title: Treated with pre-operative chemo UGI-0288 T vs N


title: Treated with pre-operative chemo UGI-0346 T vs N

status: Public on Feb 10 2017

type: genomic

city: Rotterdam

first: Askar

last: Obulkasim

state: Zuid Holland

address: Wytemaweg 80

department: Pediatric Oncology

country: Netherlands

institute: ErasmusMC - Sophia Children's Hospital

hyb_protocol: High-resolution array CGH was performed using custom design 180K Agilent microarrays (4x180k array, Agilent Technologies, Palo Alto, CA, USA, GEO platform GPL8687 containing 180,880 in situ synthesized oligonucleotides representing 169,793 unique chromosomal locations evenly distributed over the genome (spacing ~17 kb) and 4548 additional unique oligonucleotides, located at 238 of the Cancer Census genes  (http://www.sanger.ac.uk/genetics/CGP/Census/)).

scan_protocol: Agilent’s Feature Extraction software (v10.5.1.1) with default settings was applied on the microarray images to quantify the fluorescence intensities

data_processing:
After image quantification, control spots (n = 6539) were removed from the data yielding 174,340 features. Both channels were background corrected by subtracting background median signals from foreground median intensities to obtain an unbiased hybridization signal. Normalization was performed with the R-package CGHcall
The LogX ratios are thus Cy3/Cy5. Normalization was performed with using median of the intensities for the two channels, followed by a post-segmentation mode normalization as previously described. Bioinformatics. 2007 Apr 1;23(7):892-4. Epub 2007 Jan 31. CGHcall: calling aberrations for array CGH tumor profiles. van de Wiel MA1, Kim KI, Vosse SJ, van Wieringen WN, Wilting SM, Ylstra B.

molecule: genomic DNA

organism: Homo sapiens

source_name: FFPE blocks

label_protocol: Protocol following procedures and components of the ‘DNA labelling kit’ by ENZO Life Science Farmingdale, USA

extract_protocol: DNA was isolated as previously described: High-resolution copy number profiling by array CGH using DNA isolated from formalin-fixed, paraffin-embedded tissues. van Essen HF, Ylstra B. Methods Mol Biol. 2012;838:329-41.

treatment_protocol: Genomic DNA extracted using Trizol following manufacturer's instructions

tag: tissue

value: esophageal adenocarcinoma tumor

tag: treatment

value: pre-operative chemo

source_name: patient matched normal DNA

value: normal esophageal tissue


title: T-ALL sample 5

type: RNA

city: lille

first: frédéric

last: leprêtre

address: Boulevard du Pr Leclercq

department: CHU of Lille, CBP

country: France

institute: Lille University

description:
SAMPLE 17
Gene expression data from acute leukemic cell samples.

hyb_protocol: RNA were hybridized according to the manufacturer's protocols. The arrays were washed and stained using Fluidics Station 450.

scan_protocol: The images were scanned with GeneChip Scanner 3000 (Affymetrix).

data_processing:
Data were analysed with GeneChip Operating Software (GCOS; Affymetrix).
A genomics signature for the PDC samples has been established with the probes shown in the supplementary file 'genomics_signature.txt'.

label: biotin

molecule: total RNA

source_name: T-ALL sample

label_protocol: RNA were labelled according to the manufacturer's protocols.

extract_protocol: According to manufacturer's recommendations.

value: Bone marrow/blood >65% infiltration

tag: disease state

value: T-acute lymphoblastic leukemia (T-ALL)

tag: type

value: ND


title: Treated with pre-operative chemo UGI-0268 T vs N


title: T-ALL sample 9

description:
SAMPLE 21
Gene expression data from acute leukemic cell samples.

value: IMG


title: T-ALL sample 6

description:
SAMPLE 18
Gene expression data from acute leukemic cell samples.


title: Treated with pre-operative chemo UGI-0163 T vs N


title: T-ALL sample 1

description:
SAMPLE 13
Gene expression data from acute leukemic cell samples.

value: IMB


title: T-ALL sample 8

description:
SAMPLE 20
Gene expression data from acute leukemic cell samples.


title: Treated with pre-operative chemo UGI-0120 T vs N


title: Treated with pre-operative chemo UGI-0132 T vs N


title: Treated with pre-operative chemo UGI-0165 T vs N


title: Treated with pre-operative chemo UGI-0101 T vs N


title: T-ALL sample 2

description:
SAMPLE 14
Gene expression data from acute leukemic cell samples.

value: T


title: Treated with pre-operative chemo UGI-0192 T vs N


title: Treated with pre-operative chemo UGI-0215 T vs N


title: BPDCN sample 12

description:
SAMPLE 12
Gene expression data from acute leukemic cell samples.

source_name: BPDCN sample

value: Blastic plasmacytoid dendritic cell neoplasm (BPDCN)

value: PDC


title: Treated with pre-operative chemo UGI-0100 T vs N


title: T-ALL sample 7

description:
SAMPLE 19
Gene expression data from acute leukemic cell samples.


title: BPDCN sample 10

description:
SAMPLE 10
Gene expression data from acute leukemic cell samples.


title: T-ALL sample 4

description:
SAMPLE 16
Gene expression data from acute leukemic cell samples.

value: TCRab


title: Treated with pre-operative chemo UGI-0149 T vs N


title: Treated with pre-operative chemo UGI-0217 T vs N


title: BPDCN sample 11

description:
SAMPLE 11
Gene expression data from acute leukemic cell samples.


title: Treated with pre-operative chemo UGI-0112 T vs N


title: T-ALL sample 3

description:
SAMPLE 15
Gene expression data from acute leukemic cell samples.


title: Treated with pre-operative chemo UGI-0145 T vs N


title: BPDCN sample 7

description:
SAMPLE 7
Gene expression data from acute leukemic cell samples.


title: Treated with pre-operative chemo UGI-0094 T vs N


title: T-ALL sample 10

description:
SAMPLE 22
Gene expression data from acute leukemic cell samples.

value: Pre-ab


title: BPDCN sample 6

description:
SAMPLE 6
Gene expression data from acute leukemic cell samples.


title: Treated with pre-operative chemo UGI-0091 T vs N


title: Treated with pre-operative chemo UGI-0074 T vs N


title: BPDCN sample 3

description:
SAMPLE 3
Gene expression data from acute leukemic cell samples.


city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

country: USA

institute: NIH

description: Gene expression data from Staphylococcus aureus day 1 abscess left rep 3

hyb_protocol: All cRNAs were hybridized to a custom Affymetrix GeneChip

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

data_processing: The data were analyzed with Expression Console

organism: Staphylococcus aureus

label_protocol: Total RNA was obtained and treated with MICROBEnrichTM (Ambion/Life Technologies) to increase the concentration of prokaryotic RNA. Approximately, 500 ng of prokaryotic RNA was amplified, biotin-dUTP-labeled (Biotin-16-dUTP; Roche Applied Science, Indianapolis, IN) and fragmented using MessageAmp II-Bacteria kit (Ambion/Life Technologies) according to manufacturer protocol.

growth_protocol: S. aureus strain USA300 (LAC) was cultured in trypticase soy broth (TSB; Becton Dickinson, Franklin Lakes, NJ) in a rotary shaker at 225 rpm and 37 °C. Bacteria from overnight (18 h) culture were diluted 1:200 with fresh media and grown to mid-log (OD600 = 0.75). To prepare the inoculum, bacteria at early stationary phase of growth were collected by centrifugation, washed twice with Dulbecco’s phosphate buffered saline (DPBS; St. Louis, MO) and resuspended to 5 × 109 CFUs/ml in DPBS

extract_protocol: Samples were treated with QIAzol Lysis Reagent (Qiagen, Valencia, CA) and subsequently homogenized with a FastPrep®-24 sample preparation system (MP Biomedicals, Santa Ana, CA) followed by RNA extraction using a RNeasy® Microarray Tissue kit (Qiagen), according to the manufacturer’s protocol

treatment_protocol: 5 × 108 CFUs of USA300 strain LAC in 0.1 ml sterile phosphate-buffered saline by subcutaneous injection

tag: strain

value: USA300 strain LAC

tag: sample type


title: BPDCN sample 4

description:
SAMPLE 4
Gene expression data from acute leukemic cell samples.


description: Gene expression data from Staphylococcus aureus day 1 abscess right rep 2


title: BPDCN sample 5

description:
SAMPLE 5
Gene expression data from acute leukemic cell samples.


description: Gene expression data from Staphylococcus aureus day 1 abscess right rep 4


title: Treated with pre-operative chemo UGI-0092 T vs N


description: Gene expression data from Staphylococcus aureus day 1 abscess left rep 1


title: Treated with pre-operative chemo UGI-0046 T vs N


title: Treated with pre-operative chemo UGI-0002 T vs N


title: Treated with pre-operative chemo UGI-0042 T vs N


title: Staphylococcus aureus inoculum rep 2

description: Gene expression data from Staphylococcus aureus inoculum rep 2

source_name: Staphylococcus aureus inoculum rep 2

value: Staphylococcus aureus inoculum


title: Staphylococcus aureus inoculum rep 3

description: Gene expression data from Staphylococcus aureus inoculum rep 3

source_name: Staphylococcus aureus inoculum rep 3


title: BPDCN sample 9

description:
SAMPLE 9
Gene expression data from acute leukemic cell samples.


title: Staphylococcus aureus inoculum rep 1

description: Gene expression data from Staphylococcus aureus inoculum rep 1

source_name: Staphylococcus aureus inoculum rep 1


title: BPDCN sample 1

description:
SAMPLE 1
Gene expression data from acute leukemic cell samples.


title: BPDCN sample 2

description:
SAMPLE 2
Gene expression data from acute leukemic cell samples.


title: Day 12 p.i. Rep3

city: Jena

first: Himanshu

last: Manchanda

address: Beutenbergstraße 11a

department: Systems Biology and Bioinformatics

country: Germany

institute: Hans Knoell Institute

description: Replicate 3

hyb_protocol: according Illuminas instructions (Bead chip standard hybridisation protocol) using Mouse Ref-8 v2.0 Bead Chips (Illumina, San Diego, USA)

scan_protocol: Direct Hyb scan settings provided by the iScan Bead Array scanner (Illumina, San Diego, USA)

data_processing: The data were normalised using VST transformation and normalisation in R using the with lumiN package. The R package, Limma was used to identify differentially expressed genes with a criteria of having log2 fold change of >= 1 & <= -1 with having p-value of <= 0.05.

organism: Mus musculus

source_name: Mouse lung

label_protocol: Epicentre TargetAmp™- Nano Labeling Kit for Illumina® Expression BeadChip® (Biozym, Hess. Oldendorf, Germany)

extract_protocol: The RNA was isolated from frozen lung samples of each 4 mice infected with mpJena/5258 per time point as well as samples of 4 mock-infected animals

treatment_protocol: 7-to 8-week-old female BALB/c mice (16 -18 g; Charles River, Bad Sulzfeld, Germany) were infected intranasally with 106TCID50/20μl of mpJena/5258 under isoflurane anesthesia. Mock-infected mice were used as control

tag: time

value: Day 12 p.i.

value: BALB/c

tag: genter

value: female

value: lung


title: Day 12 p.i. Rep4

description: Replicate 4

label: TargetAmp™- Nano Labeling Kit for Illumina® Expression BeadChip®


title: Day 12 p.i. Rep1

description: Replicate 1


title: Day 12 p.i. Rep2

description: Replicate 2


title: Smad3 knockout ES cells

city: Hong Kong

first: Ping

last: Yuan

address: Prince Wales Hospital

department: Chemical Pathology

country: Hong Kong

institute: The Chinese University of Hong Kong

description: Smad3 knockout ES cells

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using Expression Console software. MAT background correction were applied to probe intensities, gene level expression were summarized from the corrected intensities and then quantile normalized.
MoEx-1_0-st-v1.r2.pgf
MoEx-1_0-st-v1.r2.dt1.mm8.mps

label: Biotin

source_name: embryonic stem cells

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

growth_protocol: ES cells were cultured in ES cell medium supplied with 2i (CHIR99021 and PD0325901) and LIF.

extract_protocol: Total RNA was extract by Trizol and then purified with QIAGEN Rneasy purification kit.

treatment_protocol: Not applicable

tag: genotype

value: Smad3 knockout

tag: cell type

value: embryonic stem cells

tag: genetic background


title: Wild type ES cells

description: Wild type ES cells

value: wild type


title: Day 9 p.i. Rep3

description: Replicate 3

value: Day 9 p.i.


title: Day 9 p.i. Rep1

description: Replicate 1


title: Day 9 p.i. Rep4

description: Replicate 4


title: Day 9 p.i. Rep2

description: Replicate 2


title: Day 7 p.i. Rep4

description: Replicate 4

value: Day 7 p.i.


title: Day 7 p.i. Rep3

description: Replicate 3


title: Day 7 p.i. Rep1

description: Replicate 1


title: Day 6 p.i. Rep4

description: Replicate 4

value: Day 6 p.i.


title: Day 7 p.i. Rep2

description: Replicate 2


title: Day 6 p.i. Rep1

description: Replicate 1


title: Day 4 p.i. Rep4

description: Replicate 4

value: Day 4 p.i.


title: Saponin-treated_iRBCs_rep1

city: Obihiro

first: Ryo

last: Takano

state: Hokkaido

address: Inada-cho

department: National Research Center for Protozoan Diseases

country: Japan

institute: Obihiro University of Agriculture and Veterinary Medicine

description: Gene expression after 2hr in human macrophages co-cultured with saponin-treated iRBCs

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent GE hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE 8x60K Microarrays (G4858A) for 17 hours at 65 °C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37 °C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned with an Agilent's High-Resolution Microarray Scanner using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green).

data_processing: The scanned images were analyzed with Agilent Feature Extraction Software ver. 10.7.3.1. using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: Human monocyte-derived macrophages, saponin-treated iRBCs, replicate 1

label_protocol: Cy3-labeled cRNA probe synthesis was initiated with 50 ng of total RNAs by using the Agilent Low Input Quick Amp Labeling kit, one color (Agilent Technologies).

growth_protocol: Peripheral blood mononuclear cells were independently separated from the buffy coat of healthy donors. Monocytes were purified by adherence and were allowed to differentiate for 14 days in RPMI 1640 medium supplemented with recombinant human GM-CSF and IFN-γ.

extract_protocol: Adherent macrophages co-cultured for 2 h with synchronized-iRBCs, saponin-treated iRBCs, or human non-infected RBC (n=3) were washed with ice-cold PBS and lysed with TRIzol Reagent (Invitrogen) for RNA extraction. Chloroform-isoamyl alchol (5:1) was added to the lysed cells, which were then vortexed and centrifuged for 15 min at 12,000 g at 4 °C. The resulting aqueous layer was subjected to RNA extraction by using RNeasy Mini kit columns (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Human monocyte-derived macrophages were co-cultured with synchronized-iRBCs, saponin-treated iRBCs, or human non-infected RBCs at a ratio of 1:20 in Plasmodium-culturing medium for 2 h.

value: Human-monocyte-derived macrophage


title: Day 5 p.i. Rep3

description: Replicate 3

value: Day 5 p.i.


title: Day 6 p.i. Rep2

description: Replicate 2


title: Day 4 p.i. Rep3

description: Replicate 3


title: Day 4 p.i. Rep2

description: Replicate 2


title: Saponin-treated_iRBCs_rep2

source_name: Human monocyte-derived macrophages, saponin-treated iRBCs, replicate 2


title: iRBCs_rep1

description: Gene expression after 2hr in human macrophages co-cultured with iRBCs

source_name: Human monocyte-derived macrophages, iRBCs, replicate 1


title: iRBCs_rep2

source_name: Human monocyte-derived macrophages, iRBCs, replicate 2


title: RBCs_rep2

description: Gene expression after 2hr in human macrophages co-cultured with RBCs

source_name: Human monocyte-derived macrophages, RBCs, replicate 2


title: Day 5 p.i. Rep4

description: Replicate 4


title: Day 5 p.i. Rep1

description: Replicate 1


title: Day 4 p.i. Rep1

description: Replicate 1


title: BPDCN sample 8

description:
SAMPLE 8
Gene expression data from acute leukemic cell samples.

value: Bone marrow/blood >65% infiltration

value: Blastic plasmacytoid dendritic cell neoplasm (BPDCN)

value: PDC


title: RBCs_rep1

source_name: Human monocyte-derived macrophages, RBCs, replicate 1


title: RBCs_rep3

source_name: Human monocyte-derived macrophages, RBCs, replicate 3


title: Day 5 p.i. Rep2

description: Replicate 2


title: Day 3 p.i. Rep4

description: Replicate 4

value: Day 3 p.i.


title: iRBCs_rep3

source_name: Human monocyte-derived macrophages, iRBCs, replicate 3


title: Day 6 p.i. Rep3

description: Replicate 3


title: Day 3 p.i. Rep2

description: Replicate 2


title: Day 3 p.i. Rep1

description: Replicate 1


title: prostate cancer 49

type: protein

city: Homburg

first: Nicole

last: Ludwig

address: Kirrberger Strasse

department: Human Genetics

institute: Saarland University

description:
Sample name: PCA9
level of autoantibodies

hyb_protocol: In brief, macroarrays were washed two times in TBSTT (TBS, 0.05% Tween 20, 0.5% Triton X-100) and four times in TBS. After blocking with 3% non-fat dry milk in TBST (TBS, 0.05% Tween 20), macroarrays were incubated over night with diluted sera (1:1000). After incubation, sera were stored for a second round of incubation. The macroarrays were subjected to three washing steps with TBST followed by incubation with 70°C stripping solution. Afterwards macroarrays were washed two times in TBST and four times in TBS. After incubation with blocking solution macroarrays were subjected to the second round of serum incubation. Macroarrays were washed three times in TBST, and incubated with secondary antibody (rabbit anti-human IgG, IgA, IgM-Cy5 (H+L), Dianova, 1:1000). Finally, macroarrays were washed four times in TBST, two times in TBS and dried overnight.

scan_protocol: Signals were detected by scanning with Typhoon 9410 scanner (GE Healthcare).

data_processing: Spot intensity values were computed by ARCADIA, an image analysis software that we developed specifically for protein array evaluation. In brief, the image of the macroarray was divided in subgrids. Those subgrids were further divided in spot areas containing one protein spot. Finally, the intensity of each spot was calculated as the mean value of all pixels of the respective protein spot. Mean value of duplicate spots was calculated for each cDNA clone.

molecule: protein

source_name: Serum

extract_protocol: serum obtained from blood

value: prostate carcinoma


title: Day 3 p.i. Rep3

description: Replicate 3

value: BALB/c


title: prostate cancer 48

description:
Sample name: pca8
level of autoantibodies

label_protocol: In brief, macroarrays were washed two times in TBSTT (TBS, 0.05% Tween 20, 0.5% Triton X-100) and four times in TBS. After blocking with 3% non-fat dry milk in TBST (TBS, 0.05% Tween 20), macroarrays were incubated over night with diluted sera (1:1000). After incubation, sera were stored for a second round of incubation. The macroarrays were subjected to three washing steps with TBST followed by incubation with 70°C stripping solution. Afterwards macroarrays were washed two times in TBST and four times in TBS. After incubation with blocking solution macroarrays were subjected to the second round of serum incubation. Macroarrays were washed three times in TBST, and incubated with secondary antibody (rabbit anti-human IgG, IgA, IgM-Cy5 (H+L), Dianova, 1:1000). Finally, macroarrays were washed four times in TBST, two times in TBS and dried overnight.


title: prostate cancer 47

description:
Sample name: PCA67
level of autoantibodies

label: rabbit anti-human IgG, IgA, IgM-Cy5 (H+L), Dianova


title: prostate cancer 46

description:
Sample name: PCA65
level of autoantibodies


title: Day 2 p.i. Rep3

description: Replicate 3

value: Day 2 p.i.

value: female


title: Day 2 p.i. Rep2

description: Replicate 2

value: lung


title: prostate cancer 44

description:
Sample name: PCA63
level of autoantibodies


title: prostate cancer 45

description:
Sample name: PCA64
level of autoantibodies


title: prostate cancer 43

description:
Sample name: PCA62
level of autoantibodies


title: Day 2 p.i. Rep1

description: Replicate 1


title: prostate cancer 42

description:
Sample name: PCA61
level of autoantibodies


title: Control day 12 rep2

description: Replicate 2

value: Control day 12


title: prostate cancer 38

description:
Sample name: PCA57
level of autoantibodies


title: prostate cancer 39

description:
Sample name: PCA58
level of autoantibodies


title: prostate cancer 41

description:
Sample name: PCA60
level of autoantibodies


title: T1437 Sp-UA.AVG_Signal

city: Oslo

first: Biljana

last: Stangeland

address: Sognsvannsveien 20

department: Institute of Surgical Research

country: Norway

institute: Oslo University Hospital

description: biological replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were imported to gene expression analysis software “JExpress” (Molmine, Bergen, Norway) http://jexpress.bioinfo.no) and  normalised using quantile normalisation

source_name: patient cells growing as spheres

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

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

tag: culture

value: Grown as spheres

tag: cell or tissue type

value: GBM sphere cultures

value: GBM sphere cultures isolated from ultrasonic aspirate (Sp-UA)

tag: biological replicate


title: prostate cancer 40

description:
Sample name: PCA59
level of autoantibodies


title: Control day 12 rep1

description: Replicate 1


title: Day 1 p.i. Rep4

description: Replicate 4

value: Day 1 p.i.


title: prostate cancer 37

description:
Sample name: PCA56
level of autoantibodies


title: T1311 Sp-UA.AVG_Signal

description: biological replicate 1


title: Day 1 p.i. Rep3

description: Replicate 3


title: T1348 Sp-Co.AVG_Signal

description: biological replicate 3

value: GBM sphere cultures isolated from core biopsy (Sp-Co)


title: T1344 Sp-Co.AVG_Signal

description: biological replicate 2


title: T1311 Sp-Co.AVG_Signal

description: biological replicate 1


title: Control day 7 rep2

description: Replicate 2

value: Control day 7


title: Day 1 p.i. Rep2

description: Replicate 2


title: T1370 Sp-Co.AVG_Signal

description: biological replicate 5


title: Day 1 p.i. Rep1

description: Replicate 1


title: Control day 7 rep1

description: Replicate 1


title: T1370 Fr_Co.AVG_Signal

description: biological replicate 4

source_name: Fresh tissues tripsinized /from glioblastoma patient

value: GBM tissue

value: Fresh GBM tissue isolated from core biopsy (Fr-Co)


title: T1402 Sp-Co.AVG_Signal

description: biological replicate 6


title: T1349 Sp-Co.AVG_Signal

description: biological replicate 4


title: prostate cancer 36

description:
Sample name: PCA55
level of autoantibodies


title: prostate cancer 35

description:
Sample name: PCA54
level of autoantibodies


title: prostate cancer 34

description:
Sample name: PCA53
level of autoantibodies


title: T1349 Fr-Co.AVG_Signal

description: biological replicate 3


title: prostate cancer 33

description:
Sample name: PCA52
level of autoantibodies


title: T1344 Fr-Co.AVG_Signal

description: biological replicate 1


title: T1348 Fr-Co.AVG_Signal

description: biological replicate 2


title: homozygote_rep4

city: Neuherberg

first: Martin

last: Irmler

state: Bayern

address: Ingolstaedter Landstrasse 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum München GmbH

description:
SAMPLE 8
replicate 4

scan_protocol: Standard Illumina scanning protocol using HiScan

data_processing: The data were normalized using cubic spline normalization with Illumina Genomestudio 2011.1; background subtraction was performed

source_name: kidney

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up with QIAGEN RNeasy midi kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with gel electrophoreses.

tag: genotype/variation

value: homozygote

tag: allele

tag: age

value: 29 weeks

tag: mouse id

tag: gender

value: male


title: homozygote_rep2

description:
SAMPLE 6
replicate 2


title: homozygote_rep3

description:
SAMPLE 7
replicate 3


title: JC24

city: Chicago

first: John

last: Crispino

state: IL

address: 303 E Superior

department: Medicine-Hematology/Oncology

institute: Northwestern University

description:
JC24_PMF 8 41+42+
SAMPLE 24

hyb_protocol: The hybridization, washing and staining of the arrays was performed according to Illumina provided protocols.

scan_protocol: The arrays were scanned using the Illumina HiScan or BeadArray Reader (Cleveland)

data_processing: The data were processed and normalised using Illumina GenomeStudio

source_name: CD34+ isolated from human blood sample

label_protocol: Biotinylated, amplified RNA for hybridization with the Illumina HT12v4 arrays was prepared using the Illumina® TotalPrep™ RNA Amplification Kit (Ambion, Cat. no: AMIL1791)

growth_protocol: Cells were maintained in IMDM supplemented with 100 U /ml penicillin/streptomycin, 2 mM l-glutamine, 76nM α-monothioglycerol, 1.5% BSA, 20 μg/ml lipids, insulin transferrin selenium and 10ng/mL of recombinant human thrombopoietin

extract_protocol: Total RNA were extracted using RNeasy Micro Kit (Qiagen) according to manufacturer's instructions. The quantity and quality of the isolated RNAs was determined using ND-1000 Spectrophotometer.

treatment_protocol: The cells were not treated in any way

value: megakaryocytes

tag: disease state

value: PMF patient


title: wild type_rep4

description:
SAMPLE 4
replicate 4

value: wild type


title: prostate cancer 31

description:
Sample name: pca47
level of autoantibodies

value: prostate carcinoma


title: prostate cancer 32

description:
Sample name: pca50
level of autoantibodies


title: JC22

description:
JC22_PMF 7 41+42+
SAMPLE 22


title: JC21

description:
JC21_PMF 9 41+42-
SAMPLE 21


title: homozygote_rep1

description:
SAMPLE 5
replicate 1


title: JC23

description:
JC23_PMF 9 41+42+
SAMPLE 23


title: prostate cancer 27

description:
Sample name: pca42
level of autoantibodies


title: prostate cancer 29

description:
Sample name: pca44
level of autoantibodies


title: prostate cancer 30

description:
Sample name: pca45
level of autoantibodies


title: JC19

description:
JC19_PMF 6 41+42-
SAMPLE 19


title: JC18

description:
JC18_PMF 5 41+42+
SAMPLE 18


title: prostate cancer 25

description:
Sample name: pca40
level of autoantibodies


title: prostate cancer 28

description:
Sample name: pca43
level of autoantibodies


title: prostate cancer 24

description:
Sample name: pca39
level of autoantibodies


title: prostate cancer 26

description:
Sample name: pca41
level of autoantibodies


title: JC16

description:
JC16_Control 4 41+42+
SAMPLE 16

value: control


title: wild type_rep1

description:
SAMPLE 1
replicate 1


title: wild type_rep2

description:
SAMPLE 2
replicate 2


title: JC17

description:
JC17_PMF 5 41+42-
SAMPLE 17


title: JC20

description:
JC20_PMF 6 41+42+
SAMPLE 20


title: prostate cancer 22

description:
Sample name: pca33
level of autoantibodies


title: prostate cancer 23

description:
Sample name: pca34
level of autoantibodies


title: JC15

description:
JC15_Control 4 41+42-
SAMPLE 15


title: prostate cancer 21

description:
Sample name: pca32
level of autoantibodies


title: JC14

description:
JC14_Control 3 41+42+
SAMPLE 14


title: JC11

description:
JC11_PMF 4 41+42-
SAMPLE 11


title: prostate cancer 20

description:
Sample name: pca31
level of autoantibodies


title: wild type_rep3

description:
SAMPLE 3
replicate 3


title: JC12

description:
JC12_PMF 4 41+42+
SAMPLE 12


title: JC13

description:
JC13_Control 3 41+42-
SAMPLE 13


title: prostate cancer 19

description:
Sample name: pca30
level of autoantibodies


title: prostate cancer 18

description:
Sample name: pca3
level of autoantibodies


title: prostate cancer 17

description:
Sample name: pca29
level of autoantibodies


title: JC10

description:
JC10_PMF 3 41+42+
SAMPLE 10


title: prostate cancer 15

description:
Sample name: pca27
level of autoantibodies


title: JC9

description:
JC9_PMF 3 41+42-
SAMPLE 9


title: prostate cancer 16

description:
Sample name: pca28
level of autoantibodies


title: genomic DNA from primary triple negative breast tumour 68 (validation)

city: New Lambton Heights

first: Kelly

last: Avery-Kiejda

state: NSW

address: Kookaburra Circuit

department: Medical Genetics

country: Australia

institute: Hunter Medical Research Institute

description: triple negative breast cancer (TNBC) invasive ductal carcinoma (IDC)

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using iScan using standard recommended Illumina scanner setting

data_processing: GenomeStudio software V2011.1

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted from FFPE samples using Qiagen Gentra Puregene Tissue Kit

value: female

tag: tumour grade

tag: age at diagnosis

tag: survival

value: dead

tag: disease specific death

value: TRUE

tag: month of follow up/to death

tag: tissue type

value: IDC


title: genomic DNA from primary triple negative breast tumour 70 (validation)


title: JC7

description:
JC7_PMF 2  41+42-
SAMPLE 7

tag: cell type


title: JC8

description:
JC8_PMF 2 41+42+
SAMPLE 8


title: JC5

description:
JC5_PMF 1 41+42-
SAMPLE 5


title: JC4

description:
JC4_Control 2 41+42+
SAMPLE 4


title: genomic DNA from primary triple negative breast tumour 65 (validation)

value: FALSE


title: JC6

description:
JC6_PMF 1 41+42+
SAMPLE 6


title: genomic DNA from primary triple negative breast tumour 69 (validation)


title: genomic DNA from primary triple negative breast tumour 67 (validation)


title: JC2

description:
JC2_Control 1 41+42+
SAMPLE 2


title: genomic DNA from primary triple negative breast tumour 64 (validation)


title: genomic DNA from primary triple negative breast tumour 63 (validation)


title: prostate cancer 13

description:
Sample name: pca24
level of autoantibodies


title: prostate cancer 10

description:
Sample name: pca21
level of autoantibodies


title: prostate cancer 12

description:
Sample name: pca23
level of autoantibodies


title: prostate cancer 11

description:
Sample name: pca22
level of autoantibodies


title: prostate cancer 9

description:
Sample name: PCA20
level of autoantibodies


title: JC3

description:
JC3_Control 2 41+42-
SAMPLE 3


title: JC1

description:
JC1_Control 1 41+42-
SAMPLE 1


title: prostate cancer 14

description:
Sample name: pca25
level of autoantibodies


title: ESC1

city: San Diego

first: Ronald

middle: L

last: Coleman

state: California

address: 3215 Merryfield Row

department: Chemical Physiology

institute: The Scripps Research Institute

data_processing: Raw data extraction was performed with Genome Studio (Illumina) and probes without a detection p-value (a measure of confidence that the signal observed is above background fluorescence) of less than 0.01 in at least 1 sample were removed. The remaining probes were then quantile-normalized to correct for between-sample variation. Normalized data were then analyzed using Qlucore Omics Explorer (Qlucore).

source_name: cell pellet

extract_protocol: RNA was extracte using the Life Technologies mirVana isolation kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: cell line source

value: ESC line

tag: cell status

value: WA09 ESC line


title: ESC2


title: iPSC2

value: pluripotent cell line

value: HDF69iPSC pluripotent cell line


title: prostate cancer 8

description:
Sample name: pca19
level of autoantibodies


title: iPSC1

value: HDF51iPSC pluripotent cell line


title: genomic DNA from primary triple negative breast tumour 60 (validation)


title: genomic DNA from primary triple negative breast tumour 61 (validation)


title: genomic DNA from primary triple negative breast tumour 59 (validation)

value: alive


title: genomic DNA from primary triple negative breast tumour 57 (validation)


title: prostate cancer 6

description:
Sample name: PCA17
level of autoantibodies


title: prostate cancer 7

description:
Sample name: pca18
level of autoantibodies


title: genomic DNA from primary triple negative breast tumour 66 (validation)


title: prostate cancer 5

description:
Sample name: pca13
level of autoantibodies


title: HDF

value: HDF

value: Human dermal fibrolast control line


title: prostate cancer 3

description:
Sample name: PCA11
level of autoantibodies


title: ebNPC3

value: neural precursor cell (NPCs) line

value: Multistep Differentiation through EB stage from HDF51iPSC line


title: eNPC6

value: Directed Differentiation from WA09 Cells


title: genomic DNA from primary triple negative breast tumour 62 (validation)


title: genomic DNA from primary triple negative breast tumour 56 (validation)


title: genomic DNA from primary triple negative breast tumour 58 (validation)


title: normal control 28

description:
Sample name: n99
level of autoantibodies

value: Normal


title: prostate cancer 1

description:
Sample name: PCA1
level of autoantibodies

value: prostate carcinoma


title: prostate cancer 4

description:
Sample name: pca12
level of autoantibodies


title: eNPC4


title: genomic DNA from primary triple negative breast tumour 51 (validation)

value: female

value: dead


title: normal control 26

description:
Sample name: n81
level of autoantibodies


title: iNPC3

value: Directed Differentiation from HDF69iPSC line


title: eNPC2


title: ebNPC2


title: ebNPC1


title: genomic DNA from primary triple negative breast tumour 55 (validation)

value: TRUE

value: IDC


title: normal control 25

description:
Sample name: n79
level of autoantibodies


title: eNPC3


title: genomic DNA from primary triple negative breast tumour 52 (validation)

description: triple negative breast cancer (TNBC) invasive ductal carcinoma (IDC)

value: FALSE


title: genomic DNA from primary triple negative breast tumour 54 (validation)


title: genomic DNA from primary triple negative breast tumour 53 (validation)


title: normal control 27

description:
Sample name: n9
level of autoantibodies


title: prostate cancer 2

description:
Sample name: PCA10
level of autoantibodies


title: normal control 24

description:
Sample name: n78
level of autoantibodies


title: genomic DNA from primary triple negative breast tumour 49 (validation)


title: eNPC5


title: genomic DNA from primary triple negative breast tumour 46 (validation)


title: 1NPC2

value: Directed Differentiation from HDF51iPSC line


title: genomic DNA from primary triple negative breast tumour 50 (validation)


title: genomic DNA from primary triple negative breast tumour 48 (validation)


title: normal control 23

description:
Sample name: n69
level of autoantibodies


title: genomic DNA from primary triple negative breast tumour 45 (validation)


title: genomic DNA from primary triple negative breast tumour 47 (validation)


title: iNPC1


title: normal control 21

description:
Sample name: n44
level of autoantibodies


title: normal control 20

description:
Sample name: n41
level of autoantibodies


title: normal control 22

description:
Sample name: n46
level of autoantibodies


title: normal control 19

description:
Sample name: n258
level of autoantibodies


title: normal control 18

description:
Sample name: n254
level of autoantibodies


title: eNPC1


title: normal control 17

description:
Sample name: n244
level of autoantibodies


title: normal control 16

description:
Sample name: n243
level of autoantibodies


title: normal control 15

description:
Sample name: n224
level of autoantibodies


title: genomic DNA from primary triple negative breast tumour 43 (validation)


title: genomic DNA from primary triple negative breast tumour 42 (validation)


title: normal control 13

description:
Sample name: n187
level of autoantibodies


title: normal control 12

description:
Sample name: n183
level of autoantibodies


title: normal control 14

description:
Sample name: n198
level of autoantibodies


title: normal control 11

description:
Sample name: n176
level of autoantibodies


title: normal control 10

description:
Sample name: n166
level of autoantibodies


title: normal control 8

description:
Sample name: n161
level of autoantibodies


title: genomic DNA from primary triple negative breast tumour 44 (validation)

description: triple negative breast cancer (TNBC) invasive ductal carcinoma (IDC)


title: genomic DNA from primary triple negative breast tumour 38 (validation)


title: normal control 9

description:
Sample name: n162
level of autoantibodies


title: normal control 7

description:
Sample name: n152
level of autoantibodies


title: genomic DNA from primary triple negative breast tumour 41 (validation)


title: normal control 5

description:
Sample name: n144
level of autoantibodies


title: genomic DNA from primary triple negative breast tumour 40 (validation)


title: normal control 4

description:
Sample name: n141
level of autoantibodies


title: normal control 3

description:
Sample name: n136
level of autoantibodies


title: genomic DNA from primary triple negative breast tumour 39 (validation)


title: genomic DNA from primary triple negative breast tumour 23 (validation)


title: genomic DNA from primary triple negative breast tumour 32 (validation)


title: genomic DNA from primary triple negative breast tumour 26 (validation)


title: genomic DNA from primary triple negative breast tumour 37 (validation)


title: genomic DNA from primary triple negative breast tumour 29 (validation)


title: genomic DNA from primary triple negative breast tumour 36 (validation)


title: genomic DNA from primary triple negative breast tumour 27 (validation)


title: genomic DNA from primary triple negative breast tumour 30 (validation)


title: genomic DNA from primary triple negative breast tumour 31 (validation)


title: genomic DNA from primary triple negative breast tumour 34 (validation)


title: BPH control 69

description:
Sample name: bph9
level of autoantibodies

value: benign prostate hyperplasia


title: genomic DNA from primary triple negative breast tumour 25 (validation)


title: normal control 2

description:
Sample name: n113
level of autoantibodies


title: genomic DNA from primary triple negative breast tumour 35 (validation)


title: genomic DNA from primary triple negative breast tumour 28 (validation)


title: normal control 1

description:
Sample name: n103
level of autoantibodies


title: genomic DNA from primary triple negative breast tumour 33 (validation)


title: BPH control 68

description:
Sample name: bph89
level of autoantibodies


title: BPH control 67

description:
Sample name: bph88
level of autoantibodies


title: genomic DNA from primary triple negative breast tumour 24 (validation)


title: mirMM.464-MM95db

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

country: Italy

institute: IRCCS Istituto Nazionale dei Tumori

description: lncRNA expression data from multiple myeloma newly-diagnosed primary tumor.

hyb_protocol: The fragmented labeled single-stranded DNA target was hybridized for 16 hours and 30 minutes at 45°C on GeneChip Gene 1.0 ST array, according to the standard Affymetrix protocol, using the GeneChip Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Scanning  of the arrays was performed using the GeneChip Scanner 7G.

data_processing: Expression data has been normalized using RMA procedure at the probe cluster ID annotation level. Cross-hybridization probes were filtered-out. We combined annotated probes with both Ensembl transcripts (GRCh37/hg19 assembly) and lncRNAs from v4 database on LNCipedia repository (http://www. lncipedia.org/), based on the chromosome localization of the target sequence identified by each probe; afterwards, we considered only probes univocally referable to lncRNA transcripts (i.e. that do not overlap with Ensembl transcripts). To summarize probes related to each lncRNA, we considered their median expression value

source_name: Newly-diagnosed MM patient 464

label_protocol: Biotinylated single stranded cDNA samples were prepared starting from 100 nanograms of purified total RNA, according to the standard Affymetrix protocol (GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual).

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

treatment_protocol: Plasma cells were purified from bone marrow samples using CD138 immunomagnetic microbeads according to the manufacturer's instructions (MidiMACS system, Miltenyi Biotec); the purity of the positively selected PCs was assessed by morphology and flow cytometry and was > 90% in all cases.

tag: diagnosis

value: multiple myeloma

tag: tissue

value: primary tumor

tag: t(4;14) translocation

value: n


title: mirMM.449-MM95db

source_name: Newly-diagnosed MM patient 449


title: BPH control 64

description:
Sample name: bph85
level of autoantibodies


title: BPH control 65

description:
Sample name: bph86
level of autoantibodies


title: BPH control 63

description:
Sample name: bph84
level of autoantibodies


title: BPH control 66

description:
Sample name: bph87
level of autoantibodies


title: mirMM.448-MM95db

source_name: Newly-diagnosed MM patient 448


title: genomic DNA from primary triple negative breast tumour 22 (validation)

value: alive


title: normal control 6

description:
Sample name: n145
level of autoantibodies


title: genomic DNA from primary triple negative breast tumour 17 (validation)

description: triple negative breast cancer (TNBC) invasive ductal carcinoma (IDC)


title: BPH control 62

description:
Sample name: bph83
level of autoantibodies


title: genomic DNA from primary triple negative breast tumour 18 (validation)


title: BPH control 61

description:
Sample name: bph82
level of autoantibodies


title: mirMM.437-MM95db

source_name: Newly-diagnosed MM patient 437


title: mirMM.447-MM95db

source_name: Newly-diagnosed MM patient 447


title: BPH control 60

description:
Sample name: bph81
level of autoantibodies


title: mirMM.435-MM95db

source_name: Newly-diagnosed MM patient 435


title: genomic DNA from primary triple negative breast tumour 19 (validation)


title: genomic DNA from primary triple negative breast tumour 21 (validation)


title: BPH control 59

description:
Sample name: bph79
level of autoantibodies


title: mirMM.434-MM95db

source_name: Newly-diagnosed MM patient 434


title: genomic DNA from primary triple negative breast tumour 20 (validation)


title: BPH control 70

description:
Sample name: bph90
level of autoantibodies


title: mirMM.433-MM95db

source_name: Newly-diagnosed MM patient 433


title: genomic DNA from primary triple negative breast tumour 14 (validation)


title: mirMM.431-MM95db

source_name: Newly-diagnosed MM patient 431

value: y


title: BPH control 57

description:
Sample name: bph75
level of autoantibodies


title: genomic DNA from primary triple negative breast tumour 9 (validation)


title: BPH control 56

description:
Sample name: bph74
level of autoantibodies


title: BPH control 58

description:
Sample name: bph77
level of autoantibodies


title: genomic DNA from primary triple negative breast tumour 11 (validation)


title: PBS-4

city: Sendai

first: Hiroshi

last: Fujii

state: MIyagi

address: Seiryo 1-1, Aoba-ku

department: Department of Hematotology and Rheumatology

institute: Tohoku University, School of Medicine

description:
PBS-4
Replicate 3

hyb_protocol: 0.6ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE 8x60K Microarray (Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: Spleen tissue, PBS

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1ug Total RNA using the Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: RNA was extracted from the spleen samples using RNAiso Plus (TaKaRa Biotech, Shiga, Japan) and cleaned up with RNeasy MiniElute Cleanup kit (QIAGEN) according to the manufacturer's instructions.

treatment_protocol: Fourteen-week-old MRL/lpr mice were injected with bortezomib (750 µg/kg, subcutaneously), cyclophosphamide (1mg/body, intraperitoneally) or PBS. The mice were sacrificed, and the spleens were removed 6 h after injecting the drugs. To clarify the change of gene expression profiling, total RNA from spleen tissues were extracted and analysed with microarray.

tag: strain/background

value: MRL/lpr

value: spleen

value: 14 weeks

tag: treatment

value: PBS


title: PBS-3

description:
PBS-3
Replicate 2

value: female

tag: age


title: Cyc-4

description:
Cyc-4
Replicate 3

source_name: Spleen tissue, cyclophosphamide

tag: gender

value: cyclophosphamide


title: mirMM.430-MM95db

source_name: Newly-diagnosed MM patient 430


title: PBS-1

description:
PBS-1
Replicate 1


title: genomic DNA from primary triple negative breast tumour 12 (validation)


title: BPH control 55

description:
Sample name: bph7
level of autoantibodies

source_name: Serum

tag: disease state


title: genomic DNA from primary triple negative breast tumour 8 (validation)

tag: tumour grade


title: genomic DNA from primary triple negative breast tumour 6 (validation)

tag: age at diagnosis

value: dead


title: mirMM.425-MM95db

source_name: Newly-diagnosed MM patient 425


title: BPH control 54

description:
Sample name: bph68
level of autoantibodies


title: genomic DNA from primary triple negative breast tumour 13 (validation)

tag: survival

value: TRUE


title: genomic DNA from primary triple negative breast tumour 15 (validation)

tag: disease specific death

value: IDC


title: genomic DNA from primary triple negative breast tumour 5 (validation)

value: FALSE

tag: month of follow up/to death


title: genomic DNA from primary triple negative breast tumour 10 (validation)

tag: tissue type


title: BPH control 53

description:
Sample name: bph67
level of autoantibodies


title: mirMM.429-MM95db

description: lncRNA expression data from multiple myeloma newly-diagnosed primary tumor.

source_name: Newly-diagnosed MM patient 429


title: mirMM.424-MM95db

source_name: Newly-diagnosed MM patient 424


title: Cyc-3

description:
Cyc-3
Replicate 2


title: mirMM.423-MM95db

source_name: Newly-diagnosed MM patient 423


title: genomic DNA from primary triple negative breast tumour 7 (validation)


title: BPH control 52

description:
Sample name: bph65
level of autoantibodies


title: PBS-6

description:
PBS-6
Replicate 4


title: Bor-4

description:
Bor-4
Replicate 4

source_name: Spleen tissue, bortezomib

value: bortezomib


title: Cyc-2

description:
Cyc-2
Replicate 1


title: mirMM.422-MM95db

source_name: Newly-diagnosed MM patient 422


title: genomic DNA from primary triple negative breast tumour 3 (validation)


title: Bor-3

description:
Bor-3
Replicate 3


title: genomic DNA from primary triple negative breast tumour 4 (validation)


title: BPH control 50

description:
Sample name: bph63
level of autoantibodies

value: benign prostate hyperplasia


title: genomic DNA from primary triple negative breast tumour 2 (validation)


title: mirMM.413-MM95db

source_name: Newly-diagnosed MM patient 413

value: multiple myeloma


title: genomic DNA from primary triple negative breast tumour 1 (validation)


title: mirMM.414-MM95db

source_name: Newly-diagnosed MM patient 414

value: primary tumor


title: BPH control 48

description:
Sample name: bph61
level of autoantibodies


title: BPH control 49

description:
Sample name: bph62
level of autoantibodies


title: mirMM.411-MM95db

source_name: Newly-diagnosed MM patient 411

value: n


title: Bor-2

description:
Bor-2
Replicate 2


title: BPH control 47

description:
Sample name: bph60
level of autoantibodies


title: Bor-1

description:
Bor-1
Replicate 1


title: genomic DNA from primary triple negative breast tumour 16 (validation)

description: triple negative breast cancer (TNBC) invasive ductal carcinoma (IDC)


title: mirMM.407-MM95db

source_name: Newly-diagnosed MM patient 407


title: WT-Treg-replicate1

city: Ichikawa

first: Takashi

last: Sekiya

state: Chiba

address: 1-7-1 Kohnodai

institute: National Center for Global Health and Medicine

description: transcriptome of wild-type Treg cells

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was hybridized to Agilent SurePrint G3 Mouse GE 8x60K microarray slide (G4852A) for 17 hours at 65°C in a rotating DNA Microarray Hybridization Oven (Agilent).  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution  3 um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 028005_D_F_20140728) to obtain background subtracted and spatially detrended Processed Signal intensities.  Global normalization, recommended by Agilent, was performed with parameters as follows: Threshold raw signals to 0, Nromalization algorithm: Percentile shift, and Shift to percentile: 75.

source_name: wild-type Treg cells, replicate1

label_protocol: Cy3 labeled cRNA was prepared from 10 ng RNA using the One Color Spike Mix Kit (Agilent) and Quick-Amp Labeling kit (for one color, Agilent), according to the One-Color Microarray-Based Gene Expression Analysis Ver 6.5 (Low Input Quick Amp Labeling), followed by RNAeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using a lysis buffer RNAiso (TaKaRa, Japan) following the manufacturer's recommendations. RNA samples were further cleaned-up with RNAeasy micro kit (QIAGEN). RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Freshly prepared CD4SP T cells from mice thymus. Cells were directly lysed in RNAiso (TAKARA, Japan), without culturing.

tag: genotype

value: wild-type

tag: cell type

value: thymic Treg cell


title: WT-Treg-replicate2

description: transcriptome of wild-type Treg cells

source_name: wild-type Treg cells, replicate2


title: mirMM.406-MM95db

source_name: Newly-diagnosed MM patient 406


title: BPH control 46

description:
Sample name: bph6
level of autoantibodies


title: mirMM.402-MM95db

source_name: Newly-diagnosed MM patient 402


title: genomic DNA from matched normal adjacent tissue Patient 2 (study)

description: triple negative breast cancer (TNBC) normal adjacent tissue (NAT)

value: NAT


title: genomic DNA from matched normal adjacent tissue Patient 1 (study)


title: BPH control 44

description:
Sample name: bph58
level of autoantibodies


title: genomic DNA from lymph node metastasis 12 (study)

description: triple negative breast cancer (TNBC) lymph node metastasis (LN)

value: LN


title: BPH control 45

description:
Sample name: bph59
level of autoantibodies


title: mirMM.398-MM95db

source_name: Newly-diagnosed MM patient 398


title: genomic DNA from matched normal adjacent tissue Patient 4 (study)


title: Foxp3-KO-preTreg-replicate1

description: transcriptome of Foxp3-KO preTreg cells

source_name: Foxp3-KO preTreg cells, replicate1

value: Treg precursor cell


title: BPH control 43

description:
Sample name: bph57
level of autoantibodies

source_name: Serum


title: mirMM.392-MM95db

source_name: Newly-diagnosed MM patient 392


title: Nr4a-TKO-preTreg-replicate1

description: transcriptome of Nr4a-TKO preTreg cells

source_name: Nr4a-TKO preTreg cells, replicate1


title: BPH control 42

description:
Sample name: bph56
level of autoantibodies


title: Foxp3-KO-preTreg-replicate2

description: transcriptome of Foxp3-KO preTreg cells

source_name: Foxp3-KO preTreg cells, replicate2


title: mirMM.387-MM95db

source_name: Newly-diagnosed MM patient 387


title: BPH control 41

description:
Sample name: bph55
level of autoantibodies


title: mirMM.385-MM95db

source_name: Newly-diagnosed MM patient 385


title: genomic DNA from lymph node metastasis 11 (study)


title: BPH control 40

description:
Sample name: bph54
level of autoantibodies


title: WT-Tconv-replicate2

description: transcriptome of wild-type thymic conventional CD4 T cells

source_name: wild-type Tconv cells, replicate2

value: thymic conventional CD4 T cells


title: genomic DNA from lymph node metastasis 10 (study)

value: female


title: mirMM.382-MM95db

description: lncRNA expression data from multiple myeloma newly-diagnosed primary tumor.

source_name: Newly-diagnosed MM patient 382


title: BPH control 51

description:
Sample name: bph64
level of autoantibodies


title: genomic DNA from lymph node metastasis 9 (study)


title: mirMM.375-MM95db

source_name: Newly-diagnosed MM patient 375

value: y


title: BPH control 38

description:
Sample name: bph52
level of autoantibodies


title: CD8+ TC-Treated-B6#4 26/10/12

city: Paris

first: Sylvaine

last: You

address: Hôpital Necker, Bâtiment Hamburger, 5ème étage, 149  rue de Sèvres

department: Immunology

institute: INSERM U1151 - University Paris Descartes

hyb_protocol: The Cy3+labeled cDNAs were hybridized overnight to the  Agilent Mouse Genome Oligo Microarrays 8x60k..

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (Agilent Technologies).

data_processing: The Agilent Feature Extraction Software (FES) was used to read out and process the microarray image files. FES derived output data files were further analyzed using the Rosetta Resolver gene expression data analysis system

source_name: Graft-infiltrating CD8+ T cells-Treated-B6#4 26/10/12

label_protocol: cDNAs were used as template for Cy3 labeling.

extract_protocol: SuperAmp RNA amplification was performed according to Miltenyi Biotec's undisclosed procedure. mRNA was isolated via magnetic bead technology. Amplified cDNA were quantified and DNA integrity was checked

treatment_protocol: Cell samples were lysed using SuperAmp Lysis Buffer.

value: pancreatic islet allograft

value: CD8+ T cells

value: CD3 antibody-treated


title: mirMM.362-MM95db

source_name: Newly-diagnosed MM patient 362


title: genomic DNA from lymph node metastasis 7 (study)


title: BPH control 37

description:
Sample name: bph51
level of autoantibodies


title: genomic DNA from lymph node metastasis 6 (study)


title: CD8+ TC-Treated-B6#6 08/10/12

source_name: Graft-infiltrating CD8+ T cells-Treated-B6#6 08/10/12


title: WT-Tconv-replicate1

source_name: wild-type Tconv cells, replicate1


title: Nr4a-TKO-preTreg-replicate2

description: transcriptome of Nr4a-TKO preTreg cells

source_name: Nr4a-TKO preTreg cells, replicate2


title: genomic DNA from lymph node metastasis 8 (study)


title: CD8+ TC-Treated-B6#3 17/10/12

source_name: Graft-infiltrating CD8+ T cells-Treated-B6#3 17/10/12


title: genomic DNA from lymph node metastasis 5 (study)


title: mirMM.340-MM95db

source_name: Newly-diagnosed MM patient 340


title: CD8+ TC-Treated-B6#5 08/10/12

source_name: Graft-infiltrating CD8+ T cells-Treated-B6#5 08/10/12


title: genomic DNA from matched normal adjacent tissue Patient 3 (study)


title: BPH control 36

description:
Sample name: bph50
level of autoantibodies

source_name: Serum


title: mirMM.335-MM95db

source_name: Newly-diagnosed MM patient 335


title: BPH control 35

description:
Sample name: BPH5
level of autoantibodies


title: genomic DNA from lymph node metastasis 4 (study)


title: CD8+ TC-Treated-B6#3 08/10/12

source_name: Graft-infiltrating CD8+ T cells-Treated-B6#3 08/10/12


title: mirMM.330-MM95db

source_name: Newly-diagnosed MM patient 330


title: genomic DNA from lymph node metastasis 3 (study)


title: mirMM.327-MM95db

source_name: Newly-diagnosed MM patient 327


title: mirMM.321-MM95db

source_name: Newly-diagnosed MM patient 321


title: BPH control 39

description:
Sample name: bph53
level of autoantibodies


title: genomic DNA from lymph node metastasis 2 (study)


title: BPH control 32

description:
Sample name: bph44
level of autoantibodies


title: mirMM.317-MM95db

source_name: Newly-diagnosed MM patient 317


title: BPH control 33

description:
Sample name: bph47
level of autoantibodies


title: CD8+ TC-Treated-B6#3 01/08/12

source_name: Graft-infiltrating CD8+ T cells-Treated-B6#3 01/08/12


title: genomic DNA from primary triple negative breast tumour 22 (study)

description: triple negative breast cancer (TNBC) invasive ductal carcinoma (IDC)

value: IDC


title: CD8+ TC-Treated-B6#2 01/08/12

source_name: Graft-infiltrating CD8+ T cells-Treated-B6#2 01/08/12


title: BPH control 31

description:
Sample name: bph43
level of autoantibodies


title: genomic DNA from lymph node metastasis 1 (study)

description: triple negative breast cancer (TNBC) lymph node metastasis (LN)


title: mirMM.313-MM95db

source_name: Newly-diagnosed MM patient 313


title: mirMM.314-MM95db

source_name: Newly-diagnosed MM patient 314


title: CD8+ TC-Untreated-B6#3 26/10/12

source_name: Graft-infiltrating CD8+ T cells-Untreated-B6#3 26/10/12

value: Untreated


title: genomic DNA from primary triple negative breast tumour 23 (study)


title: genomic DNA from primary triple negative breast tumour 21 (study)


title: CD8+ TC-Untreated-B6#5 26/10/12

source_name: Graft-infiltrating CD8+ T cells-Untreated-B6#5 26/10/12


title: BPH control 30

description:
Sample name: bph42
level of autoantibodies

value: benign prostate hyperplasia


title: BPH control 29

description:
Sample name: bph41
level of autoantibodies


title: CD8+ TC-Treated-B6#5 17/09/12

source_name: Graft-infiltrating CD8+ T cells-Treated-B6#5 17/09/12


title: BPH control 28

description:
Sample name: bph39
level of autoantibodies


title: CD8+ TC-Untreated-B6#6 26/10/12

source_name: Graft-infiltrating CD8+ T cells-Untreated-B6#6 26/10/12


title: CD8+ TC-Untreated-B6#4 26/10/12

source_name: Graft-infiltrating CD8+ T cells-Untreated-B6#4 26/10/12


title: mirMM.310-MM95db

source_name: Newly-diagnosed MM patient 310

value: multiple myeloma


title: genomic DNA from primary triple negative breast tumour 19 (study)


title: genomic DNA from primary triple negative breast tumour 20 (study)


title: mirMM.308-MM95db

source_name: Newly-diagnosed MM patient 308

value: primary tumor


title: mirMM.301-MM95db

source_name: Newly-diagnosed MM patient 301

value: n


title: BPH control 27

description:
Sample name: bph38
level of autoantibodies

source_name: Serum


title: CD8+ TC-Untreated-B6#6 15/10/12

source_name: Graft-infiltrating CD8+ T cells-Untreated-B6#6 15/10/12


title: BPH control 26

description:
Sample name: bph37
level of autoantibodies


title: CD8+ TC-Untreated-B6#5 15/10/12

source_name: Graft-infiltrating CD8+ T cells-Untreated-B6#5 15/10/12


title: mirMM.295-MM95db

description: lncRNA expression data from multiple myeloma newly-diagnosed primary tumor.

source_name: Newly-diagnosed MM patient 295


title: mirMM.286-MM95db

source_name: Newly-diagnosed MM patient 286


title: BPH control 25

description:
Sample name: bph36
level of autoantibodies


title: BPH control 23

description:
Sample name: bph34
level of autoantibodies


title: BPH control 22

description:
Sample name: bph30
level of autoantibodies


title: CD8+ TC-Untreated-B6#2 15/10/12

source_name: Graft-infiltrating CD8+ T cells-Untreated-B6#2 15/10/12


title: BPH control 24

description:
Sample name: bph35
level of autoantibodies


title: mirMM.282-MM95db

source_name: Newly-diagnosed MM patient 282


title: BPH control 34

description:
Sample name: bph48
level of autoantibodies


title: BPH control 21

description:
Sample name: BPH3
level of autoantibodies


title: CD8+ TC-Untreated-B6#1 15/10/12

source_name: Graft-infiltrating CD8+ T cells-Untreated-B6#1 15/10/12


title: genomic DNA from primary triple negative breast tumour 17 (study)


title: mirMM.300-MM95db

source_name: Newly-diagnosed MM patient 300


title: genomic DNA from primary triple negative breast tumour 16 (study)


title: BPH control 20

description:
Sample name: bph29
level of autoantibodies


title: genomic DNA from primary triple negative breast tumour 15 (study)


title: genomic DNA from primary triple negative breast tumour 14 (study)


title: mirMM.280-MM95db

source_name: Newly-diagnosed MM patient 280


title: mirMM.278-MM95db

source_name: Newly-diagnosed MM patient 278


title: mirMM.274-MM95db

source_name: Newly-diagnosed MM patient 274


title: BPH control 19

description:
Sample name: bph28
level of autoantibodies


title: mirMM.269-MM95db

source_name: Newly-diagnosed MM patient 269


title: genomic DNA from primary triple negative breast tumour 13 (study)

description: triple negative breast cancer (TNBC) invasive ductal carcinoma (IDC)


title: mirMM.268-MM95db

source_name: Newly-diagnosed MM patient 268


title: BPH control 18

description:
Sample name: bph27
level of autoantibodies


title: 6myc-RIO1-alfa factor_SUP

city: Milan

first: Peter

last: De Wulf

address: via Adamello 16

department: Department of Experimental Oncology

institute: European Institute of Oncology

description: 6myc-RIO1 cells were grown in YPD medium (24°C) till an OD=0.3 and then treated for 3h with 5 μg/ml α−factor to arrest them in G1 (>95%).

hyb_protocol: Labelled probes were hybridized to Affymetrix S.cerevisiae whole genome tiling R arrays

scan_protocol: Arrays were scanned on an Affymetrix Scanner

data_processing: Bed files were produced with Tiling Array Suite 1.1 from the command line with these options: tilecore -analysis -bpmap Sc03b_MR_v04.bpmap -type 1 -n 1 -nt 1 -export 1 -output_type 0 -format_type 1 -band 150 -pval_scale 0 -sig_scale 2 -tail_type 1 -nscale 1 -tgt 500 [files]

organism: Saccharomyces cerevisiae

source_name: Treatment with α−factor (3h, 5 μg/ml).

label_protocol: Synthesis of cDNA, IVT amplification, and labeling were carried out following the Affymetrix GeneChip Expression Anaysis protocol.

growth_protocol: Cells were grown in YPD medium at 24°C.

extract_protocol: Extraction was performed as described in Bermejo R. et al., Meth. Mol. Biol. 582: 103-18 (2009).

treatment_protocol: Cells were synchronised in G1 following treatment with α−factor (3h, 5 μg/ml) or in metaphase following treatment with nocodazole (3h, 15 μg/ml) in YPD medium at 24°C.

tag: antibody

tag: strain

value: W303, 6myc-RIO1


title: 6myc-RIO1-nocodazole_SUP

description: 6myc-RIO1 cells were grown in YPD medium (24°C) till an OD=0.3 and then treated for 3h with 15 μg/ml nocodazole to arrest them in metaphase (>95%).

source_name: Treatment with nocodazole (3h, 15 μg/ml).


title: genomic DNA from primary triple negative breast tumour 11 (study)


title: genomic DNA from primary triple negative breast tumour 12 (study)


title: BPH control 16

description:
Sample name: bph24
level of autoantibodies


title: BPH control 17

description:
Sample name: bph25
level of autoantibodies


title: 6myc-RIO1-nocodazole_IP

value: anti-myc 9E10 antibody (Covance, USA)


title: mirMM.267-MM95db

source_name: Newly-diagnosed MM patient 267

tag: diagnosis

tag: tissue


title: BPH control 15

description:
Sample name: bph23
level of autoantibodies

source_name: Serum


title: mirMM.263-MM95db

source_name: Newly-diagnosed MM patient 263

tag: t(4;14) translocation


title: RIO1-cycling_SUP

description: Wild-type cells were grown in YPD medium (24°) till an OD=1.0.

source_name: No treatment.


title: 6myc-RIO1-alfa factor_IP


title: BPH control 14

description:
Sample name: bph22
level of autoantibodies


title: BPH control 13

description:
Sample name: bph21
level of autoantibodies


title: RIO1-cycling_IP


title: genomic DNA from primary triple negative breast tumour 10 (study)


title: mirMM.262-MM95db

description: lncRNA expression data from multiple myeloma newly-diagnosed primary tumor.

source_name: Newly-diagnosed MM patient 262


title: mirMM.261-MM95db

source_name: Newly-diagnosed MM patient 261


title: mirMM.253-MM95db

source_name: Newly-diagnosed MM patient 253


title: genomic DNA from primary triple negative breast tumour 8 (study)


title: genomic DNA from primary triple negative breast tumour 7 (study)


title: mirMM.243-MM95db

source_name: Newly-diagnosed MM patient 243


title: BPH control 12

description:
Sample name: bph20
level of autoantibodies


title: BPH control 11

description:
Sample name: BPH2
level of autoantibodies


title: genomic DNA from primary triple negative breast tumour 9 (study)


title: mirMM.229-MM95db

source_name: Newly-diagnosed MM patient 229


title: BPH control 10

description:
Sample name: bph19
level of autoantibodies


title: mirMM.239-MM95db

source_name: Newly-diagnosed MM patient 239


title: BPH control 9

description:
Sample name: bph18
level of autoantibodies


title: mirMM.302-MM95db

source_name: Newly-diagnosed MM patient 302


title: BPH control 8

description:
Sample name: bph17
level of autoantibodies


title: genomic DNA from primary triple negative breast tumour 5 (study)


title: genomic DNA from primary triple negative breast tumour 4 (study)


title: genomic DNA from primary triple negative breast tumour 3 (study)


title: tetraploid hepatocyte, biological rep2

city: Boston

first: Shang-Yi

last: Chiu

state: MA

address: 44 Binney St.

institute: Dana-Farber Cancer Institute

description: Gene expression data from tetraploid hepatocyte.

hyb_protocol: Fragmented cRNA were hybridized on Mouse Genome 430A v2.0 chips, washed and stained using phycoerythrin-conjugated streptavidin (SAPE) by the DFCI Microarray Core Facility.

scan_protocol: Chip scanning was performed by the DFCI Microarray Core Facility.

data_processing: Dana were normalized using RMA with ExpressionFileCreator module from GenePattern (Broad Institute) with default setting.

source_name: tetraploid hepatocyte from mouse rep2

label_protocol: Biotinylated cRNA were prepared by the DFCI Microarray Core Facility according to the standard Affymetrix protocol.

growth_protocol: Wild type animals with standard housing and care conditions (following institutional guidelines established by the Dana-Farber Cancer Institute) were used.

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

treatment_protocol: Fresh isolated primary hepatocytes were stained with Hoechst 33342 and FACS sorted into diploid and tetraploid fractions.  Cells were subject to RNA extraction right after sorting.

value: liver

value: hepatocyte

tag: ploidy

value: tetraploid

tag: genetic background

value: C57BL/6 wild type

value: 3 week old


title: mirMM.219-MM95db

source_name: Newly-diagnosed MM patient 219


title: tetraploid hepatocyte, biological rep1

source_name: tetraploid hepatocyte from mouse rep1

tag: age


title: mirMM.213-MM95db

source_name: Newly-diagnosed MM patient 213


title: BPH control 7

description:
Sample name: bph16
level of autoantibodies

tag: disease state


title: BPH control 6

description:
Sample name: bph15
level of autoantibodies


title: genomic DNA from primary triple negative breast tumour 6 (study)

description: triple negative breast cancer (TNBC) invasive ductal carcinoma (IDC)

tag: gender

value: female

tag: tumour grade


title: mirMM.212-MM95db

source_name: Newly-diagnosed MM patient 212


title: mirMM.206-MM95db

source_name: Newly-diagnosed MM patient 206

value: y


title: BPH control 5

description:
Sample name: bph14
level of autoantibodies


title: genomic DNA from primary triple negative breast tumour 18 (study)


title: genomic DNA from primary triple negative breast tumour 2 (study)


title: genomic DNA from primary triple negative breast tumour 1 (study)


title: mirMM.177-MM95db

source_name: Newly-diagnosed MM patient 177


title: tetraploid hepatocyte, biological rep3

source_name: tetraploid hepatocyte from mouse rep3


title: BPH control 4

description:
Sample name: bph12
level of autoantibodies

source_name: Serum


title: mirMM.159-MM95db

source_name: Newly-diagnosed MM patient 159


title: mirMM.179-MM95db

source_name: Newly-diagnosed MM patient 179


title: mirMM.154-MM95db

source_name: Newly-diagnosed MM patient 154


title: mirMM.143-MM95db

source_name: Newly-diagnosed MM patient 143


title: BPH control 3

description:
Sample name: bph11
level of autoantibodies


title: mirMM.131-MM95db

source_name: Newly-diagnosed MM patient 131


title: BPH control 1

description:
Sample name: BPH1
level of autoantibodies


title: BPH control 2

description:
Sample name: bph10
level of autoantibodies


title: diploid hepatocyte, biological rep1

description: Gene expression data from diploid hepatocyte.

source_name: diploid hepatocyte from mouse rep1

value: diploid


title: diploid hepatocyte, biological rep2

source_name: diploid hepatocyte from mouse rep2


title: mirMM.115-MM95db

source_name: Newly-diagnosed MM patient 115


title: mirMM.104-MM95db

source_name: Newly-diagnosed MM patient 104


title: diploid hepatocyte, biological rep3

source_name: diploid hepatocyte from mouse rep3


title: mirMM.087-MM95db

source_name: Newly-diagnosed MM patient 087


title: Blood_Bo_B2_7W_rep2

city: shanghai

first: yang

middle: jian

last: mei

address: minhang district ziyue road No.518

country: China

institute: shanghai veterinary research institute

description: Gene expression profile of peripheral blood from buffalo infected with scistosoma japonicum 49d, replicate 2

hyb_protocol: Each Slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.

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

data_processing: The scanned images were analyzed with Feature Extraction software (Agilent technologies, Santa Clara, CA, US)with default settings.

organism: Bubalus bubalis

source_name: Peripheral Blood from Buffalo infected with schistosoma japonicum,49d

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

growth_protocol: Peripheral blood were collected from the jugular vein of cattle,buffalo,1-2 year old,healthy,were kept in non-infected areas.And cercariae were provided by Jiangsu Institute of Schistosomiasis Control

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: Cattle and buffalo were infected with cercariae by back patch.Before infection and after infection with 49d ,we collected peripheral blood from tha animals, and treated with TRIZOL Reagent as quickly as possible.

tag: infection time

value: whole blood


title: Blood_Bo_B1_7W_rep1

description: Gene expression profile of peripheral blood from buffalo infected with scistosoma japonicum 49d, replicate 1


title: Blood_Bo_B2_0W_rep2

description: Gene expression profile of peripheral blood from buffalo before infected with scistosoma japonicum, replicate 2

source_name: Peripheral Blood from Buffalo before infected with schistosoma japonicum


title: Blood_Bo_B3_7W_rep3

description: Gene expression profile of peripheral blood from buffalo infected with scistosoma japonicum 49d, replicate 3


title: Blood_Bo_B3_0W_rep3

description: Gene expression profile of peripheral blood from buffalo before infected with scistosoma japonicum, replicate 3


title: Blood_Bo_B1_0W_rep1

description: Gene expression profile of peripheral blood from buffalo before infected with scistosoma japonicum, replicate 1


title: Blood_Bo_C3_7W_rep3

description: Gene expression profile of peripheral blood from cattle infected with scistosoma japonicum 49d, replicate 3

organism: Bos taurus

source_name: Peripheral Blood from Cattle infected with schistosoma japonicum,49d


title: Blood_Bo_C2_7W_rep2

description: Gene expression profile of peripheral blood from cattle infected with scistosoma japonicum 49d, replicate 2


title: mirMM.074-MM95db

description: lncRNA expression data from multiple myeloma newly-diagnosed primary tumor.

source_name: Newly-diagnosed MM patient 074


title: mirMM.078-MM95db

source_name: Newly-diagnosed MM patient 078


title: mirMM.069-MM95db

source_name: Newly-diagnosed MM patient 069


title: Blood_Bo_C1_7W_rep1

description: Gene expression profile of peripheral blood from cattle infected with scistosoma japonicum 49d, replicate 1


title: mirMM.056-MM95db

source_name: Newly-diagnosed MM patient 056


title: mirMM.055-MM95db

source_name: Newly-diagnosed MM patient 055


title: mirMM.123-MM95db

source_name: Newly-diagnosed MM patient 123


title: mirMM.052-MM95db

source_name: Newly-diagnosed MM patient 052


title: mirMM.050-MM95db

source_name: Newly-diagnosed MM patient 050


title: mirMM.049-MM95db

source_name: Newly-diagnosed MM patient 049


title: mirMM.043-MM95db

source_name: Newly-diagnosed MM patient 043


title: Blood_Bo_C2_0W_rep2

description: Gene expression profile of peripheral blood from cattle before infected with scistosoma japonicum, replicate2

source_name: Peripheral Blood from Cattle before infected with schistosoma japonicum


title: mirMM.066-MM95db

source_name: Newly-diagnosed MM patient 066


title: mirMM.042-MM95db

source_name: Newly-diagnosed MM patient 042


title: mirMM.040-MM95db

source_name: Newly-diagnosed MM patient 040


title: mirMM.036-MM95db

source_name: Newly-diagnosed MM patient 036


title: Blood_Bo_C3_0W_rep3

description: Gene expression profile of peripheral blood from cattle before infected with scistosoma japonicum, replicate3


title: mirMM.039-MM95db

source_name: Newly-diagnosed MM patient 039


title: Blood_Bo_C1_0W_rep1

description: Gene expression profile of peripheral blood from cattle before infected with scistosoma japonicum, replicate 1


title: L-55-L5

city: Castellón

first: Josep

middle: A

last: Calduch-Giner

address: Ribera de Cabanes

country: Spain

institute: Institute of Aquaculture Torre de la Sal (CSIC)

hyb_protocol: Each cRNA sample (1.65 µg) was hybridized to the Microarray at 65 ºC for 17 h using Agilent GE hybridization kit

scan_protocol: Arrays were scanned with Agilent scanner G2505B

data_processing: Spot intensities and other quality control features were extracted with Agilent Feature Extraction software version 10.4.0.0, and was further analyzed, including percentile shift normalization, one-way ANOVA, principal components analysis and k-means clustering of differentially expressed genes, by means of GeneSpring GX 13.0 software (Agilent)

organism: Sparus aurata

source_name: 55 ‰ salinity_Liver

label_protocol: Total RNA (100 ng) from individual fish were labelled with cyanine 3-CTP (Low Input Quick Amp Labelling Kit, Agilent) along with Agilent One-color RNA SpikeIn kit

extract_protocol: Total RNA was extracted using the NucleoSpin®RNA II kit (Macherey-Nagel) according to manufacturer's instructions. Tissue samples were incubated with RNase free DNase during 30 min at 37 °C to eliminate potential genomic DNA contamination.

value: male

tag: developemental stage

value: Immature; 80-100 g body mass

tag: sample group

value: high salinity water (HSW; hyperosmotic environment)

tag: exposed to

value: 55 ‰ salinity

value: Liver


title: L-55-L3


title: mirMM.035-MM95db

source_name: Newly-diagnosed MM patient 035

value: multiple myeloma

value: primary tumor

value: n


title: mirMM.030-MM95db

source_name: Newly-diagnosed MM patient 030


title: L-40-L5

source_name: 40 ‰ salinity_Liver

value: 40 ‰ salinity


title: L-55-L2


title: mirMM.027-MM95db

source_name: Newly-diagnosed MM patient 027


title: L-40-L4

value: seawater (SW); control group


title: L-40-L2


title: mirMM.034-MM95db

source_name: Newly-diagnosed MM patient 034


title: mirMM.021-MM95db

source_name: Newly-diagnosed MM patient 021


title: mirMM.016-MM95db

source_name: Newly-diagnosed MM patient 016


title: mirMM.025-MM95db

source_name: Newly-diagnosed MM patient 025


title: L-40-L1


title: L-55-L1


title: mirMM.015-MM95db

source_name: Newly-diagnosed MM patient 015


title: L-40-L3


title: L-05-L1

source_name: 5 ‰ salinity_Liver

value: low salinity water (LSW; hypo-osmotic environment)

value: 5 ‰ salinity


title: L-05-L3


title: H-55-H3

source_name: 55 ‰ salinity_Hypothalamus

value: Hypothalamus


title: mirMM.026-MM95db

source_name: Newly-diagnosed MM patient 026


title: H-40-H5

source_name: 40 ‰ salinity_Hypothalamus


title: H-55-H2


title: H-55-H1


title: H-40-H2


title: H-40-H4


title: L-05-L2


title: H-55-H5


title: mirMM.004-MM95db

source_name: Newly-diagnosed MM patient 004


title: H-40-H3


title: H-05-H3

source_name: 5 ‰ salinity_Hypothalamus


title: H-05-H1


title: H-05-H2


title: G-55-G5

source_name: 55 ‰ salinity_Gill

value: Gill


title: MCF12A control for soft agar selected

city: Torrance

first: Robert

last: Gelfand

state: CA

address: 1124 W. Carson St

department: surgery

institute: LABiomed at Harbor UCLA,  and Charles Drew Univ

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing:
Samples were analyzed using the Affymetrix protocols and data are presented as rma values.
RMA is an arbitrary value for relative gene expression calculated using normalization and control values.

source_name: MCF12A monolayer

label_protocol: Samples were transferred to the UCLA DNA Microarray core facility (1 week exposures) or to the UCLA Pathology Lab (4 week exposures) and analyzed by Affymetrix human Gene 1.0 ST (1 week exposures) or Affymetrix human Gene 1.1 ST (4 week exposures) according to Affymetrix guidelines.

growth_protocol: MCF12A Cells obtained from the American Type Culture Collection (ATCC) were grown in 6 well plastic culture plates in DMEM/F12 plus antibiotic/antimycotic in the presence of 2.5% horse serum supplemented with epidermal growth factor, hydrocortisone, bovine insulin, and cholera toxin. Cells were passaged when they reached 80% confluence.

extract_protocol: For DNA microarray analysis, cells were washed with phosphate buffered saline, pH 7.4, and RNA was extracted using the RNeasy Plus Micro kit. For microRNA analysis, cells were washed with phosphate buffered saline pH 7.4 and RNA was extracted using the miRVana kit.

treatment_protocol: Cells were exposed to 25 mM ethanol or 2.5 mM acetaldehyde for 1 week, following which RNA was extracted. In other experiments, cells were cultured for 4 weeks either in the presence of 2.5% ethanol or 1% acetaldehyde. In one experiment, cells were selected for their ability to grow in soft agar, following which a cellular clone was grown on 6 well plates for further experimental exposure to ethanol and RNA extraction.

tag: cell line

value: human breast cultures

value: none (control)

tag: selected on

value: soft agar


title: G-55-G3

value: male


title: MCF12A cont2 for acetaldehyde expt

description:
control for 1 week acetaldehyde
MCF12A cont2

tag: cell type


title: G-55-G2

value: Immature; 80-100 g body mass


title: G-55-G4

value: high salinity water (HSW; hyperosmotic environment)


title: MCF12A cont1 for ethanol expt

description:
control 1 for 1 week etoh
MCF12A cont1


title: MCF12A soft agar selected ethanol

description: SA

value: 2.5% ethanol  for 4 wks


title: A1843

city: Guangzhou

first: YE

last: SONG

state: Guangdong

address: 1838 Guangzhoudadaobei Road

department: Department of Neurosurgery

institute: Nanfang Hospital, Southern Medical University

description: Gene expression data from normal brain tissue samples

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45℃ on the Affymetrix GeneChip Hybridization Oven. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: Affymetrix GeneChip Scanner 3000 was used to scan the genechips.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain raw data. Raw data were normalized in quantile algorithm with Genespring 13.0(Agilent). Differentially expressed genes were identified when the gene expression ratio between the normal control group and cancer group was more than 2-fold and the P-value was under 0.05.    The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain raw data. Raw data were normalized in quantile algorithm with Genespring 13.0(Agilent). Differentially expressed genes were identified when the gene expression ratio between the normal control group and cancer group was more than 2-fold and the P-value is under 0.05.    The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain raw data. Raw data were normalized in quantile algorithm with Genespring 13.0(Agilent). Differentially expressed genes were identified when the gene expression ratio between the normal control group and cancer group was more than 2-fold and the P-value is under 0.05.

source_name: normal brain tissue samples from epilepsy surgery 9

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (GeneChip 3’IVT Express Kit, Affymetrix).

extract_protocol: Trizol(Invitrogen, Carlsbad, CA) extraction of total RNA was performed according to the manufacturer's instructions.

value: normal brain


title: A2269

source_name: normal brain tissue samples from epilepsy surgery 6


title: G-40-G3

source_name: 40 ‰ salinity_Gill


title: G-40-G5


title: A1839

source_name: normal brain tissue samples from epilepsy surgery 8


title: A2266

source_name: normal brain tissue samples from epilepsy surgery 5


title: MCF12A Etoh 1 week

description:
1 week etoh exposure
MCF12A Etoh

value: 25 mM ethanol for 1 wk


title: MCF12A Acetaldehyde 1 week

description:
1 week acetaldehyde
MCF12A Acet

value: 2.5 mM acetaldehyde for 1 week


title: A1831

source_name: normal brain tissue samples from epilepsy surgery 7


title: G-55-G1

value: 55 ‰ salinity


title: G-40-G2

value: 40 ‰ salinity


title: monocytes-control-15

city: Jerusalem

first: Michelle

last: Grunin

address: Hadassah Ein Kerem Medical Center

department: Ophthalmology

country: Israel

institute: Hadassah-Hebrew University Medical Center

description: gene expression data-Affymetrix Gene 1.0 ST array

hyb_protocol: Following fragmentation, 5.5µg of Biotinylated ssDNA were hybridized for 17 hrs at 45 degrees Celsius on the GeneChip Human 1.0 ST Array.

scan_protocol: The GeneChips were washed and stained in the Affymetrix Fluidic Station 450. GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: Processing was performed with Partek, using RMA values, default analysis settings.

source_name: total blood monocytes, age-matched control

label_protocol: Amplified and biotinylated sense-strand DNA were prepared according to the standard Affymetrix protocol from 200ng total RNA (Expression Analysis Technical Manual, 2005, Affymetrix).

extract_protocol: Total monocyte mRNA was extracted via TriReagent (Sigma), and cleaned using MiniElute columns (Quiagen). RNA Integrity Number (RIN) was evaluated using the Agilent Bioanalzer (RIN>8).

treatment_protocol: Peripheral blood mononuclear cells were separated using Histopaque (Sigma) separation, and total blood monocytes including the CD16+ positive monocytes were separated using negative selection via magnetic beads (Stemcell Technologies).

value: healthy


title: H-55-H4


title: A2267

source_name: normal brain tissue samples from epilepsy surgery 4


title: A2262

source_name: normal brain tissue samples from epilepsy surgery 2


title: A2263

source_name: normal brain tissue samples from epilepsy surgery 3


title: G-40-G1

value: seawater (SW); control group


title: monocytes-control-13


title: Cloning of FLAG-dmDis3l2-CM-associated RNA_39894

type: SRA

city: Vienna

first: Thomas

middle: Rainer

last: Burkard

address: Dr. Bohrgasse 7

country: Austria

institute: IMBA

library_source: transcriptomic

data_processing:
Only the second read of a pair was used. The random 4mers on the 5' were removed with fastx_trimmer of the fastx-toolkit (v0.0.13). The sequences were reverse complemented. The reads were aligned with tailor (v1.1) with a minimal prefix match length of 18 and a mismatch allowed in the middle of the query. Counts were calculated with htseq-count (v0.6.1p1). The parameters were stranded=yes and  “intersection-nonempty”. A GTF containing the FlyBase r5.57 annotation supplemented with cisNATs and structured loci was used. The pre-miRNA annotation was split in two halves assigned to 5' and 3' of each miRNA region, respectively. Reads with multiple alignments were counted as their fraction to each location/feature. Feature types are summarized by following hierarchy (AS = antisense): mitochondrial mapping, rRNA, rRNA_AS, tRNA, tRNA_AS, pre_miRNA_5p3p, pre_miRNA_5p3p_AS, pre_miRNA, pre_miRNA_AS, transposable_element, transposable_element_AS, __no_feature, cisNATs, cisNATs_AS, structured_loci, structured_loci_AS, pseudogene, pseudogene_AS, ncRNA, ncRNA_AS, snoRNA, snoRNA_AS, snRNA, snRNA_AS, mRNA, mRNA_AS, intron, intron_AS.
Genome_build: Flybase r5.57
Supplementary_files_format_and_content: TXT (RPM): tab separated text containing 4mer and it's RPM (read per million); TXT (SEQCNT) tab separated text file containing alignment position, feature, tail statistics and count; XLSX: Excel file containing summary statistics (length, nt count, nt count from 3' to 5')

organism: Drosophila melanogaster

source_name: RNA associated with FLAG-dmDi3l2-CM expressed in Drosophila S2 cells

extract_protocol: Immunopurification of FLAG-dmDis3l2-CM for 4 h in the presence of 10 mM EDTA, followed by RNA extraction and 3´ adpter ligation; library generation using Lexogen FLEX Kit (Lexogen, Vienna, Austria)

tag: strain

tag: genotype/variation

value: stably expressing FLAG-dmDis3l2-CM under Actin5C promoter

tag: molecule subtype

value: RNA associated with dmDis3l2-CM


title: G-05-G5

source_name: 5 ‰ salinity_Gill

value: low salinity water (LSW; hypo-osmotic environment)

value: 5 ‰ salinity

tag: tissue

value: Gill


title: monocytes-control-11


title: monocytes-control-14


title: monocytes-control-10


title: monocytes-control-12


title: A2261

source_name: normal brain tissue samples from epilepsy surgery 1


title: A2260

description: Gene expression data from glioblastoma tissue

source_name: glioblastoma tissue 9

value: glioblastoma


title: A1838

source_name: glioblastoma tissue 6


title: monocytes-control-8


title: A1840

source_name: glioblastoma tissue 7


title: monocytes-control-9


title: G-05-G1

value: male


title: A1841

source_name: glioblastoma tissue 8


title: A1829

source_name: glioblastoma tissue 4


title: G-05-G3

value: Immature; 80-100 g body mass


title: monocytes-control-6


title: A1822

source_name: glioblastoma tissue 5


title: monocytes-control-5


title: HepG2-Bcl-2 cell lines

city: Tianjin

first: baocun

last: sun

address: No.22 Qixiangtai Road, Heping District

department: Department of Pathology

institute: Tianjin Medical University

description: Raw data file: sample 3+4.txt

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

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

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

source_name: HepG2 hepatocellular carcinoma cell line transfected with pcDNA-Bcl-2 plasmid

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

extract_protocol: Total RNA from each sample was extracted using TRK1001 (LC Sciences, Cat. TRK-1001, Total RNA Purification Kit) according to the manufacturer's procedure. Total RNA was quantified by the NanoDrop ND-2000 (Thermo Scientific) and the RNA integrity was assessed using Agilent Bioanalyzer 2100 (Agilent Technologies).

tag: transfection construct

value: pcDNA-Bcl-2 plasmid


title: monocytes-control-7


title: HepG2-Twist1_Bcl-2 cell lines

description: Raw data file: sample 3+4.txt

source_name: HepG2 hepatocellular carcionma cell line co-transfected withTwist1/Bcl-2 plasmids

value: pcDNA-Twist1 plasmid and pcDNA-Bcl-2 plasmid


title: monocytes-control-4


title: B. subtilis 168 Day 4

city: Amsterdam

first: Martijs

last: Jonker

address: Science Park 904

department: Microarray Department

institute: University of Amsterdam

hyb_protocol: Hybridization, washing, and scanning was performed as described in the Two-Color Microarray-Based Gene Expression Analysis manual (Version 6.6, Agilent Technologies). Briefly, hybridization mixtures were made by combining 300 ng test (Cy3) and 300 ng common reference (Cy5) material and were subsequently hybridized to the Agilent SurePrint Custom 8x15k microarrays G2509F (Agilent Technologies).

scan_protocol: The slides were scanned with the Agilent G2505C scanner as described in the Agilent Two-Color Microarray-Based Gene Expression Analysis guide (G4140-90050, Agilent technologies).

data_processing: Data were extracted with Feature Extraction software (Agilent Technologies). The data were analyzed in R-2.14.1 (http://cran.r-project.org/). All arrays were subjected to a set of quality control checks, such as visual inspection of the scans, checking for spatial effects through pseudo-color plots, and inspection of pre- and post-normalized data with box plots, density plots, ratio-intensity plots and principal component analysis. The data from B. subtilis strains PG479 and 168 were normalized, together with data from other strains, using the robust multi-array average (RMA) algorithm (Irizarry et al.).

organism: Bacillus subtilis

source_name: B. subtilis 168 Day 4

label_protocol: Labeling was performed by reverse transcription using random octamers, incorporating Cy3 for the test samples and Cy5 for the common reference

growth_protocol: B. subtilis strains were grown in LB at 37°C in the presence of 1.5% xylose and 1 mM IPTG (inducers were added in all cultures because some of the strains tested in the same experiment required induction). Cells were harvested at O.D.600 0.4-0.6.

extract_protocol: To isolate RNA, cell pellets were flash frozen in liquid nitrogen immediately after harvesting and stored at -80°C. Frozen pellets were grounded and subjected to RNA extraction

treatment_protocol: No treatment was applied.

tag: time (day)

source_name: Pool of different samples of different B. subtilis strains

treatment_protocol: No specific treatment was applied.

tag: sample type


title: monocytes-control-2

source_name: total blood monocytes, age-matched control

tag: disease state


title: HepG2-Twist1_cell lines

description: Raw data file: sample 1+2.txt

source_name: HepG2 hepatocellular carcinoma cell line transfected with pcDNA-Twist1


title: B. subtilis PG479 Day 3

source_name: B. subtilis PG479 Day 3

treatment_protocol: To construct B. subtilis strain PG479 (kre::erm), kre was replaced with an erythromycin resistance cassette amplified from pMutin4. Competent B. subtilis cells were transformed directly with the ligation products and mutants were verified with PCR.

value: Pool of different samples of different B. subtilis strains


title: monocytes-control-1


title: B. subtilis PG479 Day 5

source_name: B. subtilis PG479 Day 5


title: monocytes-control-3


title: monocytes-NVAMD-14

source_name: total blood monocytes, neovascular AMD patient

value: macular degeneration


title: B. subtilis 168 Day 1

source_name: B. subtilis 168 Day 1


title: HepG2-vector cell lines

description: Raw data file: sample 1+2.txt

source_name: HepG2 hepatocellular carcinoma cell line


title: A1837

source_name: glioblastoma tissue 2


title: monocytes-NVAMD-13


title: monocytes-NVAMD-11


title: monocytes-NVAMD-9


title: monocytes-NVAMD-10


title: A1832

source_name: glioblastoma tissue 1


title: A1828

source_name: glioblastoma tissue 3


title: monocytes-NVAMD-3


title: monocytes-NVAMD-7


title: monocytes-NVAMD-4