key Laboratory of Medical Science and Laboratory Medicine

description: microRNAs expression after 5 day in cisplatin treated kidney with MSCs administrated at day 1

hyb_protocol: Labeled RNA were resuspended in 18μL nuclease-free water and gently vortexed with 4.5μL 10×GE Blocking Agent and 22.5μL 2×Hi-RPM Hybridization Buffer (Agilgent). The culture was incubated at 100℃ for 5 minutes and transferred to ice water bath for 5 minutes immediately. Then shifted all volume to SureHyb chamber and hybridized at 55℃ for 20 hours following the manufacturers instructions. The hybridization chamber gasket slide contained 8 microarrays. After hybridization, microarrays were washed 5 minutes at room temperature with GE Wash Buffer 1 (Agilent) and 5 minutes at 37℃ with GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation using Gene Expression Wash Buffer Kit(Agilent, p/n 5188-5237)

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner(p/n G2565BA) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.3 (Agilent) using miRNA_QCM_Apr07 to obtain background subtracted and spatially detrended Processed Signal intensities. Extraction Configuration Set used miRNA-v1_95_May07.

organism: Rattus norvegicus

source_name: kidney,ciplatin,CELL,replicate 3

label_protocol: 0.1μg RNA was first dephosphorylated and denaturated, and  labeled using an Agilent's miRNA Complete Labeling and Hyb Kit (p/n 5190-0456) with Cy3 according to the manufacturer's instructions, followed by purification.

extract_protocol: RNA was prepared using the TRIZOL Reagent(100 ml)(Life technology) following the manufacturer's recommendations. microRNA was purified by AM1560 mirVana miRNA Isolation Kit(Ambion,USA) . RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: 200±20g Sprague Dawley rats were injected with 6mg/kg cisplatin at 0 day, with none treated rats used as control.24h after injection, equal volume PBS and 1×106MSCs dissolved in PBS were administrated by vein casual seperately.Tissues were colleced at 5 day.

tag: treatment

value: cisplatin + MSC

value: kidney

value: Sprague-Dawley


title: mock_D7 (sample 54)

description:
SAMPLE 54
donor 7, mock-infected blood, 4h post infection

tag: tissue


title: kidney_ciplatin_CELL_rep2

source_name: kidney,ciplatin,CELL,replicate 2


title: kidney_ciplatin_CELL_rep1

source_name: kidney,ciplatin,CELL,replicate 1


title: 01-276-T

value: Female

tag: sample type


title: 01-255-N

value: Normal


title: BS66770-N


title: 01-298-T


title: 01-340-T


title: kidney_ciplatin_PBS_rep3

description: microRNAs expression after 5 day in cisplatin treated kidney

source_name: kidney,ciplatin,PBS,replicate 3

value: cisplatin + PBS


title: 01-367-T

value: ER Positive


title: kidney_ciplatin_PBS_rep1

source_name: kidney,ciplatin,PBS,replicate 1


title: 01-367-N


title: kidney_ciplatin_PBS_rep2

source_name: kidney,ciplatin,PBS,replicate 2


title: mock_D6 (sample 50)

description:
SAMPLE 50
donor 6, mock-infected blood, 4h post infection


title: 01-262-T

source_name: Tumor

value: Tumor


title: Af_8h_D5 (sample 49)

description:
SAMPLE 49
donor 5, Aspergillus fumigatus-infected blood, 8h post infection

value: donor 5


title: Af_4h_D5 (sample 48)

description:
SAMPLE 48
donor 5, Aspergillus fumigatus-infected blood, 4h post infection


title: 01-280-T


title: 01-273-T


title: kidney_no treatment_rep2

description: microRNAs expression in kidney

source_name: kidney,no treatment,replicate 2


title: Af_8h_D6 (sample 53)

description:
SAMPLE 53
donor 6, Aspergillus fumigatus-infected blood, 8h post infection


title: kidney_no treatment_rep1

description: microRNAs expression in kidney

source_name: kidney,no treatment,replicate 1


title: 01-219-T


title: Ec_8h_D4 (sample 45)

description:
SAMPLE 45
donor 4, Escherichia coli-infected blood, 8h post infection

value: donor 4

value: Escherichia coli


title: 01-218-T


title: 405_NS AMI

city: Beijing

first: Xiangdong

last: Li

address: No. 167 Beilishi Rd

department: Cardiology

institute: Fuwai Hospital, National Center for Cardiovascular Diseases

description: Peripheral blood samples (5 mL) were collected in the cardiac catheterization laboratory, and were separated into plasma and cellular fractions within 2 h of collection.

hyb_protocol: Each slide is formatted with 8 identical arrays and hybridized with 100 ng Cy3-labeled RNA according to the protocols in the Agilent miRNA microarray system.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565BA, Agilent technologies, USA) Images were quantified using Feature Extraction software 10.7 (Agilent technologies, USA).

data_processing: Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, USA)

source_name: Plasma

label_protocol: miRNA molecular in total RNA was labeled by miRNA Complete Labeling and Hyb Kit(Cat#5190-0456, Agilent technologies, Santa Clara, CA, US)followed the manufacturer’s instructions, labeling section.

extract_protocol: Total RNA was isolated from plasma with TRIzol LS Reagent (Invitrogen, USA) according to the manufacturer’s protocol.

value: AMI

value: plasma


title: mock_D5 (sample 46)

description:
SAMPLE 46
donor 5, mock-infected blood, 4h post infection

value: mock

value: male

value: blood


title: 99-066-N

source_name: Normal


title: mock_D6 (sample 51)

description:
SAMPLE 51
donor 6, mock-infected blood, 8h post infection

value: donor 6

value: 8h post infection


title: Ec_4h_D4 (sample 44)

description:
SAMPLE 44
donor 4, Escherichia coli-infected blood, 4h post infection

value: 4h post infection


title: 399_NS AMI


title: Sa_4h_D4 (sample 42)

description:
SAMPLE 42
donor 4, Staphylococcus aureus-infected blood, 4h post infection

value: Staphylococcus aureus


title: Sa_8h_D4 (sample 43)

description:
SAMPLE 43
donor 4, Staphylococcus aureus-infected blood, 8h post infection


title: 99-260-T

value: Female


title: 99-188-T


title: 01-201-T


title: 99-225-T


title: 00-301-T


title: 139_NS AMI


title: 00-292-T


title: 99-165-T


title: Ca_8h_D4 (sample 41)

description:
SAMPLE 41
donor 4, Candida albicans-infected blood, 8h post infection

value: Candida albicans


title: 00-200-T


title: Ca_4h_D4 (sample 40)

description:
SAMPLE 40
donor 4, Candida albicans-infected blood, 4h post infection


title: mock_D4 (sample 39)

description:
SAMPLE 39
donor 4, mock-infected blood, 4h post infection, sample 3


title: mock_D5 (sample 47)

description:
SAMPLE 47
donor 5, mock-infected blood, 8h post infection


title: 66_NS AMI


title: 54_NS AMI


title: PM_SCC28

description: squamous cell carcinoma sample 28

hyb_protocol: Differentially labeled tumor and reference DNAs were combined and hybridized to Agilent Human Genome CGH 244A microarrays at 65°C for 40 hr. The hybridized arrays were washed and scanned using Agilent scanner

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version 9.5.3.1).

data_processing: Agilent Feature Extraction Software (v 9.5.3.1) was used for background subtraction

source_name: squamous carcinoma cell

label_protocol: 1.5 μg of tumor DNA and gender-matched reference DNA were digested. The digested DNAs were labeled by random priming with Cy3-dUTP (reference DNA) and Cy5-dUTP (tumor DNA) using Agilent Labeling Kit. The labeled DNAs were purified.

extract_protocol: Genomic DNA extracted using Dneasy Tissue Kit (Qiagen) following manufacturer's instructions

tag: cell type

value: squamous carcinoma

value: lung

source_name: normal lymphocytes (reference)

value: normal lymphocytes


title: PM_SCC30

description: squamous cell carcinoma sample 30


title: PM_SCC29

description: squamous cell carcinoma sample 29


title: 99-029-T

value: ER Positive

value: Tumor


title: mock_D4 (sample 38)

description:
SAMPLE 38
donor 4, mock-infected blood, 4h post infection, sample 2

value: donor 4


title: 99-066-T


title: 309_NS Quality Control

value: Quality Control


title: mock_D4 (sample 37)

description:
SAMPLE 37
donor 4, mock-infected blood, 4h post infection, sample 1


title: PM_SCC43

description: squamous cell carcinoma sample 43


title: 00-525-T

value: ER Negative


title: 00-525-N

value: Normal


title: Ec_8h_D1 (sample 36)

description:
SAMPLE 36
donor 1, Escherichia coli-infected blood, 8h post infection

value: donor 1

value: Escherichia coli

value: male


title: 325_NS AMI

value: AMI

value: plasma


title: 200_NS AMI


title: Ec_4h_D1 (sample 35)

description:
SAMPLE 35
donor 1, Escherichia coli-infected blood, 4h post infection

value: 4h post infection

value: blood


title: PM_SCC26

description: squamous cell carcinoma sample 26


title: PM_SCC27

description: squamous cell carcinoma sample 27


title: 99-301-T

value: Female


title: 306_1_NS Quality Control


title: 515_NS Stable Angina

value: Stable Angina


title: 00-462-N


title: PM_SCC25

description: squamous cell carcinoma sample 25

value: squamous carcinoma

value: lung


title: PM_SCC33

description: squamous cell carcinoma sample 33

value: normal lymphocytes


title: 00-225-T

value: Tumor


title: 00-529-T


title: PM_SCC35

description: squamous cell carcinoma sample 35


title: Sa_8h_D1 (sample 34)

description:
SAMPLE 34
donor 1, Staphylococcus aureus-infected blood, 8h post infection

value: Staphylococcus aureus

value: 8h post infection


title: Sa_4h_D1 (sample 33)

description:
SAMPLE 33
donor 1, Staphylococcus aureus-infected blood, 4h post infection


title: 421_NS Stable Angina


title: 381_NS AMI


title: 442_NS Stable Angina


title: 360_NS Stable Angina


title: 350_NS Stable Angina


title: mock_D1 (sample 30)

description:
SAMPLE 30
donor 1, mock-infected blood, 4h post infection, sample 3

value: mock


title: PM_SCC32

description: squamous cell carcinoma sample 32


title: PM_SCC31

description: squamous cell carcinoma sample 31


title: Ca_4h_D1 (sample 31)

description:
SAMPLE 31
donor 1, Candida albicans-infected blood, 4h post infection

value: Candida albicans


title: 249_NS Stable Angina

description: Peripheral blood samples (5 mL) were collected in the cardiac catheterization laboratory, and were separated into plasma and cellular fractions within 2 h of collection.


title: 00-522-T

value: ER Negative


title: mock_D1 (sample 29)

description:
SAMPLE 29
donor 1, mock-infected blood, 4h post infection, sample 2

value: donor 1


title: 00-185-T


title: 224_NS Stable Angina


title: 308_1_NS Quality Control

value: Quality Control


title: PM_SCC21

description: squamous cell carcinoma sample 21


title: Ca_8h_D1 (sample 32)

description:
SAMPLE 32
donor 1, Candida albicans-infected blood, 8h post infection

value: male


title: PM_SCC22

description: squamous cell carcinoma sample 22


title: 00-401-T


title: Ec_8h_D3 (sample 27)

description:
SAMPLE 27
donor 3, Escherichia coli-infected blood, 8h post infection

value: donor 3

value: Escherichia coli


title: PM_SCC20

description: squamous cell carcinoma sample 20

value: blood


title: Ec_4h_D3 (sample 26)

description:
SAMPLE 26
donor 3, Escherichia coli-infected blood, 4h post infection

value: 4h post infection


title: PM_SCC19

description: squamous cell carcinoma sample 19


title: 438_NS Highrisk

value: High risk

value: plasma


title: 00-530-T

value: Female


title: PM_SCC8

description: squamous cell carcinoma sample 8

value: squamous carcinoma

value: lung

value: normal lymphocytes


title: 00-151-T

value: Tumor


title: mock_D1 (sample 28)

description:
SAMPLE 28
donor 1, mock-infected blood, 4h post infection, sample 1

value: mock


title: 179_NS Stable Angina

value: Stable Angina


title: 420_NS Highrisk


title: 288_NS Highrisk


title: Sa_8h_D3 (sample 25)

description:
SAMPLE 25
donor 3, Staphylococcus aureus-infected blood, 8h post infection

value: Staphylococcus aureus

value: 8h post infection


title: 00-409-T

value: ER Negative


title: Sa_4h_D3 (sample 24)

description:
SAMPLE 24
donor 3, Staphylococcus aureus-infected blood, 4h post infection

value: male


title: Ca_8h_D3 (sample 23)

description:
SAMPLE 23
donor 3, Candida albicans-infected blood, 8h post infection

value: donor 3

value: Candida albicans


title: PM_SCC7

description: squamous cell carcinoma sample 7

value: blood


title: 282_NS Highrisk


title: 251_NS Highrisk


title: 00-480-T


title: 00-172-T


title: PM_SCC6

description: squamous cell carcinoma sample 6


title: 00-135-T


title: Ca_4h_D3 (sample 22)

description:
SAMPLE 22
donor 3, Candida albicans-infected blood, 4h post infection

value: 4h post infection


title: 188_NS Highrisk

value: High risk


title: PM_SCC4

description: squamous cell carcinoma sample 4


title: 00-105-T


title: 00-395-T


title: 169_NS Highrisk

value: plasma


title: mock_D3 (sample 20)

description:
SAMPLE 20
donor 3, mock-infected blood, 4h post infection, sample 2


title: PM_SCC5

description: squamous cell carcinoma sample 5


title: 01-302-T

value: Female


title: mock_D3 (sample 21)

description:
SAMPLE 21
donor 3, mock-infected blood, 4h post infection, sample 3


title: PM_SCC2

description: squamous cell carcinoma sample 2

value: squamous carcinoma


title: Ec_8h_D2 (sample 18)

description:
SAMPLE 18
donor 2, Escherichia coli-infected blood, 8h post infection

value: donor 2

value: Escherichia coli


title: mock_D3 (sample 19)

description:
SAMPLE 19
donor 3, mock-infected blood, 4h post infection, sample 1


title: PM_SCC3

description: squamous cell carcinoma sample 3

value: lung

value: normal lymphocytes


title: 25_NS Highrisk


title: 516_NS Health

value: Health


title: 01-242-T

value: Tumor


title: MSCs untransduced and treated with BMP4 - rep 3

city: Toulouse

first: Anne

last: PREL

address: 1 Avenue J Poulhes

department: Stromalab

country: France

institute: CNRS 5273 INSERM1031

hyb_protocol: The fragmented end labeled cDNA was hybridized to gene chip Human Gene 1.1 ST array strip (Affymetrix) for 20H ate 48°C.

scan_protocol: GeneChips were scanned using a gene chip Array scanner (Affymetrix)

data_processing: Supervised analyses for generation of each specific gene expression signature were obtained by using of Partek Genomics Suite software with the sample-paired t test that matched each donor treatment.

source_name: MSCs untransduced and treated with BMP4

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

growth_protocol: cells were kept in 37°C incubator until the extraction  process

extract_protocol: Total RNA were extracted with Rneasy microkit (Qiagen) using manufacturer' instructions.

treatment_protocol: Cells were transduced with lentiviral vectors containing mRNAs

value: Immature bone marrow mesenchymal stem cells

tag: treated with

value: none (untransduced control)

tag: transduced with

tag: time point

value: 58h post-transduction


title: 365_NS Health

tag: disease state


title: PM_SCC9

description: squamous cell carcinoma sample 9


title: 339_NS Health


title: MSCs untransduced and treated with BMP4 - rep 2


title: MSCs untransduced  - rep4

source_name: MSCs untransduced


title: MSCs untransduced and treated with BMP4 - rep 1


title: MSCs untransduced  - rep3


title: Sa_4h_D2 (sample 15)

description:
SAMPLE 15
donor 2, Staphylococcus aureus-infected blood, 4h post infection

value: Staphylococcus aureus

value: male


title: Sa_8h_D2 (sample 16)

description:
SAMPLE 16
donor 2, Staphylococcus aureus-infected blood, 8h post infection

value: 8h post infection

value: blood


title: PM_SCC1

description: squamous cell carcinoma sample 1


title: 284_NS Health


title: 01-237-N

value: Normal


title: 01-265-T

value: ER Negative


title: Ec_4h_D2 (sample 17)

description:
SAMPLE 17
donor 2, Escherichia coli-infected blood, 4h post infection

value: 4h post infection


title: 245_NS Health

description: Peripheral blood samples (5 mL) were collected in the cardiac catheterization laboratory, and were separated into plasma and cellular fractions within 2 h of collection.

value: plasma


title: MSCs untransduced  - rep2


title: Ca_8h_D2 (sample 14)

description:
SAMPLE 14
donor 2, Candida albicans-infected blood, 8h post infection

value: donor 2

value: Candida albicans


title: 01-265-N

value: Female


title: 01-212-T


title: Ca_4h_D2 (sample 13)

description:
SAMPLE 13
donor 2, Candida albicans-infected blood, 4h post infection


title: 100_NS Health


title: 195_NS Health


title: MSCs untransduced  - rep1


title: MSCs transduced with IDLV-Luc - rep 4 [re-analysis]

source_name: MSCs transduced with IDLV-Luc

value: viral particles containing IDLV-Luc


title: MSCs transduced with IDLV-Luc - rep 3 [re-analysis]


title: MSCs untransduced and treated with BMP4 - rep 4


title: 01-302-N


title: mock_D2 (sample 11)

description:
SAMPLE 11
donor 2, mock-infected blood, 4h post infection, sample 2

source_name: Whole blood

value: mock


title: 01-254-T

value: Tumor


title: 79_NS Health

value: Health


title: Ec_8h_D1 (sample 9)

description:
SAMPLE 9
donor 1, Escherichia coli-infected blood, 8h post infection

value: donor 1

value: Escherichia coli


title: Ventral midbrain lysates, 10wks, Control dopaminergic neurons 4

city: Durham

first: Pavle

last: Matak

state: North Carolina

address: 450 Research Drive, LSRC C-125

department: Pharmacology and Cancer Biology

institute: Duke University

description: SAMPLE 14

hyb_protocol: Targets were hybridized to the Mouse430 2.0 GeneChip (Affymetrix, Santa Clara, CA).  Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse 430 2.0  Array in the Affymetrix Hybridization Oven.  GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Partek Genomics Suite 6.5 (Partek Inc., St. Louis, MO) was used to perform data analysis. Robust multi-chip analysis (RMA) normalization was done on each dataset separately, 3 week old mice were RMA normalized together and then the 10 week old mice were normalized together. Multi-way ANOVA and fold change were performed to select target genes that were differentially expressed between Tfr1fl/+ CRE; Rpl22+/- and Tfr1fl/fl CRE; Rpl22+/- mice. Differentially expressed genes were selected with a p-value cut-off of 0.05 based on the ANOVA test and a fold change cut-off of 2.   Gene Set Enrichment Analysis [(GSEA/MSigDB v4.5) was performed on genes with >2-fold change.

source_name: 10 wks_Control dopaminergic neurons

label_protocol: 50 ng of total RNA was amplified according to the NuGEN Ovation RNA Amplification System V2. Affymetrix GeneChip analysis was performed according to the manufacturer’s instructions,

growth_protocol: Tfr1ΔDN and CTR mice were maintained until 3 and 10 wks of age after which they were sacrificed

extract_protocol: Fresh ventral midbrains from mice were isolated and actively translated mRNAs from dopaminergic neurons immunoprecipitated accroding to prevoiously published protocol (Sanz et al, PNAS, 2009, Cell-type-specific isolation of ribosome-associated mRNA from complex tissues).

treatment_protocol: Tfr1ΔDN condiitonal knockout mice carry a deletion of Transferrin receptor 1 specifically in dopaminergic neurons. These mice and respective controls (heterozygotes for Tfr1 allele) were bred onto a Ribotag mouse background to enable subsequent mRNA extraction

tag: strain background

value: F2 mice of 129Sv and C57BL/6

value: CTR; control

value: 10 wks

value: ventral midbrain

value: dopaminergic neurons


title: MSCs transduced with IDLV-Luc - rep 1 [re-analysis]

value: Immature bone marrow mesenchymal stem cells

value: 58h post-transduction


title: 01-212-N

value: Normal


title: mock_D2 (sample 10)

description:
SAMPLE 10
donor 2, mock-infected blood, 4h post infection, sample 1

value: donor 2

tag: time

value: 4h post infection

value: male

value: blood


title: Ec_4h_D1 (sample 8)

description:
SAMPLE 8
donor 1, Escherichia coli-infected blood, 4h post infection

tag: gender


title: 01-208-T

value: Female

value: ER Negative


title: MSCs transduced with MS2RLP Runx2 - rep 4

source_name: MSCs transduced with MS2RLP Runx2

value: viral particles containing MS2RLP-RUNX2


title: Ventral midbrain lysates, 10wks, Control dopaminergic neurons 2

description: SAMPLE 12


title: Ventral midbrain lysates, 10wks, Tfr1-null dopaminergic neurons 2

description: SAMPLE 9

source_name: 10 wks_Tfr1-null dopaminergic neurons

value: Tfr1ΔDN; Tfr1-null


title: MSCs transduced with MS2RLP Runx2 - rep 3


title: MSCs transduced with IDLV-Luc - rep 4

value: viral particles containing IDLV-Luc


title: Ventral midbrain lysates, 10wks, Control dopaminergic neurons 1

description: SAMPLE 11

value: F2 mice of 129Sv and C57BL/6


title: MSCs transduced with MS2RLP Runx2 - rep 1


title: Ventral midbrain lysates, 10wks, Control dopaminergic neurons 3

description: SAMPLE 13

value: CTR; control


title: MSCs transduced with MS2RLP Runx2 - rep 2


title: Ventral midbrain lysates, 10wks, Tfr1-null dopaminergic neurons 3

description: SAMPLE 10

value: 10 wks


title: Ca_8h_D1 (sample 5)

description:
SAMPLE 5
donor 1, Candida albicans-infected blood, 8h post infection

value: donor 1

value: Candida albicans

value: 8h post infection


title: Sa_4h_D1 (sample 6)

description:
SAMPLE 6
donor 1, Staphylococcus aureus-infected blood, 4h post infection

value: Staphylococcus aureus


title: MSCs transduced with IDLV-Luc - rep 2 [re-analysis]

value: Immature bone marrow mesenchymal stem cells

value: 58h post-transduction


title: Ventral midbrain lysates, 10wks, Tfr1-null dopaminergic neurons 1

description: SAMPLE 8

value: ventral midbrain

value: dopaminergic neurons


title: epic1

city: Beaucouzé

first: Etienne

last: Bucher

address: 42 rue Georges Morel

institute: IRHS

description: epic1 mutant Arabidopsis RNA chip 2

hyb_protocol: Approximately 7.5 μg of fragmented cDNA was hybridized for 16 hours at 60 rpm

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

data_processing: Data was processed in R as described in Naouar et al. Quantitative RNA expression analysis with Affymetrix Tiling 1.0R arrays identifies new E2F target genes. Plant J (2009) vol. 57 (1) pp. 184-94

organism: Arabidopsis thaliana

source_name: whole seedlings RNA

label_protocol: RNA (5-μg aliquots) was reverse transcribed using T7 oligodT (Ambion) and Superscript II (Invitrogen) and the second strand synthesised using DNA polymerase I. cDNA was then amplified using IVT (Affymetrix). The resulting cRNA was cleaned up with the GeneChip Sample Cleanup Module (Affymetrix). cRNA (7-μg aliquots) was then reverse transcribed and made double-stranded in the presence of dUTP. Following cleanup (Qiagen kit), the cDNA was fragmented and labelled using the Affymetrix kit 900812 GeneChip® WT Double Stranded DNA Terminal Labeling Kit.

growth_protocol: Plants were grown under standard growth condition with 16 hours of light (long day)

extract_protocol: RNA was extracted using the Ambion miRVANA RNA isolation kit

treatment_protocol: no treatment was performed

value: epic1 mutant

value: leaves


title: MSCs transduced with IDLV-Luc - rep 3


title: Ca_4h_D1 (sample 4)

description:
SAMPLE 4
donor 1, Candida albicans-infected blood, 4h post infection

value: 4h post infection

value: male

value: blood


title: mock_D1 (sample 2)

description:
SAMPLE 2
donor 1, mock-infected blood, 4h post infection, sample 2

value: mock


title: 01-242-N

value: Female

value: Normal


title: mock_D2 (sample 12)

description:
SAMPLE 12
donor 2, mock-infected blood, 4h post infection, sample 3

value: donor 2


title: MSCs transduced with IDLV-Luc - rep 2

value: viral particles containing IDLV-Luc


title: Ventral midbrain lysates, 3wks, Tfr1-null dopaminergic neurons 4

description: SAMPLE 7

source_name: 3 wks_Tfr1-null dopaminergic neurons

value: F2 mice of 129Sv and C57BL/6

value: Tfr1ΔDN; Tfr1-null

value: 3 wks


title: silex

description: silex wild-type Arabidopsis RNA chip 1

value: silex wild-type


title: mock_D1 (sample 3)

description:
SAMPLE 3
donor 1, mock-infected blood, 4h post infection, sample 3

value: donor 1


title: mock_D1 (sample 1)

description:
SAMPLE 1
donor 1, mock-infected blood, 4h post infection, sample 1


title: Ventral midbrain lysates, 3wks, Tfr1-null dopaminergic neurons 3

description: SAMPLE 6

value: ventral midbrain


title: MSCs transduced with IDLV-Luc - rep 1

value: Immature bone marrow mesenchymal stem cells

value: 58h post-transduction


title: Liver_LPS/GalN_rep1

city: Tianjin

first: chang

last: antao

address: 94 Weijin Road

department: School of Medicine

institute: Nankai university

description: This sample is of LPS/GalN treated mice. It is the first of three LPS/GalN treated biological replicates used in this experiment, each from separate treatments.

hyb_protocol: Hybridization was performed in NimbleGen Hybridization System following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by an Axon GenePix 4000 B scanner (Molecular Devices Corporation) piloted by GenePix Pro 6.0 software (Axon) following their standard operating protocol.

data_processing: Scanned images (TIFF format) were imported into NimbleScan software (version 2.5) for grid alignment and expression data analysis. Expression data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the NimbleScan software. The Probe level (*_norm_RMA.pair) files and Gene level (*_RMA.calls) files were generated after normalization. All gene level files were imported into Agilent GeneSpring Software (version 11.0) for further analysis.

source_name: Liver tissue of LPS/GalN treated mice

label_protocol: Labeling was performed by NimbleGen One-Color DNA Labeling Kit following their standard operating protocol. See www.nimblegen.com.

growth_protocol: 9-10 weeks old male C57 BL/6 mice received the human care under the guidelines on laboratory animals of Nankai University.

extract_protocol: Total RNA was extracted by PureYield™ RNA Midiprep System (Promega). RNA concentration and quality were determined by NanoDrop ND-1000A, and RNA integrity and gDNA contamination were tested by denaturing agarose gel electrophoresis.

treatment_protocol: Mice were treated with 0.01μg LPS alone or together with 20mg GalN for 2.5 hours.

value: LPS/GalN

tag: genotype

value: Wild-type

tag: strain

value: Male

value: 9-10 weeks

value: Liver


title: Liver_LPS_rep1

description: This sample is of LPS treated mice. It is the first of three LPS treated biological replicates used in this experiment, each from separate treatments.

source_name: Liver tissue of LPS treated mice

value: LPS

tag: age


title: Liver_LPS/GalN_rep2

description: This sample is of LPS/GalN treated mice. It is the second of three LPS/GalN treated biological replicates used in this experiment, each from separate treatments.


title: Ventral midbrain lysates, 3wks, Tfr1-null dopaminergic neurons 1

description: SAMPLE 4

source_name: 3 wks_Control dopaminergic neurons

tag: genotype/variation

value: dopaminergic neurons


title: MSCs transduced with MS2RLP DLX5 - rep 3

source_name: MSCs transduced with MS2RLP DLX5

value: viral particles containing MS2RLP-DLX5


title: MSCs transduced with MS2RLP DLX5 - rep 4


title: MSCs transduced with MS2RLP DLX5 - rep 1


title: MSCs transduced with MS2RLP DLX5 - rep 2


title: Liver_LPS/GalN_rep3

description: This sample is of LPS/GalN treated mice. It is the third of three LPS/GalN treated biological replicates used in this experiment, each from separate treatments.


title: Liver_LPS_rep2

description: This sample is of LPS treated mice. It is the second of three LPS treated biological replicates used in this experiment, each from separate treatments.


title: Ventral midbrain lysates, 3wks, Control dopaminergic neurons 1

description: SAMPLE 1

value: CTR; control


title: Ventral midbrain lysates, 3wks, Tfr1-null dopaminergic neurons 2

description: SAMPLE 5

value: F2 mice of 129Sv and C57BL/6


title: Ventral midbrain lysates, 3wks, Control dopaminergic neurons 3

description: SAMPLE 3


title: Liver_LPS_rep3

description: This sample is of LPS treated mice. It is the third of three LPS treated biological replicates used in this experiment, each from separate treatments.


title: HT-1376 vs. KSHV-infected HT-1376

status: Public on Mar 10 2015

city: Daejeon

first: Myung-Shin

last: Lee

address: Yongdu-dong, Jung-gu

department: Microbiology and Immunology

institute: Eulji University School of Medicine

description: HT-1376 vs. KSHV-infected HT-1376

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing:
Agilent Feature Extraction Software (v 9.3.2.1) was used for background subtraction and LOWESS normalization.
The averages of normalized ratios were calculated by dividing the average of normalized signal channel intensity by the average of normalized control channel intensity.

label_protocol: 0.2ug of total RNA was labeled using Low Input Quick Amp Labeling Kit, Two-Color (Agilent Technology) as following manufacturer's instructions.

growth_protocol: Cultured in DMEM with 10~20% FBS and 200ug/ml of hygromycin

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

treatment_protocol: KSHV BAC16 was infected and culture for 2 weeks with 200ug/ml of hygromycin

tag: cell line

value: bladder cancer

source_name: KSHV 1376


title: U937_EVI1 cells, control, biological replicate 2

city: Vienna

first: Rotraud

last: Wieser

address: Waehringer Guertel 18-20

department: Clinic of Medicine I

country: Austria

institute: Medical University of Vienna

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: RMA

source_name: U937_EVI1 cells, no treatment, 48 h

label_protocol: Affymetrix standard protocol

growth_protocol: RPMI1640, 10% FCS, 1% penicillin/streptomycin/glutamine

extract_protocol: RNeasy Plus Mini kit (Quiagen)

treatment_protocol: Logarithmically growing cells were treated or not with 400 nM etoposide for 48 h

tag: vector

value: EVI1 expression vector


title: U937_EVI1 cells, etoposide treatment, biological replicate 2

source_name: U937_EVI1 cells, 400 nM etoposide, 48 h

tag: treatment

value: 400 nM etoposide for 48h


title: U937_vec cells, etoposide treatment, biological replicate 2

source_name: U937_vec cells, 400 nM etoposide, 48 h

value: empty vector


title: U937_EVI1 cells, control, biological replicate 1


title: U937_vec cells, etoposide treatment, biological replicate 1


title: U937_EVI1 cells, etoposide treatment, biological replicate 1