title: Needles November Whorl 3 Replicate 3

city: Malaga

first: Rafael

middle: A

last: Cañas

address: Facultad de Ciencias, Campus de Teatinos

department: Biología Molecular y Bioquímica

country: Spain

institute: Universidad de Málaga

description: Biological replicate 3 of 3. November Whorl 3

hyb_protocol: Before the microarray hybridizations the slides were pre-incubated during 1 h at 45ºC in a solution with 5X SSC buffer, 1% BSA and 0.1% SDS. Then, the slides were washed twice with 0.01 SSC buffer during 30 s and dry in a centrifuge during 2 min at 2000 xg. Before the hybridization 40 μl of hybridization solution (62.5 % (v/v) formamide, 6.25X SSC, 0.125 mg/mL salmon sperm, 0.625 % BSA, 0.125 5 SDS, 12.5 μg/mL polyA) were added to a10 μL solution with 2 μg of the problem sample labelled with Cy3 and 2 μg of the reference sample labelled with Cy5. The samples in this mix were denatured at 65ºC during 10 min in a thermal cycler. After this incubation the sample mix was load into a PINARRAY2 slide and covered with a HybriSlipTM hybridization cover (Grace Bio-Labs, OR, USA). Microarray hybridization was performed in a Genetix Hybridization Chamber (Genetix, New Milton, UK) at 42ºC for 16 h.

scan_protocol: Hybridized slides were scanned at 5 μm resolution and their signal intensities were detected by a GenePix 4100A microarray scanner (Molecular devices, Sunnyvale, CA, USA).

data_processing: The raw data were preprocessed and normalized with the R package for common reference design microarrays BABAR. The gene co-expression network analyses were carried out with the R package WGCNA. Genes with too many missing values were eliminated and the sample w2rep2november was also removed after an outlier verification through hierarchical clustering. Before the network construction the proper soft-thresholding power was determined performing an analysis of the network topology. We use the one-step network construction option with a soft-thresholding power value of 14. Genes with a kME >0.3 were assigned to an eigengene module or to a grey module if they did not meet the above criteria. The gene network screening was made with weighted and Pearson correlations using the WGCNA networkScreening function. The q-values (FDR) were calculated and the correlations were considered significant with a q-value < 0.05.

organism: Pinus pinaster

source_name: Total RNA from adult needles

label_protocol: Dye labeled aRNA was synthesized with the Amino allyl MessageAmp II aRNA amplification kit (Ambion Inc., Austin, TX)

growth_protocol: Field-grown adult trees from Sierra Bermeja (Estepona, Spain).

extract_protocol: Total RNA was isolated following the method of Chang S et al. Plant Mol Biol Rep 1993, 11:113–116

treatment_protocol: Pinus pinaster needles from 20-25 years old trees were sampled at Los Reales de Sierra Bermeja (Estepona, Spain) (30S X:303.095 Y:4.039.618) at 1245 m of altitude in the south side of the mountain. The harvest was carried out during the year 2012. Always we obtained the needles from the same 6 specific trees. The needles were isolated by whorl. Three whorls were considered from January to April and four whorls for the rest of months due to the emergence of a new whorl of needles in May. As in P. pinaster each needle whorl corresponds to the needles growth in a single year the whorls samples were named by numbers corresponding “0” to the new needles of 2012, “1” for 2011, “2” for 2010 and “3” for 2009 (Supporting Information Fig. S1). We harvested needles those were placed between 3 and 4 m of height in the trees always in the south side of the tree. The samplings were always carried out between 4 and 5 hours after the dawn.

value: 20-25 years old

value: Needles

tag: month

value: November

tag: harvesting date

tag: whorl

tag: biological replicate

source_name: Total RNA pool from all the RNA January samples

value: May


title: Needles September Whorl 3 Replicate 3

status: Public on Feb 27 2015

type: RNA

description: Biological replicate 3 of 3. September Whorl 3

molecule: total RNA

tag: age

tag: tissue

value: September

value: June


title: Needles May Whorl 3 Replicate 3

description: Biological replicate 3 of 3. May Whorl 3

value: April


title: 1W_DNA_methylation_2

type: genomic

city: Montreal

first: Moshe

last: Szyf

state: Quebec

address: McIntyre Medical Building, 3655 Promenade Sir William Osler, Room 1309

department: Pharmacology

country: Canada

institute: McGill University

description: 1 day withdrawal

hyb_protocol: All the steps of hybridization, washing, scanning and feature extraction were performed following the Agilent protocols for chip-on-chip analysis (MeDIP).

scan_protocol: Scanning was performed using the Agilent Technologies Scanner G2505B Images were quantified using Agilent Feature Extraction Software (version 10.5).

data_processing: The extracted intensities were then analyzed using the R software environment for statistical computing (R Development Core Team, 2007). Log-ratios of the bound (Cy5) and input (Cy3) microarray channel intensities were computed for each microarray and then microarrays were normalized to one another using quantile-normalization (Bolstad et al., 2003) under the assumption that all samples have identical overall methylation levels. Methylation levels were estimated from normalized probe intensities by applying a Bayesian deconvolution algorithm (Down et al., 2008). Promoter methylation levels were obtained taking the median estimated methylation level across each promoter.

molecule: genomic DNA

organism: Rattus norvegicus

source_name: 1 day withdrawal_IP genomic DNA

label_protocol: After the sonication step, methylated DNA was immunoprecipitated with 10 μg of anti-5methylCytosine antibody (Calbiochem) that is specific to DNA methylation, does not recognize hydroxymethylated DNA, and reveals changes in 5-methylcytoine exclusively. Prior to sonication, two control plasmids were added to the DNA (6pg each), an unmethylated GFP plasmid and an in vitro methylated Luciferase plasmid. The DNA-antibody complex was immuno-precipitated with 5 mg protein A and the methylated DNA was eluted with 150μl of TE at 1.5% SDS. The input and bound fraction were then amplified using the Whole Genome Amplification kit (Sigma). The amplified input and bound fractions were labeled for microarray hybridization with either Cy3-dUTP or Cy5-dUTP (Perkin Elmer), respectively, using the CGH labeling kit (Invitrogen) following the manufacturer’s instructions.

growth_protocol: Male Sprague-Dawley rats (Harlan, Israel) weighing 250-350g were  maintained on a 12-hr light/12-hr dark reversed cycle, with food and water available ad libitum. Rats were housed 2 per cage with a metal divider between them. Experiments were conducted during the dark cycle. Rats were anesthetized with xylazine and ketamine (10mg/kg and 100mg/kg, respectively). Jugular vein catheterization: Immediately after cannula implantation, rats were implanted with intravenous silastic catheters (ID 0.55 mm, OD 0.94 mm, Dow Corning, MI) into the right jugular vein. The catheter was secured to the vein with silk sutures and was passed subcutaneously to the top of the skull, where it exited into a connector (a modified 22-gauge cannula; Plastics One, VA, USA) mounted to the skull with MX-80 screws (Small Parts, Inc., FL, USA) and dental cement (Yates and Bird, IL, USA). Cocaine self-administration: Rats were trained to self-administer cocaine for 6 hrs per day, over 10 days. The self-administration chambers (Med-Associates, Inc.; St Albans, VT, USA) had two levers, one active and one inactive. An active lever press generated a cocaine infusion (0.75 mg/kg, 0.13 ml, 5 sec/infusion; cocaine obtained from the National Institutes on Drug Abuse, MD, USA) through the i.v. catheter, and also activated a light located above the lever, which was lit for 40 sec. Active lever presses during the last 35 sec of the light cue did not result in additional cocaine infusions. Presses on the inactive lever did not activate the infusion pump and light. Control rats were subjected to saline self-administration under the same conditions. The number of active lever responses, infusions, and inactive lever responses were recorded for both treatment and control groups. Rats were returned to their home cages at the end of the daily sessions. Cocaine withdrawal (forced abstinence): After the 10-day period of self-administration training sessions, rats were subjected to either a 1-day period of withdrawal (for cocaine-trained and saline-trained rats) or 30-day period of withdrawal (cocaine-trained rats). During the withdrawal periods, rats were left in their home cages and handled 3 times a week. Extinction test : Rats were placed in the self-administration chambers, and only the contingent light cue appeared during active lever presses, without cocaine reinforcement. Cocaine-seeking behavior was assessed for 60 min. For examining DNA methylation alterations, brains were removed one hour after completion of the session, and the NAc was isolated for further epigenetic analysis.

extract_protocol: Briefly, 3 pools of NAc DNA, each including the DNA of 2 to 3 rats, were used per condition (total 8 rats per condition). Each pool was made up of 2 μg DNA (2 X 1μg for pools of 2 rats, 3 x 700ng for pools of 3 rats) that were sonicated.the dark cycle.

tag: gender

value: males

tag: weight

value: Nucleus Accumbens

tag: strain

value: Sprague-Dawley

tag: chip antibody

value: anti-5 methylcytosine antibody (Calbiochem, Cat. #NA81, Lot:D00048001)

source_name: 1 day withdrawal_Input genomic DNA


title: Sal_DNA_methylation_1

description: Saline

source_name: Saline_IP genomic DNA

source_name: Saline_Input genomic DNA


title: Sal_DNA_methylation_3

description: Saline


title: 1C_DNA_methylation_3

description: 1 day withdrawal + extinction test

source_name: 1 day withdrawal + extinction test_IP genomic DNA

source_name: 1 day withdrawal + extinction test_Input genomic DNA


title: Muse_27_DISCOVERY_Myocardial Infarction

status: Public on Feb 28 2015

city: La Jolla

first: Eri

last: Kramer

state: CA

address: 10550 N Torrey Pines Rd

country: USA

institute: The Scripps Research Institute

hyb_protocol: The amplified cDNA targets were hybridized to Affymetrix human U133 Plus 2.0 array following protocols as suggested by the supplier (Affymetrix, Santa Clara, CA).

scan_protocol: Following hybridization, arrays were washed and stained using standard Affymetrix procedures before scanning on the Affymetrix GeneChip Scanner from which data was extracted using the Affymetrix Expression Console

data_processing: Data were processessed using the RMA normalization method, including background and quantile normalization.

label: biotin

organism: Homo sapiens

source_name: CD146+ Circulating Endothelial Cells

label_protocol: Purified cDNA underwent a two-step fragmentation and labeling process using the Encore Biotin Module (NuGEN).

growth_protocol: Arterial blood was collected from AMI patients into both EDTA containing (Becton Dickinson, Franklin Lakes, NJ, USA) and CellSave (Veridex, Raritan, NJ, USA) tubes in the cardiac catheterization laboratory following the placement of an arterial sheath prior to the introduction of any guide wires or coronary catheters.  The samples were maintained at room temperature and processed within 36 hours of collection.

extract_protocol: Enriched CEC‑derived RNA was isolated using Trizol Reagent (Life Technologies, Carlsbad, CA) according to the manufacturer's instructions

treatment_protocol: The CellTracks®AutoPrep® system was used in conjunction with the CellSearch®CEC kit and the CellSearch®profile kit (Veridex) to immunomagnetically enrich and enumerate CD146+ CECs as previously described 12. The enriched CEC samples were analyzed with the CellTracks®Analyzer II and the number of CECs in the sample determined. For CEC microarray profiling, the AutoPrep tube with the sample from the CellTracks®AutoPrep® system was removed and placed into the MagCellect Magnet for 10-min incubation. With the tube still in the MagCellect Magnet, the supernatant liquid was aspirated without disrupting the ferrofluid bound cells from which RNA was subsequently isolated.  For whole blood samples in EDTA tubes leukocytes and cellular debris was obtained for RNA isolation following RBC lysis with Erythrocyte Lysis Buffer (Qiagen, Valencia, CA).

value: Myocardial Infarction

tag: cohort

value: DISCOVERY

tag: cell type

value: CD146+ Circulating Endothelial Cells


title: 30W_DNA_methylation_2

description: 30 days withdrawal

source_name: 30 days withdrawal_IP genomic DNA

source_name: 30 days withdrawal_Input genomic DNA


title: 1W_DNA_methylation_1

description: 1 day withdrawal


title: Sal_DNA_methylation_4

description: Saline


title: Sal_DNA_methylation_2

description: Saline


title: 30C_DNA_methylation_2

description: 30 days withdrawal + extinction test

source_name: 30 days withdrawal + extinction test_IP genomic DNA

source_name: 30 days withdrawal + extinction test_Input genomic DNA


title: 30W_DNA_methylation_1

description: 30 days withdrawal


title: Needles September Whorl 3 Replicate 2

description: Biological replicate 2 of 3. September Whorl 3

value: December


title: 1W_DNA_methylation_3

description: 1 day withdrawal


title: RG108_DNA_methylation_3

source_name: 30 days withdrawal + RG108 injection + extinction test_IP genomic DNA

growth_protocol: Male Sprague-Dawley rats (Harlan, Israel) weighing 250-350g were  maintained on a 12-hr light/12-hr dark reversed cycle, with food and water available ad libitum. Rats were housed 2 per cage with a metal divider between them. Experiments were conducted during the dark cycle. Rats were anesthetized with xylazine and ketamine (10mg/kg and 100mg/kg, respectively). Guide cannula implantation :  Rats were anesthetized with xylazine and ketamine (10mg/kg and 100mg/kg, respectively). A 20-gauge guide cannula was then unilaterally implanted into the NAc (AP, +1.4 mm; LM, +1.2 mm to bregma and DV, -5.6 mm) of rats with the aid of a stereotactic device (David-Kopf Instruments, CA, USA). See Fig 1C for sample image of guide cannula placement in the NAc. Jugular vein catheterization: Immediately after cannula implantation, rats were implanted with intravenous silastic catheters (ID 0.55 mm, OD 0.94 mm, Dow Corning, MI) into the right jugular vein. The catheter was secured to the vein with silk sutures and was passed subcutaneously to the top of the skull, where it exited into a connector (a modified 22-gauge cannula; Plastics One, VA, USA) mounted to the skull with MX-80 screws (Small Parts, Inc., FL, USA) and dental cement (Yates and Bird, IL, USA). Cocaine self-administration: Rats were trained to self-administer cocaine for 6 hrs per day, over 10 days. The self-administration chambers (Med-Associates, Inc.; St Albans, VT, USA) had two levers, one active and one inactive. An active lever press generated a cocaine infusion (0.75 mg/kg, 0.13 ml, 5 sec/infusion; cocaine obtained from the National Institutes on Drug Abuse, MD, USA) through the i.v. catheter, and also activated a light located above the lever, which was lit for 40 sec. Active lever presses during the last 35 sec of the light cue did not result in additional cocaine infusions. Presses on the inactive lever did not activate the infusion pump and light. The number of active lever responses, infusions, and inactive lever responses were recorded for both treatment and control groups. Rats were returned to their home cages at the end of the daily sessions. Cocaine withdrawal (forced abstinence): After the 10-day period of self-administration training sessions, rats were subjected to 30-day period of withdrawal During the withdrawal period, rats were left in their home cages and handled 3 times a week. Modulation of NAc DNA methylation. On day 29 and on day 30 of withdrawal, rats received an intra-NAc injection of either the DNA methyltransferase (DNMT) inhibitor RG108 (Sigma, MO, USA; 100 µM; n=16) or the methyl donor S-adenosylmethionine (SAM, Sigma, MO, USA; 500 µM; n=13). Control rats (n=13) received intra-NAc injections of artificial cerebrospinal fluid (aCSF) at the same time points. The drugs were infused (5 min, 0.2µl/min) into the NAc via an injection cannula inserted into the guide cannula, and using an electronical syringe pump (CMA 400, CMA/Microdialysis). The injection cannula remained in place for 5 min after infusion, to avoid reflux.  On day 29, rats were returned to their home cage after infusions. On day 30, immediately (<5 min) after infusions, rats underwent an extinction test to assess cue-induced cocaine-seeking behavior. Extinction test : Rats were placed in the self-administration chambers, and only the contingent light cue appeared during active lever presses, without cocaine reinforcement. Cocaine-seeking behavior was assessed for 60 min. For examining DNA methylation alterations, brains were removed one hour after completion of the session, and the NAc was isolated for further epigenetic analysis.

extract_protocol: In total, we used 3 RG108-treated, 4 SAM-treated and 3 aCSF-treated rats. 2µg DNA from the NAc of each single rat were sonicated.

source_name: 30 days withdrawal + RG108 injection + extinction test_input genomic DNA


title: SAM_DNA_methylation_2

source_name: 30 days withdrawal + SAM injection + extinction test_IP genomic DNA

source_name: 30 days withdrawal + SAM injection + extinction test_input genomic DNA


title: RG108_DNA_methylation_2

description: 30 days withdrawal + RG108 injection + extinction test


title: 30C_DNA_methylation_1

description: 30 days withdrawal + extinction test


title: SAM_DNA_methylation_4

description: 30 days withdrawal + SAM injection + extinction test


title: SAM_DNA_methylation_3


title: 1C_DNA_methylation_1

description: 1 day withdrawal + extinction test


title: Needles November Whorl 3 Replicate 2

description: Biological replicate 2 of 3. November Whorl 3

source_name: Total RNA from adult needles


title: RG108_DNA_methylation_1


title: SAM_DNA_methylation_1


title: aCSF_DNA_methylation_3

source_name: 30 days withdrawal + aCSF injection + extinction test_IP genomic DNA

source_name: 30 days withdrawal + aCSF injection + extinction test_input genomic DNA


title: Needles January Whorl 3 Replicate 3

description: Biological replicate 3 of 3. January Whorl 3

value: January

source_name: Total RNA pool from all the RNA January samples


title: Needles March Whorl 3 Replicate 3

description: Biological replicate 3 of 3. March Whorl 3

value: March


title: aCSF_DNA_methylation_2

description: 30 days withdrawal + aCSF injection + extinction test


title: Needles July Whorl 3 Replicate 3

description: Biological replicate 3 of 3. July Whorl 3

value: 20-25 years old

value: July

value: February


title: Needles September Whorl 3 Replicate 1

description: Biological replicate 1 of 3. September Whorl 3

value: Needles


title: aCSF_DNA_methylation_1


title: Needles January Whorl 3 Replicate 1

description: Biological replicate 1 of 3. January Whorl 3


title: Needles May Whorl 3 Replicate 2

description: Biological replicate 2 of 3. May Whorl 3

value: May

value: October


title: Needles May Whorl 3 Replicate 1

description: Biological replicate 1 of 3. May Whorl 3

value: April


title: Needles July Whorl 3 Replicate 1

description: Biological replicate 1 of 3. July Whorl 3


title: Needles November Whorl 3 Replicate 1

description: Biological replicate 1 of 3. November Whorl 3

value: November


title: Needles January Whorl 3 Replicate 2

description: Biological replicate 2 of 3. January Whorl 3


title: Needles March Whorl 3 Replicate 1

description: Biological replicate 1 of 3. March Whorl 3


title: Needles July Whorl 3 Replicate 2

description: Biological replicate 2 of 3. July Whorl 3

value: August


title: Needles March Whorl 3 Replicate 2

description: Biological replicate 2 of 3. March Whorl 3

value: September


title: 1C_DNA_methylation_2

description: 1 day withdrawal + extinction test

value: males

value: Nucleus Accumbens

value: Sprague-Dawley

value: anti-5 methylcytosine antibody (Calbiochem, Cat. #NA81, Lot:D00048001)


title: Needles January Whorl 2 Replicate 2

description: Biological replicate 2 of 3. January Whorl 2


title: Needles September Whorl 2 Replicate 2

description: Biological replicate 2 of 3. September Whorl 2

value: June


title: Needles September Whorl 2 Replicate 3

description: Biological replicate 3 of 3. September Whorl 2

value: December


title: Needles July Whorl 2 Replicate 2

description: Biological replicate 2 of 3. July Whorl 2


title: Needles September Whorl 2 Replicate 1

description: Biological replicate 1 of 3. September Whorl 2


title: Needles March Whorl 2 Replicate 2

description: Biological replicate 2 of 3. March Whorl 2

value: March


title: Needles May Whorl 2 Replicate 3

description: Biological replicate 3 of 3. May Whorl 2

value: 20-25 years old


title: Needles March Whorl 2 Replicate 3

description: Biological replicate 3 of 3. March Whorl 2


title: Needles November Whorl 2 Replicate 1

description: Biological replicate 1 of 3. November Whorl 2


title: Needles January Whorl 2 Replicate 3

description: Biological replicate 3 of 3. January Whorl 2

value: January

value: July


title: Needles May Whorl 2 Replicate 1

description: Biological replicate 1 of 3. May Whorl 2

value: Needles


title: Needles July Whorl 2 Replicate 3

description: Biological replicate 3 of 3. July Whorl 2


title: Needles May Whorl 2 Replicate 2

description: Biological replicate 2 of 3. May Whorl 2

value: May


title: Needles November Whorl 2 Replicate 2

description: Biological replicate 2 of 3. November Whorl 2


title: Needles March Whorl 2 Replicate 1

description: Biological replicate 1 of 3. March Whorl 2


title: Needles January Whorl 2 Replicate 1

description: Biological replicate 1 of 3. January Whorl 2


title: Needles July Whorl 2 Replicate 1

description: Biological replicate 1 of 3. July Whorl 2


title: Needles November Whorl 2 Replicate 3

description: Biological replicate 3 of 3. November Whorl 2


title: Needles May Whorl 1 Replicate 3

description: Biological replicate 3 of 3. May Whorl 1


title: Needles July Whorl 1 Replicate 3

description: Biological replicate 3 of 3. July Whorl 1

value: February


title: Needles January Whorl 1 Replicate 3

description: Biological replicate 3 of 3. January Whorl 1


title: Needles November Whorl 1 Replicate 3

description: Biological replicate 3 of 3. November Whorl 1


title: Needles September Whorl 1 Replicate 3

description: Biological replicate 3 of 3. September Whorl 1


title: Needles September Whorl 1 Replicate 2

description: Biological replicate 2 of 3. September Whorl 1


title: Needles May Whorl 1 Replicate 2

description: Biological replicate 2 of 3. May Whorl 1

value: October


title: Needles March Whorl 1 Replicate 3

description: Biological replicate 3 of 3. March Whorl 1


title: Needles November Whorl 1 Replicate 1

description: Biological replicate 1 of 3. November Whorl 1

value: November


title: Needles July Whorl 0 Replicate 3

description: Biological replicate 3 of 3. July Whorl 0


title: Needles November Whorl 0 Replicate 2

description: Biological replicate 2 of 3. November Whorl 0


title: Needles May Whorl 0 Replicate 3

description: Biological replicate 3 of 3. May Whorl 0


title: Needles September Whorl 1 Replicate 1

description: Biological replicate 1 of 3. September Whorl 1


title: Needles May Whorl 1 Replicate 1

description: Biological replicate 1 of 3. May Whorl 1

value: April


title: Needles May Whorl 0 Replicate 2

description: Biological replicate 2 of 3. May Whorl 0


title: Needles July Whorl 1 Replicate 1

description: Biological replicate 1 of 3. July Whorl 1


title: Needles November Whorl 1 Replicate 2

description: Biological replicate 2 of 3. November Whorl 1


title: Needles September Whorl 0 Replicate 2

description: Biological replicate 2 of 3. September Whorl 0

value: September

value: August


title: Needles November Whorl 0 Replicate 3

description: Biological replicate 3 of 3. November Whorl 0


title: Needles November Whorl 0 Replicate 1

description: Biological replicate 1 of 3. November Whorl 0


title: Pancreatic carcinoma ICGC_0532

city: Brisbane

first: Katia

last: Nones

state: QLD

address: 300 Herston Road

country: Australia

institute: QIMR Berghofer MEdical Research Institute

description: Raw data for arrays used for copy number analysis using GAP (Popova, et al 2009)

hyb_protocol: As per manufacturer’s instructions (Illumina, San Diego CA)

scan_protocol: Arrays were scanned  on iScan

data_processing: Data was extracted using Genotyping module (v1.8.4) in Genomestudio v2010.3 (Illumina, San Diego CA) to calculate B-allele frequencies (BAF) and logR values.

source_name: Cell Line Derived From Tumour

label_protocol: DNA was assayed using Illumina SNP BeadChips as per manufacturer’s instructions (Illumina, San Diego CA) (HumanOmni1-Quad or HumanOmni2.5-8 BeadChips).

extract_protocol: Nucleic acids were then extracted using the Qiagen Allprep® Kit in accordance with the manufacturers instructions with purification of DNA and RNA from the same sample. DNA was quantified using Qubit HS DNA Assay (Invitrogen). Throughout the process, all samples were tracked using unique identifiers.

value: Cell Line Derived From Tumour

tag: disease

value: Pancreatic Adenocarcinoma


title: Pancreatic carcinoma ICGC_0326

source_name: Primary Tumour

value: Primary Tumour


title: Pancreatic carcinoma ICGC_0420


title: Needles July Whorl 1 Replicate 2

description: Biological replicate 2 of 3. July Whorl 1


title: Pancreatic carcinoma ICGC_0548


title: Pancreatic carcinoma ICGC_0549


title: Needles March Whorl 1 Replicate 1

description: Biological replicate 1 of 3. March Whorl 1


title: Needles January Whorl 1 Replicate 2

description: Biological replicate 2 of 3. January Whorl 1


title: Needles May Whorl 0 Replicate 1

description: Biological replicate 1 of 3. May Whorl 0


title: Pancreatic carcinoma ICGC_0312


title: Needles July Whorl 0 Replicate 1

description: Biological replicate 1 of 3. July Whorl 0


title: Needles March Whorl 1 Replicate 2

description: Biological replicate 2 of 3. March Whorl 1


title: Needles September Whorl 0 Replicate 3

description: Biological replicate 3 of 3. September Whorl 0


title: Needles January Whorl 1 Replicate 1

description: Biological replicate 1 of 3. January Whorl 1


title: Needles July Whorl 0 Replicate 2

description: Biological replicate 2 of 3. July Whorl 0


title: Needles September Whorl 0 Replicate 1

description: Biological replicate 1 of 3. September Whorl 0


title: Pancreatic carcinoma ICGC_0309


title: Pancreatic carcinoma ICGC_0321


title: Pancreatic carcinoma ICGC_0303


title: Pancreatic carcinoma ICGC_0338


title: Pancreatic carcinoma ICGC_0300


title: Pancreatic carcinoma ICGC_0235


title: Pancreatic carcinoma ICGC_0296


title: Pancreatic carcinoma ICGC_0295


title: Pancreatic carcinoma ICGC_0223


title: Pancreatic carcinoma ICGC_0215


title: Pancreatic carcinoma ICGC_0315


title: Pancreatic carcinoma ICGC_0304


title: Pancreatic carcinoma ICGC_0201


title: Pancreatic carcinoma ICGC_0214


title: Pancreatic carcinoma ICGC_0169


title: Pancreatic carcinoma ICGC_0289


title: Pancreatic carcinoma ICGC_0154


title: Pancreatic carcinoma ICGC_0149


title: Pancreatic carcinoma ICGC_0182


title: Pancreatic carcinoma ICGC_0188


title: Pancreatic carcinoma ICGC_0139


title: Pancreatic carcinoma ICGC_0257


title: Pancreatic carcinoma ICGC_0242


title: Pancreatic carcinoma ICGC_0283


title: Pancreatic carcinoma ICGC_0144


title: Pancreatic carcinoma ICGC_0134


title: Pancreatic carcinoma ICGC_0140


title: Pancreatic carcinoma ICGC_0255


title: Pancreatic carcinoma ICGC_0143


title: Pancreatic carcinoma ICGC_0119

source_name: Cell Line Derived From Xenograft

value: Cell Line Derived From Xenograft


title: Pancreatic carcinoma ICGC_0121


title: Pancreatic carcinoma ICGC_0118


title: Pancreatic carcinoma ICGC_0185


title: Pancreatic carcinoma ICGC_0153


title: Pancreatic carcinoma ICGC_0199


title: Pancreatic carcinoma ICGC_0290


title: Pancreatic carcinoma ICGC_0116


title: Pancreatic carcinoma ICGC_0212


title: Pancreatic carcinoma ICGC_0206


title: Pancreatic carcinoma ICGC_0109


title: Pancreatic carcinoma ICGC_0327


title: Pancreatic carcinoma ICGC_0063


title: Pancreatic carcinoma ICGC_0239


title: Pancreatic carcinoma ICGC_0137


title: Pancreatic carcinoma ICGC_0207


title: Pancreatic carcinoma ICGC_0205


title: Pancreatic carcinoma ICGC_0062


title: Pancreatic carcinoma ICGC_0051


title: Pancreatic carcinoma ICGC_0042


title: Pancreatic carcinoma ICGC_0033


title: Pancreatic carcinoma ICGC_0115


title: Pancreatic carcinoma ICGC_0035


title: Pancreatic carcinoma ICGC_0016


title: Pancreatic carcinoma ICGC_0034


title: Pancreatic carcinoma ICGC_0032


title: Pancreatic carcinoma ICGC_0025


title: Pancreatic carcinoma ICGC_0114


title: Pancreatic carcinoma ICGC_0069


title: Pancreatic carcinoma ICGC_0103


title: Pancreatic carcinoma ICGC_0328


title: Pancreatic carcinoma ICGC_0059


title: Pancreatic carcinoma ICGC_0037


title: Pancreatic carcinoma ICGC_0040


title: Pancreatic carcinoma ICGC_0098


title: Homo sapiens_prostate cancer_cell line_CWR e-4

city: shanghai

first: shibao

last: li

address: libing road

country: China

institute: chip

description: Gene expression of CWR22rv1/shControl cell line

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

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

data_processing:
Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US).
Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

source_name: CWR22rv1/shEphA6-1 Cell

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

growth_protocol: CWR22rv1 cells were cultured in RPMI 1640 media supplemented with 10 % FBS and incubated at 37ºC in a humidified incubator containing 5 % CO2. PC-3M cells were cultured in DMEM/F12 media supplemented with 10 % FBS.

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

treatment_protocol: Lentiviruses expressing EphA6 shRNA (shEphA6-1) or control shRNA were used for RNA interference. Viruses were generated in   HEK293T cells harboring pLP/VSVg packaging plasmid and either plko-control shRNA or plko-EphA6 shRNA plasmid (shEphA6-1: GCAGCAGGGTTTACAACAT,  ).  PC-3M and CWR22rv1 cells were grown in 24-well plates to 80-90 % confluence overnight and then transfected with 25 nmol of control or shRNAs against EphA6 gene for 24 h using Lipofectamine TM reagent (Invitrogen) following the manufacturer's protocol.

tag: cell line

tag: tumor type

value: prostate cancer

tag: shRNA


title: Homo sapiens_prostate cancer_cell line_PC3M e-4

description: Gene expression of PC-3M/shEphA6-1 cell line

source_name: PC-3M/shEphA6-1 Cell


title: ASH2L_KD_SH272_DHT_12HRS_2

city: Ann Arbor

first: Marcin

middle: Piotr

last: Cieslik

state: Michigan

address: 500 S State St

department: Pathology

institute: University of Michigan

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

scan_protocol: Scanned on an Agilent G2505B scanner. Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization. Control Features were omitted. The LogRatio columns from each feature file were used for further analyses.

source_name: LNCaP, ASH2L shRNA and DHT

label_protocol: 10 ug of total RNA were primed with 2 ul of 100 uM T16N2 DNA primer at 70_C for 10 min, then reversed transcribed at 42_C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 uM each dATP, dTTP, dGTP, with 25 uM dCTP, 25 uM Cy3-label.

growth_protocol: VCaP and LNCaP cells were grown in DMEM-Glutmax (Invitrogen) and RPMI 1640 (Invitrogen) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin, respectively.

extract_protocol: Total RNA was isolated using Trizol and an RNeasy Kit (Invitrogen) with DNase I digestion according to the manufacturer's instructions.

treatment_protocol: Cells were plated in 100mM plates at a desired concentration and infected with shRNA or siRNA targeting ASH2L, Menin or MLL1 vs. a non-targeting shRNA or siRNA. Knockdown efficiency was determined by qPCR.

value: LNCaP

value: prostate cancer cell line

tag: treatment

value: ASH2L shRNA and DHT

source_name: LNCaP, GIPZ and ethanol

value: GIPZ and ethanol


title: MEN1_KD_SH1_DHT_12hr_1

source_name: LNCaP, Menin shRNA and DHT

value: Menin shRNA and DHT


title: GIPZ_DHT_12HR_1

source_name: LNCaP, GIPZ and DHT

value: GIPZ and DHT


title: ASH2L_KD_SH148_R1881_24HRS

source_name: VCaP, GIPZ and ethanol

value: VCaP

source_name: VCaP, ASH2L shRNA and R1881

value: ASH2L shRNA and R1881


title: Homo sapiens_prostate cancer_cell line_CWR plko

source_name: CWR22rv1/shControl Cell

value: control


title: MLL1_KD_SH12_DHT_24HRS

source_name: VCaP, MLL1 shRNA and DHT

value: MLL1 shRNA and DHT


title: MLL1_KD_SH13_DHT_24HRS


title: ASH2L_KD_SH272_R1881_24HRS


title: ASH2L_KD_SH272_DHT_12HRS_1


title: ASH2L_KD_SH148_DHT_12HRS_2


title: GIPZ_DHT_12HR_2


title: Homo sapiens_prostate cancer_cell line_PC3M plko

description: Gene expression of PC3M/shControl cell line

source_name: PC-3M/shControl Cell


title: MEN1_KD_SH3_DHT_12hr_1


title: Control_3-7_DHT_2

source_name: VCaP, control 3.7 drug and DHT

value: control 3.7 drug and DHT

source_name: VCaP, control 3.7 drug and ethanol

value: control 3.7 drug and ethanol


title: MEN1_KD_SH3_DHT_12hr_2


title: GIPZ_R1881_24HRS

source_name: VCaP, GIPZ and R1881

value: GIPZ and R1881


title: GIPZ_DHT_24HRS

source_name: VCaP, GIPZ and DHT


title: BD136_DHT_2

source_name: VCaP, BD136 drug and DHT

value: BD136 drug and DHT


title: Control_3-7_DHT_1


title: ASH2L_KD_SH148_DHT_12HRS_1


title: MEN1_KD_SH1_DHT_12hr_2


title: ASH2L_KD_si8_R1881_3

source_name: VCaP, non-targeting siRNA and ethanol

value: non-targeting siRNA and ethanol

source_name: VCaP, ASH2L siRNA 2 and R1881

value: ASH2L siRNA 2 and R1881


title: ASH2L_KD_si8_R1881_2


title: ASH2L_KD_si5_R1881_2

source_name: VCaP, ASH2L siRNA 1 and R1881

value: ASH2L siRNA 1 and R1881


title: BD136_DHT_1


title: ASH2L_KD_si8_R1881_1


title: ASH2L_KD_si5_R1881_1


title: ASH2L_KD_si5_R1881_3


title: Penile_Cancer_L3_AC_Camargo_Hospital

city: Sao Paulo

first: Fabio

middle: Albuquerque

last: Marchi

address: Av Dr Arnaldo

department: CTO

country: Brazil

institute: ICESP

description: Tumor sample Cy3-labeled mixed with reference sample Cy5-labeled

hyb_protocol: The yield and labeling efficiency was obtained and 825ng of reference and test samples with similar efficiencies were combined. 10x Blocking agent and 25x fragmentation buffer were added to each reaction, it was denatured at 95°C for 3 min and incubated at 37°C for 30min. The samples were applied onto the 4x44 k (Agilent) slides and kept at 65°C at 10rpm for 17 hours.

scan_protocol: The array images were acquired with a microarray scanner using the Scan Control (version 8.1) software program (Agilent Technologies, CA, USA). Images were quantified using Agilent Feature Extraction Software version v.10.1.1.1 (Agilent Technologies, CA, USA).

data_processing: All values represents the comparison between tumor and control samples and were filtered using R software with a script developed by us that was not published. This script just open each text file, extract Cy3 (tumor) and Cy5 (control) column and get the ratio between them for each probe.

source_name: penile squamous cell carcinoma sample

label_protocol: Tumor and reference samples (500ng) were differentially labeled using the Quick Amp Labeling Kit (Agilent Technologies, CA, USA), according to manufacturer´s instructions.  Tumor were labeled using Cy3 and references were labeled by Cy5.

extract_protocol: RNA from 39 penile cancer and five glans control samples was isolated using the RNeasy Mini Kit (Qiagen, TE, USA) or Trizol reagent (Invitrogen, CA, USA).

value: carcinoma

value: male

source_name: Pool from five autopsy glans

tag: sample type

value: reference


title: R1881_2

value: prostate cancer cell line

source_name: VCaP, non-targeting siRNA and R1881

value: non-targeting siRNA and R1881


title: Penile_Cancer_L1_AC_Camargo_Hospital


title: Penile_Cancer_E23_Barretos_Hospital


title: Penile_Cancer_1411_AC_Camargo_Hospital


title: R1881_1


title: Penile_Cancer_1388_AC_Camargo_Hospital


title: Penile_Cancer_E25_Barretos_Hospital


title: Penile_Cancer_E24_Barretos_Hospital


title: Penile_Cancer_E22_Barretos_Hospital


title: Penile_Cancer_L2_AC_Camargo_Hospital


title: Penile_Cancer_E19_Barretos_Hospital


title: Penile_Cancer_E15_Barretos_Hospital


title: Penile_Cancer_E8_Barretos_Hospital


title: Penile_Cancer_E21_Barretos_Hospital


title: Penile_Cancer_E17_Barretos_Hospital


title: Penile_Cancer_E6_Barretos_Hospital


title: Penile_Cancer_E16_Barretos_Hospital


title: Penile_Cancer_1389_AC_Camargo_Hospital


title: Penile_Cancer_E11_Barretos_Hospital


title: Penile_Cancer_E18_Barretos_Hospital


title: Penile_Cancer_E12_Barretos_Hospital


title: Penile_Cancer_1410_AC_Camargo_Hospital


title: Penile_Cancer_E2_Barretos_Hospital


title: Penile_Cancer_E9_Barretos_Hospital


title: Penile_Cancer_E10_Barretos_Hospital


title: Penile_Cancer_E1_Barretos_Hospital


title: Penile_Cancer_E26_Barretos_Hospital


title: Penile_Cancer_A22_AC_Camargo_Hospital


title: Penile_Cancer_A29_AC_Camargo_Hospital


title: Penile_Cancer_A19_AC_Camargo_Hospital


title: Penile_Cancer_A6_AC_Camargo_Hospital


title: Penile_Cancer_A12_AC_Camargo_Hospital


title: Penile_Cancer_A5_AC_Camargo_Hospital


title: Penile_Cancer_A10_AC_Camargo_Hospital


title: Penile_Cancer_A17_AC_Camargo_Hospital


title: Penile_Cancer_A20_AC_Camargo_Hospital


title: Penile_Cancer_A13_AC_Camargo_Hospital


title: Penile_Cancer_A9_AC_Camargo_Hospital


title: Unstimulated DC, rep7

city: Lyon

first: Julien

last: Textoris

address: Hôpital Edouard herriot - Pavillon P; 5 place d'Arsonval

department: Medical Diagnostic Discovery Department (MD3)

country: France

institute: bioMérieux

description: Whole blood transcriptome (PAXgene derived).

hyb_protocol: The hybridization was carried out for 17 hours at 65°C using the QIamp labeling kit.

scan_protocol: The microarray slides were scanned with the DNA Microarray scanner G2505C at resolution of 5 µm. The scanned images were analyzed with Feature Extraction Software 10.5.1.

data_processing: The analysis of microarray data was performed and the figures were created using the R (v.2.13) and the Bioconductor software suite. The raw data were filtered and normalized using the Agi4x44PreProcess library. Unsupervised and supervised analyses were carried out using hierarchical clustering, principal component analysis (made4 library) and the Linear Models for Microarray Analysis (limma library). We considered genes as differentially expressed when corrected p-value was below 0.05 and the absolute fold change (FC) was higher than 2. Twenty four microarrays are presented.

source_name: unstimulated DC

label_protocol: In brief, 400 ng of RNA were labeled with cyanine-3 CTP using a Low RNA Input Fluorescent Amplification kit.

extract_protocol: RNA was extracted using RNeasy Kit (Qiagen) with a DNase I step to eliminate DNA contaminants, according to the manufacturer recommendations. The quantity and the quality of RNA were assessed using Nanodrop (Thermo Science, Orsay, France) and a 2100 Bioanalyseur (Agilent Technologies, Massy, France), respectively.

treatment_protocol: DCs were stimulated with a MOI of 20:1.

value: monocyte-derived dendritic cells


title: Unstimulated DC, rep9


title: B. abortus infected DC, rep2

source_name: B. abortus-infected DC

value: BA infection


title: Unstimulated DC, rep5


title: O. tsutsugamushi infected DCs, rep2

source_name: O. tsutsugamushi-infected DCs

value: OT infection


title: O. tsutsugamushi infected DCs, rep1


title: B. abortus infected DC, rep3


title: B. abortus infected DC, rep1


title: Unstimulated DC, rep6


title: Unstimulated DC, rep4


title: Unstimulated DC, rep8


title: T. whipplei infected DCs, rep3

source_name: T. whipplei-infected DCs

value: TW infection


title: Penile_Cancer_A7_AC_Camargo_Hospital


title: T. whipplei infected DCs, rep2


title: O. tsutsugamushi infected DCs, rep3


title: Unstimulated DC, rep3


title: GSC11_FBS7D_3

city: Houston

first: Sangbae

last: Kim

state: TX

address: 1 Baylor plaza

department: HGSC

institute: Baylor Colleage of Medicine

hyb_protocol: Labeled, amplified material (750 ng per array) was hybridized to the Illumina HumanHT-12 V3.0 expression beadchip according to the Manufacturer's instructions (Illumina, Inc., San Diego, CA).

scan_protocol: Arrays were scanned with an Illumina Bead array Reader confocal scanner (BeadStation 500GXDW; Illumina, Inc., San Diego, CA) according to the Manufacturer's instructions

data_processing: Array data processing were performed on Illumina BeadStudio software. We normalized gene expression data using Quantile normalization and log2 transformatoin. To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software. The whole 48803 probes on the Human-12 beadChip ver. 3 were used.

label: Biotin

source_name: Glioblastoma stem cell line

label_protocol: Biotin-labeled cRNA samples for hybridization were prepared according to Illumina's recommended sample labeling procedure: 500 ng of total RNA was used for cDNA synthesis, followed by an amplification/labeling step (in vitro transcription) to synthesize biotin-labeled cRNA using the Illumina. TotalPrep RNA Amplification kit (Ambion Inc., Austin, TX). cRNA concentrations using spectrophotometer (Nanodrop, ND-1000)

extract_protocol: Total RNA was isolated from tissues with mirVana RNA Isolation labeling kit (Ambion Inc) according to the manufacturer protocol. RNA quality and integrity were confirmed by ExperionTM Automated Electrophoresis System (BIO-RAD).

tag: culture condition

value: culture under differentiated conditions for 7 day


title: LPS stimulated DC, rep3

source_name: LPS-stimulated DC

value: LPS stimulation


title: T. whipplei infected DCs, rep1


title: LPS stimulated DC, rep2


title: GSC11_FBS7D_1

description: To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software. The whole 48803 probes on the Human-12 beadChip ver. 3 were used.


title: Treg.Neonate.Thymus#3

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

hyb_protocol: Ambion WT Expression Kit

scan_protocol: Affymetrix GeneChip Scanner

data_processing: The datasets was pre-filtered to keep only those probesets for which a gene symbol could be found in the Affymetrix annotation. CEL files were normalized using Affymetrix Power Tools on the predefined probeset ID list mentioned above, and using the standard RMA workflow (background adjustment, quantile normalization, median polish probeset summarization). Output on 2^ scale.

organism: Mus musculus

label_protocol: Affymetrix GeneChip WT Terminal Labeling and Controls Kit

extract_protocol: TriZol

tag: genetic background

value: NOD

value: Male

value: 4 Days

value: Thymus

tag: exclusion markers

tag: phenotype markers

value: CD4+ GFP+

tag: separation method

value: MoFlo Sorter


title: Unstimulated DC, rep1


title: Unstimulated DC, rep2


title: C. burnetii infected DC, rep3

source_name: C. burnetii-infected DC

value: CB infection


title: LPS stimulated DC, rep1


title: GSC11_FBS3D_3

value: culture under differentiated conditions for 3 day


title: Treg.Neonate.Thymus#2

tag: gender

tag: age

tag: tissue


title: GSC11_FBS3D_1


title: GSC11_FBS7D_2


title: C. burnetii infected DC, rep1


title: C. burnetii infected DC, rep2


title: GSC11_FBS1D_3

value: culture under differentiated conditions for 1 day


title: Treg.Adult.Thymus#1

value: 5 Weeks


title: Treg.Neonate.Thymus#1


title: Treg.Adult.Thymus#3


title: GSC11_FBS3D_2


title: Treg.Adult.Thymus#2


title: GSC11_FBS1D_1


title: MEChi.GFP+.Neonate.KO#3

source_name: Thymic Medulla_MEChi.GFP+.Neonate.KO

value: Mixed

value: 3 Days

value: Thymic Medulla

value: CD45- Ly51- MHCIIhi GFP+


title: GSC11_FBS1D_2


title: MEChi.GFP+.Neonate.KO#2


title: GSC11_CTRL_3

value: culture in stem cell medium


title: MEChi.GFP+.Neonate.KO#1


title: MEChi.GFP+.Neonate#7

source_name: Thymic Medulla_MEChi.GFP+.Neonate


title: MEChi.GFP+.Adult.KO#2

source_name: Thymic Medulla_MEChi.GFP+.Adult.KO


title: MEChi.GFP+.Adult.KO#3


title: MEChi.GFP+.Adult.KO#1


title: MEChi.GFP-.Adult#6

source_name: Thymic Medulla_MEChi.GFP-.Adult

value: CD45- Ly51- MHCIIhi GFP-


title: MEChi.GFP+.Adult#8

source_name: Thymic Medulla_MEChi.GFP+.Adult


title: MEChi.GFP-.Adult#8


title: MEChi.GFP-.Neonate#1

source_name: Thymic Medulla_MEChi.GFP-.Neonate


title: PA_0784_1

city: Aurora

first: Andrew

middle: M

last: Donson

state: CO

department: Pediatrics

institute: CU Anschutz Medical Campus

description: reanalysis of GSM1214960

hyb_protocol: Following fragmentation, 11.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the Affymetrix Gene Chip Scanner 7G.

data_processing: Microarray .CEL file data was background corrected and normalized using the gcRMA algorithm, resulting in log 2 expression values. The Affymetrix HG-U133 plus 2 microarray contains 54,675 probe sets including multiple probe sets for the same gene. In order to reduce error associated with multiple testing we used only a single probe set for each gene that possessed the highest gcRMA expression level across all our samples. This filtered list of the best expressed probe sets contained 21,050 genes. This list was further filtered to remove probe sets that were expressed below a threshold level that denoted absence of expression in any sample.

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

extract_protocol:
[collection protocol] Tumor samples were snap frozen in liquid nitrogen or transferred to RNAlater immediately after surgical removal as part of patient care. All samples were collected with appropriate IRB approval (COM-IRB#95-500 and 09-0906 )
RNeasy (Qiagen) extraction of total RNA was performed according to the manufacturer's instructions.

tag: disease state

value: brain tumor

value: pilocytic astrocytoma


title: MEChi.GFP-.Neonate#2


title: MEChi.GFP+.Neonate#5


title: MEChi.GFP-.Adult#7


title: PA_0653_1

description: reanalysis of GSM1214958


title: GSC11_CTRL_1


title: PA_0879_1

description: reanalysis of GSM1214962


title: MEChi.GFP+.Adult#7


title: Penile_Cancer_E4_Barretos_Hospital

value: carcinoma

value: male

value: reference


title: PA_0855_1

description: reanalysis of GSM1214961


title: GSC11_CTRL_2


title: PA_0882_1

description: reanalysis of GSM1214963


title: MEChi.GFP+.Adult#6


title: MEChi.GFP+.Neonate#6


title: GFP+YFP-Neo#4

value: NOD

value: Female

value: 60 Days

value: Spleen

value: GFP+ YFP-

value: FACSAria


title: GFP+YFP-Neo#5


title: GFP+YFP-Neo#3


title: GFP+YFP-Adu#5


title: PA_0631_1

description: reanalysis of GSM1214957


title: PA_0748_1

description: reanalysis of GSM1214959


title: GFP+YFP-Adu#4


title: PA_0563_1

description: reanalysis of GSM1214956


title: GFP+YFP-Adu#3


title: GFP+YFP+Neo#5

value: GFP+ YFP+


title: PA_0519_1

description: reanalysis of GSM1214955


title: GFP+YFP+Adu#3


title: FL.Treg#5

value: Male

value: 12 Weeks


title: GFP+YFP+Adu#2


title: PA_0476_1

description: reanalysis of GSM1214954


title: GFP+YFP+Adu#1


title: PA_0378_1

description: reanalysis of GSM1214953


title: BM.Treg#4


title: FL.Treg#4


title: GFP+YFP+Neo#4


title: BM.Treg#3


title: BM.Treg#5


title: GFP+YFP+Neo#2


title: PA_0249_1

description: reanalysis of GSM1214950


title: PA_0160_1

description: reanalysis of GSM1214949


title: PA_0257_1

description: reanalysis of GSM1214951


title: PA_0363_1

description: reanalysis of GSM1214952


title: NORMAL_E00003_Frontal_1

description: reanalysis of GSM1214948

value: normal brain

value: frontal lobe of cerebral cortex


title: NORMAL_0605_Parietal

description: reanalysis of GSM1214947

value: parietal lobe of cerebral cortex


title: GM-CSF derived dendritic cell_3

city: London

first: Julie

last: Helft

address: 44 Lincoln's Inn Fields

department: London Research Institute

country: United Kingdom

institute: Cancer Research UK

hyb_protocol: Following fragmentation, 10ug of cRNA were hybridised for 16hrs at 45c on Genechip Mouse Gene 1.0 arrays. Genechips were washed and stained in the Affymetrix Fludics station 450.

scan_protocol: Genechips were scanned using the Affymetrix Genechip Scanner 3000G

data_processing: Data were analyzed using Bioconductor 2.13 running on R 3.0.2. Probeset expression measures were calculated using the Affymetrix package’s Robust Multichip Average (RMA) default method.

source_name: GM-CSF bone marrow culture

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

growth_protocol: Bone marrow cells from tibia and femur of C57B/6 mice were culture in single cell suspension with 20ng/ml of recombinant GM-CSF for 6 days

extract_protocol: RLT buffer (+beta-ME) extraction of total RNA was performed and purified further with the Rneasy kit (Qiagen) according to the manufacturers instructions

treatment_protocol: GM-DC and GM-MF received no treatment

value: dendritic

value: unstimulated


title: FL.Treg#3


title: GM-CSF derived macrophage cell_2

value: macrophage


title: GM-CSF derived macrophage cell_3


title: GM-CSF derived dendritic cell_2


title: NORMAL_0605_Occipital

description: reanalysis of GSM1214946

value: occipital lobe of cerebral cortex


title: GM-CSF derived macrophage cell_1


title: NORMAL_0605_Cerebellum

description: reanalysis of GSM1214944

value: cerebellum


title: NORMAL_0514_Thal

description: reanalysis of GSM1214943

value: thalamus


title: GM-CSF derived dendritic cell_1


title: Control Pre 48

city: New York

first: Michael

middle: S

last: Breen

state: NY

address: 1468 Madison Ave

department: Depts. of Psychiatry, Genetics and Genomic Sciences

institute: Ichan School of Medicine at Mount Sinai

hyb_protocol: Following fragmentation, RNA were hybridized to the Affymetrix HuGene-1_0-st-v1 chip according to the protocols provided by the manufacturer.

scan_protocol: Arrays were scanned with the Affymetrix GeneChip Scanner 7G Plus.

data_processing:
The data were background adjusted, normalized and summarized to the transcript level using RMA normalization using R software, publically available through Bioconductor. Following, only probesets found in common across RNA-Sequencing data for this specific project were retained.
GSE63878_final_list_of_normalized_data.txt: Includes the normalized data only for probesets found in common across RNA-Sequencing data.

source_name: Human peripheral blood leukocytes, control, pre-deployment

label_protocol: Microarray target preparation from RNA (200 ng/each sample for input) was done with the Ambion WT Expression Kit following standard Affymetrix protocol. Sense strand cDNA (5.5ug) was fragmented and labeled using Affymetrix GeneChip WT Terminal Labeling Kit (Affymetrix).

extract_protocol: RNA was isolated from peripheral blood leukocytes using LeukoLOCK Total RNA isolation.

treatment_protocol: Each whole blood sample (10ml) was collected into an EDTA-coated collection tube.

value: peripheral blood leukocytes

tag: condition

value: control

tag: time-point

value: pre-deployment

tag: individual


title: Control Post 47

source_name: Human peripheral blood leukocytes, control, post-deployment

tag: cell type

value: post-deployment


title: Control Post 45


title: Control Post 46


title: Control Pre 45


title: NORMAL_0514_Temporal

description: reanalysis of GSM1214942

value: temporal lobe of cerebral cortex


title: NORMAL_0514_Parietal

description: reanalysis of GSM1214941


title: Control Pre 43


title: Control Post 48


title: Control Pre 46


title: Control Post 43


title: Control Pre 47


title: Control Post 44


title: Control Post 41


title: Control Pre 42


title: Control Pre 44


title: NORMAL_0605_Frontal_1

description: reanalysis of GSM1214945


title: Control Post 42


title: Control Pre 41


title: Control Post 40


title: NORMAL_0514_Medulla

description: reanalysis of GSM1214938

value: medulla


title: Control Pre 40


title: NORMAL_0514_Occipital

description: reanalysis of GSM1214940


title: NORMAL_0514_Frontal

description: reanalysis of GSM1214937


title: Control Post 39


title: MEDSHH_0898_1

description: reanalysis of GSM1214933

value: brain tumor

value: sonic hedgehog group medulloblastoma


title: Control Post 38


title: Control Post 37


title: Control Pre 37


title: Control Pre 39


title: MEDSHH_0877_1

description: reanalysis of GSM1214932


title: Control Pre 38


title: Control Post 36


title: NORMAL_0514_Cerebellum

description: reanalysis of GSM1214936

value: normal brain


title: MEDSHH_0719_1

description: reanalysis of GSM1214927


title: MEDSHH_0565_1

description: reanalysis of GSM1214924


title: Control Post 35


title: Control Post 34


title: Control Pre 35


title: Control Pre 36


title: Control Pre 33


title: Control Post 33


title: Control Pre 34


title: MEDSHH_0288_1

description: reanalysis of GSM1214920


title: Control Post 31


title: Control Pre 31


title: MEDSHH_0529_1

description: reanalysis of GSM1214923


title: Control Pre 32


title: MEDSHH_0258_1

description: reanalysis of GSM1214917


title: MEDSHH_0801_1

description: reanalysis of GSM1214930


title: Control Pre 30


title: MEDGP4_0797_1

description: reanalysis of GSM1214929

value: group 4 medulloblastoma


title: Control Post 30


title: MEDGP4_0791_1

description: reanalysis of GSM1214928


title: Control Post 29


title: MEDGP4_0437_1

description: reanalysis of GSM1214922


title: Control Post 32


title: Control Pre 29


title: Control Post 27


title: Control Pre 27


title: Control Pre 28


title: Control Pre 26


title: MEDGP4_0254_1

description: reanalysis of GSM1214916


title: Control Post 28


title: Control Post 25


title: Control Pre 25


title: Case Pre 24

source_name: Human peripheral blood leukocytes, PTSD risk, pre-deployment

value: case (PTSD risk)


title: MEDGP4_0262_1

description: reanalysis of GSM1214918


title: MEDGP4_0186_1

description: reanalysis of GSM1214915


title: Case Post 23

source_name: Human peripheral blood leukocytes, PTSD, post-deployment

value: case (PTSD)


title: MEDGP4_0330_1

description: reanalysis of GSM1214921


title: Case Pre 23


title: Control Post 26


title: MEDGP3_0945_1

description: reanalysis of GSM1214914

value: group 3 medulloblastoma


title: MEDGP3_0925_1

description: reanalysis of GSM1214934


title: Case Pre 22


title: Case Pre 21


title: Case Pre 20


title: Case Post 20


title: Case Post 24


title: Case Post 21


title: MEDGP3_0277_1

description: reanalysis of GSM1214919


title: Case Pre 17


title: Case Pre 19


title: Case Post 17


title: Case Post 22


title: Case Post 19


title: GBM_xB00017_1

description: reanalysis of GSM1214903

value: adult high grade glioma


title: Case Post 18


title: GBM_xB00057_1

description: reanalysis of GSM1214906


title: Case Pre 15


title: Case Pre 16


title: Case Post 15


title: GBM_xB00012_1

description: reanalysis of GSM1214902


title: GBM_xB00010_1

description: reanalysis of GSM1214900


title: Case Post 14


title: GBM_xB00016_1

description: reanalysis of GSM824296


title: Case Post 13


title: Case Post 16


title: Case Pre 13


title: Case Pre 18


title: GBM_xB00056_1

description: reanalysis of GSM1214905


title: GBM_xB00011_1

description: reanalysis of GSM1214901


title: Case Pre 14


title: Case Post 12


title: Case Pre 12


title: NORMAL_0514_Midbrain

description: reanalysis of GSM1214939

value: midbrain


title: Case Pre 11


title: GBM_0678_1

description: reanalysis of GSM869679

value: pediatric high grade glioma


title: Case Post 9


title: Case Pre 10


title: Case Post 8


title: GBM_0637_1

description: reanalysis of GSM1214894


title: Case Post 7


title: GBM_0309_1

description: reanalysis of GSM1214888


title: GBM_0668_1

description: reanalysis of GSM1214895


title: GBM_0281_1

description: reanalysis of GSM1214887


title: Case Pre 7


title: Case Post 10


title: GBM_0434_1

description: reanalysis of GSM1214890


title: Case Post 6


title: Case Pre 9


title: Case Post 11


title: Case Pre 8


title: Case Post 4


title: Case Pre 5


title: GBM_0098_1

description: reanalysis of GSM1214884


title: Case Pre 4


title: GBM_0391_1

description: reanalysis of GSM1214889


title: Case Post 3


title: Case Pre 6


title: Case Pre 2


title: Case Post 5


title: Case Post 2


title: GBM_0057_1

description: reanalysis of GSM1214882


title: GBM_0271_1

description: reanalysis of GSM1214885


title: GBM_0000_1

description: reanalysis of GSM1214880


title: Case Pre 3


title: Case Post 1


title: Case Pre 1


title: GBM_0089_1

description: reanalysis of GSM1214883


title: EPNST_0870_1

description: reanalysis of GSM1217913

value: supratentorial ependymoma


title: EPNST_0388_1

description: reanalysis of GSM1217879


title: EPNST_0790_1

description: reanalysis of GSM1217903


title: EPNST_0909_1

description: reanalysis of GSM1217915


title: EPNST_0285_1

description: reanalysis of GSM1217869


title: EPNST_0135_1

description: reanalysis of GSM1217858


title: CSA19 treatment replicate 1

city: Mainz

first: Onat

last: Kadioglu

address: Staudinger Weg 5

department: Institute of Pharmacy and Biochemistry

country: Germany

institute: Johannes Gutenberg University

description: Gene expression after 72hr in CSA19 treated MCF-7 cells

hyb_protocol: 1.65 µg of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 30 µL containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 30 µL of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Whole Human Genome RNA chips (8 × 60K, Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately for 2 minutes at 30°C.

scan_protocol: Slides were scanned immediately after washing on the Agilent Technologies Scanner G2505C using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 10µm, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent) using default parameters (protocol: GE1_1010_Sep10 and Grid: 028004_D_F_20120411) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: MCF-7 cells, 72hr, CSA19 treated, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the Quick Amp Kit, One-Color (Agilent) according to the manufacturer's instructions followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the ND-1000 UV-VIS Spectrophotometer version 3.2.1.

growth_protocol: MCF-7 cells were grown in DMEM medium supplemented with 10% fetal bovine serum and 1% penicillin (100 U/mL), streptomycin (100 μg/mL) mixture. Cells were maintained in a humidified environment at 37°C with 5% CO2.

extract_protocol: Total RNA was isolated using the RNeasy Kit from Qiagen (Hilden, Germany) according to the manufacture's instruction.  RNA concentration was measured using a NanoDrop-1000 spectrophotometer and the quality of total RNA was checked by gel analysis using the total RNA Nano chip assay on an Agilent 2100 Bioanalyzer (Agilent Technologies GmbH, Germany)

treatment_protocol: MCF-7 cells (in the logarithmic growth phase) were treated with the compounds (IC50 concentrations) or DMSO for 72 hours. Cells were maintained in a humidified environment at 37°C with 5% CO2.

tag: breast cancer cell line

value: MCF-7 cells

value: female

value: 72hr in CSA19


title: CSA9 treatment replicate 1

description: Gene expression after 72hr in CSA9 treated MCF-7 cells

source_name: MCF-7 cells, 72hr, CSA9 treated, replicate 1

value: 72hr in CSA9


title: CSA9 treatment replicate 2

source_name: MCF-7 cells, 72hr, CSA9 treated, replicate 2


title: CSA19 treatment replicate 2

source_name: MCF-7 cells, 72hr, CSA19 treated, replicate 2


title: EPNST_0534_1

description: reanalysis of GSM1217892


title: CSA6 treatment replicate 2

description: Gene expression after 72hr in CSA6 treated MCF-7 cells

source_name: MCF-7 cells, 72hr, CSA6 treated, replicate 2

value: 72hr in CSA6


title: Apoptosis vector 3

city: Cambridge

first: Suraj

last: Menon

address: Li Ka Shing Center, Robinson Way

institute: Cambridge Research Institute, Cancer Research UK

description:
Apoptosis IMR90 vector
4157064153_F_1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Raw intensity data from the array scanner was processed using the BASH and HULK algorithms as implemented in the beadarray package. Log2 transformation and quantile normalization of the data were performed across all sample groups.

source_name: IMR90_Apoptosis vector

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

growth_protocol: cultured in 5%O2 in DMEM with 10% FBS and Pen/Strep and Glutamine

extract_protocol: Qiagen RNeasy protocol

treatment_protocol: 24 or 48 hours Etoposide (100microM),pBabe-Puro H-RasG12V, pWXL-Hygro E2A, H-RasG12V, pLNCX-Neo ER:H-RasG12V overexpression, conflunecy 3 days

tag: cell line

value: normal human diploid fibroblasts

tag: sample group

value: L.V.E1A_Ras; Apoptosis vector


title: CSA6 treatment replicate 1

source_name: MCF-7 cells, 72hr, CSA6 treated, replicate 1

tag: treatment


title: EPNST_0333_1

description: reanalysis of GSM1217876

value: brain tumor


title: DMSO control replicate 3

description: Gene expression after 72hr in DMSO treated (control) MCF-7 cells

source_name: MCF-7 cells, 72hr, DMSO treated (control), replicate 3

value: 72hr in DMSO


title: Quiescence p53 knockdown 3

description:
Quiescence IMR90 p53 knockdown
4157064153_E_1

source_name: IMR90_Quiescence p53 knockdown

value: L.53.1.QUIES; Quiescence p53 knockdown


title: EPNST_0416_1

description: reanalysis of GSM1217883


title: CSA treatment replicate 2

description: Gene expression after 72hr in CSA treated MCF-7 cells

source_name: MCF-7 cells, 72hr, CSA treated, replicate 2

value: 72hr in CSA


title: DMSO control replicate 2

source_name: MCF-7 cells, 72hr, DMSO treated (control), replicate 2


title: Growing vector 5

description:
Growing IMR90 vector
4157064153_C_1

source_name: IMR90_Growing vector

value: L.V.V_V; Growing vector


title: DMSO control replicate 4

source_name: MCF-7 cells, 72hr, DMSO treated (control), replicate 4


title: CSA treatment replicate 1

source_name: MCF-7 cells, 72hr, CSA treated, replicate 1


title: DMSO control replicate 1

source_name: MCF-7 cells, 72hr, DMSO treated (control), replicate 1


title: Ras Senescence p53 knockdown 3

description:
Ras Senescence IMR90 p53 knockdown
4157064153_D_1

source_name: IMR90_Ras Senescence p53 knockdown

value: L.53.1.Ras_V; Ras Senescence p53 knockdown


title: MEDGP3_0676_1

description: reanalysis of GSM1214926

value: group 3 medulloblastoma


title: Apoptosis p53 knockdown 3

description:
Apoptosis IMR90 p53 knockdown
4157064153_B_1

source_name: IMR90_Apoptosis p53 knockdown

value: L.53.1.E1A_Ras; Apoptosis p53 knockdown


title: Growing p53 knockdown 6

description:
Growing IMR90 p53 knockdown
4157064153_A_1

source_name: IMR90_Growing p53 knockdown

value: L.53.1.V_V; Growing p53 knockdown


title: Apoptosis p53 knockdown 2

description:
Apoptosis IMR90 p53 knockdown
4157064089_E_1


title: Growing p53 knockdown 5

description:
Growing IMR90 p53 knockdown
4157064089_F_1


title: EPNPFB_0700_1

description: reanalysis of GSM1217897

value: posterior fossa group B ependymoma


title: Growing vector 4

description:
Growing IMR90 vector
4157064089_D_1


title: EPNPFB_0811_1

description: reanalysis of GSM1217904


title: Quiescence Vector 5

description:
Quiescence IMR90 vector
4157064089_A_1

source_name: IMR90_Quiescence vector

value: L.V.QUIES; Quiescence vector


title: EPNPFB_0483_1

description: reanalysis of GSM1217887


title: Quiescence p53 knockdown 2

description:
Quiescence IMR90 p53 knockdown
4158260077_A_1


title: Quiescence Vector 3

description:
Quiescence IMR90 vector
4158260076_F_1


title: EPNPFB_0723_1

description: reanalysis of GSM1217898


title: EPNPFB_0246_1

description: reanalysis of GSM1217867


title: EPNPFB_0392_1

description: reanalysis of GSM1217880


title: Apoptosis p53 knockdown 1

description:
Apoptosis IMR90 p53 knockdown
4158260077_B_1


title: Quiescence p53 knockdown 1

description:
Quiescence IMR90 p53 knockdown
4158260076_D_1


title: Apoptosis vector 2

description:
Apoptosis IMR90 vector
4157064089_B_1


title: Growing p53 knockdown 4

description:
Growing IMR90 p53 knockdown
4158260077_C_1


title: EPNPFB_0364_1

description: reanalysis of GSM1217877


title: Growing vector 3

description:
Growing IMR90 vector
4158260076_B_1


title: Ras Senescence vector 2

description:
Ras Senescence IMR90 vector
4158260077_F_1

source_name: IMR90_Ras Senescence vector

value: L.V.Ras_V; Ras Senescence vector


title: Ras Senescence p53 knockdown 1

description:
Ras Senescence IMR90 p53 knockdown
4158260076_C_1


title: Apoptosis vector 1

description:
Apoptosis IMR90 vector
4158260076_A_1


title: Ras Senescence vector 1

description:
Ras Senescence IMR90 vector
4158260076_E_1


title: Growing p53 knockdown 3

description:
Growing IMR90 p53 knockdown
4158260054_F_1

value: L.53.G; Growing p53 knockdown


title: EPNPFB_0110_1

description: reanalysis of GSM1217857


title: Ras Senescence vector 3

description:
Ras Senescence IMR90 vector
4157064089_C_1


title: Ras Senescence p53 knockdown 2

description:
Ras Senescence IMR90 p53 knockdown
4158260077_D_1


title: Quiescence Vector 4

description:
Quiescence IMR90 vector
4158260077_E_1


title: EPNPFB_0080_1

description: reanalysis of GSM1217856


title: Checkpoint 48 hours p53 knockdown 3

description:
Checkpoint 48 hours IMR90 p53 knockdown
4158260054_E_1

source_name: IMR90_Checkpoint 48 hrs p53 knockdown

value: L.53.D2E; Checkpoint 48 hrs p53 knockdown


title: Checkpoint 24 hours p53 knockdown 3

description:
Checkpoint 24 hours IMR90 p53 knockdown
4158260054_B_1

source_name: IMR90_Checkpoint 24 hrs p53 knockdown

value: L.53.D1E; Checkpoint 24 hrs p53 knockdown


title: Growing vector 2

description:
Growing IMR90 vector
4158260054_D_1

value: normal human diploid fibroblasts

value: L.V.G; Growing vector


title: Checkpoint 24 hours vector 3

description:
Checkpoint 24 hours IMR90 vector
4158260054_C_1

source_name: IMR90_Checkpoint 24 hrs vector

value: L.V.D1E; Checkpoint 24 hrs vector


title: EPNPFA_0691_1

description: reanalysis of GSM1217893

value: brain tumor

value: posterior fossa group A ependymoma


title: DNA damage Senescence vector 2

description:
DNA damage Senescnece IMR90 vector
4158260039_D_1

source_name: IMR90_DNA damage Senescence vector

value: L.V.S; DNA damage Senescence vector


title: Checkpoint 48 hours vector 3

description:
Checkpoint 48 hours IMR90 vector
4158260054_A_1

source_name: IMR90_Checkpoint 48 hrs vector

value: L.V.D2E; Checkpoint 48 hrs vector


title: Checkpoint 48 hours p53 knockdown 2

description:
Checkpoint 48 hours IMR90 p53 knockdown
4158260059_B_1


title: EPNPFA_0812_1

description: reanalysis of GSM1217906


title: EPNPFA_0492_1

description: reanalysis of GSM1217889


title: Growing p53 knockdown 2

description:
Growing IMR90 p53 knockdown
4158260059_D_1


title: Checkpoint 48 hours vector 1

description:
Checkpoint 48 hours IMR90 vector
4158260039_E_1


title: DNA damage Senescence p53 knockdown 3

description:
DNA damage Senescence IMR90 p53 knockdown
4158260059_E_1

source_name: IMR90_DNA damage Senescence p53 knockdown

value: L.53.S; DNA damage Senescence p53 knockdown


title: Checkpoint 48 hours vector 2

description:
Checkpoint 48 hours IMR90 vector
4158260059_C_1


title: Checkpoint 24 hours p53 knockdown 2

description:
Checkpoint 24 hours IMR90 p53 knockdown
4158260059_A_1


title: EPNPFA_0507_1

description: reanalysis of GSM1217890


title: EPNPFA_0821_2

description: reanalysis of GSM1217910


title: EPNPFA_0859_1

description: reanalysis of GSM1217912


title: DNA damage Senescence p53 knockdown 2

description:
DNA damage Senescence IMR90 p53 knockdown
4158260039_B_1


title: EPNPFA_0393_1

description: reanalysis of GSM1217881


title: EPNPFA_0419_1

description: reanalysis of GSM1217884


title: Checkpoint 24 hours p53 knockdown 1

description:
Checkpoint 24 hours IMR90 p53 knockdown
4158260039_C_1


title: Checkpoint 24 hours vector 1

description:
Checkpoint 24 hours IMR90 vector
4158260038_D_1


title: Differentiated mouse podocytes Stretched Replicate 3

city: Greifswald

first: Karlhans

last: Endlich

address: Friedrich-Loeffler-Str. 23c

department: Anatomy and Cell Biology

institute: University Medicine Greifswald

hyb_protocol: Hybridization (16 h at 45°C) was performed according to the standard Affymetrix protocol.

scan_protocol: Scanning was performed with a GeneArray Scanner 3001 (Affymetrix).

data_processing: Data were processed using JMP Genomics 4.0 with RMA background correction and quantile normalization.

source_name: Conditionally immortalized mouse podocyte cell line SVI, stretched

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol.

growth_protocol: Podocytes were differentiated for 1-2 weeks in RPMI + 10% FBS at 38°C. Medium was changed 2-3 times weekly.

extract_protocol: Total RNA was isolated using Trizol reagent. Samples for microarray analysis were subjected to a quality control using an Agilent Bioanalyzer with the Pico RNA-Kit.

treatment_protocol: Cyclic biaxial stretch (0.5 Hz, 5% maximum linear strain) was applied for 3 d.

value: Kidney glomerulus

value: SVI

tag: stress

value: stretched


title: Checkpoint 48 hours p53 knockdown 1

description:
Checkpoint 48 hours IMR90 p53 knockdown
4158260038_B_1


title: Quiescence Vector 2

description:
Quiescence IMR90 vector
4158260039_F_1

value: L.V.Q; Quiescence vector


title: Differentiated mouse podocytes Stretched Replicate 2


title: DNA damage Senescence vector 1

description:
DNA damage Senescnece IMR90 vector
4158260038_C_1


title: Growing p53 knockdown 1

description:
Growing IMR90 p53 knockdown
4158260039_A_1


title: DNA damage Senescence p53 knockdown 1

description:
DNA damage Senescence IMR90 p53 knockdown
4158260038_F_1


title: Quiescence vector 1

description:
Quiescence IMR90 vector
4158260038_E_1


title: Growing vector 1

description:
Growing IMR90 vector
4158260038_A_1


title: Differentiated mouse podocytes Stretched Replicate 1


title: Pancreatic carcinoma ICGC_0285

description: Raw data for arrays used for copy number analysis using GAP (Popova, et al 2009)

source_name: Primary Tumour

value: Primary Tumour

tag: disease

value: Pancreatic Adenocarcinoma


title: Pancreatic carcinoma ICGC_0141


title: Pancreatic carcinoma ICGC_0146


title: Pancreatic carcinoma ICGC_0135


title: Pancreatic carcinoma ICGC_0138


title: Differentiated mouse podocytes Unstretched Replicate 3

source_name: Conditionally immortalized mouse podocyte cell line SVI, unstretched

value: unstretched


title: Pancreatic carcinoma ICGC_0131


title: Differentiated mouse podocytes Unstretched Replicate 2


title: Differentiated mouse podocytes Unstretched Replicate 1


title: 1C_expression_3

hyb_protocol: After fragmentation, 12.5ug of cDNA was hybridized to Affymetrix Rat Gene 1.0 ST microarrays

scan_protocol: GeneChips were then scanned with the GeneChip scanner 3000 (Affymetrix)

data_processing: Microarray probe intensities were normalized to each other using Robust Multi-array Average (RMA).

source_name: 1 day withdrawal + extinction test

label_protocol: In vitro transcription was performed to produce biotin-labeled cDNA using Affymetrix Gene Chip 3’ IVT Express reagent kit according to manufacturer’s instructions (Affymetrix, Santa Clara, CA)

extract_protocol: Double stranded cDNA was synthesized from total RNA from the NAc.

treatment_protocol: Male Sprague-Dawley rats (Harlan, Israel) weighing 250-350g were maintained on a 12-hr light/12-hr dark reversed cycle, with food and water available ad libitum. Rats were housed 2 per cage with a metal divider between them. Experiments were conducted during the dark cycle. Rats were anesthetized with xylazine and ketamine (10mg/kg and 100mg/kg, respectively). Jugular vein catheterization: Immediately after cannula implantation, rats were implanted with intravenous silastic catheters (ID 0.55 mm, OD 0.94 mm, Dow Corning, MI) into the right jugular vein. The catheter was secured to the vein with silk sutures and was passed subcutaneously to the top of the skull, where it exited into a connector (a modified 22-gauge cannula; Plastics One, VA, USA) mounted to the skull with MX-80 screws (Small Parts, Inc., FL, USA) and dental cement (Yates and Bird, IL, USA). Cocaine self-administration: Rats were trained to self-administer cocaine for 6 hrs per day, over 10 days. The self-administration chambers (Med-Associates, Inc.; St Albans, VT, USA) had two levers, one active and one inactive. An active lever press generated a cocaine infusion (0.75 mg/kg, 0.13 ml, 5 sec/infusion; cocaine obtained from the National Institutes on Drug Abuse, MD, USA) through the i.v. catheter, and also activated a light located above the lever, which was lit for 40 sec. Active lever presses during the last 35 sec of the light cue did not result in additional cocaine infusions. Presses on the inactive lever did not activate the infusion pump and light. Control rats were subjected to saline self-administration under the same conditions. The number of active lever responses, infusions, and inactive lever responses were recorded for both treatment and control groups. Rats were returned to their home cages at the end of the daily sessions. Cocaine withdrawal (forced abstinence): After the 10-day period of self-administration training sessions, rats were subjected to either a 1-day period of withdrawal (for cocaine-trained and saline-trained rats) or 30-day period of withdrawal (cocaine-trained rats). During the withdrawal periods, rats were left in their home cages and handled 3 times a week. Extinction test : Rats were placed in the self-administration chambers, and only the contingent light cue appeared during active lever presses, without cocaine reinforcement. Cocaine-seeking behavior was assessed for 60 min. For examining DNA methylation alterations, brains were removed one hour after completion of the session, and the NAc was isolated for further epigenetic analysis.

value: males

tag: weight

value: Nucleus Accumbens

tag: strain

value: Sprague-Dawley


title: Pancreatic carcinoma ICGC_0329

source_name: Cell Line Derived From Tumour

value: Cell Line Derived From Tumour


title: EPNPFA_0064_2

description: reanalysis of GSM1217855


title: 1C_expression_2


title: Pancreatic carcinoma ICGC_0105


title: 30C_expression_2

source_name: 30 days withdrawal + extinction test


title: 30C_expression_3


title: EPNPFA_0064_1

description: reanalysis of GSM1217854


title: Pancreatic carcinoma ICGC_0061


title: Pancreatic carcinoma ICGC_0055


title: Pancreatic carcinoma ICGC_0066


title: EPNPFA_0195_1

description: reanalysis of GSM1217862


title: ATRT_VN90005_1

description: reanalysis of GSM869633

value: atypical teratoid/rhabdoid tumor


title: ATRT_0737_1

description: reanalysis of GSM869631

value: brain tumor


title: ATRT_0687_1

description: reanalysis of GSM869630


title: ATRT_AS93161_1

description: reanalysis of GSM869617


title: ATRT_VN90007_1

description: reanalysis of GSM869634


title: ATRT_VN90004_1

description: reanalysis of GSM869632


title: 30W_expression_3

source_name: 30 days withdrawal


title: 30C_expression_1


title: 1C_expression_1


title: 1W_expression_3

source_name: 1 day withdrawal


title: 1W_expression_2


title: ATRT_0663_1

description: reanalysis of GSM869629


title: 30W_expression_1


title: Pancreatic carcinoma ICGC_0054

source_name: Cell Line Derived From Xenograft

value: Cell Line Derived From Xenograft


title: Pancreatic carcinoma ICGC_0052


title: 1W_expression_1


title: Pancreatic carcinoma ICGC_0089


title: ATRT_0605_1

description: reanalysis of GSM869628


title: ATRT_0517_1

description: reanalysis of GSM869627


title: Pancreatic carcinoma ICGC_0088


title: Pancreatic carcinoma ICGC_0087


title: Sal_expression_3

source_name: Saline


title: ATRT_0504_1

description: reanalysis of GSM869624


title: Pancreatic carcinoma ICGC_0036


title: Pancreatic carcinoma ICGC_0031


title: Pancreatic carcinoma ICGC_0026


title: Pancreatic carcinoma ICGC_0077


title: ATRT_0404_1

description: reanalysis of GSM869622


title: ATRT_0413_1

description: reanalysis of GSM869623


title: Pancreatic carcinoma ICGC_0076


title: ATRT_0370_1

description: reanalysis of GSM869621


title: Pancreatic carcinoma ICGC_0075


title: Pancreatic carcinoma ICGC_0009


title: ATRT_0003_1

description: reanalysis of GSM869618


title: ATRT_0515_1

description: reanalysis of GSM869626


title: Sal_expression_1


title: Control_7d_rep1

city: Yangzhou

first: Ji

last: Miao

state: Jiangsu

address: No.12, Wenhui East Road

department: College of Veterinary Medicine

institute: Yangzhou University

description:
Gene expression after 7dpi in CEF
REV_022
con 7-1.txt

hyb_protocol: The labelled cRNAs were hybridised onto Agilent Chicken Gene Expression (4*44K, Design ID: 026441) microarrays.

scan_protocol: After washing, the arrays were scanned using an Agilent Scanner G2505C (Agilent Technologies, US).

data_processing: To analyse array images, raw data were extracted using Feature Extraction software (version10.7.1.1, Agilent Technologies) and then analysed.

organism: Gallus gallus

source_name: chicken embryo fibroblasts_7dpi_control

label_protocol: RNA quality was assessed using an Agilent Bioanalyzer (Agilent Technologies, USA). Sample RNA integrity numbers (RINs) were obtained to assign values to RNA measurements in an unambiguous manner. Total RNAs were reverse transcribed to produce double-stranded cDNA, from which cRNAs were synthesised and then labelled with cyanine-3-CTP.

growth_protocol: Reticuloendotheliosis virus strain HA1101 (GenBank accession number: KF305089.1) was isolated from commercial layer chickens in Jiangsu, China, and stored at the Key Laboratory of Jiangsu Preventive Veterinary Medicine. The virus was propagated on a monolayer of primary CEFs prepared from 10-day-old specific-pathogen free (SPF) chicken embryos (Merial Vital Laboratory Animal Technology, China). CEFs were plated at a density of 1×104 cells per well in 24-well culture plates and then inoculated with pre-treated virus suspensions.

extract_protocol: Cellular and viral RNAs were extracted using the AxyPrepTM Multisource Total RNA Miniprep Kit (AXYGEN, China) according to the manufacturer’s protocol. Sample RNAs were quantified using a spectrophotometer and maintained at -70°C for future use.

treatment_protocol: The CEFs were infected with REV at a multiplicity of infection (MOI) of 1. After a 2 h exposure to virus, the cells were washed three times and cultured in Dulbecco’s modified Eagle medium (DMEM; GIBCO, China) supplemented with 1% foetal bovine serum (FBS; GIBCO, China) at 37°C in a 5% CO2 atmosphere. REV infection was verified using an indirect immunofluorescence assay with a mouse anti-REV monoclonal antibody. All cell cultures were seeded simultaneously. Cells were harvested at 1, 3, 5, and 7 days post-infection (dpi).

value: chicken embryo fibroblasts (CEFs)

tag: infected with

value: none (control)

tag: time point

value: 7 days post-infection


title: ATRT_0119_1

description: reanalysis of GSM869619


title: Pancreatic carcinoma ICGC_0008


title: Control_7d_rep2

description:
Gene expression after 7dpi in CEF
REV_023
con 7-2.txt


title: ATRT_0343_1

description: reanalysis of GSM869620


title: Infection_7d_rep1

description:
Gene expression after 7dpi with REV infection in CEF
REV_019
inf 7-1.txt

value: Reticuloendotheliosis virus


title: Pancreatic carcinoma ICGC_0007


title: Infection_7d_rep2

description:
Gene expression after 7dpi with REV infection in CEF
REV_020
inf 7-2.txt


title: AA_0512_1

description: reanalysis of GSM824274

value: pediatric high grade glioma


title: Infection_7d_rep3

description:
Gene expression after 7dpi with REV infection in CEF
REV_021
inf 7-3.txt


title: Control_7d_rep3

description:
Gene expression after 7dpi in CEF
REV_024
con 7-3.txt


title: AA_0137_1

description: reanalysis of GSM824273


title: Pancreatic carcinoma ICGC_0006


title: ∆zta1_vs_wt_H2O2_repl3

city: Badalona

first: Lauro

last: Sumoy

state: Barcelona

address: Ctra. Can Ruti, Camí de les escoles s/n

department: High Content Genomics and Bioinformatics

institute: IGTP

description: ∆zta1 vs wt, H2O2 stress, biological replicate 2 of 3, technical replicate 1 of 2

hyb_protocol: After fragmentation, 825 ng of cRNA labelled with two different dyes were co-hybridized on the same array using in situ hybridization buffer (Agilent) for 17 h, at 65ºC, and washed at room temperature for 1 min in Gene Expression Wash Buffer 1 (Agilent), and 1 min at 37ºC in Gene Expression Wash Buffer 2 (Agilent).

scan_protocol: Fluorescent images were obtained using an Agilent G2565BA scanner at 100% photomultiplier tube intensity and 100% laser power settings.

data_processing: TIFF image spot intensities were extracted and quantified with GenePix 6.0 software (Axon, Molecular Devices, Sunnyvale, CA) using the irregular-feature-finding option. The extracted raw data were processed with Bioconductor project software developed in the R statistical programming environment [Gentleman et al., 2004] using the Limma package [Smyth and Speed, 2003]. After normexp background subtraction was applied [Ritchie et al., 2007], the two channels on each array were balanced by lowess normalization using 0.3 as the span parameter with reduced weights in control and poor-quality spots, followed by a scaling step to make all arrays comparable,. For statistical assessment of differential gene expression, the Statistical Analysis of Microarrays (SAM) algorithm was used by applying the samr library in R [Tusher et al., 2001]. All analysis was performed using a Web interface implementation of the R-based software by Lozano and collaborators (unpublished data). Log2 ratio values from data obtained upon microarray analysis for all replicate probes of the same gene were reduced to a single value corresponding to the median of the log2ratios of all spots. Preliminary statistical analysis comparing the log2ratios from the six arrays from untreated samples with those of the 6 arrays from treated samples revealed no significant differences associated to hydrogen peroxide treatment likely due to the low dose used. Since there was no discernible effect by hydrogen peroxide, we were able to focus on the Zta1 dependent changes in gene expression that could help us understand the function of this gene. We pooled all 12 array datasets in order to increase the statistical power to detect any differences between both strains.

organism: Saccharomyces cerevisiae

source_name: mutant yeast, defective for ZTA1 (YBR046C) zeta-crystallin, 30 minute treatment with 10mM hydrogen peroxide

label_protocol: Five-hundred nanograms of total RNA from each sample were reverse transcribed after priming with Oligo-dT- and labelled by in vitro transcription with T7 RNA polymerase in the presence of Cy5-CTP or Cy3-CTP using the Quick Amp Labeling Kit (Agilent) and purified using RNAeasy columns (Qiagen).

growth_protocol: Yeast cells from wild-type FY834α and ∆zta1 strains were grown to exponential phase (OD600≈0.7-0.8) in rich YPD medium at 30ºC.

extract_protocol: Total RNA was isolated with RiboPure™-Yeast Kit from Ambion, following the manufacturer’s instructions.

treatment_protocol: Cultures were treated with or without 10 mM hydrogen peroxide treatment for 30 min.

value: treated 30 min with 10 mM hydrogen peroxide

source_name: wild type yeast, 30 minute treatment with 10mM hydrogen peroxide


title: ∆zta1_vs_wt_H2O2_repl2


title: ∆zta1_vs_wt_H2O2_repl3_dye_swap

description: ∆zta1 vs wt, H2O2 stress, biological replicate 3 of 3, technical replicate 2 of 2


title: Control_5d_rep2

description:
Gene expression after 5dpi in CEF
REV_017
con 5-2.txt

source_name: chicken embryo fibroblasts_5dpi_control

value: 5 days post-infection


title: Pancreatic carcinoma ICGC_0072


title: ∆zta1_vs_wt_H2O2_repl2_dye_swap

description: ∆zta1 vs wt, H2O2 stress, biological replicate 2 of 3, technical replicate 2 of 2


title: Pancreatic carcinoma ICGC_0005


title: Checkpoint 24 hours vector 2

description:
Checkpoint 24 hours IMR90 vector
4158260059_F_1

source_name: IMR90_Checkpoint 24 hrs vector

value: normal human diploid fibroblasts

value: L.V.D1E; Checkpoint 24 hrs vector


title: Pancreatic carcinoma ICGC_0004

value: Primary Tumour

value: Pancreatic Adenocarcinoma


title: Pancreatic carcinoma ICGC_0002


title: Control_5d_rep3

description:
Gene expression after 5dpi in CEF
REV_018
con 5-3.txt


title: Infection_5d_rep3

description:
Gene expression after 5dpi with REV infection in CEF
REV_015
inf 5-3.txt


title: Control_5d_rep1

description:
Gene expression after 5dpi in CEF
REV_016
con 5-1.txt


title: ∆zta1_vs_wt_H2O2_repl1_dye_swap

description: ∆zta1 vs wt, H2O2 stress, biological replicate 1 of 3, technical replicate 2 of 2


title: Infection_5d_rep2

description:
Gene expression after 5dpi with REV infection in CEF
REV_014
inf 5-2.txt


title: ∆zta1_vs_wt_H2O2_repl1

description: ∆zta1 vs wt, H2O2 stress, biological replicate 1 of 3, technical replicate 1 of 2


title: ∆zta1_vs_wt_control_repl3_dye_swap

description: ∆zta1 vs wt, control, biological replicate 3 of 3, technical replicate 2 of 2

source_name: wild type yeast

value: untreated

source_name: mutant yeast, defective for ZTA1 (YBR046C) zeta-crystallin


title: ∆zta1_vs_wt_control_repl2_dye_swap

description: ∆zta1 vs wt, control, biological replicate 2 of 3, technical replicate 2 of 2


title: ∆zta1_vs_wt_control_repl3

description: ∆zta1 vs wt, control, biological replicate 2 of 3, technical replicate 1 of 2


title: Control_3d_rep2

description:
Gene expression after 3dpi in CEF
REV_011
con 3-2.txt

source_name: chicken embryo fibroblasts_3dpi_control

value: 3 days post-infection


title: T

city: Hefei

first: Fang

last: Ni

address: Huang shan Road

institute: University of Science and Technology of China

description: miRNA expression in human T cells

hyb_protocol: Cy3-labelled RNA was hybridized according Agilent’s miRNA Complete Labeling and Hyb Kit.  After hybridization, microarrays were washed , then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner  using Agilent Scan Control software

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.3 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: freshly purified peripheral blood T cells

label_protocol: Cyanine-3 (Cy3) labeled RNA was prepared from 100 ng RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and RNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.RNAs from 6 donors with equal amount were pooled together to get each cell sample

treatment_protocol: Freshly purified human NK cells /NKT and T cells were used as the microRNA array samples

value: peripheral blood

value: T


title: Infection_5d_rep1

description:
Gene expression after 5dpi with REV infection in CEF
REV_013
inf 5-1.txt


title: NKT

description: miRNA expression in human NKTcells

source_name: freshly purified peripheral blood NKT cells

value: NKT


title: Infection_3d_rep2

description:
Gene expression after 3dpi with REV infection in CEF
REV_008
inf 3-2.txt


title: Control_3d_rep1

description:
Gene expression after 3dpi in CEF
REV_010
con 3-1.txt


title: pNK

description: miRNA expression in human pNK cells

source_name: freshly purified peripheral blood NK cells

value: NK


title: cNK

description: miRNA expression in human cNK cells

source_name: freshly purified cord blood NK cells

value: cord blood


title: Infection_3d_rep1

description:
Gene expression after 3dpi with REV infection in CEF
REV_007
inf 3-1.txt

value: chicken embryo fibroblasts (CEFs)


title: Control_3d_rep3

description:
Gene expression after 3dpi in CEF
REV_012
con 3-3.txt

value: none (control)


title: ∆zta1_vs_wt_control_repl2


title: Control_1d_rep1

description:
Gene expression after 1dpi in CEF
REV_004
con 1-1.txt

source_name: chicken embryo fibroblasts_1dpi_control

value: 1 day post-infection


title: ∆zta1_vs_wt_control_repl1

description: ∆zta1 vs wt, control, biological replicate 1 of 3, technical replicate 1 of 2


title: Infection_3d_rep3

description:
Gene expression after 3dpi with REV infection in CEF
REV_009
inf 3-3.txt

value: Reticuloendotheliosis virus


title: ∆zta1_vs_wt_control_repl1_dye_swap

description: ∆zta1 vs wt, control, biological replicate 1 of 3, technical replicate 2 of 2


title: Control_1d_rep3

description:
Gene expression after 1dpi in CEF
REV_006
con 1-3.txt


title: Control_1d_rep2

description:
Gene expression after 1dpi in CEF
REV_005
con 1-2.txt


title: Infection_1d_rep2

description:
Gene expression after 1dpi with REV infection in CEF
REV_002
inf 1-2.txt


title: Infection_1d_rep3

description:
Gene expression after 1dpi with REV infection in CEF
REV_003
inf 1-3.txt


title: dNK

description: miRNA expression in human dNK cells

source_name: freshly purified decidual NK cells

value: uterine decidual tissues


title: Infection_1d_rep1

description:
Gene expression after 1dpi with REV infection in CEF
REV_001
inf 1-1.txt


title: 30W_expression_2

city: Montreal

first: Moshe

last: Szyf

address: McIntyre Medical Building, 3655 Promenade Sir William Osler, Room 1309

institute: McGill University

source_name: 30 days withdrawal

tag: gender

value: males

value: Nucleus Accumbens

value: Sprague-Dawley


title: NASH [0661_SEN_252185018682_S01_CGH_107_Sep09_1_2]

status: Public on Feb 26 2015

city: kuala lumpur

first: shamsul mohd

last: zain

address: jalan lembah pantai

department: department of pharmacology

country: Malaysia

institute: univeristy of malaya

description: Normalised ratios between patients and controls were used for CNV calls

hyb_protocol: Hybridization mix was prepared. The target was denatured and the mixture was incubated. The Agilent SureHyb Gasket was placed into an Agilent Chamber base. Immediately, hybridisation mix was pipetted onto the gasket slide. OGT array was placed onto the Gasket slide. The hybridisation chamber was placed in the hybridisation oven and hybridised. After hybridization, slides were washed sequential.

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing: Data were extracted using Feature Extraction Software (version 10.7.3.1) and uploaded into the CytoSure™ Interpret software (version 4.2.5), normalized and converted into .cgh files. The data were segmented using a modified Circular Binary Segmentation (CBS) algorithm.

source_name: NAFLD

label_protocol: Reaction tubes were prepared as a mixture of 18 μL of genomic DNA sample (or reference), 10 μL of random primer and 10 μL of reaction buffer. The reactions were mixed and centrifuged for 15 s, followed by denaturation in a PCR block with a heated lid at 99°C for 20 min. Immediately after, the tubes were placed on ice for 5 min. On ice, the followings were added to the tubes: 10 μL of dCTP labelling mix, 1 μL of Cy3-dCTP (for sample) / 1 μL of Cy5-dCTP (for reference), and 1 μL of Klenow. The mixture was centrifuged for 15 s and incubated at 37°C for 2 h. Following that, the mixture was incubated at 65°C for 10 min, then placed on ice for 5 min. The mixture was centrifuged for 15 s.

extract_protocol: Genomic DNA were extracted using Qiagen as recommended by the manufacturer

tag: Stage

value: NASH

tag: blood

value: lymphocytes

tag: age

value: Male

source_name: Control


title: NASH [0661_SEN_252185018680_S01_CGH_107_Sep09_1_1]

value: Female


title: NASH [0661_SEN_252185018679_S01_CGH_107_Sep09_1_2]


title: Sal_expression_2

source_name: Saline

tag: tissue


title: NASH [0661_SEN_252185018681_S01_CGH_107_Sep09_1_1]


title: NASH [0661_SEN_252185018682_S01_CGH_107_Sep09_1_1]


title: NASH [0661_SEN_252185018681_S01_CGH_107_Sep09_1_2]


title: NASH [0661_SEN_252185018680_S01_CGH_107_Sep09_1_2]


title: NASH [0661_SEN_252185018679_S01_CGH_107_Sep09_1_1]


title: NASH [0661_SEN_252185018678_S01_CGH_107_Sep09_1_2]


title: NASH [0661_SEN_252185018609_S01_CGH_107_Sep09_1_1]


title: NASH [0661_SEN_252185018607_S01_CGH_107_Sep09_1_1]


title: NASH [0661_SEN_252185018608_S01_CGH_107_Sep09_1_2]


title: NASH [0661_SEN_252185018606_S01_CGH_107_Sep09_1_2]


title: NASH [0661_SEN_252185018608_S01_CGH_107_Sep09_1_1]


title: NASH [0661_SEN_252185018607_S01_CGH_107_Sep09_1_2]


title: NASH [0661_SEN_252185018609_S01_CGH_107_Sep09_1_2]


title: NASH [0661_SEN_252185018598_S01_CGH_107_Sep09_1_2]


title: NASH [0661_SEN_252185018599_S01_CGH_107_Sep09_1_1]


title: NASH [0661_SEN_252185018605_S01_CGH_107_Sep09_1_1]


title: NASH [0661_SEN_252185018596_S01_CGH_107_Sep09_1_2]


title: NASH [0661_SEN_252185018605_S01_CGH_107_Sep09_1_2]


title: NASH [0661_SEN_252185018597_S01_CGH_107_Sep09_1_2]


title: NASH [0661_SEN_252185018598_S01_CGH_107_Sep09_1_1]


title: NASH [0661_SEN_252185018599_S01_CGH_107_Sep09_1_2]


title: NASH [0661_SEN_252185018596_S01_CGH_107_Sep09_1_1]


title: NASH [0661_SEN_252185018597_S01_CGH_107_Sep09_1_1]


title: NASH [0661_SEN_252185018606_S01_CGH_107_Sep09_1_1]


title: NASH [0661_SEN_252185018678_S01_CGH_107_Sep09_1_1]


title: Simple steatosis [0599_SEN_252185017050_S01_CGH_107_Sep09_1_1]

value: Simple steatosis


title: NASH [0661_SEN_252185018595_S01_CGH_107_Sep09_1_2]


title: NASH [0661_SEN_252185018595_S01_CGH_107_Sep09_1_1]