title: Replicate: Post-temsirolimus patient 7

status: Public on Mar 08 2013

city: Charlottesville

first: Aubrey

last: Wagenseller

state: Virginia

address: 345 Crispell Drive

department: Surgery

institute: University of Virginia

description:
Rep: PT-Mel-pt7
Melanoma metastasis following 1d of temsirolimus treatment

hyb_protocol: Hy3-labeled samples and Hy5-labeled reference RNA sample were mixed pair-wise and hybridized to the miRCURY LNA microRNA Array (6th gen- has, mmu, and mo). Hybridization was performed according to the miRCURY LNA microRNA Array instruction manual using a Tecan HS 4800 hybridization station (Tecan, Austria).

scan_protocol: Agilent G2565BA Microarray Scanner Images were quantified using ImaGene 9.0 data analysis software

data_processing:
LOWESS normalized, background subtracted data obtained from log2 of processed Hy3/processed Hy5 signal
The 2681 rows in GPL11434 list all the probes for the human, mouse, rat and related viral miRNAs. This project involved analysis of a single species (human), so information from capture probes specific for the other species are not included in this dataset.

source_name: Melanoma metastasis- treated with temsirolimus

label_protocol: 500ng of total RNA from sample and reference were labeled with Hy3 and Hy5 fluorescent label, respectively, using the miRCURY LNA microRNA Hi-Power Labeling Kit, Hy3/Hy5 (Exiqon, Denmark), following the procedure described by the manufacturer

extract_protocol: microRNA extracted from sections cut from FFPE tissue using the miRNeasy FFPE kit

treatment_protocol: Biopsies of melanoma metastases were obtained prior to treatment and one day following treatment with temsirolimus alone. The following week patients received both bevacizumab and temsirolimus. One week later, they received temsirolimus alone and then the following week (day 23) they received bevacizumab and temsirolimus, after which another biopsy was obtained.

tag: patient

value: temsirolimus

tag: days after treatment

value: 1 d

tag: tumor

value: lymph node

tag: tumor stage

source_name: total pooled microRNA from all samples

value: reference (total pooled microRNA from all samples)


title: Replicate: Pre-treatment patient 7

type: RNA

country: USA

description:
Rep: Pre-Mel-pt6
Control, pretreatment melanoma metastasis

molecule: total RNA

organism: Homo sapiens

source_name: Melanoma metastasis- untreated

tag: treatment

value: untreated

value: 0 d

value: melanoma

tag: tissue

tag: gender

value: male

tag: sample type


title: BMMCs_Pla2g3+/+_Rep1

status: Public on Mar 09 2013

city: Tokyo

first: Yoshitaka

last: Taketomi

address: 7-3-1 Hongo, Bunkyo-ku,

department: CDBIM, Graduate School of Medicine,

country: Japan

institute: The University of Tokyo

description: Gene expression before coculture

hyb_protocol: 1.65 µg of Cy3-labeled cRNA was fragmented using the Agilent Gene Expression Hybridization Kit protocol. Hybridizations were performed for 17 hours at 65ºC at 10 rpm in a rotating hybridization oven.

scan_protocol: Slides were scanned with a Laser Scanner GenePix 4000B (Molecular Devices) using a scan resolution of 5µm and appropriate gains on the photomultiplier (PMT) to obtain the highest intensity without saturation.

data_processing: Data was obtained using the Agilent Feature Extraction software (v9.5.1.1), using default for all parameters. Data were subsequently imported into GeneSpringGX11.5 (Agilent Technologies) for the analysis of gene expression microarray data. Probes were normalized by quantile normalization among all microarray data.

organism: Mus musculus

source_name: Pla2g3+/+, BMMC

label_protocol: 450 ng of total RNA was amplified and labeled using the Agilent Quick Amp Labeling Kit according to the manufacturer's protocol.

growth_protocol: Mouse BM cells were cultured in IL-3-containing BMMC-complete medium. After 4–6 weeks of culture, > 97% of the cells were identified as Kit+FcεRIα+ mast cells by flow cytometry.

extract_protocol: Total RNA was extracted from BMMCs derived from Pla2g3–/– and Pla2g3+/+ mice before and after coculture and purified using the RNeasy Mini Kit (Qiagen). The quality of RNA was assessed with a 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: BMMCs were seeded onto the Swiss 3T3 fibroblast monolayer and cocultured for 4 days in the presence of mouse SCF (100 ng/ml). The cells were trypsinized and reseeded in culture dishes, and nonadherent cells were collected. Purity (> 99%) was confirmed by flow cytometry for Kit and FcεRIα. The maturation of BMMCs into CTMC-like cells was verified by staining of their granules with alcian blue and counterstaining with safranin O.

tag: strain

tag: genotype

value: Pla2g3 wild-type

tag: maturation

value: immature


title: Replicate: Post-combination treatment patient 2

description:
Rep: PC-Mel-pt2
Melanoma metastasis following 23d of combination treatment

source_name: Melanoma metastasis- treated with temsirolimus and bevacizumab

value: temsirolimus and bevacizumab


title: Replicate: Pre-treatment patient 5

description:
Rep: Pre-Mel-pt5
Control, pretreatment melanoma metastasis


title: Blood_baseline

city: Toon

first: Junichi

last: Iga

state: Ehime

address: Shitsukawa 454

department: Neuropsychiatry

institute: Ehime University

description: Gene expression before lithium medication in human blood.

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 55ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.5.1 (Agilent) using default parameters (protocol GE1-v5_10_April08 and Grid: 014850_D_F_20080627) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Data were global intra-array normalized on to the 75.0 percentile using GeneSpring GX 12.1.

source_name: Peripheral blood, baseline

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the Agilent One-Color Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer's instructions.

growth_protocol: Freshly drawn peripheral blood from healthy volunteers was collected in the PAXgene Blood RNA tube (Qiagen, Tokyo, Japan) according to the manufacturer's recommendations.

extract_protocol: RNA was prepared using the PAXgene Blood RNA tube (Qiagen, Tokyo, Japan) following the manufacturer's recommendations. The protocol includes differential lysis of red and white blood cells, and an on-column DNase digestion. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: pool from 8 subjects

value: whole blood

tag: mean age

tag: disease status

value: healthy

tag: time point

value: baseline


title: Post-combination treatment patient 12

description:
PC-Mel-pt12
Melanoma metastasis following 23d of combination treatment


title: Post-temsirolimus patient 12

description:
PT-Mel-pt12
Melanoma metastasis following 1d of temsirolimus treatment


title: Pre-treatment patient 12

description:
Pre-Mel-pt12
Control, pretreatment melanoma metastasis


title: Blood_1wk

description: Gene expression after 1 week of lithium medication in human blood.

source_name: Peripheral blood, 1 week after medication

value: lithium

value: 1 week after medication


title: Post-temsirolimus patient 10

description:
PT-Mel-pt10
Melanoma metastasis following 1d of temsirolimus treatment

value: temsirolimus


title: Post-combination treatment patient 9

description:
PC-Mel-pt9
Melanoma metastasis following 23d of combination treatment


title: Replicate: Post-combination treatment patient 10

description:
Rep: PC-Mel-pt10
Melanoma metastasis following 23d of combination treatment


title: Pre-treatment patient 10

description:
Pre-Mel-pt10
Control, pretreatment melanoma metastasis


title: Pre-treatment patient 11

description:
Pre-Mel-pt11
Control, pretreatment melanoma metastasis


title: Post-temsirolimus patient 8

description:
PT-Mel-pt8
Melanoma metastasis following 1d of temsirolimus treatment

value: 1 d

value: female


title: Post-combination treatment patient 8

description:
PC-Mel-pt8
Melanoma metastasis following 23d of combination treatment

value: lymph node

value: reference (total pooled microRNA from all samples)


title: Post-temsirolimus patient 9

description:
PT-Mel-pt9
Melanoma metastasis following 1d of temsirolimus treatment


title: Post-temsirolimus patient 7

description:
PT-Mel-pt7
Melanoma metastasis following 1d of temsirolimus treatment


title: Pre-treatment patient 8

description:
Pre-Mel-pt8
Control, pretreatment melanoma metastasis

value: untreated

value: 0 d


title: Pre-treatment patient 9

description:
Pre-Mel-pt9
Control, pretreatment melanoma metastasis

value: melanoma

value: male


title: BMMCs_Pla2g3+/+_Rep2

description: Gene expression before coculture

value: Pla2g3 wild-type

value: immature


title: Post-temsirolimus patient 11

description:
PT-Mel-pt11
Melanoma metastasis following 1d of temsirolimus treatment


title: Post-combination treatment patient 10

description:
PC-Mel-pt10
Melanoma metastasis following 23d of combination treatment

value: temsirolimus and bevacizumab


title: Post-combination treatment patient 7

description:
PC-Mel-pt7
Melanoma metastasis following 23d of combination treatment


title: Post-temsirolimus patient 6

description:
PT-Mel-pt6
Melanoma metastasis following 1d of temsirolimus treatment


title: Pre-treatment patient 7

description:
Pre-Mel-pt7
Control, pretreatment melanoma metastasis


title: Post-combination treatment patient 5

description:
PC-Mel-pt5
Melanoma metastasis following 23d of combination treatment


title: Pre-treatment patient 6

description:
Pre-Mel-pt6
Control, pretreatment melanoma metastasis


title: Pre-treatment patient 3

description:
Pre-Mel-pt3
Control, pretreatment melanoma metastasis


title: Post-combination treatment patient 4

description:
PC-Mel-pt4
Melanoma metastasis following 23d of combination treatment


title: Post-temsirolimus patient 5

description:
PT-Mel-pt5
Melanoma metastasis following 1d of temsirolimus treatment


title: Pre-treatment patient 5

description:
Pre-Mel-pt5
Control, pretreatment melanoma metastasis


title: Post-temsirolimus patient 4

description:
PT-Mel-pt4
Melanoma metastasis following 1d of temsirolimus treatment


title: Post-temsirolimus patient 3

description:
PT-Mel-pt3
Melanoma metastasis following 1d of temsirolimus treatment


title: Post-temsirolimus patient 2

description:
PT-Mel-pt2
Melanoma metastasis following 1d of temsirolimus treatment


title: Pre-treatment patient 4

description:
Pre-Mel-pt4
Control, pretreatment melanoma metastasis


title: Post-combination treatment patient 2

description:
PC-Mel-pt2
Melanoma metastasis following 23d of combination treatment


title: Post-combination treatment patient 1

description:
PC-Mel-pt1
Melanoma metastasis following 23d of combination treatment


title: Pre-treatment patient 2

description:
Pre-Mel-pt2
Control, pretreatment melanoma metastasis


title: THP1 incubated 24 h with MV from THP1-PMA donors, repl. 1

city: Indianapolis

first: Leni

last: Moldovan

state: IN

address: 980 W Walnut St., Rm. C422

department: Ophthalmology

institute: Indiana University

description: Gene expression in THP1 cells treated with THP1+PMA-derived MV

hyb_protocol: For samples Mono1-3 and GM1-3, 15ug of biotin labeled cRNA were hybridized to the array, washed and stained in Affymetrix Fluidics Station 450, using protocol EukGE-WS2v5-450. For all other samples, GeneChips were hybridized with 3.75 ug biotin-labeled, fragmented cDNA, then washed and stained in Affymetrix Fluidics Station 400, using protocol EukGE-WS2v5.

scan_protocol: The Affymetrix GeneChip Scanner 7G was used for samples Mono1-3 and GM1-3 and Affymetrix GeneChip Scanner 3000 was used to scan all other samples.

data_processing: Presence call was obtained with GeneChip Operating Software Version 1.4.0.036. Data were processed with Partek Genomic Suite 6.4, after importing from .CEL files using robust multi-chip average with GC content adjustment (GC-RMA) for background correction, and quantile normalization. Only those genes that demonstrated a P (present) or M (marginal) call in at least two experimental samples of the triplicate per experimental conditions were futher used for analysis.

label: biotin

source_name: THP1 cells

label_protocol: For samples Mono1-3 and GM1-3, 2 ug of total RNA were processed with GeneChip® HT One-Cycle Target Labeling and Control Kit (Affymetrix). For all other samples, 30 ng RNA were processed using the Ovation™ RNA Amplification. The cDNA thus obtained was fragmented and labeled using the FL-Ovation™ cDNA Biotin Module V2 (both kits from NuGEN Technologies, Inc., San Carlos, CA).

growth_protocol: Peripheral human blood monocytes were isolated from buffy coats, on histopaque-1077, and grown in X-VIVO 15 media (Lonza) supplemented with 10 μg/ml polymyxin B, in the absence or presence of 50 ng/ml of rhGM-CSF. Monocytes were washed after 4 hours and cultured in fresh media without added rhGM-CSF. THP-1 cells (ATCC) were grown in RPMI 1640 supplemented with 10% FBS. To induce differentiation, THP-1 cells were grown in X-VIVO 15 serum-free media and treated with 65 nM PMA, or with vehicle (DMSO) as control.

extract_protocol: Total RNA was extracted using Trizol methodology. At all steps, the quantity and quality of the preparations were controlled using Nanodrop and Experion Automated Electrophoresis System (BioRad).

treatment_protocol: Microvesicles (MV) were obtained by a 30 min, 4°C, 16000 x g centrifugation of the cell-free culture supernatant. Primary monocyte-derived macrophages were treated either with GM-CSF or with MV derived from other GM-CSF-treated macrophages, for 24 h. THP1 cells were treated with PMA or DMSO (control). MV were isolated from these cells and further incubated for 24 h with new THP1 cells.

tag: cell group

value: cell line

tag: cell type

value: THP1 cells


title: THP1 incubated 24 h with MV from THP1-PMA donors, repl. 2

value: THP1 cells treated with THP1+PMA-derived MV


title: THP1+DMSO used as MV donors, repl. 3

description: Gene expression in THP1 cells treated with DMSO

value: THP1 cells treated with DMSO


title: THP1+PMA used as MV donors, repl. 1

description: Gene expression in THP1 cells treated with PMA

value: THP1 cells treated with PMA


title: Freshly isolated monocyte incubated 24 h with MV from other GM-CSF-treated MDM, repl. 2

description: Gene expression in MDM after interaction with MDM-derived MV

source_name: Monocyte-derived macrophages

value: primary

value: Monocyte-derived macrophages


title: THP1 incubated 24 h with MV from THP1-DMSO donors, repl. 1

description: Gene expression in THP1 cells treated with THP1+DMSO-derived MV


title: THP1+PMA used as MV donors, repl. 3


title: Freshly isolated monocytes used as MV recipients, repl. 2

description: Gene expression in differentiated MDM

source_name: Monocytes

value: Monocytes

value: differentiated MDM


title: THP1+DMSO used as MV donors, repl. 2


title: THP1 incubated 24 h with MV from THP1-PMA donors, repl. 3


title: Freshly isolated monocyte incubated 24 h with MV from other GM-CSF-treated MDM, repl. 1

value: MDM after interaction with MDM-derived MV


title: THP1+DMSO used as MV donors, repl. 1


title: THP1 incubated 24 h with MV from THP1-DMSO donors, repl. 3

value: THP1 cells treated with THP1+DMSO-derived MV


title: THP1 incubated 24 h with MV from THP1-DMSO donors, repl. 2


title: THP1+PMA used as MV donors, repl. 2


title: Freshly isolated monocyte incubated 24 h with MV from other GM-CSF-treated MDM, repl. 3


title: Freshly isolated monocytes used as MV recipients, repl. 1

description: Gene expression in differentiated MDM


title: Freshly isolated monocytes used as MV recipients, repl. 3

description: Gene expression in differentiated MDM


title: GM-CSF-treated macrophages used as MV donors, repl. 2

description: Gene expression in differentiated MDM


title: Freshly isolated monocytes used as MV donors, repl. 1

description: Gene expression in primary monocytes

value: primary monocytes


title: Freshly isolated monocytes used as MV donors, repl. 2

description: Gene expression in primary monocytes


title: GM-CSF-treated macrophages used as MV donors, repl. 3

description: Gene expression in differentiated MDM


title: GM-CSF-treated macrophages used as MV donors, repl. 1

description: Gene expression in differentiated MDM


title: Patient64 IFN+RBV

city: Bethesda

first: Yaron

last: Rotman

state: MD

address: 10 Center Drive, Bldg 10, Room 9C434

department: Liver Diseases Branch

institute: NIH, NIDDK

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: Data analyzed using Partek Genomics Suite with GCRMA normalization

source_name: Liver tissue IFN+RBV

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

growth_protocol: Patients treated with or without ribavirin for 4 weeks, and biopsied before or 6hr after an initial injection of peginterferon alfa-2a

extract_protocol: Trizol extraction of total RNA according to manufacturer protocol

treatment_protocol: Samples preserved in RNALater and stored in -80C

tag: group

value: D

value: IFN + RBV

tag: disease state

value: hepatitis C

value: liver biopsy


title: Patient62 RBV

source_name: Liver tissue RBV

value: C

value: RBV


title: Patient61 None

source_name: Liver tissue None

value: A


title: Freshly isolated monocytes used as MV donors, repl. 3

description: Gene expression in primary monocytes


title: SKOV3 +rhSTIP1 1

city: TauYau

first: Yun-Shien

last: Lee

state: Taiwan

address: TauYau

department: Dept. Biotechnology

country: Taiwan

institute: Ming Chuan Univ

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: Normalize with MAS5 by Affymetrix Expression Console Version 1.1

label: Biotin

source_name: SKOV3 cell treated with rhSTIP1

label_protocol: Standard Affymetrix protocol

extract_protocol: cellular RNA extraction with TRIZOL

tag: cell line


title: Patient53 None


title: Patient52 IFN

source_name: Liver tissue IFN

value: B

value: IFN


title: Patient60 IFN+RBV


title: Patient56 None


title: 40A9_Ezh2 +/+ _iPSC_biological_replicate2

city: Milano

first: Pasquale

last: Laise

address: Via Adamello,16

country: Italy

institute: IEO

hyb_protocol: Hybridization was performed according to Affimetrix guidelines

scan_protocol: Scanning was performed using the Affimetrix scanner

data_processing:
Data was processed using the affy package available on bioconductor (http://www.bioconductor.org) using standard RMA analysis settings
Probe group file: MoGene-1_0-st-v1.r4.pgf
meta-probeset file: MoGene-1_0-st-v1.r4.mps

source_name: established iPSC clone

label_protocol: Labeling was performed according to Affimetrix guidelines

growth_protocol:
Cell culture: iPSC clones were cultured in ESC medium (high glucose DMEM, 15% knockout serum replacement-Invitrogen-, 2mM L-glutamine, 50 units/ml penicillin, 50µg/ml streptomycin, 0,1 mM non-essential amino acids, 1/500 home-made leukaemia inhibitory factor, 0,1 mM 2-β-mercaptoethanol) in feeder-free conditions on gelatin coated dishes
iPSC derivation protocol: MEF at passage 1 to 3 were seeded at a density of 2x105 cells/well in a 6-well tissue culture dish. 24hr later, MEF were transduced in a 1:1 PBS/DMEM/GlutaMAX (Invitrogen) solution with 50 µg/ml of recombinant TAT-Cre recombinase. 16 hour after transduction, medium was replaced, and MEF were infected with the STEMCCA and rtTA lentiviruses. 24 hours following infection with STEMCCA and rtTA, MEF were harvested and seeded at  clonal density on a mytomycin-treated MEF feeder layer. One day after, MEF medium was replaced with ESC medium supplemented with 1 µg/ml doxycycline to induce expression of the reprogramming factors. Doxycycline treatment was replaced every other day for 23 days. Four days after doxycycline withdrawal, iPSC colonies were picked and expanded on a mitomycin-treated MEF feeder layer to establish individual iPSC clones.

extract_protocol: Total RNA was extracted with Trizol reagent and purified using QUIAGEN RNeasy Mini kit following  manufacturer's instructions

tag: genotype/variation

value: Ezh2 fl/fl

value: induced pluripotent stem cells (iPSC)


title: Patient55 IFN


title: Patient49 None


title: Patient50 RBV


title: Patient58 IFN+RBV


title: Patient47 IFN+RBV


title: Patient51 RBV


title: Patient54 None


title: Patient65 None


title: Patient44 IFN


title: Patient46 IFN


title: 786-O_AZA_SSS1

type: genomic

city: Los Angeles

first: Kurinji

last: Pandiyan

address: 1441 Eastlake Avenue NOR 7344

department: Department of Urology - Norris Comprehensive Cancer Center

institute: University of Southern California

description: male, renal cancer cell line, AZA and M.SssI treated

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to the Illumina 450k methylation array using standard Illumina protocols

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

data_processing: Mean non-background corrected signal intensities of the methylated (M) and unmethylated (U) for each CpG locus were extracted using the Illumina BeadStudio software v3.2.Data points were marked “NA” if 1) Probes contained single-nucleotide polymorphisms (SNPs), 2) those that overlap with a repetitive element that covers the targeted CpG dinucleotide, 3) those that overlap with regions of insertions and deletions in the human genome. Beta values with detection P value greater than 0.05 were also replaced as NA. Furthermore, probes containing at least one “NA” across the tumor sample set were masked as “NA”. Beta values were background subtracted.

label: Cy5 and Cy3

molecule: genomic DNA

source_name: 786-O Cell Line

label_protocol: Standard Illumina labeling protocol

growth_protocol: Cells were grown under standard conditions

extract_protocol: Genomic DNA was extracted using standard phenol chloform procedures with ethanol precipitation. Zymo EZ DNA kit was used for bisulfite conversion

treatment_protocol: 2x10^5 nuclei were treated with 1x M.SssI buffer and 50U of M.SssI for 15 minutes. A no-enzyme control was included. SAHA treatment was performed for 24hours with 1uM SAHA

tag: Sex

value: male

value: AZA and M.SssI

value: 786-O Cell Line


title: Patient43 RBV

tag: treatment


title: 786-O_SSS1

description: male, renal cancer cell line, M.SssI treated

value: M.SssI treated


title: Patient35 IFN

tag: tissue


title: Patient37 RBV


title: Patient41 IFN


title: Patient33 None


title: MCF7_NoE

description: female, breast cancer cell line, control

source_name: MCF7 Cell Line

value: female

value: control

value: MCF7 Cell Line


title: MCF7_SAHA_SSS1

description: female, breast cancer cell line, SAHA and M.SssI treated

value: SAHA and M.SssI treated


title: Patient32 None

value: hepatitis C


title: Patient34 IFN

value: liver biopsy


title: 786-O_SAHA_SSS1

description: male, renal cancer cell line, SAHA and M.SssI treated


title: C.glabrata_milbe_4

city: Lausanne

first: Dominique

last: Sanglard

address: Rue Bugnon 48

country: Switzerland

institute: University of Lausanne and University Hospital Center

description: Milbemycin-treated cells

hyb_protocol: Agilent gene expression hybridization kit protocol

scan_protocol: Agilent Scanning protocol on an Agilent DNA Microarray Scanner G2565BA  Other: Arrays were scanned at 5um resolution and 100/10% PMT XDR

data_processing: Data were extracted from the images with Feature Extraction (FE) software. Data were normalized using a combined rank consistency filtering with LOWESS intensity normalization. The gene expression values obtained from FE software were imported into GeneSpring 10.0.2 software (Agilent technologies) for preprocessing and data analysis.

organism: Nakaseomyces glabratus

label_protocol: Agilent one-color quick amp labeling kit protocol

growth_protocol: log-pase culture grown in RPMI

extract_protocol: total RNA extraction using Trizol

treatment_protocol: Milbemycin A3 oxim was given at a concentration of 10µg/ml for 1 h in RPMI mediun at 35°C under constant shaking. Same conditions were applied to untreated cells (control)

value: treated with Milbemycin A3 oxim


title: C.glabrata_milbe_3

description: Milbemycin-treated cells


title: Patient30 RBV

value: C

value: RBV


title: 786-O_AZA_NoE

description: male, renal cancer cell line, AZA treated

value: AZA treated


title: C.glabrata_milbe_2

description: Milbemycin-treated cells


title: Patient27 IFN

value: B

value: IFN


title: MCF7_AZA_NoE

description: female, breast cancer cell line, AZA treated


title: MCF7_SSS1

description: female, breast cancer cell line, M.SssI treated


title: Patient28 IFN+RBV

value: D

value: IFN + RBV


title: C.glabrata_milbe_1

description: Milbemycin-treated cells


title: MCF7_SAHA_NoE

description: female, breast cancer cell line, SAHA treated

value: SAHA treated


title: Patient25 IFN


title: DKO1_SSS1_rep1

description: male, derivative of HCT116, engineerd disruption of DNA methyltransferase , DNMT1 and DNMT3B, M.SssI treated

source_name: DKO1 Cell Line

value: male

value: DKO1 Cell Line


title: MCF7_AZA_SSS1

description: female, breast cancer cell line, AZA and M.SssI treated

value: female

value: AZA and M.SssI


title: HCT116_AZA_SSS1

description: male, colorectal carcinoma cell line, AZA and M.SssI treated

source_name: HCT116 Cell Line

value: HCT116 Cell Line


title: DKO1_AZA_SSS1

description: male, derivative of HCT116, engineerd disruption of DNA methyltransferase , DNMT1 and DNMT3B, AZA and M.SssI treated


title: Patient29 IFN+RBV


title: Patient24 None

value: A


title: C.glabrata_control_4

description: untreated cells

value: untreated


title: HCT116_SSS1

description: male, colorectal carcinoma cell line, M.SssI treated

value: M.SssI treated


title: HCT116_SAHA_SSSI

data_processing: Mean non-background corrected signal intensities of the methylated (M) and unmethylated (U) for each CpG locus were extracted using the Illumina BeadStudio software v3.2. Data points were marked null if 1) Probes contained single-nucleotide polymorphisms (SNPs), 2) those that overlap with a repetitive element that covers the targeted CpG dinucleotide, 3) those that overlap with regions of insertions and deletions in the human genome. Beta values with detection P value greater than 0.05 were also replaced as Null. Furthermore, probes containing at least one null across the tumor sample set were masked as null. Beta value was calculated as M/(M+U) and were background subtracted.  Detection P values were obtained using the Z-score formula as previously described (Noushmehr et al., 2010, Cancer Cell).

tag: gender

value: colorectal carcinoma cell

value: SAHA and M.SssI treated


title: 786-O_SAHA_NoE

description: male, renal cancer cell line, SAHA treated

value: 786-O Cell Line


title: Patient22 None

value: hepatitis C

value: liver biopsy


title: DKO1_NoE_rep1

description: male, derivative of HCT116, engineerd disruption of DNA methyltransferase DNMT1 and DNMT3B, control

value: control


title: DKO1_AZA_NoE

description: male, derivative of HCT116, engineerd disruption of DNA methyltransferase DNMT1 and DNMT3B, AZA treated

value: AZA treated


title: Patient20 IFN+RBV

value: D

value: IFN + RBV


title: C.glabrata_control_3

description: untreated cells


title: Patient17 IFN

value: B

value: IFN


title: HCT116_AZA_NoE

description: male, colorectal carcinoma cell line, AZA treated, control

value: male


title: Patient18 RBV

value: C

value: RBV


title: C.glabrata_control_2

description: untreated cells


title: HCT116_NoE

description: male, colorectal carcinoma cell line, control

value: HCT116 Cell Line


title: C.glabrata_control_1

description: untreated cells

value: untreated


title: HCT116_SAHA_NoE

value: SAHA treated, control


title: Patient15 None

value: A


title: HCT116_NoE_SSSI_rep2

value: colorectal carcinoma cell

value: M.SssI treated


title: Patient14 RBV

value: hepatitis C


title: Patient16 RBV

value: liver biopsy


title: Patient13 RBV


title: HCT116_NoE_rep2

value: control


title: Patient26 IFN+RBV


title: Nemo+CRE + CLL V211

city: Essen

first: Ludger

last: Klein-Hitpass

address: Virchowstr. 173

department: Universitaetsklinikum

country: Germany

institute: Institut fuer Zellbiologie

description:
Gene expression data of BMSC isolated from induced strain (Nemo+CRE) co-cultured with CLL V211
Nemo+CRE + CLL V211

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip MG-430_2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using the Affymetrix Hybridization, Wash and Stain Kit.

scan_protocol: Arrays were scanned in a GeneChip Scanner 3000 with G7 update

data_processing: The data were analyzed with MAS5 using Affymetrix default analysis settings and global scaling to a target intensity of 1000 as normalization method.

source_name: BMSC_Nemo KO_co-cultured with leukemic B-cells

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix ExpressKit protocol starting from 200 ng total RNA.

growth_protocol: Primary BMSCs were isolated from femora of NemoF/F and Nemoy/F-mice and cultured until they reached 90% confluence. Cells were incubated overnight in a 1:1 mixture of medium (DMEM w/o FCS) and PBS containing 1µM Tat-Cre protein10. Nemo- BMSCs were then cultured at least 8 days after transduction in DMEM supplemented with PS and 10% FCS before co-culture experiments were performed.

extract_protocol: Total RNA was extracted from BMSCs using the miRNeasy Mini Kit (Quiagen, Hilden, Germany) according to the manufacturer’s instruction.

treatment_protocol: After BMSCs had formed a confluent monolayer, primary CLL cells were co-cultured. Typically, 80 x 10x6 primary CLL cells were seeded onto a 10cm dish (56 square cm). After 5 days, CLL cells were separated from co-cultures with stromal cells by repeated washing steps with PBS. Subsequently, single cell suspensions were treated with magnetic anti-CD19 beads to allow removal of remaining CLL cells. Flow-cytometry analysis indicated that more than 99% CD5+CD19+ cells were successfully isolated from CLL-stroma-co-cultures

tag: strain background

value: Nemo knockout

tag: tissue origin

value: femora

value: bone marrow stromal cells (BMSC)

tag: co-cultured with

value: CLL V211


title: Patient12 IFN

value: B

value: IFN


title: Patient11 IFN+RBV

value: D

value: IFN + RBV


title: Patient10 RBV

value: C

value: RBV


title: Soleus_Muscle_Rep2

city: Padova

first: Gerolamo

last: Lanfranchi

address: Via U. Bassi, 58/B

department: CRIBI - Biotechnology Center and Biology Department

institute: University of Padova

description: Gene Expression profiling of murine adult soleus (slow oxidative muscle).

hyb_protocol: 1.65 µg of labeled cRNA target was mixed with 11 µl of 10X Blocking Agent, 2.2 µl of 25X Fragmentation Buffer, and water of Agilent Hybridization Kit (catalogue number 5188-5242) to a final volume of 55 µl. Reaction was incubated at 60°C for exactly 30 min to fragment cRNA. 100 µl of hybridization mix, composed by equal volumes of fragmented cRNA and 2X GEx Hybridization Buffer HI-RPM, was dispensed onto one of the 4 arrays of the Agilent Mouse Oligo Arrays 4x44K (catalogue number G4122F). The full microarray slide was loaded into an Agilent SureHyb chamber and hybridization was performed in a hybridization oven at 65°C for 17 h. Rotation was set at 10 rpm. At the end of hybridization, slides were washed for 1 min at 22 ºC in Wash Solution 1 (catalogue number 5188-5325) and 1 min in Wash Solution 2, pre-warmed to 37 ºC (catalogue number 5188-5326).

scan_protocol: Microarrays were scanned using the Agilent Technologies Scanner G2505B US22502723 (ChipScan software version A.7.0.1), scan region 61 X 21.6mm, scan resolution 5 micron single pass, extended dynamic range selected (XDR Hi 100%; XDR Lo 10%).

data_processing: Data was extracted from the scanned image using the Agilent Feature Extraction Software version. 9.1.3.1 (protocol GE1-v5_91_0806). Quantile inter-arrays normalization was performed with the Expander software (Bioinformatics 2003; 19:1787-99) on the gProcessedSignal column of the result table and normalized data is reported in the VALUE column. Mean values were calculated for multiple probes with the same Agilent Probe ID. Probes with gIsPosAndSignif value of zero were disregarded and labeled as "null".

source_name: Soleus muscle, adult CD1 mice

label_protocol: 1 µg RNA was amplified and labeled using the Agilent One-color Quick Amp Labeling Kit (catalogue number 5190-0442), following the Manufacturer’s instructions. The RNA sample was mixed to 1.2 µl T7 Promoter Primer, 5 µl Agilent One-Color RNA Spike-In (1:5,000 dilution, catalogue number 5188-5282) and denatured for 10 min at 65 ºC. First Strand Buffer, DTT, dNTP MMLV and RNaseOut were added and cDNA synthesis was carried out for 2 h at 40 ºC. After 15 min at 65 ºC to inactivate the MMLV enzyme, complementary RNA (cRNA) was generated using T7 RNA polymerase, which simultaneously amplifies target material and incorporates Cy3-labeled CTP. Run-off in vitro transcription reactions proceeded for 2 h at 40°C. RNeasy Mini spin columns (Qiagen) were used to further purify the labeled-amplified cRNA samples.

growth_protocol: Male

extract_protocol: CD1 mice (Charles River) were killed by cervical dislocation. The soleus muscles from both hind limbs of the same mouse were immediately removed by microdissection and dispersed in 1 ml TRIzol reagent (Invitrogen). Muscle tissue was homogenized with an ultra-turrax-T8 blender (IKA-Werke) before RNA extraction following the standard protocol. The Nanodrop ND-1000 was used for RNA quantification and RNA 6000 Nano LabChip kit (Agilent Technologies) was used for RNA quality control in conjunction with an Agilent Bioanalyzer 2001.

treatment_protocol: 3 months

value: Soleus muscle

tag: differentiation stage

value: Male


title: Soleus_Muscle_Rep3


title: Nemo+CRE + CLL V163

description:
Gene expression data of BMSC isolated from induced strain (Nemo+CRE) co-cultured with CLL V163
Nemo+CRE + CLL V163

value: CLL V163


title: Nemo+CRE + CLL V132

description:
Gene expression data of BMSC isolated from induced strain (Nemo+CRE) co-cultured with CLL V132
Nemo+CRE + CLL V132

value: CLL V132


title: Patient8 None

value: A

value: hepatitis C


title: Patient23 IFN+RBV

value: liver biopsy


title: EDL_Muscle_Rep3

description: Gene Expression profiling of murine adult EDL (fast glycolytic muscle).

source_name: EDL muscle, adult CD1 mice

extract_protocol: CD1 mice (Charles River) were killed by cervical dislocation. The EDL muscles from both hind limbs of the same mouse were immediately removed by microdissection and dispersed in 1 ml TRIzol reagent (Invitrogen). Muscle tissue was homogenized with an ultra-turrax-T8 blender (IKA-Werke) before RNA extraction following the standard protocol. The Nanodrop ND-1000 was used for RNA quantification and RNA 6000 Nano LabChip kit (Agilent Technologies) was used for RNA quality control in conjunction with an Agilent Bioanalyzer 2001.

value: Extensor digitorum longus muscle


title: Nemo+CRE + CLL V128

description:
Gene expression data of BMSC isolated from induced strain (Nemo+CRE) co-cultured with CLL V128
Nemo+CRE + CLL V128

value: Nemo knockout

value: femora

value: CLL V128


title: HCT116_SSS1_rep1

value: male

value: colorectal carcinoma cell

value: M.SssI treated


title: DKO1_NoE

value: DKO1 (HCT11 derivative)

value: disruption of DNA methyltransferase DNMT1 and DNMT3B

value: control


title: Patient9 IFN+RBV

value: D

value: IFN + RBV


title: Nemo+CRE + CLL V227

description:
Gene expression data of BMSC isolated from induced strain (Nemo+CRE) co-cultured with CLL V227
Nemo+CRE + CLL V227

value: bone marrow stromal cells (BMSC)

value: CLL V227


title: Nemo+CRE + CLL V147

description:
Gene expression data of BMSC isolated from induced strain (Nemo+CRE) co-cultured with CLL V147
Nemo+CRE + CLL V147

value: CLL V147


title: EDL_Muscle_Rep1

value: Male


title: Nemo+CRE + CLL V172

description:
Gene expression data of BMSC isolated from induced strain (Nemo+CRE) co-cultured with CLL V172
Nemo+CRE + CLL V172

value: CLL V172


title: EDL_Muscle_Rep2

value: Extensor digitorum longus muscle


title: HCT116_NoE_rep1


title: TIC10 treated (10uM) rep3

city: Hershey

first: Joshua

middle: E

last: Allen

state: PA

address: 500 University Drive

institute: Penn State Hershey Medical Ctr

description: Replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using the following:  Measurements less than 0.01 were then set to 0.01, arrays normalized to the 50th percentile, and individual genes normalized to the median of all arrays.

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

growth_protocol: All samples harvested from sterile cell culture 48-hours post treatment

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.

treatment_protocol: Cells were treated with .05% DMSO or TIC10 (10uM) in fresh complete media


title: Patient6 IFN

value: B

value: IFN

value: hepatitis C

value: liver biopsy


title: TIC10 treated (10uM) rep2

description: Replicate 2


title: H1_NoE

source_name: H1 Cell Line

value: male

value: human embryonic stem cells


title: Patient5 IFN


title: DKO1_SSS1

value: DKO1 (HCT11 derivative)

value: colorectal carcinoma cell

value: M.SssI treated


title: C2C12_Myotube_Rep3

description: Gene Expression profiling of purified C2C12 myotubes 96 hours after start of differentiation.

source_name: C2C12, purified myotubes

growth_protocol: C2C12 myoblasts were allowed to reach 90% confluence and then the medium was changed to differentiation medium (DM, Dulbecco’s modified Eagle medium supplemented with 2% horse serum) that was freshly replaced every day thereafter. Spontaneous twitching of fused myotubes was observed after 4-8 days of differentiation.

extract_protocol: Total RNA was isolated with TRIzol reagent (Invitrogen) following the standard protocol. The Nanodrop ND-1000 was used for RNA quantification and RNA 6000 Nano LabChip kit (Agilent Technologies) was used for RNA quality control in conjunction with an Agilent Bioanalyzer 2001.(Agilent Technologies) was used for RNA quality control in conjunction with an Agilent Bioanalyzer 2001.

treatment_protocol: C2C12 myotubes were harvested 96 hours after start of differentiation. To isolate them from the mononucleated cells present in the culture, cells were detached using diluted trypsin. After trypsinization, myotubes were plated again in fresh proliferation medium to allow the mononucleated cells to attach to the surface. After 30 min at 37°C, the floating cells which are mostly myotubes were collected and processed for RNA extraction.

value: myotubes harvested 96 hours after start of differentiation


title: Patient2 None

value: A


title: Nemo-CRE + CLL V132

description:
Gene expression data of BMSC isolated from uninduced strain (Nemo-CRE) co-cultured with CLL V132
Nemo-CRE + CLL V132

source_name: BMSC_Nemo wild type_co-cultured with leukemic B-cells

value: Nemo wild type

value: femora

value: bone marrow stromal cells (BMSC)

value: CLL V132


title: DMSO treated rep3

description: Replicate 3

value: DMSO treated


title: Nemo-CRE + CLL V163

description:
Gene expression data of BMSC isolated from uninduced strain (Nemo-CRE) co-cultured with CLL V163
Nemo-CRE + CLL V163

value: CLL V163


title: C2C12_Myotube_Rep2


title: Nemo-CRE + CLL V147

description:
Gene expression data of BMSC isolated from uninduced strain (Nemo-CRE) co-cultured with CLL V147
Nemo-CRE + CLL V147

value: CLL V147


title: DMSO treated rep2

description: Replicate 2


title: Nemo-CRE + CLL V227

description:
Gene expression data of BMSC isolated from uninduced strain (Nemo-CRE) co-cultured with CLL V227
Nemo-CRE + CLL V227

value: CLL V227


title: H1_SSS1


title: TIC10 treated (10uM) rep1

description: Replicate 1


title: Patient4 None

value: hepatitis C


title: Patient0 None

value: liver biopsy


title: Nemo-CRE + CLL V128

description:
Gene expression data of BMSC isolated from uninduced strain (Nemo-CRE) co-cultured with CLL V128
Nemo-CRE + CLL V128

value: CLL V128


title: C2C12_Myoblast_Rep3

description: Gene Expression profiling of proliferating C2C12 cells at the myoblast stage.

source_name: C2C12, 50 percent confluent myoblasts

growth_protocol: C2C12 myoblasts (from ATCC, Manassas, VA, USA) were grown at 37°C in a controlled humidified 5% CO2 atmosphere. Cells were maintained in gelatine-coated plates in proliferation medium (PM, Dulbecco’s modified Eagle medium supplemented with 10% fetal bovine serum).

treatment_protocol: When C2C12 myoblasts reached about 50% confluence, the cells were collected and processed for RNA extraction.

value: proliferating myoblasts


title: DMSO treated rep1

description: Replicate 1


title: C2C12_Myotube_Rep1


title: GliNS2_GSC line_5

city: Monza

first: Simona

last: Baronchelli

address: Via Cadore 48

institute: University of Milan-Bicocca

hyb_protocol: Hybridization was performed on Agilent-014950 Human Genome CGH microarray 4x44K, following manufacturer's instructions (www.agilent.com for details).

scan_protocol: Briefly, the arrays were scanned at 2μm resolution using Agilent microarray scanner (Agilent Technologies, Santa Clara, CA, USA).

data_processing: Data were analyzed using Feature Extraction v10.7 and Agilent Genomic Workbench v5.0 softwares. The Aberration Detection Method 2 (ADM2) algorithm was used to compute and assist the identification of aberrations for each sample.

source_name: Glioma Stem Cell line

label_protocol: 1µg of genomic DNA was labeled according to the Agilent guidelines (www.agilent.com). Sample DNA was labeled with Cy3 and the Human Genomic DNA: Male (Promega), used as reference DNA, was labeled with Cy5.

extract_protocol: Genomic DNA was isolated using the Wizard Genomic DNA Purification Kit (Promega).

source_name: Human Genomic DNA: Male (Promega)

tag: sample type

value: Genomic DNA comes from multiple anonymous donors.


title: C2C12_Myoblast_Rep1


title: Nemo-CRE + CLL V172

description:
Gene expression data of BMSC isolated from uninduced strain (Nemo-CRE) co-cultured with CLL V172
Nemo-CRE + CLL V172

value: CLL V172


title: EL08/V211

description: Gene expression data of EL08-1D2 cell line co-cultured with CLL V211 for 5 days

source_name: EL08-1D2 co-cultured with CLL

growth_protocol: 10x5 EL08-1D2 cells were plated in coated 6cm dishes.

extract_protocol: Total RNA was extracted from EL08-1D2 cells using the miRNeasy Mini Kit (Quiagen, Hilden, Germany) according to the manufacturer’s instruction.

treatment_protocol: After 24hours 30x10x6 primary CLL cells were seeded onto the feeder layer of EL08-1D2 cells. After 5 days, CLL cells were separated from co-cultures with stromal cells by repeated washing steps with PBS. Subsequently, single cell suspensions were treated with magnetic anti-CD19 beads to allow removal of remaining CLL cells. Flow-cytometry analysis indicated that more than 99% CD5+CD19+ cells were successfully isolated from CLL-stroma-co-cultures

value: stromal cells

tag: culture condition

value: co-cultured for 5 days with leukemic B-cells (CLL V211)


title: 786-O_NoE

description: male, renal cancer cell line, control

value: male

value: control

value: 786-O Cell Line


title: Patient1 IFN+RBV

source_name: Liver tissue IFN+RBV

value: D

value: IFN + RBV


title: G166_GSC line_3


title: CD8 memory T_untreated_responsive 2

city: New Haven

first: Wei

last: Zhang

state: Connecticut

institute: Yale School of Medicine

description: gene-level expression values were estimated by using IterPLIER algorithm implemented in the Affymetrix Expression Console software, core probesets analysis

hyb_protocol: Samples were tested with GeneChip Human Exon 1.0 ST Arrays (Affymetrix) by Microarray Core Facility at Yale Keck Biotechnology Resource Laboratory

scan_protocol: Samples were scanned by Microarray Core Facility at Yale Keck Biotechnology Resource Laboratory

data_processing: The gene-level expression values were estimated by using IterPLIER algorithm implemented in the Affymetrix Expression Console software. Partek Genomics Suite was used for downstream analysis to identify differentially expressed genes.

source_name: sorted CD8+CD45RO+ memory T cell, untreated, responsive individual 2

label_protocol: Samples were labeled by Microarray Core Facility at Yale Keck Biotechnology Resource Laboratory

growth_protocol: Peripheral blood mononuclear cells (PBMC) were isolated by Ficoll density gradient separation. PBMC were stained with CD3-PECy7, CD8-APC, and CD45RO-Pacific Blue, and CD3+CD8+CD45RO+ memory T cells were then separated by cell sorting with a FACSAria cell-sorting system.

extract_protocol: Total RNAs were isolated from CD8+ memory T cells by using a RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions.

treatment_protocol: FACS Sorted CD8+CD45RO+ memory T cells were either left untreated in RPMI-1640 complete medium or treated with IL-23 at 100ng/ml for 6 h at 37°C

tag: cell

value: Sorted CD8+CD45RO+ memory T cells

value: untreated

tag: il-23 responsiveness

value: responsive individual


title: CD8 memory T_untreated_Nonresponsive 2

source_name: sorted CD8+CD45RO+ memory T cell, untreated, nonresponsive individual 2

value: nonresponsive individual


title: CD8 memory T_IL23 treated_responsive 2

source_name: sorted CD8+CD45RO+ memory T cell, IL23 treated, responsive individual 2

value: IL23 treated


title: C2C12_Myoblast_Rep2


title: GBM7_GSC line_2


title: G179_GSC line_4


title: EL08/V163

description: Gene expression data of EL08-1D2 cell line co-cultured with CLL V163 for 5 days

tag: cell type

value: co-cultured for 5 days with leukemic B-cells (CLL V163)


title: CD8 memory T_IL23 treated_responsive 1

source_name: sorted CD8+CD45RO+ memory T cell, IL23 treated, responsive individual 1


title: GBM2_GSC line_1


title: EL08/V190

description: Gene expression data of EL08-1D2 cell line co-cultured with CLL V190 for 5 days

value: co-cultured for 5 days with leukemic B-cells (CLL V190)


title: Soleus_Muscle_Rep1

description: Gene Expression profiling of murine adult soleus (slow oxidative muscle).

value: Soleus muscle

value: Male


title: CD8 memory T_IL23 treated_Nonresponsive 2

source_name: sorted CD8+CD45RO+ memory T cell, IL23 treated, nonresponsive individual 2


title: EL08/V172

description: Gene expression data of EL08-1D2 cell line co-cultured with CLL V172 for 5 days

value: co-cultured for 5 days with leukemic B-cells (CLL V172)


title: Nemo-CRE + CLL V211

description:
Gene expression data of BMSC isolated from uninduced strain (Nemo-CRE) co-cultured with CLL V211
Nemo-CRE + CLL V211

value: Nemo wild type

value: femora

value: bone marrow stromal cells (BMSC)

value: CLL V211


title: CD8 memory T_IL23 treated_Nonresponsive 1

source_name: sorted CD8+CD45RO+ memory T cell, IL23 treated, nonresponsive individual 1


title: CD8 memory T_untreated_responsive 1

source_name: sorted CD8+CD45RO+ memory T cell, untreated, responsive individual 1


title: CD8 memory T_untreated_Nonresponsive 1

source_name: sorted CD8+CD45RO+ memory T cell, untreated, nonresponsive individual 1


title: FOXP3, mut, REP3, 0h

city: Milan

first: Jose

middle: Manuel

last: Garcia-Manteiga

address: Via Olgettina 58

department: Center for Translational Genomics and Bioinformatics

institute: OSR - San Raffaele Scientific Institute

description: Gene expression data from T effector cells with or without FOXP3 expression

hyb_protocol: About 5.5 μg of fragmented and labeled DNA target was hybridized to the Affymetrix GeneChip Human Gene 1.0 ST Array at 45°C for 17 h on a GeneChip Hybridization Oven 640 (Affymetrix).

scan_protocol: Hybridized arrays were washed and stained on a gene Chip Fluidics Station 450 and finally scanned on a Gene Chip Scanner 3000 7G (Affymetrix), generating an intensity file (*.CEL) for each array

data_processing: Data preprocessing was done using RMA quantile normalization by the <oligo> R package and differential gene expression was assesd by <limma> R package.

source_name: CD4+/CD25- T effector cells in resting phase

label_protocol: DNA was fragmented and end-labeled using the GeneChip WT Terminal Labeling Kit (Affymetrix)

growth_protocol: CD4+ T cell clones were stimulated by a feeder cell mixture containing 10^6 PBMCs from 3 different healthy donors/ml (irradiated with 6000 rads), 10^5 JY(Epstein Bar virus immortalized B cell limphoblastoid cell line)/ml (irradiated 10000 rads) and PHA (Roche Diagnostics 0.1 mg/ml). T cell clones were stimulated every 21 days with the same feeder mixture.

extract_protocol: Total RNA was extracted with Rnaesy Plus MINI Kit (Quiagen, Hilden, Germany) according to manufacture's instructions.

treatment_protocol: At day 14-16, T cell clones were left one day without IL2.  Cells were then left unstimulated (t0) or stimulated for 72hrs (72h) with anti-CD3 immoblized (10 mg/ml) in Tris-HCL 0.1M and soluble anti-CD28 mAB (1 mg/ml)

tag: foxp3 expression

value: NO

value: CD4+/CD25- T effector cell

value: IPEX disease carrier

tag: genotype

value: FOXP3 2T>C(mut)

value: female


title: FOXP3, mut, REP4, 72h

source_name: CD4+/CD25- T effector cells 72h after activation

tag: disease state

value: anti-CD3, anti-CD28 for 72 h


title: DKO1-SAHA-2

description: male, derivative of HCT116, engineerd disruption of DNA methyltransferase DNMT1 and DNMT3B, SAHA treated

hyb_protocol: RNA was amplified, fragmented and hybridized to the Illumina bead array using standard Illumina protocols

data_processing: Raw signal intensities for each probe were obtained using Illumina Beadstudio data analysis software and imported to the Bioconductor lumi package for data transformation and normalization. Probes with all samples ‘‘absent’’ (near or below background levels) were filtered. Loess normalization was performed

source_name: DKO1 Cell Line

extract_protocol: RNA was extracted using standard TRIzol procedure.

treatment_protocol: Cells were treated with 0.3 uM Aza and harvested after 72 hours or with 1 uM SAHA treatment and harvested after 24hours

value: SAHA treated

tag: cell line

value: DKO1 Cell Line


title: EL08/V131

description: Gene expression data of EL08-1D2 cell line co-cultured with CLL V131 for 5 days

value: stromal cells

value: co-cultured for 5 days with leukemic B-cells (CLL V131)


title: EL08/V128

description: Gene expression data of EL08-1D2 cell line co-cultured with CLL V128 for 5 days

value: co-cultured for 5 days with leukemic B-cells (CLL V128)


title: DKO1-Aza-2

description: male, derivative of HCT116, engineerd disruption of DNA methyltransferase DNMT1 and DNMT3B, AZA treated

value: AZA treated


title: DKO1-Aza-1


title: DKO1-SAHA-1


title: FOXP3, mut, REP2, 72h


title: EL08-1D2 rep2

description: Gene expression data of EL08-1D2 cell line

source_name: EL08-1D2 mono-culture

value: mono-cultured (control)


title: DKO1-2

description: male, derivative of HCT116, engineerd disruption of DNA methyltransferase DNMT1 and DNMT3B, control

value: control


title: FOXP3, mut, REP1, 0h


title: EL08-1D2 rep1


title: FOXP3, WT, REP5, 0h

value: YES

value: FOXP3 wild type


title: FOXP3, WT, REP2, 0h


title: FOXP3, WT, REP3, 72h


title: FOXP3, WT, REP1, 72h


title: FOXP3, WT, REP4, 0h


title: HCT116-SAHA-1

description: male, colorectal carcinoma cell line, SAHA treated, control

source_name: HCT116 Cell Line

value: HCT116 Cell Line


title: DKO1-1


title: HCT116-Aza-1

description: male, colorectal carcinoma cell line, AZA treated, control


title: Patient7 IFN

source_name: Liver tissue IFN

tag: group

value: B

value: IFN

value: hepatitis C

value: liver biopsy


title: veraison defoliation, replicate 3, harvest

city: Bologna

first: Chiara

last: Pastore

address: Viale Fanin, 46

institute: University of Bologna

description: Veraison defoliation,third biological replicate

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: The microarray was scanned using a ScanArray 4000XL (Perkin-Elmer) at 532 nm (Cy-3 absorption peak) and GenePix Pro7 software (Molecular Devices, Sunnyvale, CA, USA) according to the manufacturers’ instructions. Images were analyzed using NimbleScan v2.5 software (Roche).

data_processing: NimbleScan v2.5 software (Roche), produces Pair Files containing the raw signal intensity data for each probe and Calls Files with normalized expression data derived from the average of the intensities of the four probes for each gene. The normalized gene expression data were finally converted to log2 values.

organism: Vitis vinifera

source_name: Sangiovese berry

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Adult Sangiovese (Vitis vinifera L.) vines, clone 12T grafted to SO4, planted in the field in a vineyard in Bologna, Italy (44°30’N, 11°24’E), with North-South oriented rows vine spacing 1 m × 2.8 m, vertical  shoot positioned spur pruned cordon training system.

extract_protocol: Total RNA was extracted from the berry tissue without seeds using the Spectrum™ Plant Total RNA kit (Sigma-Aldrich, St. Louis, MO). RNA quality and quantity were determined using a Nanodrop 2000 instrument (Thermo Scientific, Wilmington, DE) and a Bioanalyzer Chip RNA 7500 series II (Agilent, Santa Clara, CA).

treatment_protocol: Nine vines per treatment, with the same cluster number at flowering (16 per vine), were selected in  a single uniform row and each vine was randomly assigned in three blocks to the three following groups: control (C, no treatment), pre-bloom defoliation (PBD), hand defoliation of main and lateral leaves in the first 6 basal shoot nodes at stage 17 (inflorescence fully developed, single flowers separated, according to Eichorn and Lorenz 1977, JD 147); veraison defoliation (VD), hand defoliation of main and lateral leaves in the first 6 basal shoot nodes at veraison (berries softening and °Brix ~8, JD 211).

tag: treatment

value: defoliation

tag: cultivar

value: Sangiovese

tag: phonological stage

value: veraison

tag: developmental stage

value: harvest

value: berry


title: veraison defoliation, replicate 2, harvest

description: Veraison defoliation, second biological replicate

tag: tissue


title: HCT116-2

description: male, colorectal carcinoma cell line, control


title: HCT116-SAHA-2

value: SAHA treated


title: HET-XX-4

city: Edinburgh

first: Ian

last: Adams

address: Crewe Road

department: Genome Regulation

country: United Kingdom

institute: MRC Human Genetics Unit

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: Background subtracted (method=bgAdjust), log-transformed (method=”log2”), quantile-normalized (method=”quantile”) using lumi in R.

source_name: E18.5 Tex19.1+/- XX placenta

label_protocol: Biotinylated cRNA was prepared using the Illumina TotalPrep RNA Amplification Kit (Ambion).

growth_protocol: Freshly dissected material

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen), and then treated with DNase I. Quality control was performed with Agilent Bioanalyser.

value: placenta

tag: strain

tag: gender

value: female

tag: genotype/variation


title: KO-XX-4

source_name: E18.5 Tex19.1-/- XX placenta


title: WT-XY-2

source_name: E18.5 Tex19.1+/+ XY placenta

value: male


title: pre-bloom defoliation, replicate 3, harvest

description: pre-bloom defoliation, third biological replicate

value: pre-bloom


title: veraison defoliation, replicate 1, harvest

description: Veraison defoliation, first biological replicate


title: HCT116-1

value: control


title: KO-XX-3


title: pre-bloom defoliation, replicate 2, harvest

description: pre-bloom defoliation, second biological replicate


title: HCT116-Aza-2

value: AZA treated


title: Pooled genomic DNA from adjacent normal tissue (23 patients) #2

city: Tuebingen

first: Michael

middle: H.

last: Walter

address: Calwer Str. 7

department: Department of Medical Genetics

institute: University of Tuebingen

description: Normal pool 2

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 BeadArray Reader using standard recommended Illumina scanner setting.

data_processing: BeadStudio software v3.2, Bioconductor 'methylumi' package

source_name: normal colon

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted from CRC and normal colon tissue samples using Gentra Puregene Tissue Kit (Qiagen, Hilden, Germany) according to standard instructions.

value: normal-adjacent colonic tissues

tag: methylation epigenotypes (me)

value: Control


title: HET-XX-3


title: veraison defoliation, replicate 3, end of veraison

value: end of veraison


title: KO-XY-2

source_name: E18.5 Tex19.1-/- XY placenta


title: KO-XY-1


title: Pooled genomic DNA from adjacent normal tissue (23 patients) #3

description: Normal pool 3


title: pre-bloom defoliation, replicate 1, harvest

description: pre-bloom defoliation, first biological replicate


title: veraison defoliation, replicate 2, end of veraison


title: veraison defoliation, replicate 1, end of veraison


title: HET-XX-2


title: KO-XX-2


title: WT-XY-1


title: Pooled genomic DNA from adjacent normal tissue (24 patients) #1

description: Normal pool 1


title: Pooled genomic DNA from LME-type colorectal cancer tissue (6 patients) #5

description: LME pool 5

source_name: LME-CRC

value: colorectal cancer tissues

value: low (LME)


title: Pooled genomic DNA from LME-type colorectal cancer tissue (5 patients) #4

description: LME pool 4


title: pre-bloom defoliation, replicate 3, end of veraison

value: defoliation


title: pre-bloom defoliation, replicate 2, end of veraison

value: Sangiovese


title: CypD -/-_C1

city: Philadelphia

first: Louise

middle: C

last: Showe

address: 3601 Spruce St

institute: The Wistar Institute

hyb_protocol: Hyb on Illumina Mouse-WG6 v2 Expression BeadChip Kit using Illumina whole-Genome Gene Exprssion with Intellihyb Seal system which detect signal with streptavidin-Cy3

scan_protocol: Illumina Setting with PMTFactor=2

data_processing: Illumina BeadStudio v.3.0 software was used to export expression levels and detect p-values for each probe of each sample. Arrays were quantile-normalized between each other and filtered to remove non-informative probes (probes with a detection p-value > 0.05 in all samples)

source_name: CypD KO_MEFs

label_protocol: Biotin Labeling of RNA at 250ng with Ambion Illumina® TotalPrep RNA Amplification Kit

growth_protocol: Mouse embryonic fibroblast (MEF) cultures were established from embryonic day-13.5 embryos according to standard procedures. MEFs were maintained in DMEM plus 10% FCS, l-glutamine, and penicillin/streptomycin (Invitrogen).

extract_protocol: Total RNA was extracted using the TRI Reagent (Ambion) method and treated with DNaseI (Fermentas)

tag: strain background

value: CypD knockout

tag: tissue origin

value: E13.5 embryos

value: mouse embryonic figroblasts (MEFs)

tag: replicate

value: C


title: foetal-NSCs_spinal cord

hyb_protocol: Hybridization and wash were performed following Agilent guidelines (see manufacturer's web site at http://www.agilent.com/).

scan_protocol: Scanned on an Agilent G2565AA scanner. mages were quantified using Agilent Feature Extraction Software (v 10.7.3.1).

data_processing: Data were processed using Agilent Feature Extraction Software (v 10.7.3.1) and the Agilent Genomic Workbench (v 5.0.14). The algorithm used to obtain z-score values is the Methylation status detection algorithm that is integrated in the Genomic Workbench software (Agilent Technologies). Specifically, as described in the Agilent Methylation (CH3) Analysis User Guide (available at http://www.genomics.agilent.com/files/Manual/G3800-90010_MethylationAnalysis.pdf). The algorithm first bins the probes by their melting temperature. For each bin, it applies Gaussian fits using one of three models. It fits the probe log-ratios to Gaussians, using a local searching algorithm called *random * *hill climbing*  *Z*- scores and *p*- values derived from the Gaussian data give probabilities and confidence values for methylated and unmethylated probe populations. Additionally the Z-score represents the number of standard deviations separating the smoothed adjusted log-ratio of a probe from the median of the null probes according to their Tm. The combined Z-score is the combination of both the methylated and unmethylated ZScores. For further information about the algorithm and the Z-core values please refer to the methylation analysis user guide.

source_name: human foetal NSCs isolated from the spinal cord

label_protocol: IP and Total DNA were labeled according to manufacturer's instructions with Cy5 and Cy3 fluorescent dyes, respectively (see manufacturer's web site at http://www.agilent.com/).

extract_protocol: Total DNA from cell lines was isolated using the Wizard Genomic DNA Purification Kit (Promega) following manufacturer's instructions. Total DNA from FFPE samples was isolated using Invisorb Spin FFPE Tissue Kit following manufacturer's instructions. 5µg of whole DNA were diluited in 1X PBS (for each sample).

value: CB660SP form spinal cord

tag: antibody

tag: antibody vendor

value: Eurogentec

tag: sample type

value: input DNA


title: HET-XX-1

value: placenta

value: female


title: GBM pool_5 FFPE biopsies

source_name: DNA pool isolated from 5 FFPE-GBM samples

tag: cell line

value: 1 pool from 5 GBM biopsies

source_name: DNA pool isolated from FFPE-GBM samples


title: Pooled genomic DNA from LME-type colorectal cancer tissue (5 patients) #3

description: LME pool 3


title: Pooled genomic DNA from LME-type colorectal cancer tissue (5 patients) #2

description: LME pool 2


title: Pooled genomic DNA from LME-type colorectal cancer tissue (5 patients) #1

description: LME pool 1


title: pre-bloom defoliation, replicate 1, end of veraison

value: pre-bloom

value: berry


title: pre-bloom defoliation, replicate 2, beginning of veraison

value: beginning of veraison


title: KO-XX-1


title: foetal NSCs_forebrain

source_name: human foetal NSCs isolated from the forebrain

value: CB660 from forebrain


title: pre-bloom defoliation, replicate 3, beginning of veraison


title: control, untreated, replicate 3, beginning of veraison

description: Control third biological replicate

value: control


title: GBM2_GSC line

source_name: Glioma Stem Cell line isolated from patient affected by GBM


title: WT_B1

value: wild type

tag: cell type

value: B


title: G144_GSC line


title: G166_GSC line


title: Pooled genomic DNA from LME-type colorectal cancer tissue (6 patients) #6

description: LME pool 6

value: colorectal cancer tissues

value: low (LME)


title: Pooled genomic DNA from IME-type colorectal cancer tissue (6 patients) #6

description: IME pool 6

source_name: IME-CRC

value: intermediate (IME)


title: CypD -/-_A1

value: CypD knockout

value: E13.5 embryos

value: mouse embryonic figroblasts (MEFs)

value: A


title: WT_C1

value: C


title: control, untreated, replicate 2, beginning of veraison

description: Control second biological replicate

tag: treatment

value: Sangiovese


title: Pooled genomic DNA from IME-type colorectal cancer tissue (6 patients) #5

description: IME pool 5


title: WT_A1


title: control, untreated, replicate 1, beginning of veraison

description: Control first biological replicate

tag: cultivar


title: Pooled genomic DNA from IME-type colorectal cancer tissue (5 patients) #4

description: IME pool 4


title: C.albicans_milbe_3

description: Milbemycin-treated cells

organism: Candida albicans

value: treated


title: Pooled genomic DNA from IME-type colorectal cancer tissue (5 patients) #3

description: IME pool 3


title: Pooled genomic DNA from IME-type colorectal cancer tissue (5 patients) #2

description: IME pool 2


title: Pooled genomic DNA from HME-type colorectal cancer tissue (4 patients) #6

description: HME pool 6

source_name: HME-CRC

value: high (HME)


title: control 4

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

data_processing: The data were normalised using quantile normalisation in R

source_name: mouse BM-macrophages

label_protocol: Biotinylated cRNA were prepared with the TargetAmpTM Nano-gTM Biotin-aRNA Labeling Kit for the Illumina® System

growth_protocol: Male and female C57BL/6 and vav1-/- mice were bred under specific pathogen–free conditions  and were used at 7–12 weeks of age

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit.

value: mouse BM-macrophages

tag: genotype

value: WT


title: C.albicans_milbe_1

description: Milbemycin-treated cells

extract_protocol: total RNA extraction using Trizol


title: Pooled genomic DNA from HME-type colorectal cancer tissue (4 patients) #5

description: HME pool 5


title: C.albicans_milbe_2

description: Milbemycin-treated cells


title: VAV ko 4


title: C.albicans_control_3

description: untreated cells

value: untreated


title: Pooled genomic DNA from HME-type colorectal cancer tissue (3 patients) #3

description: HME pool 3


title: Pooled genomic DNA from IME-type colorectal cancer tissue (5 patients) #1

description: IME pool 1


title: VAV ko 3


title: control 3


title: VAV ko 2


title: Pooled genomic DNA from HME-type colorectal cancer tissue (3 patients) #2

description: HME pool 2


title: Rec12_set1D

status: Public on Mar 07 2013

city: Meguro-ku

first: Shintaro

last: YAMADA

state: Tokyo

address: 3-8-1 Komaba

institute: University of Tokyo

description:
Rec12 / WCE, meiosis 5h, set1+ deletion cells
input CEL: WCE_2.CEL

hyb_protocol: 16 h at 45C using a hybridization oven 640 (affymetrix) as described in the Affymetrix Chromatin Immunoprecipitation Assay Protocol (P/N 702238)

scan_protocol: Fluidics station 400 protocol EukGE-WS2v5 (affymetrix) was performed to wash and stain arrays. The arrays were scanned on GeneChip Scanner 3000 7G (affymetrix).

data_processing: Data were quantile normalized and smoothed with Affymetrix Tiling Analysis Software

organism: Schizosaccharomyces pombe

source_name: FLAG ChIP DNA from rec12+-FLAG set1+ deletion cells harvested 5h after meiosis induction

label_protocol: Amplified DNA were labeled with biotin as described (Katou et al., Nature 424:1078-83)

growth_protocol: Cells in a pat1-114 rad50S rec12+-FLAG background were induced to enter meiosis by the haploid meiosis system, and harvested five hours after the induction.

extract_protocol: Cells were crosslinked with formaldehyde and ChIPs were performed as previously described (Yamada et al., EMBO J 23: 1792-803) except for using following antibodies. Anti-H3K9ac and -H3K14ac antibodies were purchased from Millipore.  Anti-H3K4me3, and -H3 antibodies were from Abcam. Anti-FLAG was from Sigma-Aldrich.

tag: fraction

value: ChIP

value: FLAG

source_name: Input DNA from rec12+-FLAG wild type cells harvested 5h after meiosis induction

value: input


title: Rec12_wt

description:
Rec12 / WCE, meiosis 5h, wild type cells
input CEL: WCE_2.CEL

source_name: FLAG ChIP DNA from rec12+-FLAG wild type cells harvested 5h after meiosis induction


title: C.albicans_control_2

description: untreated cells


title: Rec12_H3K9A

description:
Rec12 / WCE, meiosis 5h, H3K9A cells
input CEL: WCE_2.CEL

source_name: FLAG ChIP DNA from rec12+-FLAG H3K9A cells harvested 5h after meiosis induction

value: rec12+-FLAG wild type cells harvested 5h after meiosis induction


title: H3K14ac

description: H3K14ac / H3Cter, meiosis 1h

source_name: H3K14ac ChIP DNA from cells harvested 1h after meiosis induction

growth_protocol: Cells in a pat1-114 background were induced to enter meiosis by the haploid meiosis system, and harvested one hour after the induction.

extract_protocol: Cells were crosslinked with formaldehyde and ChIPs were performed as previously described (Yamada et al., EMBO J 23: 1792-803) except using following antibodies. Anti-H3K9ac and -H3K14ac antibodies were purchased from Millipore.  Anti-H3K4me3, and -H3 antibodies were from Abcam.

value: Millipore

source_name: H3Cter ChIP DNA from cells harvested 1h after meiosis induction

value: Abcam


title: H3K4me3

description: H3K4me3 / H3Cter, meiosis 1h

source_name: H3K4me3 ChIP DNA from cells harvested 1h after meiosis induction


title: H3Cter

description: H3Cter / WCE, meiosis 1h

source_name: Input DNA from cells harvested 1h after meiosis induction


title: H3K9ac

description: H3K9ac / H3Cter, meiosis 1h

source_name: H3K9ac ChIP DNA from cells harvested 1h after meiosis induction


title: C.albicans_control_1

description: untreated cells


title: Pooled genomic DNA from HME-type colorectal cancer tissue (3 patients) #4

description: HME pool 4

tag: tissue

value: colorectal cancer tissues


title: Pooled genomic DNA from HME-type colorectal cancer tissue (3 patients) #1

description: HME pool 1


title: VAV ko 1

tag: strain


title: control 1


title: FOXP3, mut, REP5, 0h

description: Gene expression data from T effector cells with or without FOXP3 expression

source_name: CD4+/CD25- T effector cells in resting phase

tag: foxp3 expression

value: NO

value: CD4+/CD25- T effector cell

tag: disease state

value: IPEX disease carrier

value: FOXP3 2T>C(mut)

tag: gender

value: female


title: control 2


title: pre-bloom defoliation, replicate 1, beginning of veraison

source_name: Sangiovese berry

value: defoliation

value: Sangiovese

tag: phonological stage

value: pre-bloom

tag: developmental stage

value: beginning of veraison

value: berry


title: HPV-negative OSCC #139

city: Seattle

first: Chu

last: Chen

state: Washington

address: 1100 Fairview Ave. N, PO Box 19024, M/S M5-C800

department: PHS

institute: Fred Hutchinson Cancer Research Center

hyb_protocol: The cRNA was hybridized to an Affymetrix U133 2.0 Plus GeneChip arrays per Affymetrix protocols

scan_protocol: GeneChip arrays were scanned using an Affymetrix GeneChip arrays Scanner 3000 7G in the Fred Hutchinson Cancer Research Center's Genomics Shared Resources

data_processing: We used gcRMA algorithm from Bioconductor to extract gene expression values and perform normalization. The data were analyzed using a regression-based, estimating equations approach implemented in GenePlus software. The hierarchical clustering was performed using Affymetrix GeneSpring software GX 7.3.1.

source_name: HPV-negative OSCC patient

label_protocol: Biotin-labeled cRNA were prepared from 1.0 to 2.5 ug of total RNA using the GeneChip Expression 3'-Amplification Reagents Kit per manufacturer's protocol

extract_protocol: The RNA and DNA from each specimen were simultaneously extracted using TRIzol method.

tag: tissue type

value: HPV-negative oral squamous cell carcinoma (OSCC)

tag: tumor stage

value: I/II

tag: age

tag: Sex

value: M

tag: vital

value: Alive

tag: fu time

value: uni-modality


title: HPV-negative OSCC #141

value: III/IV

value: F

value: Dead-oral ca

tag: treatment

value: multii-modality


title: HPV-negative OSCC #131


title: HPV-negative OSCC #147


title: CypD -/-_B1

source_name: CypD KO_MEFs

tag: strain background

tag: genotype/variation

value: CypD knockout

tag: tissue origin

value: E13.5 embryos

tag: cell type

value: mouse embryonic figroblasts (MEFs)

tag: replicate

value: B


title: HPV-negative OSCC #144


title: HPV-negative OSCC #143


title: HPV-negative OSCC #151


title: HPV-negative OSCC #129


title: HPV-negative OSCC #140

value: Dead -unk cause


title: 252800515186-2

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

description: KI1 syn 7/10

hyb_protocol: Agilent : 200.0 ng at 65 degree_C during 17 hours.

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

data_processing: LimmaGUI analysis within custom R script with Quantile Normalization.

source_name: KI1 syn 7/10

label_protocol: Agilent - Low RNA input QuickAmp.

extract_protocol: Chomzynski extraction protocol.

value: knock-out

tag: tissue

value: Brain synaptosome

tag: amount in (µg)

tag: rin number


title: 252800515186-1

description: WT3 syn 7/10

source_name: WT3 syn 7/10

value: wild type


title: 252800515185-8

description: WT2 syn 7/10

source_name: WT2 syn 7/10


title: HPV-negative OSCC #126

value: HPV-negative oral squamous cell carcinoma (OSCC)

value: Dead-non OC


title: HPV-negative OSCC #124

value: M


title: HPV-negative OSCC #128

value: I/II


title: HPV-negative OSCC #127

value: uni-modality


title: HPV-negative OSCC #123

value: III/IV

value: Alive


title: 252800515185-7

description: WT1 syn 7/10

source_name: WT1 syn 7/10


title: HPV-negative OSCC #121


title: HPV-negative OSCC #136


title: HPV-negative OSCC #117

value: Dead-oral ca


title: 252800515186-3

description: KI2 syn 7/10

source_name: KI2 syn 7/10


title: 252800515186-4

description: KI3 syn 7/10

source_name: KI3 syn 7/10


title: HPV-negative OSCC #119

value: F


title: HPV-negative OSCC #118


title: HPV-negative OSCC #108


title: HPV-negative OSCC #114


title: HPV-negative OSCC #100


title: HPV-negative OSCC #101

value: multii-modality


title: HPV-negative OSCC #107


title: HPV-negative OSCC #106


title: HPV-negative OSCC #115


title: HPV-negative OSCC #103


title: HPV-negative OSCC #102


title: HPV-negative OSCC #84


title: HPV-negative OSCC #110


title: HPV-negative OSCC #113


title: HPV-negative OSCC #94


title: HPV-negative OSCC #90


title: Kc vs Input rep2

city: Cambridge

first: Sarah

last: Bray

address: Downing Street

department: PDN

institute: University  of Cambridge

hyb_protocol: 34 µg labeled sample DNA and 34 µg labeled control DNA were combined, dried in a speed vac with medium heat and resuspended in 12.3 µl water.  For each hybridisation 29.5µl 2X Hybridization Buffer, 11.8µl Hybridization Component A and 1.2µl Alignment Oligo (NimbleGen Hybridization Kit) were combined and 31.7µl added to each hybridisation sample. Samples were incubated at +95°C for 5 minutes, 42°C for 5 minutes and 41 µl loaded onto the array. The hybridisation was performed to NimbleGen D. melanogaster ChIP-chip 2.1M Whole-Genome Tiling Arrays in the Nimbelegen hybridisation station at 42°C (mix mode B) for 18 hours. Post hybridisation washes were performed according to the NimbleGen Wash Buffer Kit instructions.

scan_protocol: Arrays are scanned at 5 µm resolution with a GenePix 4000B (Axon) dual laser scanner at 100% Power, with Lines to average = 1 and Focus position = 0 at their respective optimal PMT gains. Signal for Cy3 and Cy5 channels are balanced using the histogram view in the GenePix software. Images are saved as Single-image TIFF.

data_processing: Images are processed with NimbleScan v2.4 software (Roche-Nimblegen) as per manufacturer instructions. Raw data files (*.pair) are created for each channel. The *.pair data files are then loaded into limma (Bioconductor) and normalised with the vsn package (Bioconductor). The resulting ratios are log2 ratio of ChIP/Input.

organism: Drosophila melanogaster

source_name: Kc replicate 2

label_protocol: In duplicate reactions: 1 μg of amplified DNA with 30 µl 2.5X Random Primers Solution (BioPrime DNA labelling kit, Life Technologies) was incubated at 100°C for 5 minutes and then cooled on ice. The samples were labelled using the BioPrime DNA labelling kit (Life Technologies) in the presence of 4.5nmol fluorescently labelled Cy3- or Cy5-dCTP (GE Healthcare) and 72 U of Klenow at 37°C. After 2 hours the reactions were stopped with 7.5 µl Stop Buffer (BioPrime DNA labelling kit, Life Technologies). Duplicate reactions were pooled into single tubes and then precipitated with 165 µl Isopropanol and 0.2M sodium chloride and washed with cold 80% ethanol. The DNA was resuspened in 50 µl water and quantified on a Nanodrop spectrophotometer (Thermo Scientific).

growth_protocol: Schneider's Drosophila Medium (Invitrogen) supplemented with 5% fetal bovine serum (Sigma) and 1% penicillin-streptomycin in a incubator at 25°C.

extract_protocol: Kc cells were fixed with 1% fresh formaldehyde (SIGMA) after 30 minutes of 2mM EDTA treatment and then processed as described in Krejci et al. 2007.

treatment_protocol: 2mM EDTA for 30 minutes

tag: cell line

value: Kc167 cells

value: EDTA treated to elicit Notch activation

tag: chip antibody

value: Su(H) antibody (Santa Cruz, # sc-15813)

source_name: Total input replicate 2

value: none (input)


title: HPV-negative OSCC #88

tag: tissue type


title: HPV-negative OSCC #96

tag: tumor stage


title: HPV-negative OSCC #87

tag: age


title: HPV-negative OSCC #81

tag: Sex


title: HPV-negative OSCC #85

tag: vital


title: HPV-negative OSCC #116

tag: fu time


title: HPV-negative OSCC #86

tag: treatment


title: HPV-negative OSCC #83


title: HPV-negative OSCC #92


title: HPV-negative OSCC #99


title: HPV-negative OSCC #104

value: Dead -unk cause


title: HPV-negative OSCC #82


title: HPV-negative OSCC #134


title: Kc vs Input rep1

source_name: Kc replicate 1

source_name: Total input replicate 1


title: HPV-negative OSCC #80


title: HPV-negative OSCC #75


title: HPV-negative OSCC #70


title: HPV-negative OSCC #43


title: HPV-negative OSCC #73


title: HPV-negative OSCC #44


title: HPV-negative OSCC #47


title: HPV-negative OSCC #67


title: HPV-negative OSCC #68


title: HPV-negative OSCC #77


title: HPV-negative OSCC #72


title: HPV-negative OSCC #53


title: HPV-negative OSCC #58


title: HPV-negative OSCC #46

value: unknown


title: HPV-negative OSCC #45


title: HPV-negative OSCC #69


title: HPV-negative OSCC #51


title: HPV-negative OSCC #71


title: HPV-negative OSCC #55


title: HPV-negative OSCC #39


title: HPV-negative OSCC #57


title: HPV-negative OSCC #60


title: HPV-negative OSCC #38


title: Kc vs Input rep3

source_name: Kc replicate 3

source_name: Total input replicate 3


title: HPV-negative OSCC #35


title: HPV-negative OSCC #34


title: HPV-negative OSCC #41


title: HPV-negative OSCC #40


title: HPV-negative OSCC #79


title: HPV-negative OSCC #29


title: HPV-negative OSCC #49


title: HPV-negative OSCC #33


title: HPV-negative OSCC #27


title: HPV-negative OSCC #26


title: HPV-negative OSCC #21


title: HPV-negative OSCC #15


title: HPV-negative OSCC #32


title: HPV-negative OSCC #22


title: HPV-negative OSCC #24


title: HPV-negative OSCC #13


title: HPV-negative OSCC #6


title: HPV-negative OSCC #14


title: HPV-negative OSCC #8


title: HPV-negative OSCC #12


title: HPV-negative OSCC #17


title: HPV-negative OSCC #3


title: HPV-negative OSCC #23


title: HPV-negative OSCC #1


title: HPV-negative OSCC #5


title: HPV-negative OSCC #25


title: HPV-negative OSCC #28


title: DMSO 6 hour treatment - replicate 1

first: Richard

middle: A

last: Young

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

hyb_protocol: Following fragmentation, 12.5 ug of aRNA were hybridized at 45C for 16 hr at 60RPM on GeneChip Arrays (PrimeView). GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the manurfacturer's instructions, using the buffers provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 and images were extracted with Affymetrix GeneChip Expression Console. A CDF containing the ERCC probes was provided by Affymetrix.

data_processing:
A CDF provided by Affymetrix, which contained the ERCC probes (PrimeView_withERCC_binary.cdf) was used instead of the standard PrimeView cdf.
The data were analyzed with Bioconductor using the MAS5 nomalization method. Then, these data were renormalized to the external spike-ins. See manuscript for additional details.

source_name: multiple myeloma

label_protocol: Biotinylated aRNA was prepared according to the standard Affymetrix protocol from 100 ng total RNA (GeneChip 3' IVT Express Kit User Manual, 2009, Affymetrix).

growth_protocol: RPMI 1640 supplemented with 10% FCS and 1% GlutaMAX

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
External spike-in RNAs (ERCC ExFold RNA Spike-In kit, Ambion, 4456739) were added based on cell number. See manuscript for details.

treatment_protocol: 0.05% DMSO for 6 hour

value: 0.05% DMSO 6 hour


title: 50nm JQ1 6 hour treatment - replicate 2

treatment_protocol: 50nM JQ1 treatment for 6 hour

value: 50nm JQ1 6 hour


title: HPV-negative OSCC #11

value: HPV-negative oral squamous cell carcinoma (OSCC)


title: 5000nm JQ1 6 hour treatment - replicate 1

treatment_protocol: 5000nM JQ1 treatment for 6 hour

value: 5000nm JQ1 6 hour


title: 5000nm JQ1 6 hour treatment - replicate 2


title: 500nm JQ1 6 hour treatment - replicate 2

treatment_protocol: 500nM JQ1 treatment for 6 hour

value: 500nm JQ1 6 hour


title: 500nm JQ1 30 minute treatment - replicate 1

treatment_protocol: 500nM JQ1 treatment for 30 minutes

value: 500nm JQ1 30 minute


title: 500nm JQ1 30 minute treatment - replicate 2


title: 500nm JQ1 3 hour treatment - replicate 1

treatment_protocol: 500nM JQ1 treatment for 3 hour

value: 500nm JQ1 3 hour


title: 50nm JQ1 6 hour treatment - replicate 1


title: WT - replicate 1


title: 500nm JQ1 6 hour treatment - replicate 1


title: 500nm JQ1 1 hour treatment - replicate 2

treatment_protocol: 500nM JQ1 treatment for 1 hour

value: 500nm JQ1 1 hour


title: 5nm JQ1 6 hour treatment - replicate 2

treatment_protocol: 5nM JQ1 treatment for 6 hour

value: 5nm JQ1 6 hour


title: DMSO 6 hour treatment - replicate 2


title: Fat body_pool 5_dsRNA-Vg

city: São Carlos

first: Francis

middle: M. F.

last: Nunes

state: São Paulo

address: Rodovia Washington Luís, km 235, SP-310

department: Departamento de Genética e Evolução

country: Brazil

institute: Universidade Federal de São Carlos

description: small RNA fraction (enriched miRNA)

hyb_protocol: Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://microrna.sanger.ac.uk/sequences/) 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 uL 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: Background was determined using a regression-based background mapping method. The regression was performed on 5% to 25% of the lowest intensity data points excluding blank spots. Raw data matrix was then subtracted by the background matrix. Normalization was carried out using a LOWESS (Locally-weighted Regression) method on the background-subtracted data. The normalization is to remove system related variations, such as sample amount variations, different labeling dyes, and signal gain differences of scanners so that biological variations can be faithfully revealed [Bolstad BM, Irizarry RA, Astrand M, Speed TP. (2003). A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics. 19(2):185-193.]. A transcript to be listed as detectable must meet at least two conditions: signal intensity higher than 3×(background standard deviation) and spot CV < 0.5. CV is calculated by (standard deviation)/(signal intensity). When repeating probes are present on an array, a transcript is listed as detectable only if the signals from at least 50% of the repeating probes are above detection level. t-Tests were performed between “control” and “test” sample groups. T-values were calculated for each miRNA, and p-values were computed from the theoretical t-distribution. miRNAs with p-values below a critical p-value (typically 0.01) are selected for cluster analysis. The clustering was done using hierarchical method and was performed with average linkage and Euclidean distance metric. All data processes, except the clustering plot, were carried out using computer programs developed in-house at LC Sciences. The clustering plot was generated using TIGR MeV (Multiple Experimental Viewer) software from The Institute for Genomic Research.

organism: Apis mellifera

source_name: knockdown forager fat body

label_protocol: Microarray assay was performed using a service provider (LC Sciences). The assay started from 2 µg total RNA samples which were 3’-extended with a poly(A) tail using poly(A) polymerase. An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent Cy3 dye staining.

extract_protocol: The abdominal carcass (lined with fat body) of each bee was separately preserved in 500 µL of QIAzol (Qiagen) and stored at -80ºC until RNA isolation.  In order to separate large (>200 nucleotides, for knockdown validation) and small (<200 nucleotides, rich in microRNAs, for array experiments) RNA fractions, miRNeasy kit (Qiagen) and RNeasy MinElute Cleanup kit (Qiagen) were combined (including a DNase treatment), following manufacturer's instructions.

treatment_protocol: Newly-emerged workers were dorsally injected under the 5th abdominal segment with a volume of 2 µL (10 µg/µL) of double-stranded RNA (dsRNA) against Vitellogenin (dsRNA-Vg) or against Green Fluorescent Protein (dsRNA-GFP) as the sham control.

value: 15-day-old adult worker

value: fat body


title: Fat body_pool 6_dsRNA-Vg

description: small RNA fraction (enriched miRNA)

value: double-stranded RNA (dsRNA) against Vitellogenin (dsRNA-Vg)


title: 500nm JQ1 1 hour treatment - replicate 1


title: 5nm JQ1 6 hour treatment - replicate 1


title: WT - replicate 2


title: 500nm JQ1 3 hour treatment - replicate 2


title: Fat body_pool 3_dsRNA-Vg

description: small RNA fraction (enriched miRNA)


title: Patient sample 98

city: Oklahoma City

first: Bart

last: Frank

state: OK

institute: OMRF

description: SAMPLE 78

hyb_protocol: cRNA was hybridized to Illumina WG-6 version 3 Expresion BeadChips (Illumina Inc, San Diego, CA) and washed according to the manufacturer’s protocol.

scan_protocol: Microarrays were then scanned using an Illumina iSCAN scanner.

data_processing: Signal intensities were normalization (signal - average)/standard deviation after use of internal standards that discriminate expressed signal intensities from background intensities. Data were analyzed using the associative t-test (for details of normalization and analysis see: Bioinformatics. 2003;19(2):204-211; and Nucleic acids research. 2009;37(19):6323-6339)

source_name: Whole blood leukocytes

label_protocol: RNA was labeled using the Illumina TotalPrep RNA Amplification Kit according to the manufacturer's protocol (Ambion).

growth_protocol: Peripheral blood was collected in PAXgene RNA tubes.

extract_protocol: Total RNA was extracted with the PAXgene Blood RNA Kit following the manufacturer's protocol. RNA encoding α and β globin was reduced using GLOBINclear Human kit (Ambion) and the manufacturer's protocol.

treatment_protocol: PAXgene RNA tubes were incubated at room temperature for 2 hours, frozen at -20°C, and then stored at -80°C prior to RNA isolation. Prior to extraction, samples were thawed at room temperature.

tag: disease state

value: TTP remission

value: Whole blood leukocytes


title: Patient sample 67

description: SAMPLE 75


title: Patient sample 65

description: SAMPLE 73


title: Fat body_pool 2_dsRNA-Vg

description: small RNA fraction (enriched miRNA)

tag: genotype/variation


title: Patient sample 7

description: SAMPLE 74


title: Fat body_pool 4_dsRNA-GFP

description: small RNA fraction (enriched miRNA)

source_name: control forager fat body

value: double-stranded RNA (dsRNA) against Green Fluorescent Protein (dsRNA-GFP)


title: Fat body_pool 1_dsRNA-Vg

description: small RNA fraction (enriched miRNA)


title: Fat body_pool 3_dsRNA-GFP

description: small RNA fraction (enriched miRNA)


title: Fat body_pool 5_dsRNA-GFP

description: small RNA fraction (enriched miRNA)


title: Patient sample 43

description: SAMPLE 76


title: Fat body_pool 4_dsRNA-Vg

description: small RNA fraction (enriched miRNA)


title: Fat body_pool 6_dsRNA-GFP

description: small RNA fraction (enriched miRNA)


title: Patient sample 58

description: SAMPLE 70


title: Fat body_pool 2_dsRNA-GFP

description: small RNA fraction (enriched miRNA)


title: Control sample 73

description: SAMPLE 65

value: Healthy control


title: Control sample 99

description: SAMPLE 77


title: Patient sample 19

description: SAMPLE 69


title: Control sample 4

description: SAMPLE 59


title: Patient sample 66

description: SAMPLE 71


title: Control sample 25

description: SAMPLE 64


title: Patient sample 20

description: SAMPLE 72


title: Patient sample 54

description: SAMPLE 60


title: Patient sample 32

description: SAMPLE 55


title: Brain_pool 6_dsRNA-Vg

description: small RNA fraction (enriched miRNA)

source_name: knockdown forager brain

label_protocol: Microarray assay was performed using a service provider (LC Sciences). The assay started from 1 µg total RNA samples which were 3’-extended with a poly(A) tail using poly(A) polymerase. An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent Cy3 dye staining.

extract_protocol: The dissected brain of each bee was separately preserved in 500 µL of QIAzol (Qiagen) and stored at -80ºC until RNA isolation.  In order to separate large (>200 nucleotides, for knockdown validation) and small (<200 nucleotides, rich in microRNAs, for array experiments) RNA fractions, miRNeasy kit (Qiagen) and RNeasy MinElute Cleanup kit (Qiagen) were combined (including a DNase treatment), following manufacturer's instructions.

value: brain


title: Control sample 24

description: SAMPLE 62


title: Control sample 56

description: SAMPLE 57


title: Control sample 75

description: SAMPLE 67


title: Brain_pool 5_dsRNA-Vg

description: small RNA fraction (enriched miRNA)


title: Control sample 60

description: SAMPLE 54


title: Control sample 70

description: SAMPLE 58


title: Patient sample 33

description: SAMPLE 61


title: Control sample 53

description: SAMPLE 68


title: Control sample 29

description: SAMPLE 63


title: Control sample 71

description: SAMPLE 66


title: Patient sample 57

description: SAMPLE 56


title: Patient sample 68

description: SAMPLE 53


title: Brain_pool 4_dsRNA-Vg

description: small RNA fraction (enriched miRNA)


title: Control sample 48

description: SAMPLE 51


title: Brain_pool 3_dsRNA-Vg

description: small RNA fraction (enriched miRNA)


title: Brain_pool 2_dsRNA-Vg

description: small RNA fraction (enriched miRNA)


title: Fat body_pool 1_dsRNA-GFP

description: small RNA fraction (enriched miRNA)


title: Patient sample 22

description: SAMPLE 52


title: Control sample 46

description: SAMPLE 50


title: Control sample 9

description: SAMPLE 49


title: Patient sample 50

description: SAMPLE 46


title: Control sample 13

description: SAMPLE 47


title: Patient sample 51

description: SAMPLE 48


title: Control sample 45

description: SAMPLE 44


title: Control sample 76

description: SAMPLE 43


title: Brain_pool 4_dsRNA-GFP

description: small RNA fraction (enriched miRNA)

source_name: control forager brain


title: Control sample 35

description: SAMPLE 40


title: Brain_pool 5_dsRNA-GFP

description: small RNA fraction (enriched miRNA)


title: Brain_pool 2_dsRNA-GFP

description: small RNA fraction (enriched miRNA)


title: Patient sample 44

description: SAMPLE 45


title: Brain_pool 3_dsRNA-GFP

description: small RNA fraction (enriched miRNA)


title: Brain_pool 1_dsRNA-Vg

description: small RNA fraction (enriched miRNA)


title: Brain_pool 1_dsRNA-GFP

description: small RNA fraction (enriched miRNA)


title: Control sample 37

description: SAMPLE 38


title: Control sample 12

description: SAMPLE 36


title: Control sample 14

description: SAMPLE 39


title: Patient sample 40

description: SAMPLE 35


title: Control sample 42

description: SAMPLE 34


title: Patient sample 38

description: SAMPLE 37


title: Control sample 55

description: SAMPLE 32


title: Control sample 61

description: SAMPLE 33


title: Patient sample 18

description: SAMPLE 28


title: Control sample 27

description: SAMPLE 30


title: Patient sample 41

description: SAMPLE 26


title: Patient sample 63

description: SAMPLE 29


title: Patient sample 30

description: SAMPLE 27


title: Patient sample 5

description: SAMPLE 31


title: Patient sample 64

description: SAMPLE 25


title: Control sample 72

description: SAMPLE 20


title: Control sample 6

description: SAMPLE 23


title: Patient sample 36

description: SAMPLE 12


title: Control sample 8

description: SAMPLE 15


title: Control sample 74

description: SAMPLE 7


title: Control sample 10

description: SAMPLE 17


title: Control sample 11

description: SAMPLE 21


title: Patient sample 17

description: SAMPLE 10


title: Control sample 28

description: SAMPLE 18


title: Control sample 31

description: SAMPLE 5


title: Control sample 52

description: SAMPLE 22


title: Patient sample 15

description: SAMPLE 8


title: Patient sample 62

description: SAMPLE 24


title: Patient sample 1

description: SAMPLE 2


title: Control sample 69

description: SAMPLE 19


title: Patient sample 47

description: SAMPLE 13


title: Patient sample 59

description: SAMPLE 4


title: Control sample 2

description: SAMPLE 1


title: Control sample 16

description: SAMPLE 3


title: Patient sample 3

description: SAMPLE 16


title: Patient sample 39

description: SAMPLE 14


title: Patient sample 21

description: SAMPLE 11


title: Brain_pool 6_dsRNA-GFP

description: small RNA fraction (enriched miRNA)


title: Patient sample 49

description: SAMPLE 9


title: Patient sample 23

description: SAMPLE 6


title: Th0_NaCl1

city: Berkeley

first: Nir

last: Yosef

state: CA

address: Berkeley

department: EECS

institute: UC Berkeley

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Mouse 430 2.0 microarrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Expression data was preprocessed using the RMA algorithm followed by quantile normalization, with the parameters in the ExpressionFileCreator module of the GenePattern suite set to default

source_name: Th17 cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (3' IVT Express Kit, Affymetrix).

growth_protocol: Cd4+ T cells were purified from spleen and lymph nodes using anti-CD4 microbeads (Miltenyi Biotech) then stained in PBS with 1% FCS for 20 min at room temperature with anti-Cd4-PerCP, anti-Cd62l-APC, and anti-Cd44-PE antibodies (all Biolegend, CA). Naïve Cd4+ Cd62lhigh Cd44low T cells were sorted using the BD FACSAria cell sorter.  Sorted cells were activated with plate bound anti-Cd3 (2μg/ml) and anti-Cd28 (2μg/ml) in the presence of cytokines.

extract_protocol: Extraction of total RNA was performed according to the RNeasy Mini Kit (Qiagen) manufacturer's instructions.

treatment_protocol: Naïve T cells were isolated from WT mice, and cultured under Th0 condition with or without 40mM NaCl for 72 h.


title: Control sample 26

description: SAMPLE 41


title: Patient sample 34

description: SAMPLE 42


title: Th0_Ctrl2


title: Th0_Ctrl1


title: Th0_NaCl2


title: KO_TgfbpIL6_ko48

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix microarray HT_MG-430A. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

treatment_protocol: For Th17 differentiation: 2ng/mL rhTGF-β1 (Miltenyi Biotec), 25ng/mL rmIl-6 (Miltenyi Biotec), 20ng/ml rmIl-23 (Miltenyi Biotec), and 20ng/ml rmIL-β1 (Miltenyi Biotec). Cells were cultured for 48 hours.

tag: time (hr)

tag: genotype

value: IL23R knockout


title: KO_TgfbpIL6pIL23_ko49IL23

tag: cell type


title: WT_TgfbpIL6pIL23_wt54IL23

value: WT