title: MNHOC79_A-rep2

city: Biella

first: giovanna

last: chiorino

address: via malta 3

department: Cancer Genomics

country: Italy

institute: Fondo Edo Tempia

hyb_protocol: Hybridization was carried out for 17 hours at 65°C by rotating at 10 rpm. Microarray slides were washed in GE Wash Buffer-1 for 2 minutes and pre-warmed GE Wash Buffer-2 for 2 minutes at room temperature.

scan_protocol: Microarray slides were scanned in an Agilent Scanner version C (G2505C, Agilent Technologies).

data_processing: Images were analyzed using the Feature Extraction software v10.7. Raw data elaboration was carried out with Bioconductor (www.bioconductor.org), using R statistical language. Background correction was performed with the normexp method with an offset of 50 and quantile was used for between-array normalization. The LIMMA (LInear Models for Microarray Analysis) package was then used to identify differentially expressed genes in EOC-xenografts versus their corresponding patient tumors. The empirical Bayes method was used to compute a moderated t-statistics. Transcripts with a log base two fold change (logFC) greater than 1 or lower than -1 and p-value less than 0.01 were considered as differentially expressed.

source_name: Ovarian cancer from xenograft

label_protocol: Labeled cRNA target was prepared starting from100 ng of input RNA [RNA integrity number (RIN) > 7.0] by Low Input Quick Amp Labelling Kit and One-Color Spike-In Kit (Agilent Technologies) and purified with RNeasy Mini Kit (Qiagen) according to the manufacturer’s recommendation and protocols. Cyanine3CTP-labelled cRNA was quantified on a NanoDrop ND1000 Spectrophotometer using Microarray/RNA-40 measurement and the specific activity of cyanine 3 was calculated for each reaction. We set the minimum threshold of 2 μg for yield and 7 pmol/μg for the specific activity. Labeled cRNA (600ng) was fragmented by incubation with 5μl of 10× blocking reagent and 1μl of 25× fragmentation buffer in a 25μl reaction volume for 30 minutes at 60°C. Twentyfive microliters of 2× GE Hybridization Buffer Hi-RPM was added to fragmented cRNA;  40 μl of this  “hybridization mix” were placed onto the  SurePrint G3 Human GE V2 8x60K microarrays (50,599 Biological Features/array; Agilent Technologies).

growth_protocol: EOC-xenografts Subcutis models (s.c.). Tumors were dissected free of necrotic tissue repeatedly rinsed in HBSS and 2-4 mm of tissue was implanted subcutaneously  in the flank of nude mice.  Tumor growth was measured with a Vernier caliper, and tumor weights (mg = mm3) were calculated as follows: (length [mm] × width2 [mm2]) / 2.  Intraperitoneal models (i.p.). Ascites was centrifuged, washed repeatedly, resuspended in HBSS and implanted intraperitoneally in nude mice at a concentration of 10-20 ×10e6. Criteria for growing tumors were abdominal distension and palpable tumor masses in the peritoneal cavity. Mice were killed when they presented signs of discomfort (survival), ascites was harvested and the volume recorded.  Intrabursal transplantation (i.b.). Ovarian cancer cells from enzymatic digestion or ascites (1×10e6 cell suspension) were injected orthotopically under the bursa of the mouse ovary, as detailed in Supplementary data. At necroscopy, the ovary image was acquired with a macrodigital imaging system (MacroPATH; Milestone S.r.l, Sorisole, Italy); the two diameters were determined, the mean calculated and taken as measure of tumor mass. Ascites was harvested and the volume recorded.  Clinical specimens (primary ovarian tumors, metastasis, ascitic fluid) were obtained from patients undergoing surgery for ovarian tumor by laparotomy or paracentesis and in nude mice within 24hr. Established EOC-xenografts were cryopreserved frozen in DMSO and passed serially in nude mice for further studies (i.e. EOC-xenograft sample were immediately snap frozen for gene expression analysis).

extract_protocol: RNA isolation and assessment of human and mouse proportion. Qiazol and the miRNeasy Mini Kit together with a DNase I digestion step (Qiagen) were used according to the manufacturer’s recommendations to isolate total RNA from EOC-xenografts and patient tumor specimens. Total RNA quality was checked for integrity using RNA Nano Chips on Agilent Bioanalyzer 2100 (Agilent Technologies). Xenograft tumors are composed of a mixture of human- and mouse-derived cells; to assess their respective amount, total RNA was evaluated by way of species-specific TaqMan Prime Time qPCR assays for beta actin (ACTB). Briefly, 200ng tot RNA were reverse transcribed with random hexamers in a 20 microliters reaction by the High Capacity cDNA Reverse Transcription kit (Applied Biosystems); cDNA (2 microliters of the 1:20 dilution) was PCR amplified in 10 μl reaction, in presence of 500nM primers, 250nM probe (Hs PT39a22214847, MmPT53a.31778008, IDT) and the TaqMan gene expression master mix 1x (Applied Biosystem) on the Applied Biosystems 7900HT Fast Real Time PCR system (40 cycles at 94°C for 15 s, 60°C for 60s). Standard curves, generated with the following formula: [CtmouseACTB – CthumanACTB = (m-h Ct)] using known using known human and mouse tot RNA mixtures (100%, 95, 90 ,80, 75, 70, 60, 50%), were used to determine the proportions of human and mouse ACTB RNA in EOC-xenograft. The value (m-h Ct) obtained for each sample (analyzed in triplicate) was plotted against the standard curve to extrapolate the percentage of human RNA. Only samples with a human RNA content > 75%  were considered further.

treatment_protocol: EOC-xenografts collected from subcutis (sc), abdominal masses (am) and ascitic fluid (A) of mice engrafted with tumors at different passages (62 xenograft samples representing 29 EOC-xenograft models) and from 9 patient specimens, underwent one-color microarray-based gene expression profiling by way of SurePrint G3 Human GE V2 8x60K microarrays (50,599 Biological Features/array; Agilent Technologies) .

value: Epithelial Ovarian Cancer (EOC)

value: xenograft from mouse


title: MNHOC111_A-rep2

status: Public on Jan 07 2015

type: RNA

molecule: total RNA

organism: Homo sapiens

tag: cell type

tag: tissue


title: PfBDP1DD ON Shld1 36+/-4hpi_Bio 1

city: Melbourne

first: Michaela

last: Petter

state: VIC

address: 792 Elizabeth Street

department: Peter Doherty Institute

country: Australia

institute: University of Melbourne

hyb_protocol: Microarray hybridizations were carried out as described in [PMID: 12929205]. In short, hybridizations were performed for 16 hours at 65°C using a Maui hybridization system (BioMicro Systems, Salt Lake City, Utah, USA).

scan_protocol: Microarrays were scanned as described in [PMID: 12929205]. In short, scanning was performed with an Axon GenePix 4000B microarray scanner and associated GenePix Pro v6.0 software (Axon Instruments, Union City, California, USA).

data_processing: Lowess normalisation was applied to all arrays as implemented in the Acuity 4.0 software (Molecular Devices). The microarray data were then filtered to include only spots with at least 95% of pixels having signal intensity greater than two standard deviations above background for both Cy3 and Cy5 fluorescence intensity.

organism: Plasmodium falciparum 3D7

source_name: PfBDP1DD ON Shld1 36+/-4hpi

label_protocol: Labeling was carried out as described in [PMID: 12929205]

growth_protocol: Plasmodium falciparum parasites were cultured in RPMI-HEPES medium containing 5% O+ red blood cells, 0.2% sodium bicarbonate and 0.5% Albumax (Gibco). Parasitaemia was maintained at 0.5%-10%. Parasites cultures were incubated at 37ºC in 1% O2, 5% CO2 and 94% N2.

extract_protocol: Total RNA was extracted using Trizol (Life Technologies) following manufacturer's instructions

treatment_protocol: PfBDP1DD parasites grown  in the presence of 2.5 nM WR99210/500 nM Shld1 and synchronized by MACS and sorbitol treatment to an 8-hour growth window were split into two cultures at 30 hours post invasion (hpi) and Shld1 removed from one batch. This is the sample grown in the presence of Shld1.

tag: transgenic line

tag: genotype/variation

value: expressing an endogeneous PfBDP1-HA-DD fusion protein

value: whole organsim

source_name: reference pool RNA

treatment_protocol: RNA from highly synchronized cells was extracted at 6 time points across the IDC at 8 h intervals. Equal amount of RNA from each time point was mixed to prepare the cDNA which was used as a reference pool.

tag: sample type

value: reference pool


title: MNHOC78_A-rep4


title: MNHOC76_A-rep3


title: Benign endometriosis sample 17

city: Pittsburgh

first: SungHwan

last: Kim

address: 200 Lothrop, BST W1200

country: USA

institute: University of Pittsburgh

hyb_protocol: according to Nanostring instructions

scan_protocol: according to Nanostring instructions

data_processing: Used EdgeR package. Once negative binomial models were fitted and dispersion estimates were obtained, we performed testing procedures for determining differential expression using an exact test with the quantile-adjusted conditional maximum likelihood (qCML) method.

label: biotin

source_name: Benign endometriosis sample

label_protocol: according to Nanostring instructions

extract_protocol: The RNeasy FFPE Kit (Qiagen) was used to isolate total RNA from FFPE tissues. The nCounter® GX Human Immunology Kit (Nanostring) was used to profile 511 immune genes.

value: Paraffin tissue blocks

value: Peritoneal implant

tag: tissue subtype

value: Benign endometriosis


title: PfBDP1DD ON Shld1  28+/-4hpi_Bio 2

source_name: PfBDP1DD ON Shld1  28+/-4hpi


title: PfBDP1DD ON Shld1  28+/-4hpi_Bio 3


title: Benign endometriosis sample 16


title: Benign endometriosis sample 15


title: PfBDP1DD ON Shld1 36+/-4hpi_Bio 2


title: Benign endometriosis sample 14


title: MNHOC10_A-rep4


title: REP_ctr_rep2

city: Chicago

first: Ann

last: Harris

state: Illinois

address: 2430 N Halsted

institute: Northwestern University

hyb_protocol: RNA samples are sent to Mogene company for further processing and data generation.

source_name: immortalized primary fetal human epididymis cells

growth_protocol: Cells are cultured in Primaria flasks (Falcon) in CMRL 1066 medium, containing 20% foetal calf serum (FCS) (Gibco, UK); L-glutamine (4mM); insulin (0.2 unit/ml); cholera toxin (10-10M) and hydrocortisone (1μg/ml), all from Sigma. Cultures were routinely maintained at 37°C in a humidified 5% CO2 incubator.

extract_protocol: TRIzol® (Life Technologies) used for RNA extraction.

treatment_protocol: Cells are cultured in phenol-free CMRL-1066 medium containing 10% dextran coated-charcoal (C6241, Sigma) - stripped FBS for 72h prior to stimulation with 1 nM R1881 (NLP005005MG, PerkinElmer, Waltham, MA) or vehicle for a further 16h.

value: SV-40 transformed primary human fetal epididymis cells


title: PfBDP1DD ON Shld1 20+/-4hpi_Bio 3

source_name: PfBDP1DD ON Shld1 20+/-4hpi


title: PfBDP1DD ON Shld1  28+/-4hpi_Bio 1


title: PfBDP1DD ON Shld1 20+/-4hpi_Bio 2


title: Benign endometriosis sample 13


title: Benign endometriosis sample 12


title: Benign endometriosis sample 11

value: Ovary


title: PfBDP1DD ON Shld1 20+/-4hpi_Bio 1


title: MNHOC8_A-rep2


title: PfBDP1DD ON Shld1 12+/-4hpi_Bio 3

source_name: PfBDP1DD ON Shld1 12+/-4hpi


title: PfBDP1DD ON Shld1 12+/-4hpi_Bio 2


title: MNHOC8Y_A-rep3


title: MNHOC78_A-rep5


title: MNHOC84_A-rep4


title: MNHOC79_A-rep3


title: MNHOC8Y_A-rep4


title: MNHOC76_A-rep4


title: Benign endometriosis sample 10


title: Benign endometriosis sample 9


title: PfBDP1DD ON Shld1 12+/-4hpi_Bio 1


title: MNHOC8_A-rep3


title: PfBDP1DD ON Shld1 4+/-4hpi_Bio 1

source_name: PfBDP1DD ON Shld1 4+/-4hpi


title: Benign endometriosis sample 7


title: Benign endometriosis sample 8


title: PfBDP1DD ON Shld1 4+/-4hpi_Bio 3


title: Benign endometriosis sample 6


title: MNHOC10_am-rep2


title: MNHOC22_A-rep3


title: Benign endometriosis sample 5


title: Benign endometriosis sample 4


title: PfBDP1DD ON Shld1 4+/-4hpi_Bio 2


title: Benign endometriosis sample 3


title: MNHOC125_sc-rep1


title: Benign endometriosis sample 2


title: MNHOC22_A-rep4


title: Benign endometriosis sample 1


title: atypical endometriosis sample 9

source_name: atypical endometriosis sample

value: atypical endometriosis


title: Normal endometrium sample 29

source_name: Normal endometrium sample

value: Endometrium

value: Normal endometrium


title: Expression data of depletion of SP1 and overexpression of p53 in MPM cells [MES7-shControl-Vector-3]

city: Bethesda

first: Mahadev

last: Rao

state: MD

address: 10 Center drive

department: TGBI

institute: NCI

hyb_protocol: Genechip hybridization kits were used for hybridization (P/N 900720) on GeneChip Human 133 plus 2.0 array.Fluids stattion 450/250 were used

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label_protocol: cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Cells are grown in RPMI1640 media with 10% FBS with antibiotics

extract_protocol: Total RNA was performed using Qiagen RNAeasy kit according to the manufacturer's instructions.

treatment_protocol: For in vitro experiments, the MPM cells were treated with mithramycin for 24 hrs. For in vivo experiments, athymic nude mice were injected with mithramycin for Monday, Wednsday and Friday with a dose of 1 or 2 mg/kg, i.p. for 3 weeks.

value: Malignant pleural mesothelioma cells


title: MNHOC111_A-rep1


title: Normal endometrium sample 28


title: MNHOC106_sc-rep2


title: MNHOC10_A-rep5


title: Expression data of depletion of SP1 and overexpression of p53 in MPM cells [MES7-shControl-p53OEX-2]


title: Expression data of depletion of SP1 and overexpression of p53 in MPM cells [MES7-shControl-Vector-2]


title: Expression data of depletion of SP1 and overexpression of p53 in MPM cells [MES7-shControl-p53OEX-1]


title: MNHOC84_A-rep3


title: Expression data of depletion of SP1 and overexpression of p53 in MPM cells [MES7-shControl-p53OEX-3]


title: Expression data of depletion of SP1 and overexpression of p53 in MPM cells [MES7-shControl-Vector-1]


title: Normal endometrium sample 27


title: MNHOC109_sc


title: WTH4877CGH_CBS999.97_X_RTU

type: genomic

city: Taipei

first: Ting-Fang

last: Wang

address: Academia Sinica. 128 Sec. 2, Academia Rd

department: Institute of Molecular Biology

country: Taiwan

institute: Academia Sinica

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., following their standard operating protocol.(cgh_cnv_userguide_v7)

scan_protocol: The protocol for scanning two-color NimbleGen arrays with a GenePix 4000B Scanner and associated software Genepix6.0.

data_processing: Images were aligned and quantified using NimbleScan software  (V2.4) (Roche NimbleGen) which produced .pair reports of raw data and converted to ratio of Cy5 vs cy3

molecule: genomic DNA

organism: Trichoderma reesei

source_name: F1 progeny of CBS999.97 wt and the RTU strains

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol.( cgh_cnv_userguide_v7)

growth_protocol: This strain was cultured on malt extract agar plate  for 5 days. After 5 days, this strain was cultured into potato dextrose broth for 1 day to extract genomic DNA.

extract_protocol: These strains were cultured into liquid culture medium (potato dextrose broth) for 1 day to extract genomic DNA. The liquid culture medium was centrifuged at 3600rpm for 10min. The mycelia pellet was resuspended in Triton/SDS lysis buffer, and transfered into a new 2ml tube contain glassbead. Addded  Phenol/chroloform/IAA and 1X  Tris-EDTA buffer, and vortex for 15 min  at room tempture. Then, centrifuged at 13200rpm for 5min. The supernatant  was transfered into a new 1.5ml tube with 1.5X volume 100% EtOH at -20C for 2hr. The solution  was then centrifuged to remove supernatant at 13200rpm for 5min. Treat with RNaseA in  1X Tris-EDTA buffer for 1hr at 37C. Then,added  Phenol/chroloform  at 13200rpm for 5min. The supernatant was transfered into a new 1.5ml tube with chroloform at 13200rpm  for 5min. The supernatant was transfered into a new 1.5ml tube with Amino acetate, NaOAC and 100% EtOH at -20C for 2hr~overnight. Centrifuged at 13200rpm for 5min, then wash with 70% EtOH.  Centrifuged at 13200rpm for 5min to remove the supernatant. Air dry the pellet at room tempture. Dissolved the pellet(genomic DNA) with  1X  Tris-EDTA buffer.

tag: strain

source_name: Hypocrea jecorina CBS999.97  Wild-type

growth_protocol: This strain was cultured on malt extract agar plate  for 3 days. After 3 days, this strain was cultured into potato dextrose broth for 1 day to extract genomic DNA.

tag: genotype

value: Wild-type parental haploid strain


title: WTH4869CGH_CBS999.97_X_RTU

value: F1 progeny of CBS999.97 wt and the RTU strains


title: Expression data of depletion of SP1 and overexpression of p53 in MPM cells [MES1-shControl-Vector-2]


title: MNHOC10_am-rep3


title: MNHOC22_am-rep2


title: MNHOC125_sc-rep2


title: MNHOC88_sc


title: MNHOC94_sc


title: Expression data of depletion of SP1 and overexpression of p53 in MPM cells [MES1-shControl-p53OEX-3]


title: Normal endometrium sample 26


title: WTH4873CGH_CBS999.97_X_RTU


title: Expression data of depletion of SP1 and overexpression of p53 in MPM cells [MES1-shControl-Vector-3]


title: Normal endometrium sample 25


title: Expression data of depletion of SP1 and overexpression of p53 in MPM cells [MES1-shControl-Vector-1]


title: Expression data of depletion of SP1 and overexpression of p53 in MPM cells [MES1-shControl-p53OEX-2]


title: MNHOC106_sc-rep1


title: WTH0297CGH

source_name: Hypocrea jecorina CBS999.97 F1 progeny

growth_protocol: This strain was cultured on malt extract agar plate  for 3days. After 3 days, this strain was cultured into potato dextrose broth for 1 day to extract genomic DNA.

extract_protocol: This strain was cultured on malt extract agar plate  for 3days. After 3 days, this strain was cultured into liquid culture medium (potato dextrose broth) for 1 day to extract genomic DNA. The liquid culture medium was centrifuged at 3600rpm for 10min. The mycelia pellet was respened in Tirton/SDS lysis buffer, and transfered into a new 2ml tube contain glassbead. Addded  Phenol/chroloform/IAA and 1X  Tris-EDTA buffer, and vortex for 15 min  at room tempture. Then, centrifuged at 13200rpm for 5min. The supernatant  was transfered into a new 1.5ml tube with 1.5X volume 100% EtOH at -20C for 2hr. The solution  was then centrifuged to remove supernatant at 13200rpm for 5min. Treat with RNaseA in  1X Tris-EDTA buffer for 1hr at 37C. Then,added  Phenol/chroloform  at 13200rpm for 5min. The supernatant was transfered into a new 1.5ml tube with chroloform at 13200rpm  for 5min. The supernatant was transfered into a new 1.5ml tube with Amino acetate, NaOAC and 100% EtOH at -20C for 2hr~overnight. Cebtrifuged at 13200rpm for 5min, then wash with 70% EtOH.  Cebtrifuged at 13200rpm for 5min to remove the supernatant. Air dry the pellet at room tempture. Dissolved the pellet(genomis DNA) with  1X  Tris-EDTA buffer.

tag: generation

value: euploid F1 progeny

tag: reference

value: Wild-type paretal haploid strain


title: MNHOC9_sc

value: Epithelial Ovarian Cancer (EOC)

value: xenograft from mouse


title: Normal endometrium sample 24


title: Normal endometrium sample 23


title: Expression data of depletion of SP1 and overexpression of p53 in MPM cells [MES1-shControl-p53OEX-1]


title: MNHOC107_sc


title: Normal endometrium sample 22


title: WTH4865CGH_CBS999.97_X_RTU


title: Expression data of in vivo effect of mithramycin in MPM xenografts [In vivo-MES7-Saline-3]

source_name: In vivo-MES7-Saline-3

value: Malignant pleural mesothelioma xenografts


title: MNHOC142_am


title: WTH0295CGH


title: WTH0293CGH

value: aneuploid F1 progeny


title: WTH0296CGH


title: Normal endometrium sample 21

value: Paraffin tissue blocks


title: Expression data of in vivo effect of mithramycin in MPM xenografts [In vivo-MES7-Saline-2]

source_name: In vivo-MES7-Saline-2


title: Normal endometrium sample 20


title: Expression data of in vivo effect of mithramycin in MPM xenografts [In vivo-MES7-1 mgkg-3]

source_name: In vivo-MES7-1 mgkg-3


title: Normal endometrium sample 19


title: Expression data of in vivo effect of mithramycin in MPM xenografts [In vivo-MES7-Saline-1]

source_name: In vivo-MES7-Saline-1


title: WTH0292CGH


title: MNHOC18_sc

source_name: Ovarian cancer from xenograft


title: Normal endometrium sample 18


title: MNHOC164_am-rep3


title: Expression data of in vivo effect of mithramycin in MPM xenografts [In vivo-MES7-1 mgkg-2]

source_name: In vivo-MES7-1 mgkg-2


title: MNHOC182_sc-rep3


title: WTH0291CGH


title: MNHOC164_am-rep2


title: Expression data of in vivo effect of mithramycin in MPM xenografts [In vivo-MES7-1 mgkg-1]

source_name: In vivo-MES7-1 mgkg-1


title: Normal endometrium sample 16


title: WTH0288CGH


title: WTH0287CGH


title: WTH0289CGH


title: WTH0257CGH


title: MNHOC124_sc


title: Expression data of in vivo effect of mithramycin in MPM xenografts [In vivo-MES1-Saline-2]

source_name: In vivo-MES1-Saline-2


title: Normal endometrium sample 14


title: Expression data of in vivo effect of mithramycin in MPM xenografts [In vivo-MES1-Saline-3]

source_name: In vivo-MES1-Saline-3


title: MNHOC230_sc


title: MNHOC78_am-rep3


title: Normal endometrium sample 13


title: WTH0256CGH


title: Normal endometrium sample 15


title: MNHOC135_sc


title: MNHOC239_sc


title: Expression data of in vivo effect of mithramycin in MPM xenografts [In vivo-MES1-Saline-1]

source_name: In vivo-MES1-Saline-1


title: Normal endometrium sample 12


title: WTH0252CGH


title: WTH0255CGH


title: Expression data of in vivo effect of mithramycin in MPM xenografts [In vivo-MES1-MM 2mgkg-2]

source_name: In vivo-MES1-MM 2mgkg-2


title: Normal endometrium sample 11


title: Expression data of in vivo effect of mithramycin in MPM xenografts [In vivo-MES1-MM 2mgkg-1]

source_name: In vivo-MES1-MM 2mgkg-1


title: WTH0253CGH


title: MNHOC119_am-rep2


title: Normal endometrium sample 10


title: MNHOC164_am-rep1


title: Normal endometrium sample 9


title: Normal endometrium sample 8


title: WTH0251CGH


title: MNHOC8Y_am-rep2


title: Normal endometrium sample 7


title: WTH0011CGH_2


title: Expression data of in vivo effect of mithramycin in MPM xenografts [In vivo-MES1-MM 1mgkg-3]

source_name: In vivo-MES1-MM 1mgkg-3


title: MNHOC78_am-rep2


title: MNHOC84_sc-rep2


title: Expression data of in vivo effect of mithramycin in MPM xenografts [In vivo-MES1-MM 1mgkg-2]

source_name: In vivo-MES1-MM 1mgkg-2


title: MNHOC76_am-rep2


title: Expression data of in vitro effect of mithramycin in MPM cells [In vitro-MES7-Untreated 3]

source_name: In vitro-MES7-Untreated 3


title: Normal endometrium sample 6

source_name: Normal endometrium sample


title: Expression data of in vitro effect of mithramycin in MPM cells [In vitro-MES7-Untreated 1]

source_name: In vitro-MES7-Untreated 1


title: Hypocrea jecorina CBS999.97 Wild-type WTH0011CGH-34d

source_name: Hypocrea jecorina CBS999.97  Wild-type

growth_protocol: This strain was cultured on malt extract agar plate  for 33 days. After 33 days, this strain was cultured into potato dextrose broth for 1 day to extract genomic DNA.

extract_protocol: These strainswere cultured into liquid culture medium (potato dextrose broth) for 1 day to extract genomic DNA. The liquid culture medium was centrifuged at 3600rpm for 10min. The mycelia pellet was respened in Tirton/SDS lysis buffer, and transfered into a new 2ml tube contain glassbead. Addded  Phenol/chroloform/IAA and 1X  Tris-EDTA buffer, and vortex for 15 min  at room tempture. Then, centrifuged at 13200rpm for 5min. The supernatant  was transfered into a new 1.5ml tube with 1.5X volume 100% EtOH at -20C for 2hr. The solution  was then centrifuged to remove supernatant at 13200rpm for 5min. Treat with RNaseA in  1X Tris-EDTA buffer for 1hr at 37C. Then,added  Phenol/chroloform  at 13200rpm for 5min. The supernatant was transfered into a new 1.5ml tube with chroloform at 13200rpm  for 5min. The supernatant was transfered into a new 1.5ml tube with Amino acetate, NaOAC and 100% EtOH at -20C for 2hr~overnight. Cebtrifuged at 13200rpm for 5min, then wash with 70% EtOH.  Cebtrifuged at 13200rpm for 5min to remove the supernatant. Air dry the pellet at room tempture. Dissolved the pellet(genomis DNA) with  1X  Tris-EDTA buffer.

tag: genetic background

tag: age


title: Expression data of in vitro effect of mithramycin in MPM cells [In vitro-MES7-Untreated 2]

source_name: In vitro-MES7-Untreated 2


title: Hypocrea jecorina CBS999.97 F1 progeny WTH0254CGH-24d

source_name: Hypocrea jecorina CBS999.97 F1 progeny

growth_protocol: This strain was cultured on malt extract agar plate  for 23 days. After 23 days, this strain was cultured into potato dextrose broth for 1 day to extract genomic DNA.


title: Expression data of in vivo effect of mithramycin in MPM xenografts [In vivo-MES1-MM 1mgkg-1]

source_name: In vivo-MES1-MM 1mgkg-1


title: Hypocrea jecorina CBS999.97 F1 progeny WTH0254CGH-34d


title: Hypocrea jecorina CBS999.97 F1 progeny WTH0262CGH-34d


title: MNHOC182_sc-rep2

source_name: Ovarian cancer from xenograft


title: Normal endometrium sample 5


title: Normal endometrium sample 4


title: Hypocrea jecorina CBS999.97 Wild-type WTH0011CGH-24d


title: Expression data of in vitro effect of mithramycin in MPM cells [In vitro-MES7-MM 100nM-3]

source_name: In vitro-MES7-MM 100nM-3


title: Normal endometrium sample 2


title: MNHOC119_am-rep3


title: MNHOC8_am-rep1


title: Hypocrea jecorina CBS999.97 F1 progeny WTH0262CGH-24d


title: Normal endometrium sample 1


title: Expression data of in vitro effect of mithramycin in MPM cells [In vitro-MES7-MM 100nM-1]

source_name: In vitro-MES7-MM 100nM-1


title: Normal endometrium sample 3


title: Expression data of in vitro effect of mithramycin in MPM cells [In vitro-MES7-MM 25nM-2]

source_name: In vitro-MES7-MM 25nM-2


title: Hypocrea jecorina CBS999.97 F1 progeny WTH0262CGH-14d


title: Expression data of in vitro effect of mithramycin in MPM cells [In vitro-MES7-MM 100nM-2]

source_name: In vitro-MES7-MM 100nM-2


title: Expression data of in vitro effect of mithramycin in MPM cells [In vitro-MES7-MM 25nM-1]

source_name: In vitro-MES7-MM 25nM-1


title: MNHOC218_sc


title: Expression data of in vitro effect of mithramycin in MPM cells [In vitro-MES7-MM 25nM-3]

source_name: In vitro-MES7-MM 25nM-3


title: MNHOC182_sc-rep1


title: MNHOC212_sc


title: Expression data of in vitro effect of mithramycin in MPM cells [In vitro-MES1-Untreated-3]

source_name: In vitro-MES1-Untreated-3


title: MNHOC154_sc


title: Hypocrea jecorina CBS999.97 Wild-type WTH0011CGH-14d


title: Hypocrea jecorina CBS999.97 F1 progeny WTH0254CGH-14d


title: Expression data of in vitro effect of mithramycin in MPM cells [In vitro-MES1-Untreated-2]

source_name: In vitro-MES1-Untreated-2


title: Normal endometrium sample 17


title: MNHOC244_sc


title: WTH0285CGH

hyb_protocol: Agilent Oligo aCGH Hybridization Kit  and Agilent Oligo aCGH Wash Buffers  were used according to manufacturer protocols.

scan_protocol: Agilent G2565CA Scanner was used according to manufacturer protocol. CGH_105_Dec08

data_processing: Data extraction has been performed with Agilent Feature Extraction Software v10.5.1.1.

label_protocol: 0.5 ug genomic DNA was labelled with Cy5-dUTP  from random primers extended with the exo- Klenow fragment of DNA polymerase (NEB). The final products were purified with MinElute columns (Qiagen) and labelling efficiencies were quantified spectrophotometrically.

extract_protocol: This strain was cultured on malt extract agar plate  for 3days. After 3 days, this strain was cultured into liquid culture medium (potato dextrose broth) for 1 day to extract genomic DNA. The liquid culture medium was centrifuged at 3600rpm for 10min. The mycelia pellet was respened in Tirton/SDS lysis buffer, and transfered into a new 2ml tube contain glassbead. Addded  Phenol/chroloform/IAA and 1X  Tris-EDTA buffer, and vortex for 15 min  at room tempture. Then, centrifuged at 13200rpm for 5min. The supernatant  was transfered into a new 1.5ml tube with 1.5X volume 100% EtOH at -20C for 2hr. The solution  was then centrifuged to remove supernatant at 13200rpm for 5min. Treat with RNaseA in  1X Tris-EDTA buffer for 1hr at 37C. Then,added  Phenol/chroloform  at 13200rpm for 5min. The supernatant was transfered into a new 1.5ml tube with chroloform at 13200rpm  for 5min. The supernatant was transfered into a new 1.5ml tube with Amino acetate, NaOAC and 100% EtOH at -20C for 2hr~overnight. Centrifuged at 13200rpm for 5min, then wash with 70% EtOH.  Centrifuged at 13200rpm for 5min to remove the supernatant. Air dry the pellet at room tempture. Dissolved the pellet(genomic DNA) with  1X  Tris-EDTA buffer.

value: F1 haploid progeny

value: parental

value: wild-type


title: WTH0377CGH

data_processing:
Images were aligned and quantified using NimbleScan software (V2.4) (Roche NimbleGen) which produced .pair reports of raw data and converted to ratio of Cy5 vs Cy3.
All the scanning and image processing follow the NimbleGen Array User's Guide: CGH Analysis v3.0.   The raw data have been normalized with Scanner hardware, let the red and  green intensity superimposed.
We used Agilent's GeneSpring 12.1 (build 170166) Analysis Platform to analysis our array CGH data.

growth_protocol: This strain was cultured on malt extract agar plate for 3days. After 3 days, this strain was cultured into potato dextrose broth for 1 day to extract genomic DNA.

source_name: Hypocrea jecorina CBS999.97 Wild-type

value: Wild-type paretal haploid


title: WTH0381CGH


title: Expression data of in vitro effect of mithramycin in MPM cells [In vitro-MES1-MM 100nM-3]

source_name: In vitro-MES1-MM 100nM-3


title: Expression data of in vitro effect of mithramycin in MPM cells [In vitro-MES1-MM 100nM-2]

source_name: In vitro-MES1-MM 100nM-2


title: Expression data of in vitro effect of mithramycin in MPM cells [In vitro-MES1-Untreated-1]

source_name: In vitro-MES1-Untreated-1


title: WTH0373CGH


title: WTH0284CGH

source_name: Hypocrea jecorina CBS999.97  Wild-type


title: Expression data of in vitro effect of mithramycin in MPM cells [In vitro-MES1-MM 25nM-3]

source_name: In vitro-MES1-MM 25nM-3


title: WTH0286CGH

source_name: Hypocrea jecorina CBS999.97 F1 progeny


title: WTH0278CGH


title: WTH0282CGH


title: WTH0294CGH


title: WTH0290CGH


title: Expression data of in vivo effect of mithramycin in MPM xenografts [In vivo-MES1-MM 2mgkg-3]

source_name: In vivo-MES1-MM 2mgkg-3


title: WTH0282CGH


title: WTH0270CGH


title: WTH0281CGH


title: WTH0283CGH


title: Expression data of in vitro effect of mithramycin in MPM cells [In vitro-MES1-MM 25nM-2]

source_name: In vitro-MES1-MM 25nM-2


title: Expression data of in vitro effect of mithramycin in MPM cells [In vitro-MES1-MM 100nM-1]

source_name: In vitro-MES1-MM 100nM-1


title: WTH0274CGH


title: WTH0278CGH


title: NALM-6 GSK126 0.5 uM at 72 hrs, Biological rep2

city: London

first: Matteo

last: Righi

state: London

address: The MediaWorks, 191 Wood Ln

country: United Kingdom

institute: Autolus Therapeutics

description: Gene expression data from NALM-6 GSK126 0.5 uM at 72 hrs

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 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: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and robust multi-array average (RMA )as normalization method. Log2 Transformed

source_name: NALM-6 GSK126 0.5 uM at 72 hrs

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

growth_protocol: Cancer cell lines

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

treatment_protocol: Cell lines were treated for 72 hours with DMSO or 0.5 uM EZH2 inhibitor GSK126

tag: cell line

tag: treatment

tag: time

value: 72 hrs


title: Expression data of in vitro effect of mithramycin in MPM cells [In vitro-MES1-MM 25nM-1]

source_name: In vitro-MES1-MM 25nM-1


title: WTH0279CGH


title: WTH0280CGH


title: NALM-6 GSK126 0.5 uM at 72 hrs, Biological rep1


title: WTH0262CGH


title: WTH0276CGH


title: MNHOC84_sc-rep1

source_name: Ovarian cancer from xenograft


title: WTH0266CGH


title: WTH0277CGH


title: WTH0275CGH


title: MNHOC119_am-rep1


title: NALM-6 DMSO vehicle at 72 hrs, Biological rep2

description: Gene expression data from NALM-6 DMSO vehicle at 72 hrs

source_name: NALM-6 DMSO vehicle at 72 hrs

value: vehicle


title: SUP-B8 GSK126 0.5 uM at 72 hrs, Biological rep2

description: Gene expression data from SUP-B8 GSK126 0.5 uM at 72 hrs

source_name: SUP-B8 GSK126 0.5 uM at 72 hrs


title: NALM-6 DMSO vehicle at 72 hrs, Biological rep1


title: WTH0274CGH


title: WTH0273CGH


title: MNHOC78_am-rep1


title: MNHOC8Y_am-rep1


title: WTH0254CGH


title: WTH0250CGH


title: WTH0272CGH


title: WTH0013CGH

value: Wild-type parental haploid


title: MNHOC10_am-rep1


title: WTH0258CGH


title: MNHOC79_am-rep1


title: SUP-B8 DMSO vehicle at 72 hrs, Biological rep2

description: Gene expression data from SUP-B8 DMSO vehicle at 72 hrs

source_name: SUP-B8 DMSO vehicle at 72 hrs


title: WTH0271CGH


title: WTH0270CGH


title: Severely injured patient (12980132)

status: Public on Jan 06 2015

city: Gainesville

first: M Cecilia

last: Lopez

state: FL

address: 1376 Mowry Road

department: Molecular Genetics and Microbiology

institute: University of Florida

hyb_protocol: 7.5 ug labeled and fragmented cDNA were  hybridized on a Human Transcriptome Array (GGH) for 18hrs at 45C

scan_protocol: The GeneChip arrays were stained and scanned in an Affymetrix GCS 3000 7G Scanner.

data_processing: The data was normalized using RMA. Analyzed using BRB array tools

source_name: Whole Blood

label_protocol: label cDNA was prepared Using the Nugen Ovation PICO WTA System and labeled and fragemented using Nugen Encore® Biotin Module

extract_protocol: Extraction of total RNA was performed with QIAGEN Rneasy mini kit according to the manufacturer's instructions.

value: PMNs (isolated peripheral neutrophils )

tag: Sex

value: F

tag: age(years)

tag: injury

value: trauma


title: WTH0011CGH

source_name: Hypocrea jecorina CBS999.97 Wild-type


title: MNHOC76_am-rep1

tag: cell type

tag: tissue


title: Severely injured patient (21647111)


title: Severely injured patient (12093936)


title: SUP-B8 DMSO vehicle at 72 hrs, Biological rep1


title: Severely injured patient (5245890)


title: Severely injured patient (16084092)

value: M


title: Severely injured patient (648417)


title: MNHOC22_am-rep1


title: Severely injured patient (4966687)


title: Severely injured patient (265370)


title: Severely injured patient (24757022)


title: Severely injured patient (6484868)


title: SUP-B8 GSK126 0.5 uM at 72 hrs, Biological rep1


title: Severely injured patient (13703789)


title: Severely injured patient (29445705)


title: Severely injured patient (12562356)


title: Severely injured patient (11518240)


title: Severely injured patient (24548518)


title: Severely injured patient (29811049)


title: Severely injured patient (10045508)


title: Severely injured patient (387697)


title: Severely injured patient (33626206)


title: Severely injured patient (34926458)


title: Severely injured patient (21124171)


title: Severely injured patient (14016785)


title: Severely injured patient (33155902)


title: Severely injured patient (6432772)


title: Severely injured patient (4824118)


title: Severely injured patient (32403479)


title: Severely injured patient (34634837)


title: Severely injured patient (4338103)


title: Severely injured patient (32306270)


title: Severely injured patient (15355118)


title: Severely injured patient (13825527)


title: Severely injured patient (30903000)


title: Severely injured patient (12198619)


title: Severely injured patient (21998872)


title: Severely injured patient (2232958)


title: Severely injured patient (28341101)


title: Severely injured patient (19632033)


title: Severely injured patient (3824557)


title: Severely injured patient (5570285)


title: Severely injured patient (17018445)


title: Severely injured patient (34224871)


title: Severely injured patient (11781213)


title: Severely injured patient (3484620)


title: Severely injured patient (6590090)


title: Severely injured patient (10081558)


title: Severely injured patient (29440205)


title: Severely injured patient (3118002)


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title: Severely injured patient (18530330)


title: Severely injured patient (29099922)


title: Severely injured patient (21843158)


title: Severely injured patient (6856979)


title: Severely injured patient (16682521)


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title: Severely injured patient (8435066)


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title: Severely injured patient (17260140)


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title: Severely injured patient (122824)


title: Severely injured patient (3066270)


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title: Severely injured patient (2461728)


title: Severely injured patient (5697231)


title: Severely injured patient (7306731)


title: Severely injured patient (22663053)


title: Severely injured patient (16229218)


title: Severely injured patient (28836053)


title: Severely injured patient (3747596)


title: Severely injured patient (31235249)


title: Severely injured patient (29955168)


title: Severely injured patient (26150026)


title: Severely injured patient (13736214)


title: Severely injured patient (33979128)


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title: Severely injured patient (11357976)


title: Severely injured patient (26097001)


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title: Severely injured patient (21785634)


title: Severely injured patient (18882803)


title: Severely injured patient (2944962)


title: Severely injured patient (29385153)


title: Severely injured patient (32937351)


title: Severely injured patient (32848072)


title: Severely injured patient (3684976)


title: Severely injured patient (29734543)


title: Severely injured patient (2194683)


title: Severely injured patient (11998025)


title: Severely injured patient (11813511)


title: Severely injured patient (8299598)


title: Severely injured patient (17737204)


title: Severely injured patient (28347308)


title: Severely injured patient (8501088)


title: Severely injured patient (7195459)


title: Severely injured patient (12216479)


title: Severely injured patient (13888966)


title: Severely injured patient (6650564)


title: Severely injured patient (1821858)


title: Severely injured patient (26070683)


title: Severely injured patient (25599597)


title: Severely injured patient (543799)


title: Severely injured patient (34444593)


title: Severely injured patient (26876523)


title: Severely injured patient (1793856)


title: Severely injured patient (18341626)


title: Severely injured patient (13823558)


title: Severely injured patient (8002866)


title: Severely injured patient (34453925)


title: Severely injured patient (23452902)


title: Severely injured patient (15964592)


title: Severely injured patient (2591063)


title: Severely injured patient (14889463)


title: Severely injured patient (17399874)


title: Severely injured patient (6603874)


title: Severely injured patient (1384103)


title: Severely injured patient (31747751)


title: Severely injured patient (25712745)


title: Severely injured patient (14516108)


title: Severely injured patient (26678241)


title: Severely injured patient (11496579)


title: Severely injured patient (12957703)


title: Severely injured patient (2770081)


title: Severely injured patient (2537924)


title: Severely injured patient (30752042)


title: Severely injured patient (31060317)


title: Severely injured patient (33703099)


title: Severely injured patient (18937854)


title: Severely injured patient (9924621)


title: Severely injured patient (30057671)


title: Severely injured patient (9533146)


title: Severely injured patient (5660879)


title: Severely injured patient (28529718)


title: Severely injured patient (18034523)


title: Severely injured patient (4369453)


title: Severely injured patient (26557751)


title: Severely injured patient (21101805)


title: Severely injured patient (6383220)


title: Severely injured patient (23973399)


title: Severely injured patient (11993174)


title: Severely injured patient (24502172)


title: Severely injured patient (1699608)


title: Severely injured patient (33410636)


title: Severely injured patient (20639547)


title: Severely injured patient (7832672)


title: Severely injured patient (33708729)


title: Severely injured patient (147763)


title: Severely injured patient (9570647)


title: Severely injured patient (29254335)


title: Severely injured patient (21697189)


title: Severely injured patient (3695523)


title: Severely injured patient (22413253)


title: Severely injured patient (17600494)


title: Severely injured patient (25042105)


title: Severely injured patient (1340452)


title: Control 15

value: control


title: Control 17


title: Severely injured patient (31266684)


title: Severely injured patient (15099008)


title: Control 14


title: Control 16


title: Control 13


title: Control 4


title: Control 9


title: Control 11


title: Control 1


title: Severely injured patient (27626059)


title: Control 2


title: Control 7


title: Control 5


title: Control 12


title: Severely injured patient (10086412)


title: Control 3


title: Severely injured patient (17103994)


title: Severely injured patient (29538717)


title: Control 8


title: Severely injured patient (26029920)


title: Severely injured patient (31418283)


title: Control 6


title: Control 10


title: Severely injured patient (6893543)


title: Severely injured patient (24256241)


title: Severely injured patient (24658845)


title: Severely injured patient (23345422)


title: Severely injured patient (27391296)


title: Severely injured patient (32750581)


title: Severely injured patient (33419346)


title: Severely injured patient (6327735)


title: Severely injured patient (5818091)


title: Severely injured patient (28162576)


title: Severely injured patient (8495723)


title: Severely injured patient (22808080)


title: Severely injured patient (28193682)


title: Severely injured patient (12351237)


title: Severely injured patient (22451912)


title: Severely injured patient (11146930)


title: Severely injured patient (29532546)


title: Severely injured patient (6461536)


title: Severely injured patient (13312831)


title: Severely injured patient (376529)


title: Severely injured patient (18839039)


title: Severely injured patient (33643240)


title: Severely injured patient (33512461)


title: Severely injured patient (5283007)


title: Severely injured patient (27050319)


title: Severely injured patient (9366022)


title: Severely injured patient (2814521)


title: Severely injured patient (7159530)


title: Severely injured patient (20533987)


title: Severely injured patient (11626800)


title: Severely injured patient (14174719)


title: Severely injured patient (16451519)


title: Severely injured patient (20926587)


title: Severely injured patient (15011325)


title: Severely injured patient (27599917)


title: Severely injured patient (713866)


title: Severely injured patient (25758336)


title: Severely injured patient (33784548)


title: Severely injured patient (11325272)


title: Severely injured patient (6173571)


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title: Severely injured patient (34908308)


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title: Severely injured patient (12490256)


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title: Severely injured patient (1329857)


title: Severely injured patient (27848448)


title: Severely injured patient (11237659)


title: Severely injured patient (33983655)


title: Severely injured patient (15102920)


title: Severely injured patient (4929809)


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title: Severely injured patient (23081017)


title: Severely injured patient (7942024)


title: Severely injured patient (7030514)


title: Severely injured patient (2978082)


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title: Severely injured patient (12718937)


title: Severely injured patient (11112472)


title: Severely injured patient (211088)


title: Severely injured patient (26571367)


title: Severely injured patient (14539512)


title: Severely injured patient (19330128)


title: Severely injured patient (20659135)


title: Severely injured patient (497415)


title: Severely injured patient (10616717)


title: Severely injured patient (27556946)


title: Severely injured patient (23955372)


title: Severely injured patient (3461008)


title: Severely injured patient (9617757)


title: Severely injured patient (29275807)


title: Severely injured patient (23269802)


title: Severely injured patient (20428748)


title: Severely injured patient (17206218)


title: Severely injured patient (8890756)


title: Severely injured patient (12567935)


title: Severely injured patient (25410896)


title: Severely injured patient (7456622)


title: Severely injured patient (31811929)


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title: Severely injured patient (12029360)


title: Severely injured patient (4067646)


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title: Severely injured patient (10076909)


title: Severely injured patient (27770931)


title: Severely injured patient (29917756)


title: Severely injured patient (4958819)


title: Severely injured patient (25325860)


title: Severely injured patient (11520627)


title: Severely injured patient (33997415)


title: Severely injured patient (23077337)


title: Severely injured patient (5843140)


title: Severely injured patient (31062742)


title: Severely injured patient (22782253)


title: Severely injured patient (30358462)


title: Severely injured patient (34593188)


title: Severely injured patient (31183577)


title: Severely injured patient (10722171)


title: Severely injured patient (30761333)


title: Severely injured patient (28962381)


title: Severely injured patient (5941282)


title: Severely injured patient (17486554)


title: Severely injured patient (17326055)


title: Severely injured patient (13285844)


title: Severely injured patient (29630062)


title: Severely injured patient (20809285)


title: Severely injured patient (32617331)


title: Severely injured patient (18017661)


title: Severely injured patient (5332134)


title: Severely injured patient (28069647)


title: Severely injured patient (5794490)


title: Severely injured patient (5277417)


title: Severely injured patient (28119710)


title: Severely injured patient (11668553)


title: Severely injured patient (8964889)


title: Severely injured patient (29557050)


title: Severely injured patient (4684630)


title: Severely injured patient (1879662)


title: Severely injured patient (13811134)


title: Severely injured patient (25889234)


title: Severely injured patient (13648187)


title: Severely injured patient (1045350)


title: Severely injured patient (14853401)


title: Severely injured patient (9602872)


title: Severely injured patient (15968591)


title: Severely injured patient (4358009)


title: Severely injured patient (34715972)


title: Severely injured patient (12620731)


title: Severely injured patient (2700537)


title: Severely injured patient (13950301)


title: Severely injured patient (25135346)


title: Severely injured patient (13551249)


title: Severely injured patient (9389663)


title: Severely injured patient (33505478)


title: Severely injured patient (18629890)


title: Severely injured patient (12423263)


title: Severely injured patient (12994676)


title: Severely injured patient (24334540)


title: Severely injured patient (13753565)


title: Severely injured patient (32142520)


title: Severely injured patient (28127850)


title: Severely injured patient (18250371)


title: Severely injured patient (9944351)


title: Severely injured patient (4937485)


title: Severely injured patient (21745344)


title: Severely injured patient (33096304)


title: Severely injured patient (4504175)


title: Severely injured patient (9198745)


title: Severely injured patient (10415224)


title: Severely injured patient (19271003)


title: Severely injured patient (13464905)


title: Severely injured patient (10759205)


title: Severely injured patient (14149374)


title: Severely injured patient (3665717)


title: Severely injured patient (12163765)


title: Severely injured patient (35010435)


title: Severely injured patient (19971735)


title: Severely injured patient (19851404)


title: Severely injured patient (17668970)


title: Severely injured patient (25289437)


title: Severely injured patient (4083061)


title: Severely injured patient (30348275)


title: Severely injured patient (22394200)


title: Severely injured patient (14653150)


title: Severely injured patient (8596023)


title: Severely injured patient (13629358)


title: Severely injured patient (2971540)


title: Severely injured patient (32058850)


title: Severely injured patient (26924163)


title: Severely injured patient (952678)


title: Severely injured patient (22841755)


title: Severely injured patient (8907118)


title: Severely injured patient (11963610)


title: Severely injured patient (16938865)


title: Severely injured patient (27542384)


title: Severely injured patient (33970198)


title: Severely injured patient (2791363)


title: Severely injured patient (2924830)


title: Severely injured patient (26886598)


title: Severely injured patient (32539466)


title: Severely injured patient (3699228)


title: tam45_41_60min_rep1

city: Kyoto

first: Shinichi

last: Oide

address: 9-2 Kizugawadai, Kizugawa

country: Japan

institute: Research institute of Innovative Technology for the Earth (RITE)

description: gene expression 60 minutes after growth temperature upshift

hyb_protocol: Hybridization was performed using Gene Expression Hybridization Kit according to the manufacture’s manual (Agilent). The labeled cDNA was hybridized to microarrays in an Agilent Technologies Microarray chamber at 65˚C for 17 h in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent), and 1 minute with 37˚C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) at a resolution of 5 µm using single color scan setting for 4x44k array slides. PMT is set to 100% for Cy3 channels.

data_processing: The scanned images were analyzed quantified with Feature Extraction Software 10.5.5.1 (Agilent) using default parameters (protocol GE1_105_Dec08). Feature extracted data were analyzed using GeneSpring GX v 12.0 software from Agilent. Normalization of the data was done in GeneSpring GX using the recommended Percentile shift normalization (50th percentile).

organism: Corynebacterium glutamicum

source_name: tam45 cells, 41 ℃, 60 minute, replicate 1

label_protocol: The cDNAs were synthesized from RNA by using reverse transcriptase from 10 μg of total RNAs and labeled with cyanine 3 (Cy3) using the SuperScript Indirect cDNA Labeling system (Life Technologies).

growth_protocol: All strains were grown in 10 ml A medium supplemented with 4 % glucose at 33 ℃ with agitation (200 rpm).

extract_protocol: Total RNA was extacted from each sample with NucleoSpin RNA (TaKaRa Bio Inc., JAPAN), according to the manufacturer's recommendations.

treatment_protocol: When OD610 of the cultures reached around 7, the growth temperature increased to 41 ℃, and the cultures were incubated for additional 1 hour.

tag: sampling time

value: 60 minutes


title: tam45_41_15min_rep1

description: gene expression 15 minutes after growth temperature upshift

source_name: tam45 cells, 41 ℃, 15 minute, replicate 1

value: 15 minutes


title: Severely injured patient (211594)


title: tam45_41_0min_rep1

description: gene expression 0 minute after growth temperature upshift

source_name: tam45 cells, 41 ℃, 0 minute, replicate 1

value: 0 minute


title: Severely injured patient (21655117)


title: Severely injured patient (2030418)


title: Severely injured patient (17478915)


title: trm2_41_60min_rep1

source_name: trm2 cells, 41 ℃, 0 minute, replicate 1


title: tam45_41_30min_rep1

description: gene expression 30 minutes after growth temperature upshift

source_name: tam45 cells, 41 ℃, 30 minute, replicate 1

value: 30 minutes


title: Severely injured patient (23475244)


title: tam44_41_15min_rep1

source_name: tam44 cells, 41 ℃, 15 minute, replicate 1


title: tam44_41_0min_rep1

source_name: tam44 cells, 41 ℃, 0 minute, replicate 1


title: Severely injured patient (27379160)


title: Severely injured patient (15295454)


title: trm2_41_0min_rep1


title: tam44_41_60min_rep1

source_name: tam44 cells, 41 ℃, 60 minutes, replicate 1


title: tam44_41_30min_rep1

source_name: tam44 cells, 41 ℃, 30 minutes, replicate 1


title: GLY3_41_60min_rep1

description:
gene expression 60 minutes after growth temperature upshift
parental strain

source_name: GLY3 cells, 41 ℃, 60 minutes, replicate 1


title: Severely injured patient (29651128)


title: Severely injured patient (25233640)


title: Severely injured patient (10330501)


title: Severely injured patient (12278819)


title: Severely injured patient (16126330)


title: GLY3_41_0min_rep1

description:
gene expression 0 minute after growth temperature upshift
parental strain

source_name: GLY3 cells, 41 ℃, 0 minute, replicate 1


title: Severely injured patient (9335780)


title: Severely injured patient (21889401)


title: Severely injured patient (19346493)


title: trm2_41_30min_rep1

source_name: trm2 cells, 41 ℃, 30 minutes, replicate 1


title: Severely injured patient (26592085)


title: Severely injured patient (9182019)


title: GLY3_41_15min_rep1

description:
gene expression 15 minutes after growth temperature upshift
parental strain

source_name: GLY3 cells, 41 ℃, 15 minutes, replicate 1


title: GLY3_41_30min_rep1

description:
gene expression 30 minutes after growth temperature upshift
parental strain

source_name: GLY3 cells, 41 ℃, 30 minutes, replicate 1


title: trm2_41_15min_rep1

source_name: trm2 cells, 41 ℃, 15 minutes, replicate 1


title: Severely injured patient (31426617)

source_name: Whole Blood


title: Severely injured patient (933201)


title: Severely injured patient (4914849)


title: Severely injured patient (13605905)


title: Severely injured patient (5309033)


title: Severely injured patient (6457078)


title: Severely injured patient (29888593)


title: Severely injured patient (15126507)


title: Severely injured patient (8311420)


title: Severely injured patient (18711782)


title: Severely injured patient (7883201)


title: Severely injured patient (33495747)


title: Severely injured patient (2012127)


title: Severely injured patient (33248761)


title: Severely injured patient (31082491)


title: Severely injured patient (4708645)


title: Severely injured patient (27652186)


title: Severely injured patient (29632840)


title: Severely injured patient (9129788)


title: Severely injured patient (25639786)


title: Severely injured patient (17365488)


title: Severely injured patient (676064)


title: Severely injured patient (7259981)


title: Severely injured patient (32790867)


title: Severely injured patient (3995987)


title: Severely injured patient (2714944)


title: Severely injured patient (14990317)


title: Severely injured patient (3211256)


title: Severely injured patient (21820177)


title: Severely injured patient (1337911)


title: Severely injured patient (6690371)


title: Severely injured patient (6728949)


title: Severely injured patient (28778395)


title: Severely injured patient (17697278)


title: Severely injured patient (25782105)


title: Severely injured patient (33555591)


title: Severely injured patient (24788354)


title: Severely injured patient (24579207)


title: Severely injured patient (21650597)


title: genomic_DNA_from_Surgical_resection_GBM-1730

city: Acton

first: Sebastian

last: Kurscheid

state: ACT

address: 57 Garran Road

department: JCSMR

institute: Australian National University

hyb_protocol: Labeled test and reference DNAs together with 100 µg human Cot-1 DNA were hybridized for ~48 hrs at 37º C.

scan_protocol: 16-bit DAPI, Cy3 and Cy5 images were acquired using a custom built CCD camera system (Hamilton et al. 2006. A large field CCD system for quantitative imaging of microarrays. Nuc. Acids Res. 34, e58).

data_processing:
Image and data analysis was carried out using UCSF SPOT (Jain AN et al. 2002. Fully automatic quantification of microarray image data. Genome Res. 12:325-332). Ratios for each spot were calculated as the total background-corrected fluorescence intensity ratios for the test and reference channels. In addition, array CGH data were corrected for BAC clone specific GC content and in some hybridizations a geometrical dependence of the ratios on the array. Data were derived from two different versions of arrays: HumArray2.0 and HumArray3.1. For compatibility, data are presented in the HumArray 3.1 format.
Matrix signal intensities: Cy3/Cy5 ratio (Relative Ratio, RR) and average of signals per clone were computed.
Log2(RR) – The Lift Genome Annotations Tools was used to convert the coordinates of 1986 BACs for the Assembly GRCh37 (https://genome.ucsc.edu/cgi-bin/hgLiftOver). The data processing was completed by signals normalization to the median RR per hybridization and the computation of log2RR. An additional smoothing procedure was applied to remove the wave bias for more accurate breakpoint detection in profiles as proposed by van de Wiel et al. (van de Wiel et al., 2009). The copy number alteration (CNA) data was analysed by circular binary segmentation (CBS) (Olshen et al., 2004; Venkatraman and Olshen, 2007) performed on normalized log2(RR) values for each sample.

source_name: Surgical resection GBM-1730

label_protocol: Genomic DNA (600 ng) was labeled by random priming to incorporate Cy5/Cy3 dCTP in a 50 µl reaction.

extract_protocol: Genomic DNA was isolated using Qiagen AllPrep DNA/RNA Kit (Qiagen, 80204).

tag: gender

tag: disease state

value: GBM

tag: os

tag: clinical trial phase

value: III

source_name: Reference DNA

value: synthetic normal reference DNA


title: genomic_DNA_from_Surgical_resection_GBM-1704

source_name: Surgical resection GBM-1704

value: U


title: genomic_DNA_from_Surgical_resection_GBM-1543

source_name: Surgical resection GBM-1543


title: genomic_DNA_from_Surgical_resection_GBM-1621

source_name: Surgical resection GBM-1621

value: II


title: Severely injured patient (3025944)


title: Severely injured patient (27045511)


title: Severely injured patient (2928539)


title: Severely injured patient (24626847)


title: Severely injured patient (3974501)


title: Severely injured patient (17075415)


title: genomic_DNA_from_Surgical_resection_GBM-1705

source_name: Surgical resection GBM-1705


title: genomic_DNA_from_recurrent_GBM-1613,_originating_tumor_GBM-1543

source_name: recurrent GBM-1613, originating tumor GBM-1543


title: Severely injured patient (17086294)


title: Severely injured patient (13477597)


title: Severely injured patient (268970)


title: Severely injured patient (20646917)


title: Severely injured patient (21850433)


title: Severely injured patient (8410562)


title: Severely injured patient (17670937)


title: Severely injured patient (3237808)


title: Severely injured patient (6536278)


title: Severely injured patient (29574522)


title: genomic_DNA_from_Surgical_resection_GBM-1617

source_name: Surgical resection GBM-1617


title: genomic_DNA_from_Surgical_resection_GBM-1628

source_name: Surgical resection GBM-1628


title: Severely injured patient (7215223)


title: genomic_DNA_from_Surgical_resection_GBM-1437

source_name: Surgical resection GBM-1437


title: Severely injured patient (27897114)


title: genomic_DNA_from_Surgical_resection_GBM-1709

source_name: Surgical resection GBM-1709


title: genomic_DNA_from_Surgical_resection_GBM-1614

source_name: Surgical resection GBM-1614


title: genomic_DNA_from_Surgical_resection_GBM-1612

source_name: Surgical resection GBM-1612


title: genomic_DNA_from_Surgical_resection_GBM-1591

source_name: Surgical resection GBM-1591


title: genomic_DNA_from_Surgical_resection_GBM-1763

source_name: Surgical resection GBM-1763


title: genomic_DNA_from_Surgical_resection_GBM-1748

source_name: Surgical resection GBM-1748


title: Severely injured patient (31061653)

source_name: Whole Blood


title: genomic_DNA_from_Surgical_resection_GBM-1552

source_name: Surgical resection GBM-1552


title: genomic_DNA_from_Surgical_resection_GBM-1756

source_name: Surgical resection GBM-1756

source_name: Reference DNA


title: genomic_DNA_from_Surgical_resection_GBM-1761

source_name: Surgical resection GBM-1761


title: genomic_DNA_from_Surgical_resection_GBM-1601

source_name: Surgical resection GBM-1601


title: genomic_DNA_from_Surgical_resection_GBM-1589

source_name: Surgical resection GBM-1589


title: genomic_DNA_from_Surgical_resection_GBM-1706

source_name: Surgical resection GBM-1706


title: genomic_DNA_from_Surgical_resection_GBM-1587

source_name: Surgical resection GBM-1587


title: genomic_DNA_from_Surgical_resection_GBM-1545

source_name: Surgical resection GBM-1545


title: genomic_DNA_from_Surgical_resection_GBM-1760

source_name: Surgical resection GBM-1760


title: genomic_DNA_from_Surgical_resection_GBM-1566

source_name: Surgical resection GBM-1566


title: genomic_DNA_from_Surgical_resection_GBM-1732

source_name: Surgical resection GBM-1732


title: Severely injured patient (17782669)


title: genomic_DNA_from_Surgical_resection_GBM-1759

source_name: Surgical resection GBM-1759


title: Severely injured patient (34326209)


title: Severely injured patient (21367224)


title: Severely injured patient (34734923)


title: Severely injured patient (22114967)


title: Severely injured patient (30795590)


title: Severely injured patient (11093077)


title: Severely injured patient (14728445)


title: genomic_DNA_from_Surgical_resection_GBM-1729

source_name: Surgical resection GBM-1729


title: genomic_DNA_from_Surgical_resection_GBM-1703

source_name: Surgical resection GBM-1703


title: genomic_DNA_from_Surgical_resection_GBM-1774

source_name: Surgical resection GBM-1774


title: genomic_DNA_from_Surgical_resection_GBM-1357

source_name: Surgical resection GBM-1357


title: genomic_DNA_from_Surgical_resection_GBM-1758

source_name: Surgical resection GBM-1758


title: genomic_DNA_from_Surgical_resection_GBM-1755

source_name: Surgical resection GBM-1755


title: genomic_DNA_from_Surgical_resection_GBM-1714

source_name: Surgical resection GBM-1714

source_name: Reference DNA


title: genomic_DNA_from_Surgical_resection_GBM-1766

source_name: Surgical resection GBM-1766


title: genomic_DNA_from_Surgical_resection_GBM-1317

source_name: Surgical resection GBM-1317


title: genomic_DNA_from_Surgical_resection_GBM-1639

source_name: Surgical resection GBM-1639


title: genomic_DNA_from_Surgical_resection_GBM-1682

source_name: Surgical resection GBM-1682


title: genomic_DNA_from_Surgical_resection_GBM-1752

source_name: Surgical resection GBM-1752


title: genomic_DNA_from_Surgical_resection_GBM-1646

source_name: Surgical resection GBM-1646


title: genomic_DNA_from_Surgical_resection_GBM-1584

source_name: Surgical resection GBM-1584


title: genomic_DNA_from_Surgical_resection_GBM-1496

source_name: Surgical resection GBM-1496


title: Severely injured patient (2073353)

source_name: Whole Blood


title: genomic_DNA_from_recurrent_GBM-1622,_originating_tumor_GBM-1621

source_name: recurrent GBM-1622, originating tumor GBM-1621


title: Severely injured patient (5656641)


title: genomic_DNA_from_recurrent_GBM-1775,_originating_tumor_GBM-1714

source_name: recurrent GBM-1775, originating tumor GBM-1714


title: Severely injured patient (4930727)


title: genomic_DNA_from_recurrent_GBM-1497,_originating_tumor_GBM-1430

source_name: recurrent GBM-1497, originating tumor GBM-1430


title: genomic_DNA_from_Surgical_resection_GBM-1769

source_name: Surgical resection GBM-1769


title: Severely injured patient (20037566)


title: Severely injured patient (19720060)


title: Severely injured patient (21269988)


title: Severely injured patient (29831499)


title: genomic_DNA_from_Surgical_resection_GBM-1768

source_name: Surgical resection GBM-1768


title: Severely injured patient (8392032)


title: genomic_DNA_from_Surgical_resection_GBM-1564

source_name: Surgical resection GBM-1564


title: genomic_DNA_from_Surgical_resection_GBM-1399

source_name: Surgical resection GBM-1399


title: Severely injured patient (13673659)


title: genomic_DNA_from_Surgical_resection_GBM-1707

source_name: Surgical resection GBM-1707

source_name: Reference DNA


title: genomic_DNA_from_Surgical_resection_GBM-1430

source_name: Surgical resection GBM-1430


title: genomic_DNA_from_Surgical_resection_GBM-1360

source_name: Surgical resection GBM-1360


title: genomic_DNA_from_Surgical_resection_GBM-1308

source_name: Surgical resection GBM-1308


title: genomic_DNA_from_Surgical_resection_GBM-1647

source_name: Surgical resection GBM-1647


title: genomic_DNA_from_Surgical_resection_GBM-1297

source_name: Surgical resection GBM-1297


title: genomic_DNA_from_Surgical_resection_GBM-1562

source_name: Surgical resection GBM-1562


title: genomic_DNA_from_Surgical_resection_GBM-1731

source_name: Surgical resection GBM-1731


title: genomic_DNA_from_Surgical_resection_GBM-1603

source_name: Surgical resection GBM-1603


title: genomic_DNA_from_Surgical_resection_GBM-1710

source_name: Surgical resection GBM-1710


title: genomic_DNA_from_Surgical_resection_GBM-1749

source_name: Surgical resection GBM-1749


title: genomic_DNA_from_Surgical_resection_GBM-1764

source_name: Surgical resection GBM-1764


title: genomic_DNA_from_Surgical_resection_GBM-1316

source_name: Surgical resection GBM-1316


title: genomic_DNA_from_Surgical_resection_GBM-1419

source_name: Surgical resection GBM-1419


title: Severely injured patient (20820146)

source_name: Whole Blood


title: Severely injured patient (4975259)


title: genomic_DNA_from_Surgical_resection_GBM-1606

source_name: Surgical resection GBM-1606


title: Severely injured patient (9956587)


title: Severely injured patient (4277162)


title: Severely injured patient (21900468)


title: Severely injured patient (5914004)


title: Severely injured patient (22317442)


title: Capan2_NC-2 biological rep1

city: Hong Kong

first: Chi Han Samson

last: Li

address: Shatin

department: School of Biomedical Sciences

country: Hong Kong

institute: The Chinese University of Hong Kong

description: Gene expression data from CAPAN2 cells transduced with control lentivirus

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in GeneChip® Fluidics Station 450.

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

data_processing: The data were analyzed with Partek Suite version 6.6 using Affymetrix default analysis settings and RMA as normalization method.

source_name: Capan2 cells transduced with control lentivirus

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

growth_protocol: Cultured in standard condition according to America Type Culture Condition (ATCC) with DMEM supplemented with 10% FBS and 1x penicillin and streptomycin

extract_protocol: Total RNA were extracted using Trizol reagent (Invitrogen)

treatment_protocol: Cells were transduced with lentivirus in the presence of 8µg/ml hexadimethrine bromide (Sigma) overnight

value: Pancreatic ductal adenocarcinoma

tag: transfection

value: control lentivirus


title: Severely injured patient (15863994)


title: Severely injured patient (17105131)


title: Severely injured patient (212182)


title: Severely injured patient (25351929)


title: Severely injured patient (2246649)


title: Severely injured patient (28666724)


title: NBM17

city: Oxford

first: Andrea

last: Pellagatti

address: John Radcliffe Hospital

department: NDCLS, RDM

institute: University of Oxford

description:
Healthy control 17
Gene expression data from bone marrow CD34+ cells

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using an Affymetrix GeneChip Scanner 3000

data_processing: Affymetrix CEL files were pre-processed using GC Robust Multi-array Average (GC-RMA)

label: Biotin

source_name: Bone marrow CD34+ cells

label_protocol: 50 ng of total RNA were amplified and biotin-labelled with the Two-Cycle cDNA Synthesis and the Two-Cycle Target Labelling and Control Reagent packages according to the standard Affymetrix protocol

extract_protocol: Total RNA was extracted using TRIZOL following the manufacturer’s protocol

treatment_protocol: Mononuclear cells were separated using Histopaque density gradient centrifugation, labelled with CD34 MicroBeads, and then CD34+ cells were isolated using MACS magnetic cell separation columns according to the manufacturer’s recommendations.

value: bone marrow

value: bone marrow CD34+ cells

tag: disease status

value: Healthy control


title: NBM09

description:
Healthy control 9
Gene expression data from bone marrow CD34+ cells


title: Severely injured patient (33344376)

value: PMNs (isolated peripheral neutrophils )

value: trauma


title: Severely injured patient (18036846)

value: M


title: Severely injured patient (4393368)


title: Capan2_siLLGL1-2 biological rep2

description: Gene expression data from CAPAN2 cells transduced with lentivirus carrying shRNAs targeting LLGL1 transcript

source_name: Capan2 cells transduced with lentivirus carrying shRNAs targeting LLGL1 transcript


title: Severely injured patient (17762934)

value: F


title: NBM13

description:
Healthy control 13
Gene expression data from bone marrow CD34+ cells


title: NBM14

description:
Healthy control 14
Gene expression data from bone marrow CD34+ cells


title: NBM12

description:
Healthy control 12
Gene expression data from bone marrow CD34+ cells


title: NBM16

description:
Healthy control 16
Gene expression data from bone marrow CD34+ cells


title: NBM08

description:
Healthy control 8
Gene expression data from bone marrow CD34+ cells


title: NBM15

description:
Healthy control 15
Gene expression data from bone marrow CD34+ cells


title: NBM04

description:
Healthy control 4
Gene expression data from bone marrow CD34+ cells


title: NBM11

description:
Healthy control 11
Gene expression data from bone marrow CD34+ cells


title: Severely injured patient (14873450)


title: NBM05

description:
Healthy control 5
Gene expression data from bone marrow CD34+ cells


title: NBM10

description:
Healthy control 10
Gene expression data from bone marrow CD34+ cells


title: NBM06

description:
Healthy control 6
Gene expression data from bone marrow CD34+ cells


title: Capan2_siLLGL1-2 biological rep1

value: lentivirus carrying shRNAs targeting LLGL1 transcript


title: Severely injured patient (4816971)


title: NBM07

description:
Healthy control 7
Gene expression data from bone marrow CD34+ cells


title: Capan2_NC-2 biological rep2


title: 292M_LowFat_Muscle (Mm)

city: Baltimore

first: Andrew

middle: P

last: Feinberg

state: Maryland

address: 855 N Wolfe St

department: Department of Medicine

institute: Johns Hopkins School of Medicine

description:
processed data file: Muscle_processed_data.txt
DNA methylation

hyb_protocol: as per manufacturer's protocol (NimbleGen Arrays User’s Guide, CGH Arrays v 9.1)

data_processing:
QC scores generated and normalization performed as per CHARM R package (available on Bioconductor)
Processed data description: Methylation beta-values (range from 0-1, differences in beta-values represent relative methylation differences)

organism: Mus musculus

extract_protocol: MasterPure DNA Purification Kit (epicentre, WI, USA)

tag: strain

value: male

value: Muscle

tag: diet

value: LowFat

tag: mouse weight

tag: glucose tolerance test

tag: insulin tolerance test

tag: fasting glucose


title: NBM01

description:
Healthy control 1
Gene expression data from bone marrow CD34+ cells


title: Severely injured patient (14360450)

tag: Sex

tag: age(years)


title: Severely injured patient (25567765)

tag: injury


title: Severely injured patient (29563818)

tag: tissue


title: MDS179

description:
MDS patient 179
Gene expression data from bone marrow CD34+ cells

tag: cell type

value: MDS


title: MDS178

description:
MDS patient 178
Gene expression data from bone marrow CD34+ cells


title: 172M_HighFat_Muscle (Mm)

scan_protocol: as per manufacturer's protocol (NimbleGen Arrays User’s Guide, CGH Arrays v 9.1)

tag: gender

value: HighFat


title: 145M_LowFat_Muscle (Mm)

label_protocol: as per manufacturer's protocol (NimbleGen Arrays User’s Guide, CGH Arrays v 9.1)


title: MDS176

description:
MDS patient 176
Gene expression data from bone marrow CD34+ cells


title: NBM03

description:
Healthy control 3
Gene expression data from bone marrow CD34+ cells


title: MDS226

description:
MDS patient 226
Gene expression data from bone marrow CD34+ cells


title: MDS183

description:
MDS patient 183
Gene expression data from bone marrow CD34+ cells


title: Severely injured patient (28899447)


title: MDS174

description:
MDS patient 174
Gene expression data from bone marrow CD34+ cells


title: MDS180

description:
MDS patient 180
Gene expression data from bone marrow CD34+ cells


title: Severely injured patient (29898696)


title: 297M_LowFat_Muscle (Mm)


title: 904M_HighFat_Muscle (Mm)


title: MDS169

description:
MDS patient 169
Gene expression data from bone marrow CD34+ cells


title: MDS171

description:
MDS patient 171
Gene expression data from bone marrow CD34+ cells


title: MDS168

description:
MDS patient 168
Gene expression data from bone marrow CD34+ cells


title: MDS173

description:
MDS patient 173
Gene expression data from bone marrow CD34+ cells


title: MDS170

description:
MDS patient 170
Gene expression data from bone marrow CD34+ cells


title: MDS166

description:
MDS patient 166
Gene expression data from bone marrow CD34+ cells


title: MDS165

description:
MDS patient 165
Gene expression data from bone marrow CD34+ cells


title: 909M_LowFat_Muscle (Mm)

description:
processed data file: Muscle_processed_data.txt
DNA methylation


title: 280M_LowFat_Muscle (Mm)


title: 165M_HighFat_Muscle (Mm)


title: 131M_LowFat_Muscle (Mm)


title: NBM02

description:
Healthy control 2
Gene expression data from bone marrow CD34+ cells


title: 208M_HighFat_Muscle (Mm)


title: MDS172

description:
MDS patient 172
Gene expression data from bone marrow CD34+ cells


title: MDS164

description:
MDS patient 164
Gene expression data from bone marrow CD34+ cells


title: 220B_HighFat_Islet (Mm)

description:
processed data file: Islets_processed_data.txt
DNA methylation

value: Islet


title: 206M_HighFat_Muscle (Mm)


title: 214B_HighFat_Islet (Mm)


title: MDS225

description:
MDS patient 225
Gene expression data from bone marrow CD34+ cells


title: MDS167

description:
MDS patient 167
Gene expression data from bone marrow CD34+ cells


title: MDS160

description:
MDS patient 160
Gene expression data from bone marrow CD34+ cells


title: 902B_HighFat_Islet (Mm)


title: MDS224

description:
MDS patient 224
Gene expression data from bone marrow CD34+ cells


title: MDS163

description:
MDS patient 163
Gene expression data from bone marrow CD34+ cells


title: MDS159

description:
MDS patient 159
Gene expression data from bone marrow CD34+ cells


title: MDS223

description:
MDS patient 223
Gene expression data from bone marrow CD34+ cells


title: MDS162

description:
MDS patient 162
Gene expression data from bone marrow CD34+ cells


title: MDS158

description:
MDS patient 158
Gene expression data from bone marrow CD34+ cells


title: 287B_LowFat_Islet (Mm)


title: MDS157

description:
MDS patient 157
Gene expression data from bone marrow CD34+ cells


title: 278B_LowFat_Islet (Mm)


title: MDS155

description:
MDS patient 155
Gene expression data from bone marrow CD34+ cells


title: 905B_LowFat_Islet (Mm)


title: MDS151

description:
MDS patient 151
Gene expression data from bone marrow CD34+ cells


title: MDS156

description:
MDS patient 156
Gene expression data from bone marrow CD34+ cells


title: MDS153

description:
MDS patient 153
Gene expression data from bone marrow CD34+ cells


title: MDS147

description:
MDS patient 147
Gene expression data from bone marrow CD34+ cells


title: MDS161

description:
MDS patient 161
Gene expression data from bone marrow CD34+ cells


title: MDS221

description:
MDS patient 221
Gene expression data from bone marrow CD34+ cells


title: MDS152

description:
MDS patient 152
Gene expression data from bone marrow CD34+ cells


title: 213B_LowFat_Islet (Mm)

description:
processed data file: Islets_processed_data.txt
DNA methylation


title: MDS222

description:
MDS patient 222
Gene expression data from bone marrow CD34+ cells


title: 910B_LowFat_Islet (Mm)


title: 299B_HighFat_Islet (Mm)


title: 283B_HighFat_Islet (Mm)


title: MDS150

description:
MDS patient 150
Gene expression data from bone marrow CD34+ cells


title: MDS148

description:
MDS patient 148
Gene expression data from bone marrow CD34+ cells


title: MDS146

description:
MDS patient 146
Gene expression data from bone marrow CD34+ cells


title: 282B_HighFat_Islet (Mm)


title: MDS149

description:
MDS patient 149
Gene expression data from bone marrow CD34+ cells


title: MDS219

description:
MDS patient 219
Gene expression data from bone marrow CD34+ cells


title: 172Hy_HighFat_Hypothalamus (Mm)

description:
processed data file: Hypothalamus_processed_data.txt
DNA methylation

value: Hypothalamus


title: 165Hy_HighFat_Hypothalamus (Mm)


title: MDS216

description:
MDS patient 216
Gene expression data from bone marrow CD34+ cells


title: 297Hy_LowFat_Hypothalamus (Mm)


title: MDS215

description:
MDS patient 215
Gene expression data from bone marrow CD34+ cells


title: MDS212

description:
MDS patient 212
Gene expression data from bone marrow CD34+ cells


title: MDS220

description:
MDS patient 220
Gene expression data from bone marrow CD34+ cells


title: MDS217

description:
MDS patient 217
Gene expression data from bone marrow CD34+ cells


title: MDS214

description:
MDS patient 214
Gene expression data from bone marrow CD34+ cells


title: MDS213

description:
MDS patient 213
Gene expression data from bone marrow CD34+ cells


title: MDS144

description:
MDS patient 144
Gene expression data from bone marrow CD34+ cells


title: MDS141

description:
MDS patient 141
Gene expression data from bone marrow CD34+ cells


title: MDS142

description:
MDS patient 142
Gene expression data from bone marrow CD34+ cells


title: 280Hy_LowFat_Hypothalamus (Mm)


title: MDS138

description:
MDS patient 138
Gene expression data from bone marrow CD34+ cells


title: MDS135

description:
MDS patient 135
Gene expression data from bone marrow CD34+ cells


title: MDS210

description:
MDS patient 210
Gene expression data from bone marrow CD34+ cells


title: MDS181

description:
MDS patient 181
Gene expression data from bone marrow CD34+ cells


title: MDS134

description:
MDS patient 134
Gene expression data from bone marrow CD34+ cells


title: MDS143

description:
MDS patient 143
Gene expression data from bone marrow CD34+ cells


title: MDS218

description:
MDS patient 218
Gene expression data from bone marrow CD34+ cells


title: MDS136

description:
MDS patient 136
Gene expression data from bone marrow CD34+ cells


title: MDS139

description:
MDS patient 139
Gene expression data from bone marrow CD34+ cells


title: 87Hy_HighFat_Hypothalamus (Mm)

description:
processed data file: Hypothalamus_processed_data.txt
DNA methylation


title: 208Hy_HighFat_Hypothalamus (Mm)


title: 145Hy_LowFat_Hypothalamus (Mm)


title: MDS140

description:
MDS patient 140
Gene expression data from bone marrow CD34+ cells


title: 131Hy_LowFat_Hypothalamus (Mm)


title: 904Hy_HighFat_Hypothalamus (Mm)


title: MDS133

description:
MDS patient 133
Gene expression data from bone marrow CD34+ cells


title: MDS132

description:
MDS patient 132
Gene expression data from bone marrow CD34+ cells


title: MDS128

description:
MDS patient 128
Gene expression data from bone marrow CD34+ cells


title: MDS130

description:
MDS patient 130
Gene expression data from bone marrow CD34+ cells


title: MDS129

description:
MDS patient 129
Gene expression data from bone marrow CD34+ cells


title: MDS209

description:
MDS patient 209
Gene expression data from bone marrow CD34+ cells


title: MDS208

description:
MDS patient 208
Gene expression data from bone marrow CD34+ cells


title: MDS131

description:
MDS patient 131
Gene expression data from bone marrow CD34+ cells


title: MDS207

description:
MDS patient 207
Gene expression data from bone marrow CD34+ cells


title: MDS204

description:
MDS patient 204
Gene expression data from bone marrow CD34+ cells


title: 206Hy_HighFat_Hypothalamus (Mm)


title: MDS127

description:
MDS patient 127
Gene expression data from bone marrow CD34+ cells


title: 206L_HighFat_Hepatocytes (Mm)

description:
processed data file: Hepatocytes_processed_data.txt
DNA methylation

value: Hepatocyte


title: MDS205

description:
MDS patient 205
Gene expression data from bone marrow CD34+ cells


title: 904L_HighFat_Hepatocytes (Mm)


title: MDS206

description:
MDS patient 206
Gene expression data from bone marrow CD34+ cells


title: MDS125

description:
MDS patient 125
Gene expression data from bone marrow CD34+ cells


title: MDS201

description:
MDS patient 201
Gene expression data from bone marrow CD34+ cells


title: 172L_HighFat_Hepatocytes (Mm)


title: MDS202

description:
MDS patient 202
Gene expression data from bone marrow CD34+ cells


title: 276L_LowFat_Hepatocytes (Mm)


title: MDS203

description:
MDS patient 203
Gene expression data from bone marrow CD34+ cells


title: 292L_LowFat_Hepatocytes (Mm)


title: 145L_LowFat_Hepatocytes (Mm)


title: 174L_LowFat_Hepatocytes (Mm)


title: 125L_LowFat_Hepatocytes (Mm)


title: MDS200

description:
MDS patient 200
Gene expression data from bone marrow CD34+ cells


title: MDS199

description:
MDS patient 199
Gene expression data from bone marrow CD34+ cells


title: MDS194

description:
MDS patient 194
Gene expression data from bone marrow CD34+ cells


title: MDS197

description:
MDS patient 197
Gene expression data from bone marrow CD34+ cells


title: 208L_LowFat_Hepatocytes (Mm)


title: MDS196

description:
MDS patient 196
Gene expression data from bone marrow CD34+ cells


title: MDS195

description:
MDS patient 195
Gene expression data from bone marrow CD34+ cells


title: MDS211

description:
MDS patient 211
Gene expression data from bone marrow CD34+ cells


title: MDS192

description:
MDS patient 192
Gene expression data from bone marrow CD34+ cells


title: 293L_HighFat_Hepatocytes (Mm)


title: MDS193

description:
MDS patient 193
Gene expression data from bone marrow CD34+ cells


title: MDS124

description:
MDS patient 124
Gene expression data from bone marrow CD34+ cells


title: MDS120

description:
MDS patient 120
Gene expression data from bone marrow CD34+ cells


title: 131L_HighFat_Hepatocytes (Mm)

description:
processed data file: Hepatocytes_processed_data.txt
DNA methylation


title: 292Hy_LowFat_Hypothalamus (Mm)

description:
processed data file: Hypothalamus_processed_data.txt
DNA methylation


title: 297A_LowFat_Adipocytes (Mm)

description:
processed data file: Adipocytes_processed_data.txt
DNA methylation

value: Adipocyte


title: MDS198

description:
MDS patient 198
Gene expression data from bone marrow CD34+ cells

value: bone marrow


title: genomic DNA from Surgical resection GBM-2207

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 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 was used for primary data acqusition. Raw data was imported into R and further processed using R/Bioconductor package “methylumi”. The raw pre-processing (Illumina method) was used for data normalization.

label: Cy5 and Cy3

source_name: Surgical resection GBM-2207

label_protocol: Standard Illumina Protocol

tag: disease state

value: GBM

tag: geo expression data

tag: age


title: 909L_HighFat_Hepatocytes (Mm)


title: genomic DNA from Surgical resection GBM-2669

source_name: Surgical resection GBM-2669

tag: os


title: MDS117

description:
MDS patient 117
Gene expression data from bone marrow CD34+ cells

value: bone marrow CD34+ cells

tag: disease status


title: Y3/CD103-/--1

city: Miami

first: Thomas

middle: R

last: Malek

address: 1600 NW 10th Avenue

department: Microbiology/Immunology

institute: University of Miami

hyb_protocol: Biotinylated cRNA was hybridized to Affymetrix Gene ST1.0 arrays

scan_protocol: Image analysis was performed using the Affymetrix Command Console Software (AGCC).

data_processing: Resulting data were normalized with the RMA method using software at GeneSifter (Seattle, WA). Group comparisons of the transformed data of 3 independent biological replicates were performed using ANOVA applying the Benjamini Hochberg correction for false positives. Data analysis was based on annotated mRNAs and setting a lower signal intensity limit of 4 units (one group must pass).

source_name: regulatory T cell

label_protocol: 10-20 ng of RNA was used in a single round of linear RNA probe amplification using Ovation Pico WTA System V2 and biotin-labeled using  Encore Biotin Module (NuGEN, San Carlos, CA, USA).

extract_protocol: Total RNA was isolated using TRizol and further purified with RNAeasy Minikit (QIAGEN). RNA quantity and qulaity was confirmned by analysis with a Agilent 2100 Bioananalyzer

treatment_protocol: T regulatory cells  were FACS purified and total RNA was isolated

tag: strain

tag: genotype/variation

value: laminai propria small and large intestine

value: regulatory T cells (Tregs)


title: Y3/CD103-/--3


title: 145A_LowFat_Adipocytes (Mm)

tag: diet

tag: mouse weight


title: MDS121

description:
MDS patient 121
Gene expression data from bone marrow CD34+ cells


title: Y3/CD103-/--2


title: genomic DNA from cultured glioma spheres LN-2683GS

source_name: cultured glioma spheres LN-2683GS

value: M

tag: growth protocol

value: GS lines were cultured under stem cell conditions using DMEM-F12 medium (Invitrogen, 10565-018) supplemented with human recombinant EGF and human recombinant basic FGF (Peprotech, AF-100-15 and 100-18B), 20 ng/ml each, and 2% B27 (Invitrogen, 17504); 50% of the medium was substituted twice weekly.


title: MDS113

description:
MDS patient 113
Gene expression data from bone marrow CD34+ cells


title: MDS115

description:
MDS patient 115
Gene expression data from bone marrow CD34+ cells


title: MDS116

description:
MDS patient 116
Gene expression data from bone marrow CD34+ cells


title: MDS108

description:
MDS patient 108
Gene expression data from bone marrow CD34+ cells


title: genomic DNA from Surgical resection GBM-2540

source_name: Surgical resection GBM-2540


title: MDS118

description:
MDS patient 118
Gene expression data from bone marrow CD34+ cells


title: genomic DNA from cultured glioma spheres LN-2669GS

source_name: cultured glioma spheres LN-2669GS


title: 172A_HighFat_Adipocytes (Mm)

tag: glucose tolerance test

tag: insulin tolerance test

tag: fasting glucose


title: MDS123

description:
MDS patient 123
Gene expression data from bone marrow CD34+ cells


title: 87A_HighFat_Adipocytes (Mm)


title: Y3-1


title: Y3-3


title: MDS107

description:
MDS patient 107
Gene expression data from bone marrow CD34+ cells


title: 292A_LowFat_Adipocytes (Mm)


title: Y3-2


title: WT-3

value: WT


title: genomic DNA from Surgical resection GBM-2683

source_name: Surgical resection GBM-2683


title: 904A_HighFat_Adipocytes (Mm)

value: male


title: WT-2


title: 909A_LowFat_Adipocytes (Mm)


title: genomic DNA from cultured glioma spheres LN-2207GS

source_name: cultured glioma spheres LN-2207GS


title: MDS106

description:
MDS patient 106
Gene expression data from bone marrow CD34+ cells


title: 131A_LowFat_Adipocytes (Mm)


title: WT-1


title: 165A_HighFat_Adipocytes (Mm)


title: 280A_LowFat_Adipocytes (Mm)


title: MDS099

description:
MDS patient 99
Gene expression data from bone marrow CD34+ cells


title: genomic DNA from cultured glioma spheres LN-2540GS

source_name: cultured glioma spheres LN-2540GS


title: FTO

city: Nanjing

first: Hong-Qi

last: Fan

state: Jiangsu

address: 300 Guangzhou RD

department: Department of Endocrinology

country: China

institute: The First Affiliated Hospital of Nanjing Medical University

description: Total RNA from each sample was amplified and transcribed into fluorescent cRNA with using the manufacturer’s Agilent’s Quick Amp Labeling protocol (version 5.7, Agilent Technologies). The labeled cRNAs were hybridized onto the Whole Mouse Genome Oligo Microarray (4x44K, Agilent Technologies). After having washed the slides, the arrays were scanned by the Agilent Scanner G2505C.

hyb_protocol: The Labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60 °C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide.

scan_protocol: The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C)

data_processing:
Agilent Feature Extraction software (version 11.0.1.1) was used to analyze the acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v11.5 software package (Agilent Technologies). After quantile normalization of the raw data, genes that at least 1 out of 2 samples have flags in Detected (“All Targets Value”) were chosen for further data analysis
Differentially expressed genes were identified through Fold Change filtering. Hierarchical Clustering was performed using the Agilent GeneSpring GX software (version 11.5). GO analysis and Pathway analysis were performed in the standard enrichment computation method

source_name: MIN6, transfected with PLVX-IRES-ZsGreen-mFTO

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology). Briefly, total RNA from each sample was linearly amplified and labeled with Cy3-UTP.

growth_protocol: MIN6 cells were cultured in DMEM medium with 15% fetal bovine serum, 100 U/ml penicillin, 100 µg/ml streptomycin and 50 µM β-mercaptoethanol in 5% CO2 /95% air in a humidified atmosphere at 37 °C

extract_protocol: Total RNA was extracted using Trizol reagent (Invitrogen) following the manufacture’s procedure.

treatment_protocol: Packaging of pseudotyped recombinant lentivirus was performed by transfection of 293T cells. Briefly, FTO overexpression vector pLVX-IRES-ZsGreen1-FTO or empty vector was ransfected with package vectors pCMV Δ8.91 and pMD.G into 293T cells using Lipofectamine 2000. Lentivirus in the culture media was harvested at 72 h and filtered through a 0.45 µm low protein binding polysulfonic filter. The virus was frozen and kept in -70 °C freezer for future use. For virus infection, MIN6 cells were plated into 6-cm dishes in advance and cultured for nearly 18 hours with about 50% confluence before transduction. The lentivirus suspension in the presence of 8 µg/ml polybrene was added to the cells. After transduction for 48 h, green fluorescence was observed to indicate the transduction efficiency.

value: a transgenic C57Bl/6 mouse-derived insulinoma cells

tag: passages

tag: cell line

tag: treatment

value: FTP overexpression


title: genomic DNA from Surgical resection GBM-1430

source_name: Surgical resection GBM-1430

tag: gender


title: MDS102

description:
MDS patient 102
Gene expression data from bone marrow CD34+ cells

tag: tissue

tag: cell type

value: MDS


title: 208A_HighFat_Adipocytes (Mm)

value: HighFat


title: MDS098

description:
MDS patient 98
Gene expression data from bone marrow CD34+ cells


title: MDS104

description:
MDS patient 104
Gene expression data from bone marrow CD34+ cells


title: MDS101

description:
MDS patient 101
Gene expression data from bone marrow CD34+ cells


title: LVX

source_name: MIN6, trasfected with PLVX-IRES-ZsGreen

value: control


title: MDS103

description:
MDS patient 103
Gene expression data from bone marrow CD34+ cells


title: MDS114

description:
MDS patient 114
Gene expression data from bone marrow CD34+ cells


title: 206A_HighFat_Adipocytes (Mm)

description:
processed data file: Adipocytes_processed_data.txt
DNA methylation


title: genomic DNA from Surgical resection GBM-1399

source_name: Surgical resection GBM-1399

tag: disease state

tag: geo expression data

tag: age


title: MDS097

description:
MDS patient 97
Gene expression data from bone marrow CD34+ cells

tag: disease status


title: genomic DNA from recurrent GBM-1497, originating tumor GBM-1430

tag: os


title: genomic DNA from Surgical resection GBM-1437

source_name: Surgical resection GBM-1437

value: U


title: genomic DNA from Surgical resection GBM-1419

source_name: Surgical resection GBM-1419

value: F


title: genomic DNA from Surgical resection GBM-1360

source_name: Surgical resection GBM-1360


title: MDS094

description:
MDS patient 94
Gene expression data from bone marrow CD34+ cells

source_name: Bone marrow CD34+ cells


title: MDS092

description:
MDS patient 92
Gene expression data from bone marrow CD34+ cells


title: MDS090

description:
MDS patient 90
Gene expression data from bone marrow CD34+ cells


title: MDS096

description:
MDS patient 96
Gene expression data from bone marrow CD34+ cells


title: MDS089

description:
MDS patient 89
Gene expression data from bone marrow CD34+ cells


title: genomic DNA from Surgical resection GBM-1357

source_name: Surgical resection GBM-1357


title: MDS084

description:
MDS patient 84
Gene expression data from bone marrow CD34+ cells


title: MDS087

description:
MDS patient 87
Gene expression data from bone marrow CD34+ cells


title: MDS082

description:
MDS patient 82
Gene expression data from bone marrow CD34+ cells


title: MDS085

description:
MDS patient 85
Gene expression data from bone marrow CD34+ cells


title: MDS088

description:
MDS patient 88
Gene expression data from bone marrow CD34+ cells


title: MDS081

description:
MDS patient 81
Gene expression data from bone marrow CD34+ cells


title: MDS091

description:
MDS patient 91
Gene expression data from bone marrow CD34+ cells


title: MDS080

description:
MDS patient 80
Gene expression data from bone marrow CD34+ cells


title: genomic DNA from Surgical resection GBM-1316

source_name: Surgical resection GBM-1316


title: genomic DNA from Surgical resection GBM-1317

source_name: Surgical resection GBM-1317


title: MDS079

description:
MDS patient 79
Gene expression data from bone marrow CD34+ cells


title: genomic DNA from Surgical resection GBM-1639

source_name: Surgical resection GBM-1639


title: genomic DNA from Surgical resection GBM-1308

source_name: Surgical resection GBM-1308


title: genomic DNA from recurrent GBM-1622, originating tumor GBM-1621


title: genomic DNA from Surgical resection GBM-1564

source_name: Surgical resection GBM-1564


title: MDS075

description:
MDS patient 75
Gene expression data from bone marrow CD34+ cells


title: genomic DNA from Surgical resection GBM-1647

source_name: Surgical resection GBM-1647


title: MDS072

description:
MDS patient 72
Gene expression data from bone marrow CD34+ cells


title: MDS074

description:
MDS patient 74
Gene expression data from bone marrow CD34+ cells


title: genomic DNA from Surgical resection GBM-1297

source_name: Surgical resection GBM-1297


title: MDS071

description:
MDS patient 71
Gene expression data from bone marrow CD34+ cells


title: genomic DNA from Surgical resection GBM-1562

source_name: Surgical resection GBM-1562