title: Subject 495, region Frontal Pole

source_name: Frontal Pole, 69 yr old male


title: Subject 882, region Occipital Visual Cortex

status: Public on Aug 19 2016

type: RNA

city: New York

first: Bin

last: Zhang

state: NY

address: 1470 Madison Avenue

department: Genetics and Genomic Sciences

country: USA

institute: Icahn School of Medicine at Mount Sinai

data_processing: The raw microarray data was preprocessed using the robust multiarray Average (RMA) method function implemented in the R/Bioconductor package Affy (v1.44) using the default parameters, including quantile normalizion and log2 transformation. RMA normalization was performed separately for each brain region. For 17 brain regions profiled with both 133A and 133B arrays, 133A and 133B arrays were normalized separately and combined afterwards. Finally, the normalized gene expression data was corrected for covariates including sex, PMI (postmortem interval), pH and race using linear regression.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Occipital Visual Cortex, 90 yr old female

extract_protocol: Total RNA was isolated from 50 mg tissue aliquots from brain tissue samples, amplified to cRNA, and biotin-labeled for analysis on the Affymetrix U133AB or U133 Plus 2.0 Human genome GeneChip at Gene Logic Inc. (Gaithersburg, MD, USA) using the TRIzol method and RNeasy columns according to protocols from Affymetrix (Santa Clara, CA, USA). The 28S/18S rRNA ratio of isolated RNA was assessed using a Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) Label – biotin label protocol => followed a protocol described in the Gene Logic GeneChip® Analysis Manual (Gaithersburg, USA).

tag: subject id

tag: age

tag: Sex

value: female

tag: race

value: white

tag: postmortem interval minutes

tag: ph

tag: clinical dementia rating

tag: braak neurofibrillary tangle score

tag: neuropathological category

value: Probable AD

tag: average neuritic plaque density

tag: sum of cerad rating scores in multiple brain regions

tag: sum of neurofibrillary tangles density in multiple brain regions

tag: brain region

value: Occipital Visual Cortex

tag: tissue

value: post-mortem brain


title: Subject 523, region Frontal Pole

hyb_protocol: followed a protocol described in the Gene Logic GeneChip® Analysis Manual (Gaithersburg, USA).

source_name: Frontal Pole, 82 yr old female

value: Normal

value: Frontal Pole


title: Subject 865, region Occipital Visual Cortex

scan_protocol: followed a protocol described in the Gene Logic GeneChip® Analysis Manual (Gaithersburg, USA).

source_name: Occipital Visual Cortex, 79 yr old female

value: black

value: Possible AD


title: Subject 1006, region Amygdala

source_name: Amygdala, 98 yr old female

label_protocol: followed a protocol described in the Gene Logic GeneChip® Analysis Manual (Gaithersburg, USA).

value: Amygdala


title: Subject 1012, region Amygdala


title: Subject 869, region Occipital Visual Cortex

source_name: Occipital Visual Cortex, 93 yr old female


title: Subject 480, region Frontal Pole

source_name: Frontal Pole, 91 yr old female


title: Subject 870, region Occipital Visual Cortex

source_name: Occipital Visual Cortex, 85 yr old female

value: definite AD


title: Subject 462, region Frontal Pole

source_name: Frontal Pole, 87 yr old male

value: male


title: Subject 988, region Amygdala

source_name: Amygdala, 79 yr old female

value: hispanic


title: Subject 842, region Occipital Visual Cortex

source_name: Occipital Visual Cortex, 83 yr old female


title: Subject 879, region Occipital Visual Cortex

source_name: Occipital Visual Cortex, 91 yr old female


title: Subject 956, region Amygdala

source_name: Amygdala, 93 yr old female


title: Subject 973, region Amygdala

source_name: Amygdala, 96 yr old female


title: Subject 457, region Frontal Pole

source_name: Frontal Pole, 84 yr old female


title: Subject 836, region Occipital Visual Cortex

source_name: Occipital Visual Cortex, 64 yr old male


title: Subject 843, region Occipital Visual Cortex

source_name: Occipital Visual Cortex, 66 yr old male


title: Subject 750, region Amygdala

source_name: Amygdala, 84 yr old female


title: Subject 709, region Amygdala

source_name: Amygdala, 94 yr old female


title: Subject 963, region Amygdala

source_name: Amygdala, 90 yr old female


title: Subject 831, region Occipital Visual Cortex

source_name: Occipital Visual Cortex, 88 yr old female


title: Subject 451, region Frontal Pole

source_name: Frontal Pole, 83 yr old male


title: Subject 427, region Frontal Pole

source_name: Frontal Pole, 80 yr old male


title: Subject 914, region Amygdala

source_name: Amygdala, 89 yr old female


title: Subject 375, region Frontal Pole

source_name: Frontal Pole, 87 yr old female


title: Subject 865, region Amygdala


title: Subject 940, region Amygdala

source_name: Amygdala, 83 yr old female


title: Subject 370, region Frontal Pole

source_name: Frontal Pole, 100 yr old male


title: Subject 882, region Amygdala


title: Subject 82, region Occipital Visual Cortex

source_name: Occipital Visual Cortex, 86 yr old female


title: Subject 804, region Occipital Visual Cortex

source_name: Occipital Visual Cortex, 82 yr old male


title: Subject 367, region Frontal Pole

source_name: Frontal Pole, 93 yr old female


title: Subject 347, region Frontal Pole


title: Subject 364, region Frontal Pole


title: Subject 488, region Frontal Pole


title: Subject 800, region Occipital Visual Cortex

source_name: Occipital Visual Cortex, 89 yr old female


title: Subject 776, region Occipital Visual Cortex

source_name: Occipital Visual Cortex, 95 yr old male


title: Subject 752, region Amygdala


title: Subject 83, region Occipital Visual Cortex

source_name: Occipital Visual Cortex, 90 yr old female


title: Subject 340, region Frontal Pole


title: Subject 709, region Occipital Visual Cortex

source_name: Occipital Visual Cortex, 94 yr old female


title: Subject 665, region Amygdala

source_name: Amygdala, 92 yr old female


title: Subject 869, region Amygdala

source_name: Amygdala, 93 yr old female


title: Subject 316, region Frontal Pole

source_name: Frontal Pole, 64 yr old male


title: Subject 332, region Frontal Pole

source_name: Frontal Pole, 94 yr old female


title: Subject 233, region Amygdala

source_name: Amygdala, 100 yr old female


title: Subject 592, region Amygdala

source_name: Amygdala, 95 yr old female


title: Subject 684, region Occipital Visual Cortex

source_name: Occipital Visual Cortex, 84 yr old female


title: Subject 697, region Occipital Visual Cortex

source_name: Occipital Visual Cortex, 100 yr old female


title: Subject 234, region Frontal Pole

source_name: Frontal Pole, 99 yr old female


title: Subject 480, region Amygdala

source_name: Amygdala, 91 yr old female


title: Subject 665, region Occipital Visual Cortex

source_name: Occipital Visual Cortex, 92 yr old female


title: Subject 66, region Occipital Visual Cortex

source_name: Occipital Visual Cortex, 89 yr old male


title: Subject 256, region Frontal Pole


title: Subject 750, region Occipital Visual Cortex


title: Subject 230, region Frontal Pole

source_name: Frontal Pole, 96 yr old female


title: Subject 273, region Frontal Pole

source_name: Frontal Pole, 92 yr old male


title: Subject 215, region Frontal Pole

source_name: Frontal Pole, 91 yr old female


title: Subject 184, region Frontal Pole

source_name: Frontal Pole, 86 yr old female


title: Subject 111, region Frontal Pole

source_name: Frontal Pole, 93 yr old female


title: Subject 639, region Occipital Visual Cortex

source_name: Occipital Visual Cortex, 86 yr old female


title: Subject 618, region Occipital Visual Cortex

source_name: Occipital Visual Cortex, 82 yr old male


title: Subject 1027, region Frontal Pole

source_name: Frontal Pole, 80 yr old male


title: Subject 571, region Occipital Visual Cortex

source_name: Occipital Visual Cortex, 89 yr old female


title: Subject 551, region Occipital Visual Cortex

source_name: Occipital Visual Cortex, 85 yr old female


title: Subject 1039, region Frontal Pole

source_name: Frontal Pole, 85 yr old male


title: Subject 1006, region Frontal Pole

source_name: Frontal Pole, 98 yr old female


title: Subject 1018, region Frontal Pole

source_name: Frontal Pole, 60 yr old male


title: Subject 626, region Occipital Visual Cortex

source_name: Occipital Visual Cortex, 88 yr old female


title: Subject 2010, region Frontal Pole

source_name: Frontal Pole, 70 yr old male


title: Subject 505, region Occipital Visual Cortex

source_name: Occipital Visual Cortex, 94 yr old female


title: Subject 625, region Occipital Visual Cortex

source_name: Occipital Visual Cortex, 102 yr old female


title: Subject 523, region Occipital Visual Cortex

source_name: Occipital Visual Cortex, 82 yr old female


title: Subject 592, region Occipital Visual Cortex

source_name: Occipital Visual Cortex, 95 yr old female


title: Subject 1023, region Frontal Pole

source_name: Frontal Pole, 92 yr old female


title: Subject 495, region Occipital Visual Cortex

source_name: Occipital Visual Cortex, 69 yr old male


title: Subject 480, region Occipital Visual Cortex

source_name: Occipital Visual Cortex, 91 yr old female


title: Subject 234, region Amygdala

source_name: Amygdala, 99 yr old female


title: Subject 462, region Occipital Visual Cortex

source_name: Occipital Visual Cortex, 87 yr old male


title: Subject 504, region Occipital Visual Cortex

source_name: Occipital Visual Cortex, 85 yr old male


title: Subject 457, region Occipital Visual Cortex

source_name: Occipital Visual Cortex, 84 yr old female


title: Subject 375, region Occipital Visual Cortex

source_name: Occipital Visual Cortex, 87 yr old female


title: CLGL-90

city: Raleigh

first: Steven

middle: E

last: Suter

state: NC

address: 1051 William Moore Drive

department: Department of Clinical Sciences

institute: NC State University

description: LGL leukemia

hyb_protocol: Hybridization was performed according to Affymetrix technical protocols.

scan_protocol: Lineberger Functional Genomic Core Facility at the University of North Carolina Chapel Hill using an Affymetrix GeneChip Scanner 3000 7G Plus with Autoloader

data_processing: All downstream analysis was performed using  GeneSpring GX v10 (Agilent Technologies). Normalization  of expression array data was performed  using the GC-RMA procedure, and signals were  median-centred across all arrays.

organism: Canis lupus familiaris

source_name: lymphoid cell line

label_protocol: MessageAmp II-Biotin Enhanced Kit (Ambion, Life Technologies, Grand Island, NY)

growth_protocol: RPMI/10% FBS

extract_protocol: Total RNA  was isolated from  each cell line and from non-neoplastic lymph node  specimens following the manufacturers’ instructions (Trizol;  Invitrogen, Carlsbad, CA, USA). All samples RIN >9.

tag: cell line

value: LGL T-cell


title: GL-1

description: B-cell leukemia

value: B--cell


title: CL-1

description: Primitive a/b T-cell leukemia

value: T-cell


title: 17-71

description: B-lymphoid malignancy

value: B-cell


title: CLL-1390

description: Primitive T-cell leukemia


title: Subject 427, region Occipital Visual Cortex

source_name: Occipital Visual Cortex, 80 yr old male


title: Subject 451, region Occipital Visual Cortex

source_name: Occipital Visual Cortex, 83 yr old male


title: Subject 215, region Occipital Visual Cortex

value: female


title: UL-1

description: lymphoid cell line

hyb_protocol: According to Affymetrix technical protocols

scan_protocol: Affymetrix GeneChip® Scanner 3000 7G Plus Targeted Genotyping System

data_processing: GEP analysis was performed using GeneSpring GX v12 (Agilent Technologies). Expression array data were normalized using the GC-RMA procedure  and signals were median-centered across all arrays.

source_name: cell line

label_protocol: MessageAmp II-Biotin Enhanced Kit

extract_protocol: Total RNA extracted using Trizol (Invitrogen) using standard techiques: all samples RIN >9


title: Subject 234, region Occipital Visual Cortex

source_name: Occipital Visual Cortex, 99 yr old female

value: white


title: TL-1

description: lymphoid cell line


title: Subject 2010, region Occipital Visual Cortex

source_name: Occipital Visual Cortex, 70 yr old male


title: Subject 184, region Occipital Visual Cortex

source_name: Occipital Visual Cortex, 86 yr old female

value: Probable AD


title: Subject 13, region Occipital Visual Cortex

source_name: Occipital Visual Cortex, 94 yr old female

value: Occipital Visual Cortex


title: CLBL-1

description: lymphoid cell line


title: Aldara Treated, biological replicate 5

city: Glasgow

first: Alison

last: McColl

address: B3-34 120 University Place

country: United Kingdom

institute: University of Glasgow

description: Gene expression data of mouse brains following topical application of Aldara cream

hyb_protocol: Hybridized, washed and stained using GeneTitan hybridization, wash and stain kit for WT Array Plates and GeneTitan Operating Software

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

data_processing: GeneSpring GX software, probeset level data were normalised using RMA 16 normalisation and summarisation

label: Biotin

organism: Mus musculus

source_name: Whole mouse brain following topical application of Aldara cream

label_protocol: Labelled with biotin using Ambion WT Expression Kit following the Affymetrix GeneChip WT Terminal Labeling kit

growth_protocol: Mice were treated with 80mg Aldara cream or aquaeous control cream every 24 hours on shaved dorsal skin. Treatment was repeated for 5 consecutive applications.

extract_protocol: Brain tissue was homogenised in 1ml of QIAzol using a Rotor-Stator. RNA was extracted usingQiagen RNeasy mini kits according to manufacturer's instruction

treatment_protocol: Following treatment, perfused mouse brains were harvested and were 'snap-frozen' in liquid nitrogen

value: Whole brain

tag: strain

tag: gender

value: Female


title: Subject 332, region Occipital Visual Cortex

tag: subject id

value: post-mortem brain


title: 3132

description: lymphoid cell line


title: Aldara Treated, biological replicate 3


title: Aldara Treated, biological replicate 4


title: Ema

description: lymphoid cell line

value: Ema


title: Aldara Treated, biological replicate 1


title: Aldara Treated, biological replicate 2


title: Subject 1006, region Occipital Visual Cortex

source_name: Occipital Visual Cortex, 98 yr old female

tag: age

value: black

value: Possible AD


title: Subject 1023, region Occipital Visual Cortex

source_name: Occipital Visual Cortex, 92 yr old female

tag: Sex

value: definite AD


title: Subject 988, region Frontal Pole

source_name: Frontal Pole, 79 yr old female

tag: race

value: Frontal Pole


title: Control, biological replicate 1

description: Gene expression data of mouse brains following topical application of control cream

source_name: Whole mouse brain following topical application of control cream


title: Subject 941, region Frontal Pole

source_name: Frontal Pole, 88 yr old male

value: male

tag: postmortem interval minutes


title: Subject 992, region Frontal Pole

source_name: Frontal Pole, 88 yr old female

tag: ph


title: Subject 990, region Frontal Pole

source_name: Frontal Pole, 62 yr old female

tag: clinical dementia rating

value: Normal


title: Control, biological replicate 5


title: Control, biological replicate 3


title: Subject 923, region Frontal Pole

source_name: Frontal Pole, 69 yr old male

value: asian

tag: braak neurofibrillary tangle score


title: Control, biological replicate 4


title: Subject 914, region Frontal Pole

source_name: Frontal Pole, 89 yr old female

tag: neuropathological category


title: Lgr5-Hi fraction-CTL

city: Yokohama, Kanagawa

first: Yoshiki

last: Mochizuki

address: 1-7-22 Suehiro-cho

country: Japan

institute: RIKEN

hyb_protocol: Following fragmentation, 6 ug of cDNA were hybridized for 17 hr at 45C on GeneChip Mouse Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with RMA-Sketch using Affymetrix default analysis settings and global scaling as normalization method.

source_name: Lgr5-Hi-CTL:FACS sorted intestinal epithelial cells from Zip7flox/+ villin-CreERT2, Lgr5-EGFP-ires-CreERT2 mice, Lgr5 hi

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 6 ug total DNA (GeneChip WT Terminal Labeling and Hybridization User Manual , 2009, Affymetrix).

growth_protocol: Adult mouse small intestinal crypts were isolated after mice were treated with tamoxifen

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

treatment_protocol: Tamoxifen was given for 2 days.

tag: genotype

tag: cell type

value: intestinal epithelial cells

tag: cell population


title: Subject 940, region Frontal Pole

source_name: Frontal Pole, 83 yr old female

tag: average neuritic plaque density

tag: sum of cerad rating scores in multiple brain regions

tag: sum of neurofibrillary tangles density in multiple brain regions

tag: brain region


title: Subject 870, region Frontal Pole

source_name: Frontal Pole, 85 yr old female

tag: tissue


title: Subject 963, region Frontal Pole

source_name: Frontal Pole, 90 yr old female

tag: subject id


title: Subject 892, region Frontal Pole

source_name: Frontal Pole, 90 yr old male

tag: age


title: Control, biological replicate 2

tag: strain

tag: gender


title: Subject 869, region Frontal Pole

source_name: Frontal Pole, 93 yr old female

tag: Sex

tag: race

tag: postmortem interval minutes


title: Subject 882, region Frontal Pole

tag: ph

tag: clinical dementia rating

tag: braak neurofibrillary tangle score


title: Subject 975, region Frontal Pole

tag: neuropathological category


title: Lgr5-Mid fraction-KO

source_name: Lgr5-Med-KO: FACS sorted intestinal epithelial cells from Zip7flox/flox villin-CreERT2, Lgr5-EGFP-ires-CreERT2 mice, Lgr5 Med

tag: genotype

tag: cell type

tag: cell population


title: CCALD-iPSCs_2

city: Seoul

first: Dong-Wook

last: Kim

address: 50-1 Yonsei-ro, Seodaemun-gu

department: Dept. of Physiol.

country: South Korea

institute: Yonsei University College of Medicine

description: replicate 4

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: standard Illumina  protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: CCALD-iPSCs

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

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: no treatment

value: iPSCs


title: Lgr5-Hi fraction-KO

source_name: Lgr5-Hi-KO: FACS sorted intestinal epithelial cells from Zip7flox/flox villin-CreERT2, Lgr5-EGFP-ires-CreERT2 mice, Lgr5 hi


title: Subject 843, region Frontal Pole

source_name: Frontal Pole, 66 yr old male

tag: average neuritic plaque density

tag: sum of cerad rating scores in multiple brain regions

tag: sum of neurofibrillary tangles density in multiple brain regions


title: AMN-iPSCs_2

description: replicate 3

source_name: AMN-iPSCs


title: Subject 865, region Frontal Pole

source_name: Frontal Pole, 79 yr old female

tag: subject id

value: female

tag: brain region

tag: tissue


title: Subject 83, region Frontal Pole

tag: age

value: white


title: AMN-iPSCs_3

description: replicate 3


title: CCALD-iPSCs_3

description: replicate 4


title: Subject 82, region Frontal Pole

source_name: Frontal Pole, 86 yr old female

tag: Sex


title: CCALD-iPSCs_1

description: replicate 4


title: Subject 800, region Frontal Pole

tag: race


title: Subject 842, region Frontal Pole

tag: postmortem interval minutes


title: Lgr5-Mid fraction-CTL

source_name: Lgr5-Med-CTL: FACS sorted intestinal epithelial cells from Zip7flox/+ villin-CreERT2, Lgr5-EGFP-ires-CreERT2 mice, Lgr5 Med


title: Control-iPSCs_3

description: replicate 2

source_name: Control-iPSCs


title: Subject 786, region Frontal Pole

source_name: Frontal Pole, 95 yr old female

tag: ph


title: Control-iPSCs_2

description: replicate 2


title: Control-iPSCs_1

description: replicate 2


title: hESCs_3

description: replicate 1

source_name: hESCs

value: H9 hESCs


title: hESCs_2

description: replicate 1


title: AMN-iPSCs_1

description: replicate 3


title: Subject 790, region Frontal Pole

source_name: Frontal Pole, 73 yr old female

tag: clinical dementia rating


title: Subject 776, region Frontal Pole

source_name: Frontal Pole, 95 yr old male

value: hispanic

tag: braak neurofibrillary tangle score


title: Subject 755, region Frontal Pole

source_name: Frontal Pole, 87 yr old male

tag: neuropathological category


title: Subject 752, region Frontal Pole

source_name: Frontal Pole, 84 yr old female

value: Probable AD


title: hESCs_1

description: replicate 1


title: Subject 836, region Frontal Pole

source_name: Frontal Pole, 64 yr old male


title: Subject 639, region Frontal Pole


title: Subject 623, region Frontal Pole

source_name: Frontal Pole, 85 yr old male


title: Subject 625, region Frontal Pole

source_name: Frontal Pole, 102 yr old female


title: Subject 66, region Frontal Pole

source_name: Frontal Pole, 89 yr old male


title: cartilage, leptin-induced, rep2

city: Shanghai

first: Ziming

address: 1665 Kongjiang Road

department: School of Medicine

country: China

institute: Shanghai Jiao Tong University

description: Gene expression of leptin-induced cartilage in rat

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).

organism: Rattus norvegicus

source_name: knee joint cartilage

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).

extract_protocol: Total RNA was extracted using TAKARA RNAiso Plus#9109 following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: The rats were divided into two groups: control animals (H group, n = 12) and leptin-induced animals (L group, n = 12). In order to investigate the in vivo effects of leptin on articular cartilage, rat recombinant leptin (100 μg) (R&D Systems), in a volume of 50 μL sterile saline, was injected into the joint cavity of the right knee of rats. Cartilage from rats killed 24 hours after intra-articular administration of leptin was collected and placed into liquid nitrogen for storage and use.

tag: gender

tag: strain

value: Sprague–Dawley rat

tag: treatment

value: leptin-induced


title: cartilage, healthy control, rep2

description: Gene expression of healthy cartilage in rat

value: healthy control


title: SucroseFedRatHeart_PerfusedGlucose_rep5

city: Houston

first: Romain

last: Harmancey

state: Texas

address: 1881 East Rd.

department: Internal Medicine - Division of Cardiology

institute: The University of Texas Health Science Center at Houston

description: Gene expression in perfused left ventricular heart tissue from Sprague Dawley rats fed a high-sucrose diet for 8 to 10 weeks to induce insulin resistance; Hearts were perfused for 60 min in the working mode in Krebs-Henseleit buffer supplemented with DL-beta-hydroxybutyric acid (10 mmol/L), acetoacetate (1 mmol/L), propionate (2 mmol/L) and glucosel (25 mmol/L)

hyb_protocol: 1.65 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Hi-RPM hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Rat Gene Expression v2 8x60K Microarray (G4858A-074036) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.3 (Agilent) using default parameters (protocol GE1_1100_Jul11 and Grid: 028279_D_F_20130204) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Left ventricular tissue High-Sucrose Diet-fed rat, Perfused in Working Mode for 60 min with Glucose, replicate 5

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 150 ng RNA using the One-Color Low RNA Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop 2000c spectrophotometer.

extract_protocol: Total RNA was prepared using the RNeasy fibrous tissue kit (QIAGEN, Valencia, CA) following the manufacturer's recommendations. Residual DNA contamination was eliminated by treatment with DNase I according to the manufacturer's instructions. Total RNA concentration and purity was determined on a NanoDrop 2000c spectrophotometer (Thermo Fisher Scientific, Waltham, MA). RNA integrity was evaluated on a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Rats were anesthetized with chloral hydrate (500 mg/kg). Hearts were rapidly excised and transferred in ice-cold Krebs-Henseleit buffer. Non-perfused hearts were immediately dissected and tissue was flash-frozen in liquid nitrogen and stored at -80°C until RNA extraction. The other hearts were perfused ex vivo in normoxic and normothermic conditions for 60 min in the working mode using a filling pressure and an afterload of 15 cm H2O and 100 cm H2O, respectively. The Krebs-Henseleit perfusion buffer contained 2.5 mmol/L calcium, 10 mmol/L DL-beta-hydroxybutyric acid, 1 mmol/L acetoacetate, 2 mmol/L propionate, and 25 mmol/L glucose (or 25 mmol/L mannitol as an osmotic control for the no glucose group). Following perfusion, the hearts were quickly dissected, the tissue flash-frozen in liquid nitrogen and stored at -80°C until RNA extraction.

value: heart

value: Sprague Dawley

value: 16-18 weeks

tag: diet

value: High-Sucrose Diet


title: Subject 618, region Frontal Pole

source_name: Frontal Pole, 82 yr old male

value: male

value: Possible AD

tag: average neuritic plaque density

tag: sum of cerad rating scores in multiple brain regions

value: Frontal Pole

value: post-mortem brain


title: cartilage, healthy control, rep1


title: SucroseFedRatHeart_PerfusedGlucose_rep4

source_name: Left ventricular tissue High-Sucrose Diet-fed rat, Perfused in Working Mode for 60 min with Glucose, replicate 4


title: cartilage, leptin-induced, rep1


title: Subject 616, region Frontal Pole

source_name: Frontal Pole, 91 yr old female

tag: subject id

tag: sum of neurofibrillary tangles density in multiple brain regions


title: SucroseFedRatHeart_PerfusedGlucose_rep3

source_name: Left ventricular tissue High-Sucrose Diet-fed rat, Perfused in Working Mode for 60 min with Glucose, replicate 3

tag: tissue


title: SucroseFedRatHeart_PerfusedGlucose_rep2

source_name: Left ventricular tissue High-Sucrose Diet-fed rat, Perfused in Working Mode for 60 min with Glucose, replicate 2

tag: age


title: ChowFedRatHeart_PerfusedGlucose_rep5

description: Gene expression in perfused left ventricular heart tissue from Sprague Dawley rats fed a chow-diet (LabDiet; Laboratory Rodent diet 5001); Hearts were perfused for 60 min in the working mode in Krebs-Henseleit buffer supplemented with DL-beta-hydroxybutyric acid (10 mmol/L), acetoacetate (1 mmol/L), propionate (2 mmol/L) and glucose (25 mmol/L)

source_name: Left ventricular tissue Chow-fed rat, Perfused in Working Mode for 60 min with Glucose, replicate 5

value: Rodent Chow


title: Subject 551, region Frontal Pole

source_name: Frontal Pole, 85 yr old female

tag: Sex

value: female

value: Normal

tag: brain region


title: SucroseFedRatHeart_PerfusedGlucose_rep1

source_name: Left ventricular tissue High-Sucrose Diet-fed rat, Perfused in Working Mode for 60 min with Glucose, replicate 1


title: Subject 592, region Frontal Pole

source_name: Frontal Pole, 95 yr old female

tag: race

value: white

tag: postmortem interval minutes


title: Subject 571, region Frontal Pole

source_name: Frontal Pole, 89 yr old female

value: black

tag: ph

tag: clinical dementia rating

value: definite AD


title: Subject 523, region Frontal Pole

source_name: Frontal Pole, 82 yr old female

tag: braak neurofibrillary tangle score

tag: neuropathological category


title: ChowFedRatHeart_PerfusedGlucose_rep3

source_name: Left ventricular tissue Chow-fed rat, Perfused in Working Mode for 60 min with Glucose, replicate 3

tag: gender

tag: strain


title: Subject 495, region Frontal Pole

source_name: Frontal Pole, 69 yr old male


title: ChowFedRatHeart_PerfusedGlucose_rep1

source_name: Left ventricular tissue Chow-fed rat, Perfused in Working Mode for 60 min with Glucose, replicate 1

tag: diet


title: ChowFedRatHeart_PerfusedGlucose_rep2

source_name: Left ventricular tissue Chow-fed rat, Perfused in Working Mode for 60 min with Glucose, replicate 2


title: ChowFedRatHeart_PerfusedGlucose_rep4

source_name: Left ventricular tissue Chow-fed rat, Perfused in Working Mode for 60 min with Glucose, replicate 4


title: Subject 480, region Frontal Pole

tag: average neuritic plaque density


title: SucroseFedRatHeart_PerfusedMannitol_rep5

description: Gene expression in perfused left ventricular heart tissue from Sprague Dawley rats fed a high-sucrose diet for 8 to 10 weeks to induce insulin resistance; Hearts were perfused for 60 min in the working mode in Krebs-Henseleit buffer supplemented with DL-beta-hydroxybutyric acid (10 mmol/L), acetoacetate (1 mmol/L), propionate (2 mmol/L) and mannitol (25 mmol/L)

source_name: Left ventricular tissue High-Sucrose Diet-fed rat, Perfused in Working Mode for 60 min with Mannitol, replicate 5


title: Subject 462, region Frontal Pole

source_name: Frontal Pole, 87 yr old male

tag: sum of cerad rating scores in multiple brain regions


title: Subject 457, region Frontal Pole

source_name: Frontal Pole, 84 yr old female

tag: subject id


title: SucroseFedRatHeart_PerfusedMannitol_rep4

source_name: Left ventricular tissue High-Sucrose Diet-fed rat, Perfused in Working Mode for 60 min with Mannitol, replicate 4


title: Subject 488, region Frontal Pole

source_name: Frontal Pole, 87 yr old female

tag: sum of neurofibrillary tangles density in multiple brain regions


title: SucroseFedRatHeart_PerfusedMannitol_rep1

source_name: Left ventricular tissue High-Sucrose Diet-fed rat, Perfused in Working Mode for 60 min with Mannitol, replicate 1

tag: tissue


title: SucroseFedRatHeart_PerfusedMannitol_rep2

source_name: Left ventricular tissue High-Sucrose Diet-fed rat, Perfused in Working Mode for 60 min with Mannitol, replicate 2

tag: age


title: SucroseFedRatHeart_PerfusedMannitol_rep3

source_name: Left ventricular tissue High-Sucrose Diet-fed rat, Perfused in Working Mode for 60 min with Mannitol, replicate 3


title: Subject 427, region Frontal Pole

source_name: Frontal Pole, 80 yr old male

tag: Sex


title: Subject 370, region Frontal Pole

source_name: Frontal Pole, 100 yr old male

tag: brain region


title: Subject 375, region Frontal Pole

tag: race


title: Subject 364, region Frontal Pole

tag: postmortem interval minutes


title: Subject 367, region Frontal Pole

source_name: Frontal Pole, 93 yr old female

tag: ph

value: Probable AD


title: Subject 347, region Frontal Pole

tag: clinical dementia rating


title: ChowFedRatHeart_PerfusedMannitol_rep2

description: Gene expression in perfused left ventricular heart tissue from Sprague Dawley rats fed a chow-diet (LabDiet; Laboratory Rodent diet 5001); Hearts were perfused for 60 min in the working mode in Krebs-Henseleit buffer supplemented with DL-beta-hydroxybutyric acid (10 mmol/L), acetoacetate (1 mmol/L), propionate (2 mmol/L) and mannitol (25 mmol/L)

source_name: Left ventricular tissue Chow-fed rat, Perfused in Working Mode for 60 min with Mannitol, replicate 2


title: ChowFedRatHeart_PerfusedMannitol_rep4

source_name: Left ventricular tissue Chow-fed rat, Perfused in Working Mode for 60 min with Mannitol, replicate 4


title: Subject 451, region Frontal Pole

source_name: Frontal Pole, 83 yr old male

tag: braak neurofibrillary tangle score


title: ChowFedRatHeart_PerfusedMannitol_rep5

source_name: Left ventricular tissue Chow-fed rat, Perfused in Working Mode for 60 min with Mannitol, replicate 5


title: Subject 340, region Frontal Pole

tag: neuropathological category


title: Subject 332, region Frontal Pole

source_name: Frontal Pole, 94 yr old female


title: ChowFedRatHeart_PerfusedMannitol_rep1

source_name: Left ventricular tissue Chow-fed rat, Perfused in Working Mode for 60 min with Mannitol, replicate 1

tag: gender


title: SucroseFedRatHeart_NonPerfused_rep4

description: Gene expression in naïve left ventricular heart tissue from Sprague Dawley rats fed a high-sucrose diet for 8 to 10 weeks to induce insulin resistance (Research Diets D11725)

source_name: Left ventricular tissue High-Sucrose Diet-fed rat, Non-perfused, replicate 4

tag: strain


title: ChowFedRatHeart_PerfusedMannitol_rep3

source_name: Left ventricular tissue Chow-fed rat, Perfused in Working Mode for 60 min with Mannitol, replicate 3

tag: diet


title: SucroseFedRatHeart_NonPerfused_rep3

source_name: Left ventricular tissue High-Sucrose Diet-fed rat, Non-perfused, replicate 3


title: Subject 316, region Frontal Pole

source_name: Frontal Pole, 64 yr old male

tag: average neuritic plaque density


title: Subject 273, region Frontal Pole

source_name: Frontal Pole, 92 yr old male

tag: sum of cerad rating scores in multiple brain regions


title: Subject 256, region Frontal Pole

source_name: Frontal Pole, 99 yr old female

tag: subject id


title: SucroseFedRatHeart_NonPerfused_rep1

source_name: Left ventricular tissue High-Sucrose Diet-fed rat, Non-perfused, replicate 1


title: Subject 234, region Frontal Pole

tag: sum of neurofibrillary tangles density in multiple brain regions


title: SucroseFedRatHeart_NonPerfused_rep2

source_name: Left ventricular tissue High-Sucrose Diet-fed rat, Non-perfused, replicate 2

tag: tissue


title: ChowFedRatHeart_NonPerfused_rep4

description: Gene expression in naïve left ventricular heart tissue from Sprague Dawley rats fed a chow-diet (LabDiet; Laboratory Rodent diet 5001)

source_name: Left ventricular tissue Chow-fed rat, Non-perfused, replicate 4

tag: age


title: SucroseFedRatHeart_NonPerfused_rep5

source_name: Left ventricular tissue High-Sucrose Diet-fed rat, Non-perfused, replicate 5


title: ChowFedRatHeart_NonPerfused_rep5

source_name: Left ventricular tissue Chow-fed rat, Non-perfused, replicate 5


title: ChowFedRatHeart_NonPerfused_rep3

source_name: Left ventricular tissue Chow-fed rat, Non-perfused, replicate 3


title: Subject 230, region Frontal Pole

source_name: Frontal Pole, 96 yr old female

tag: Sex


title: ChowFedRatHeart_NonPerfused_rep2

source_name: Left ventricular tissue Chow-fed rat, Non-perfused, replicate 2


title: Subject 215, region Frontal Pole

source_name: Frontal Pole, 91 yr old female

tag: brain region


title: Subject 2010, region Frontal Pole

source_name: Frontal Pole, 70 yr old male

tag: race


title: ELDERLY 7

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

country: Italy

institute: University of Padova

description: gene expression from whole blood collected at rest, morning fasting

hyb_protocol: The cRNA labeling and hybridizations were performed according to protocols from Affymetrix Inc. (Santa Clara, CA).

scan_protocol: Affymetrix GeneChip scanner 3000

data_processing: RMA of .CEL files using affy Bioconductor library and Brainarray: HuGene10stv1_Hs_ENTREZG_15.1.0 custom CDF. In RMA, PM values have been background adjusted, normalized using quantile normalization, and expression measure calculated using median polish summarization

source_name: whole blood RNA

extract_protocol: Total RNA was isolated from each of the two blood samples using Tempus Spin RNA Isolation Kit (Applied Biosystems) as specified in the manufacturer's guidelines. To improve the detection sensitivity of transcripts on microarrays globin mRNA was depleted from a portion of each total RNA sample isolated from TEMPUS Blood RNA  tubes using the GLOBINclear™-Human kit (Ambion, TX).

treatment_protocol: Blood was sampled from antecubital vein of each subject while seated. The subjects were asked to avoid vigorous physical activity in the 24 h before blood sampling and to fasten from the evening meal until the morning, when samples were obtained.

tag: age class


title: ChowFedRatHeart_NonPerfused_rep1

source_name: Left ventricular tissue Chow-fed rat, Non-perfused, replicate 1


title: Subject 111, region Frontal Pole

source_name: Frontal Pole, 93 yr old female

tag: postmortem interval minutes

tag: ph


title: Subject 1023, region Frontal Pole

source_name: Frontal Pole, 92 yr old female

tag: clinical dementia rating

tag: braak neurofibrillary tangle score


title: Subject 1027, region Frontal Pole

source_name: Frontal Pole, 80 yr old male

tag: neuropathological category


title: ELDERLY 16

label_protocol: The cRNA labeling and hybridizations were performed according to protocols from Affymetrix Inc. (Santa Clara, CA).


title: Subject 1018, region Frontal Pole

source_name: Frontal Pole, 60 yr old male


title: ELDERLY 58


title: Subject 1039, region Frontal Pole

source_name: Frontal Pole, 85 yr old male


title: Subject 184, region Frontal Pole

source_name: Frontal Pole, 86 yr old female


title: ELDERLY 10


title: ELDERLY 13


title: Subject 1006, region Frontal Pole

source_name: Frontal Pole, 98 yr old female


title: ELDERLY 1


title: ELDERLY 22


title: Mu50 luxR-4

city: Cheongju

first: Jung Wook

address: Osong Health Technology Administration Complex, 187

department: Division of Antimicrobial resistance

institute: Korea National Research Institute of Health

description:
N_Mu50 luxR-4
This sample is of Staphylococcus aureus Mu50 delta-SAV1322, a deletion mutant in which SAV1322 locus. It is the forth of four mutant biological replicates used in this experiment, each from separate cultures.

hyb_protocol: Hybridization were carried out according to NimbleGen protocols.

scan_protocol: Arrays were scanned using the NimbleGen MS 200 Microarray Scanner

data_processing: Array data export processing and analysis was performed using NimbleScan v2.5  (RMA algorithm)

organism: Staphylococcus aureus subsp. aureus Mu50

source_name: Mu50 delta-SAV1322

label_protocol: cDNA were prepared from 10 ug total RNA using the SuperScript double-stranded cDNA   synthesis kit(Invitrogen). Labeling were carried out according to NimbleGen protocols.

growth_protocol: Cells were grown exponentially to an O.D. 600nm of approximately 0.5, then harvested.

extract_protocol: Total RNA was extracted using the Rneasy Mini Kit (Qiagen) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer at the Harvard-Partners Center for Genetics and Genomics (Harvard Medical School, Cambridge, MA USA).

treatment_protocol: The knockout mutant strains generated by allelic exchange method.

tag: genotype/variation

value: delta-SAV1322 mutant


title: Mu50 luxR-3

description:
N_Mu50 luxR-3
This sample is of Staphylococcus aureus Mu50 delta-SAV1322, a deletion mutant in which SAV1322 locus. It is the third of four mutant biological replicates used in this experiment, each from separate cultures.


title: Mu50 luxR-1

description:
N_Mu50 luxR-1
This sample is of Staphylococcus aureus Mu50 delta-SAV1322, a deletion mutant in which SAV1322 locus. It is the first of four mutant biological replicates used in this experiment, each from separate cultures.


title: Mu50-2

description:
N_Mu50-2
This sample is of wild-type Staphylococcus aureus Mu50. It is the second of four wild-type biological replicates used in this experiment, each from separate cultures.

source_name: Mu50 wild-type

value: wild type


title: Mu50 luxR-2

description:
N_Mu50 luxR-2
This sample is of Staphylococcus aureus Mu50 delta-SAV1322, a deletion mutant in which SAV1322 locus. It is the second of four mutant biological replicates used in this experiment, each from separate cultures.


title: ADULT 55


title: ELDERLY 4


title: ELDERLY 19


title: Mu50-1

description:
N_Mu50-1
This sample is of wild-type Staphylococcus aureus Mu50. It is the first of four wild-type biological replicates used in this experiment, each from separate cultures.


title: Mu50-3

description:
N_Mu50-3
This sample is of wild-type Staphylococcus aureus Mu50. It is the third of four wild-type biological replicates used in this experiment, each from separate cultures.


title: ADULT 46


title: ADULT 40


title: ADULT 37


title: ADULT 49


title: ADULT 43


title: ADULT 52


title: ADULT 31


title: ADULT 34


title: ADULT 28


title: 6H13P

status: Public on Aug 18 2016

city: Changchun

first: Shuang

last: Ji

state: Jilin

address: 5333,xi'an road

department: College of Animal Science

institute: Jilin University

description: Gene expression data from subcutaneous adipose tissue adipose tissue in Yan yellow cattle

hyb_protocol: According to AFFX Eukaryotic expression profile of single-round PCR chip experiment Protocol

scan_protocol: According to Affymetrix GeneChip data analysis

data_processing: Gene expression estimates were calculated by the Robust Multichip Analysis(RMA)and Significance Analysis of Microarrays(SAM).The differentially expressed genes were clustered with Cluster 3.0.The GO analysis was performed using the molecule annotation system 3.0 (http://bioinfo.capitalbio.com/mas3).

organism: Bos taurus

source_name: Subcutaneous Adipose tissue of Yan yellow cattle

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

growth_protocol: A total of 9 bulls of the same breed (Yan yellow cattle) with similar genetic backgrounds and were reared under identical conditions.

extract_protocol: Total RNA was extracted from adipose tissue samples using RNeasy Lipid Tissue Mini and Midi Kits (Qiagen, Valencia, CA).

treatment_protocol: At slaughter house,longissimus dorsi muscle,subcutaneous and abdominal adipose tissue samples were obtained according to standard procedures.Samples were immediately frozen in liquid nitrogen and stored at -80°C until further analysis.

tag: gender

value: 24-month old

value: Subcutaneous Adipose tissue

tag: breed

value: Yan yellow cattle


title: 4H11P


title: 8_2

description: Gene expression data from abdominal adipose tissue in Yan yellow cattle

source_name: Abdominal Adipose Tissue  of Yan yellow cattle

value: Abdominal Adipose Tissue


title: 5H22F

value: male


title: 5H12P


title: Mu50-4

description:
N_Mu50-4
This sample is of wild-type Staphylococcus aureus Mu50. It is the fourth of four wild-type biological replicates used in this experiment, each from separate cultures.


title: 6H33B

description: Gene expression data from Longissimus Dorsi Muscle in Yan yellow cattle

source_name: Longissimus Dorsi Muscle of Yan yellow cattle

value: Longissimus Dorsi Muscle


title: 4H31B


title: ADULT 25


title: Blood_af_ovarian-dysgenesis_2

type: genomic

city: Jerusalem

first: Ephrat

last: Levy-Lahad

address: Shmu'el Bait 12

country: Israel

institute: Shaare Zedek Medical Center

description: Hybridized to 250K_Nsp

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 7G.

data_processing: The array image was acquired using Affymetrix GeneChip® Command Console® Software (AGCC) . Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using the Genotyping Consule software.

molecule: genomic DNA

source_name: Peripheral blood

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from peripheral blood using a homemade DNA extraction kit based on the salting-out method, and dissolved in low TE (1mM Tris-Hcl pH=8, 0.1mM EDTA). DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and agarose gel electrophoresis.

tag: cell type

value: peripheral blood

value: Female

tag: disease state

value: XX-Ovarian dysgenesis


title: 5H32B


title: HepG2 untreated at 48hrs- 2nd set

city: Kajang

first: Yun-Kwan

last: NG

state: Selangor

address: Lot PT21144, Jalan Sungai Long, Bandar Sungai Long,

country: Malaysia

institute: Universiti Tunku Abdul Rahman

description: Gene expression data of HepG2 at 48hrs

hyb_protocol: The cRNA was then fragmented and mixed with a hybridization cocktail before subjecting to the array, which was then hybridized for 16 hours at 45 oC with rotation at 60 rpm.

scan_protocol: Immediately after hybridization, the hybridized probe arrays underwent an automated washing and staining protocol on the GeneChip” FS450 fluidic station and were then scanned on the GeneChip® Scanner 3000 7G Plus

data_processing:
Data generated from the scan was then analyzed using the Affymetrix GeneChip® Command Console software, v1.1, and the Affymetrix GeneChip® Expression Console software, v 1.1.
RMA

source_name: HepG2 cell was cultured for 48 hrs without CCL

label_protocol: Biotinylated cRNA of each sample was prepared according to the Affymetrix protocols

growth_protocol: Quantity of 5K HepG2 cell was seeded for various timepoints: 0hrs, 6hrs, 12hrs, 18hrs, 24hrs and 48hrs

extract_protocol: Total RNA of cell from each timepoint was extracted as per manufacturer's instruction

treatment_protocol: Treated HepG2 was treated with CCL and cultured at various timepoints: 6hrs, 12hrs, 18hrs, 24hrs and 48hrs

tag: cell line


title: HepG2 treated by CCL at 6hrs- 2nd set

description: Gene expression data of HepG2 after treated with CCL for 6hrs

source_name: HepG2 cell was cultured for 6 hrs with CCL


title: HepG2 treated by CCL at 6hrs- 3rd set


title: 4H21F

tag: tissue


title: HepG2 treated by CCL at 12hrs- 2nd set

description: Gene expression data of HepG2 after treated with CCL for 12hrs

source_name: HepG2 cell was cultured for 12 hrs with CCL


title: HepG2 treated by CCL at 48hrs- 2nd set

description: Gene expression data of HepG2 after treated with CCL for 48hrs

source_name: HepG2 cell was cultured for 48 hrs with CCL


title: HepG2 treated by CCL at 24hrs- 2nd set

description: Gene expression data of HepG2 after treated with CCL for 24hrs

source_name: HepG2 cell was cultured for 24 hrs with CCL


title: HepG2 treated by CCL at 12hrs- 3rd set


title: HepG2 treated by CCL at 6hrs- 1st set


title: Blood_af_ovarian-dysgenesis_1

description: Hybridized to 250K_Nsp


title: HepG2 treated by CCL at 18hrs- 1st set

description: Gene expression data of HepG2 after treated with CCL for 18hrs

source_name: HepG2 cell was cultured for 18 hrs with CCL


title: HepG2 treated by CCL at 24hrs- 1st set


title: HepG2 treated by CCL at 18hrs- 3rd set


title: HepG2 treated by CCL at 18hrs- 2nd set


title: HepG2 untreated at 48hrs- 3rd set

description: Gene expression data of HepG2 at 48hrs


title: HepG2 untreated at 48hrs- 1st set

description: Gene expression data of HepG2 at 48hrs


title: HepG2 treated by CCL at 48hrs- 1st set


title: HepG2 untreated at 24hrs- 2nd set

description: Gene expression data of HepG2 at 24hrs

source_name: HepG2 cell was cultured for 24 hrs without CCL


title: HepG2 untreated at 18hrs- 1st set

description: Gene expression data of HepG2 at 18hrs

source_name: HepG2 cell was cultured for 18 hrs without CCL


title: HepG2 untreated at 24hrs- 1st set

description: Gene expression data of HepG2 at 24hrs


title: HepG2 untreated at 12hrs- 3rd set

description: Gene expression data of HepG2 at 12hrs

source_name: HepG2 cell was cultured for 12 hrs without CCL


title: HepG2 untreated at 18hrs- 3rd set

description: Gene expression data of HepG2 at 18hrs


title: HepG2 treated by CCL at 12hrs- 1st set


title: HepG2 untreated at 24hrs- 3rd set

description: Gene expression data of HepG2 at 24hrs


title: HepG2 untreated at 12hrs- 1st set

description: Gene expression data of HepG2 at 12hrs


title: HepG2 untreated at 6hrs- 1st set

description: Gene expression data of HepG2 at 6hrs

source_name: HepG2 cell was cultured for 6 hrs without CCL


title: HepG2 untreated at 0hrs- 3rd set

description: Gene expression data of HepG2 at 0hrs

source_name: HepG2 cell without treatement at 0hrs


title: HepG2 untreated at 6hrs- 3rd set

description: Gene expression data of HepG2 at 6hrs


title: HepG2 untreated at 6hrs- 2nd set

description: Gene expression data of HepG2 at 6hrs


title: F162_F169

city: Hamburg

first: Stefan

last: Scholten

state: Hamburg

address: Ohnhorststrasse 18

department: Biocenter Klein Flottbek

country: Germany

institute: University of Hamburg

hyb_protocol: RNA labeling and hybridizations were performed according to the protocols of the maize oligonucleotide array project (http://www.maizearray.org). Both dyes (Cy3 or Cy5) were alternately used for each genotype to reduce systematic bias.

scan_protocol: The microarrays were scanned (AppliedPrecision ArrayWorx Scanner, Applied Precision Inc., USA) and the data were evaluated using the Software GenePix Pro 4.0 (Molecular Devices, Sunnyvale, USA).

data_processing: Raw data from microarray hybridization, exported from GenePix suites 6.0 (Axon, USA), was imported into LIMMA. The background was corrected by normexp method with offset 50. Background-corrected signal intensities were normalized using a two-step normalization: print-tip group loss (within-array normalization) and then between-array scale normalization.

organism: Zea mays

label_protocol: An interwoven loop design of two-color hybridizations was developed for the factorial to minimize average variance.

growth_protocol: Four seedlings of each maize inbred line were grown for 7 days under controlled conditions (25 °C 16 h day, 21 °C 8 h night, 70 per cent air humidity) with randomized plate positions.

extract_protocol: The biological replicates were pooled and homogenized prior to RNA extraction. Total RNA was isolated with mirVana miRNA isolation  20 kit (Ambion, Thermo Scientific).

treatment_protocol: The whole 7-day-old seedlings were sampled and frozen in liquid nitrogen.

tag: inbred line

tag: cultivar

value: flint

value: seedling

tag: age

value: 7 days

tag: sample type

value: pool of 4 biological replicates

source_name: gpr

value: gpr

value: dent


title: P033_F039


title: F039_S067_2


title: S067_P060


title: HL-60_exo-2

city: Portland

first: Noah

last: Hornick

state: OR

address: 3181 S.W. Sam Jackson Park Rd.

department: Pediatric Hematology Oncology

institute: OHSU

hyb_protocol: Hybridizations were performed as per Affymetrix FlashTag Biotin HSR RNA Labeling Kit User Guide with incubation at 48°C/ 60 rpm for 18 hours. Arrays were washed and stained on Fluidics Station 450 using script FS450_0002

scan_protocol: Standard Affymetrix scan protocol using GeneChip Scanner 3000 7G

data_processing: Data were analyzed with Partek Genomics Suite(v.6.6) using the RMA normalization method. Four samples from GEO accession GSE55025 (GSM1328048, GSM1328049, GSM1328044, GSM1328045) were included along with twelve new samples for the normalization.

source_name: HL-60 extracellular vesicles

label_protocol: Biotinylated RNA was prepared using Affymetrix HSR miRNA Flash Tag Biotin protocol with 130 ng total RNA input

growth_protocol: Human CD34+ cord-blood progenitors (New York Blood Center) were enriched using MACS cell separation (Miltenyi Biotec) and cultured in serum-free media (Stem Cell Technologies) supplemented with 100U/ml penicillin/streptomycin, 40ng/ml FLT3L, 25ng/ml SCF, and 50ng/ml TPO (Miltenyi Biotec) at 1% oxygen and 5% carbon dioxide for 48h, after which exosomes were isolated by differential centrifugation. HL-60 and MOLM-14 cell lines were cultured at 1% oxygen and 5% carbon dioxide in RPMI + 10% FBS and 1X Pen-Strep for 48 hours, after which extracellular vesicles were isolated by differential centrifugation.

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

value: malignant myeloid cell line

value: extracellular vesicles


title: CD34_exo-2

source_name: CD34 extracellular vesicles

value: CD34+ human hematopoietic progenitor cells


title: CD34_cel-2

source_name: CD34 cells

value: cells


title: P006_P033


title: F040_P006


title: F040_F012


title: HL-60_exo-1


title: HL-60_cel-1

source_name: HL-60 cells


title: HL-60_cel-3


title: CD34_exo-1


title: P042_F040


title: P065_P042


title: F039_P065


title: HL-60_exo-3


title: F040_L024


title: MOLM-14_cel-1

source_name: MOLM-14 cells


title: F012_F039


title: HL-60_cel-2


title: MOLM-14_exo-1

source_name: MOLM-14 extracellular vesicles


title: L024_F043


title: L024_F039


title: P060_F040


title: CD34_cel-1


title: F043_F012


title: F012_P024


title: HepG2 untreated at 12hrs- 2nd set

description: Gene expression data of HepG2 at 12hrs


title: P048_P064


title: S067_F045


title: P064_F012


title: L041_P066


title: F043_F030


title: S046_F045


title: L024_P048


title: F047_S067_2


title: F045_P033


title: L041_P084


title: F030_S067_3


title: F047_P084


title: F037_P033


title: F039_P066


title: P084_F039


title: P084_F037


title: F037_F043


title: P074_F047


title: P074_F030


title: F030_F037


title: P024_P040


title: F045_P074


title: P074_L041


title: P024_F039


title: P040_L024


title: HepG2 untreated at 0hrs- 1st set

description: Gene expression data of HepG2 at 0hrs


title: S067_F037


title: P024_F047


title: F043_L041


title: L041_P024


title: F043_F047


title: S067_L041


title: F037_P074


title: F045_F043


title: P074_F039


title: F047_S046


title: F039_P072


title: P075_L041


title: P084_F045


title: P081_F043


title: P072_S067


title: F043_P048


title: P048_F047


title: F045_P081


title: S067_P075


title: L041_P033


title: F039_F043


title: F039_S067


title: P068_F045


title: P083_P084


title: P024_F030


title: F030_P084


title: P084_P068


title: P066_S046


title: S046_F037


title: P033_P024_2


title: P027_F012


title: P080_P074


title: P074_P070


title: P070_F039


title: S018_P027


title: F030_P083


title: F012_P006_2


title: F037_P080


title: P006_S002


title: P066_F037


title: S028_F012


title: F030_S018


title: F012_F023


title: F012_L012


title: S002_F030


title: F047_P066


title: F030_S067_2


title: L012_F030


title: S015_S016


title: F023_F030


title: F043_L012


title: F023_F043


title: S067_S028


title: L012_S015


title: P024_L012


title: F169_P299


title: F169_P261


title: P312_F162


title: F023_P033_2


title: F169_P245


title: P033_P024


title: P135_F169


title: P284_F169


title: P272_F162


title: P235_F162


title: F162_P291


title: P299_F160


title: S016_F023


title: F160_P284


title: P261_F160


title: F160_P135


title: P291_F159


title: P159_F159


title: F161_P271


title: P330_F159


title: F161_P302


title: F159_P272


title: F162_P330


title: F160_P245


title: F157_P223


title: F159_P235


title: P245_F154


title: F157_P290


title: F154_P135


title: P291_F043


title: F043_P235


title: F154_P261


title: F154_P299


title: F043_P272


title: P159_F043_2


title: P312_F043


title: P284_F154


title: F159_P312


title: F151_P271


title: F043_P330


title: P261_F145


title: P135_F145


title: F145_P245


title: P330_F104


title: P291_F104


title: F151_P140


title: P235_F104


title: F101_P223


title: F101_P302


title: F145_P284


title: F104_P272


title: F047_P140


title: F099_P135


title: P245_F099


title: F099_P261


title: P299_F099


title: P261_F047


title: P312_S067


title: F047_P290


title: P159_S067


title: F099_P284


title: P272_S067


title: S067_P291


title: F104_P312


title: S067_P235


title: F145_P299


title: F104_P159_2


title: P235_P261


title: P159_P245


title: F161_F162


title: P245_F161


title: F169_P223


title: P223_P235


title: P140_P159


title: F160_P140


title: S067_P330


title: F159_F160


title: P135_F157


title: P312_P330


title: F157_F159


title: F043_F154


title: F154_P302


title: P291_P299


title: P272_P284


title: P299_F151


title: F151_F043


title: F104_F145


title: P302_P312


title: F047_S067


title: P167_P167.F117

value: hybrid


title: P284_F101


title: S067_F099


title: P271_P272


title: F145_P290


title: P290_P291


title: P167_F103


title: P167_F072


title: P167_F087


title: P167.F103_P167


title: P167.F117_F117


title: P167.F087_P167


title: P167.F087_P167.F103


title: F101_F104


title: P330_P135


title: P167.F072_P167


title: F099_P271


title: P167.F072_P167.F047


title: P167.F047_P167


title: P167.F047_P135.F117


title: P159.F117_P159.F087


title: P159.F047_P167.F117


title: P167.F117_P167.F087


title: P159.F072_P159


title: P159.F087_F087


title: P159.F087_P159.F103


title: P159_P159.F103


title: P159.F047_P159


title: P159.F103_F103


title: P159.F072_P159.F047


title: P154_P154.F072


title: P154.F117_P154


title: P154.F103_P154


title: P159_P159.F087


title: P167.F103_P167.F072


title: P154.F072_F072


title: P154.F117_P154.F087


title: P154_P154.F047


title: P154.F087_P154


title: P154.F087_P154.F103


title: P154.F047_P159.F117


title: P154.F072_P154.F047


title: P159.F117_P159


title: P154.F047_F047


title: P140.F117_P140.F087


title: P140.F117_F117


title: P159.F103_P159.F072


title: P140.F103_P140.F072


title: P140.F087_P140.F103


title: P140.F072_P140.F047


title: P140.F047_P140


title: P140.F072_P140


title: P140_P140.F087


title: P140_P140.F117


title: P140.F047_P154.F117


title: P135.F117_P135


title: P135.F103_F103


title: P135.F103_P135.F072


title: P135.F087_P135


title: P135.F087_P135.F103


title: P140.F087_F087


title: P135.F047_P135


title: P135.F072_F072


title: P135.F072_P135.F047


title: P135.F047_P140.F117


title: F087_P154.F087


title: F087_P135.F087


title: P135_P135.F103


title: F103_P140.F103


title: F087_P167.F087


title: F072_P167.F072


title: F117_P154.F117


title: F103_P154.F103


title: P135.F117_P135.F087


title: F117_P159.F117


title: F072_P159.F072


title: F072_P140.F072


title: F047_P140.F047


title: F103_P167.F103


title: F047_P135.F047


title: P135_P135.F072


title: F117_P135.F117


title: F047_P167.F047


title: P211_F124


title: P140_F124


title: S067_F137


title: P048_F137


title: F090_F062


title: F047_P159.F047


title: P167_F062


title: P048_F062


title: F047_F124


title: F047_P167


title: F047_P048


title: S067_P167


title: P165_F087


title: F062_P135


title: F062_F055


title: P048_F055


title: S067_F055


title: P204_S067


title: F124_P048


title: F124_F104


title: P092_F104


title: F062_P210


title: P209_F072


title: F124_S067


title: P209_F104


title: P150_F072


title: F117_P167


title: F103_S067


title: F117_F103


title: F117_P048


title: F138_P210


title: P204_F072


title: P214_F087


title: P214_P211


title: CDX2; Dmt1F/F/ApcF/+ Tumor

city: Ann Arbor

first: XIANG

last: XUE

state: Michigan

address: 1301 E. Catherine Street

institute: Umich

description: Gene expression data from colons.

hyb_protocol: Following fragmentation, 3.7 ug of cDNA were hybridized at 48C on Mouse Gene 2.1 ST Array strip arrays using the Affymetrix Gene Atlas system (software version 1.0.4.267)

scan_protocol: Arrays were scanned using the Affymetrix Gene Atlas system.

data_processing: Data was analyzed using the oligo Bioconductor package implemented in the R-statistical environment version 3.0.0. RMA was used to fit log2 transformed expression values.

source_name: Tumor Colon

label_protocol: Biotinylated cDNA were prepared according to the Affymetrix Plus WT kit protocol from 400 ng total RNA (GeneChip® WT Plus Reagent Kit Manual P/N 703174 Rev. 2).

growth_protocol: All mice were C57BL/6 background and maintained in standard cages in a light and temperature-controlled room and were allowed standard chow and water ad libitum.

treatment_protocol: Normal and tumor colon tissues were got from 3 months old mice

tag: background strain

value: 3 months old

tag: genotype

value: CDX2; Dmt1F/F/ApcF/+


title: F137_P211


title: CDX2; Dmt1+/+/ApcF/+ Tumor

description: Gene expression data from colons.

value: CDX2; Dmt1+/+/ApcF/+


title: P214_F134


title: F103_F101


title: F137_F136


title: P204_F090


title: P211_F103


title: F137_P140


title: P092_F101


title: F103_P048


title: P140_F103


title: F055_P140


title: F043_P150


title: P209_F101


title: F043_P209


title: F055_F043


title: F043_P092


title: CDX2; Dmt1+/+/ApcF/+ Normal

description: Gene expression data from colons.

source_name: Normal Colon


title: CDX2; Dmt1F/F/ApcF/+ Normal

description: Gene expression data from colons.


title: P211_P210


title: P150_P048


title: P154_P140


title: P210_P209


title: P135_P092


title: P140_P135


title: F055_P211


title: P154_F087


title: F104_P214


title: F072_P154


title: F101_P154


title: F072_P214


title: P154_F134


title: P092_F090


title: P150_F090


title: F072_F138


title: F104_P159


title: F138_P135


title: P048_F138


title: P167_P159


title: F104_P165


title: P167_F138


title: F090_P214


title: P048_P165


title: F138_F137


title: P165_F136


title: F101_P165


title: P159_F136


title: P159_F134


title: P159_F043


title: F090_P154


title: F087_P204


title: F087_P150


title: P165_F043


title: F136_P204


title: F136_P092


title: F087_F047


title: P210_F047


title: P135_F047


title: PSCC Patient 24 [PSCC Tumor]

city: Birmingham

first: Sunil

last: Sudarshan

state: Alabama

address: 510 20th Street South

department: Urology

institute: UAB

hyb_protocol: Samples  were hybridized to NanoString PanCancer Pathway Panel probes for 16 hours as per the manufacturer's instructions.

scan_protocol: Samples were scanned on the nCounter System as per the manufacturer's instructions.

data_processing: Gene Expression was quantified on the NanoString nCounter and raw counts were generated with nSolver. Raw counts were normalized against 40 reference genes with the geNorm algorithm. nSolver text files (.csv) and NanoString.rcc files were imported into Partek Genomic Suite 6.6 (PGS, Saint Louis, MO), and differential expressions were determined by ANOVA

label: NanoString capture and reporter probe mix

source_name: PSCC Tumor

extract_protocol: RNA was extracted from FFPE slides with the Roche High Pure FFPET RNA Isolation Kit as per the manufacturer's instructions, with the exception that proteinase K digestion times at 65C were extended to overnight

tag: vm status

value: No mets

tag: ecog ps

tag: os (in months)

tag: tnm stage


title: PSCC Patient 25 [PSCC Tumor]


title: F136_P209


title: PSCC Patient 22 [PSCC Tumor]


title: F101_P159


title: PSCC Patient 21 [PSCC Tumor]


title: PSCC Patient 20 [PSCC Tumor]


title: PSCC Patient 19 [PSCC Tumor]


title: F134_P204


title: P210_F117


title: P135_F117


title: PSCC Patient 16 [PSCC Tumor]


title: F134_P150


title: PSCC Patient 17 [PSCC Tumor]


title: PSCC Patient 23 [PSCC Tumor]


title: PSCC Patient 15 [Adjacent Normal]

source_name: Adjacent Normal


title: L005_F034


title: F030_F023


title: F013_F043


title: L012_L007


title: F012_F005


title: F134_F117


title: PSCC Patient 15 [PSCC Tumor]

value: visceral mets


title: L007_S028


title: F013_S028


title: F012_S028


title: PSCC Patient 12 [Adjacent Normal]


title: PSCC Patient 18 [PSCC Tumor]


title: S028_F023


title: F034_S028


title: PSCC Patient 11 [PSCC Tumor]


title: PSCC Patient 10 [PSCC Tumor]


title: S028_F043


title: S028_L005


title: S028_L012


title: PSCC Patient 8 [PSCC Tumor]


title: PSCC Patient 14 [Adjacent Normal]


title: PSCC Patient 14 [PSCC Tumor]


title: PSCC Patient 8 [Adjacent Normal]


title: PSCC Patient 9 [PSCC Tumor]


title: PSCC Patient 6 [Adjacent Normal]


title: L012_P006


title: F034_P006


title: PSCC Patient 12 [PSCC Tumor]


title: PSCC Patient 6 [PSCC Tumor]


title: F012_P006


title: PSCC Patient 11 [Adjacent Normal]


title: PSCC Patient 5 [PSCC Tumor]


title: F023_P006


title: P006_L005


title: 24h time point suture IN-biological rep 4

city: Linkoping

first: Neil

last: Lagali

address: sandbacksgatan 7

department: Ophthalmology

country: Sweden

institute: linkoping University

description: Gene expression data with sutures still In, but 24h after defining 0h time point

hyb_protocol: Following fragmentation, 130µl of the prepared hybridisation cocktail was hybridized into GeneChip Gene 2.0 ST 100-Format Array, and incubated for 16hr at 45ºC, and at 60 rpm (GeneChip® WT PLUS Reagent Kit, P/N 703174 Rev. 2, Affymetrix Inc).

scan_protocol: Genechips were scanned in accordance with the instructions in the Affymetrix GeneChip command Console User Manual (P/N 702569).

data_processing: Expression Console/RMA

source_name: rattus norvegicus albino-right eye cornea from 24h suture IN

label_protocol: Biotinylated cRNA was generated by In Vitro Transcription of the second-starnded cDNA template using T7 RNA polymerase, according to the mmanufactures instructions

growth_protocol: Male wistar rats, aged 12-16 weeks and weighing 350-400g were used. Animals were housed in an environment controlled by Heating, Ventilating and Air conditioning (HVAC) system. A standard dark: light cycle of 12:12 hours was maintained, while the noise levels were maintained below 85 db. Animals were provided with standard rodent food and water ad libitum. All animals were quarantined for two weeks before commencing an experiment.

extract_protocol: Cornea tissue excluding the scleral rim was disrupted using a hand held tissueRuptor and disposable Probe (Qiagen, Hilden, Germany) in a 2ml tube. Total RNA was then extracted from the lysate using RNeasy Mini Kit (Qiagen, Hilden, Germany)

treatment_protocol: Suture-Induced inflammatory corneal neovascularization was used. Two sutures were placed temporally into the cornea at a distance of 1.5mm from the limbus. At 4-5 days, sutures were removed from the eye for the suture OUT arm and then the cornea harvested for Microarray analysis. In the suture IN arm, at 4-5 days, sutures were maintained and then the cornea harvested 24h later and also used for microarray analysis

tag: strain

value: Wistar

tag: Sex

value: Male

value: Cornea


title: 24h time point suture IN-biological rep 2


title: 24h time point suture IN-biological rep 3


title: PSCC Patient 13 [PSCC Tumor]


title: P006_F043

value: seedling

value: 7 days

value: flint


title: PSCC Patient 7 [PSCC Tumor]


title: F023_P033

value: pool of 4 biological replicates

value: dent


title: PSCC Patient 2 [Adjacent Normal]


title: PSCC Patient 3 [PSCC Tumor]


title: P006_F005


title: PSCC Patient 4 [PSCC Tumor]


title: PSCC Patient 4 [Adjacent Normal]


title: PSCC Patient 2 [PSCC Tumor]


title: L005_P033


title: F043_P033


title: L012_P033


title: Mgal_WT_HS_rep2

city: Moscow

first: Tatiana

middle: A.

last: Semashko

address: Malaya Pirogovskaya

country: Russia

institute: RCPCM

description:
Transcriptome profiling of Mycoplasma gallisepticum cell culture in exponential growth phase under treatment with sublethal concentrations of oligomycin
HS_2

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >12 pmol Cy3/ug cRNA) were fragmented and hybridized to Agilent Custom Gene Expression Microarray, 8×15K  (G2509F)  according to the manufacturer's instructions.

scan_protocol: Slides were scanned on the Agilent DNA Microarray Scanner (G2505B).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent) using default parameters (Grid 069985_D_F_20140926).

organism: Mycoplasmoides gallisepticum

source_name: WT, heat stress at 46C during 15 min

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng total RNA using the Low Input Quick Amp Labeling Kit, One-Color (Agilent) according to the manufacturer's instructions exept using primer 5'-AAACGACGGCCAGTGAATTGTAATACGACTCACTATAGGCGCNNNNNN-3' instead T7 Primer, followed by PureLink RNA Mini Kit column purification (Thermofisher Scientific).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: The wild-type M. gallisepticum S6 and its mutants were grown in a liquid medium containing tryptose (20 g/l), Tris (3 g/l), NaCl (5 g/l), KCl (5 g/l), yeast extract (0,5%), horse serum (10%) and glucose (1%) at 37°C in aerobic conditions. Aliquotes of frozen cells were passaged twice for 24 hours, after that cells were diluted in the ratio 1:10 (v/v) in fresh media and harvested after 12 hours. For mutants, first cell passase was grown with 2 ug/ml tetracycline in culture media.

extract_protocol: Total RNA was prepared using direct lysis of cell culture in TRIzol LS reagent (Life Technologies) according to the manufacturer’s instructions. RNA was treated by DNase I (Thermo Scientific) followed by ethanol precipitation. RNA was quantified using a Qubit 2.0 fluorometer.

treatment_protocol: The wild-type M. gallisepticum cells were treated with sublethal concentrations of CCCP (final concentration 50 ug/ml in culture media), novobiocin (50 ug/ml) or tetracycline (8 ug/ml) during 1 hour or were under 46C during 15 min.

tag: strain background

tag: genotype/variation

value: WT


title: PSCC Patient 1 [PSCC Tumor]


title: P006_F030


title: Mgal_WT_HS_rep1

description:
Transcriptome profiling of Mycoplasma gallisepticum cell culture in exponential growth phase under treatment with sublethal concentrations of oligomycin
HS_1


title: Mgal_WT_tet_rep2

description:
Transcriptome profiling of Mycoplasma gallisepticum cell culture in exponential growth phase under treatment with sublethal concentrations of tetracycline
tet_2

source_name: WT, tetracycline treatment


title: Mgal_WT_tet_rep1

description:
Transcriptome profiling of Mycoplasma gallisepticum cell culture in exponential growth phase under treatment with sublethal concentrations of tetracycline
tet_1


title: Mgal_WT_novo_rep2

description:
Transcriptome profiling of Mycoplasma gallisepticum cell culture in exponential growth phase under treatment with sublethal concentrations of novobiocin
novo_2

source_name: WT, novobiocin treatment


title: F005_S002


title: Mgal_WT_cccp_rep2

description:
Transcriptome profiling of Mycoplasma gallisepticum cell culture in exponential growth phase under treatment with sublethal concentrations of CCCP
cccp_2

source_name: WT, CCCP treatment


title: Mgal_WT_cccp_rep1

description:
Transcriptome profiling of Mycoplasma gallisepticum cell culture in exponential growth phase under treatment with sublethal concentrations of CCCP
cccp_1


title: F030_S002


title: F043_S002


title: P033_F030


title: P033_F013


title: P033_F005


title: Mgal_WT_novo_rep1

description:
Transcriptome profiling of Mycoplasma gallisepticum cell culture in exponential growth phase under treatment with sublethal concentrations of novobiocin
novo_1


title: P033_L007


title: 24h time point suture OUT- biological rep 4

description: Gene expresion data 24h after suture removal

source_name: rattus norvegicus albino-right eye cornea from 24h after suture removal


title: 24h time point suture OUT- biological rep 3


title: 0h time point-biological rep 1

description: Gene expression data from 0h time point, 4-5 days after suture placement

source_name: rattus norvegicus albino-right eye cornea from 0h timepoint


title: 0h time point-biological rep 3


title: S002_F013


title: L005_S002


title: 24h time point suture OUT- biological rep 2


title: 24h time point suture OUT- biological rep 1


title: 24h time point suture IN-biological rep 1


title: S002_L007


title: 0h time point-biological rep 2


title: Mgal_00440_rep1

description:
Transcriptome profiling of Mycoplasma gallisepticum mutant with transposone insertion to  potential sigma factor GCW_00440 cell culture in exponential growth phase
Tn_00440_1

source_name: Tn4001opt_mini2 insertion in GCW_00440


title: Mgal_00495_rep2

description:
Transcriptome profiling of Mycoplasma gallisepticum mutant with transposone insertion to  1-deoxy-D-xylulose 5-phosphate reductoisomerase GCW_00495 cell culture in exponential growth phase
Tn_00495_2

source_name: Tn4001opt_mini1 insertion in GCW_00495


title: Control sample- biological rep2

description: Gene expression data from avascular control cornea

source_name: rattus norvegicus albino-right eye non sutured cornea


title: Control sample- biological rep1


title: S002_F034


title: Mgal_00440_rep2

description:
Transcriptome profiling of Mycoplasma gallisepticum mutant with transposone insertion to  potential sigma factor GCW_00440 cell culture in exponential growth phase
Tn_00440_2


title: Control sample- biological rep3


title: Mgal_00495_rep1

description:
Transcriptome profiling of Mycoplasma gallisepticum mutant with transposone insertion to  1-deoxy-D-xylulose 5-phosphate reductoisomerase GCW_00495 cell culture in exponential growth phase
Tn_00495_1


title: Mgal_00390_rep2

description:
Transcriptome profiling of Mycoplasma gallisepticum mutant with transposone insertion to RBS of lactate dehydrogenase GCW_00390 cell culture in exponential growth phase
Tn_RBS_00390_2

source_name: Tn4001opt_mini1 insertion in 5' UTR GCW_00390

value: CR19 = RBS GCW_00390::Tn4001opt_mini1


title: Mgal_03935_rep1

description:
Transcriptome profiling of Mycoplasma gallisepticum mutant with transposone insertion to  helicase SNF2 GCW_03935 cell culture in exponential growth phase
Tn_03935_1

source_name: Tn4001opt_mini1 insertion in GCW_03935


title: F005_S067


title: S002_F012


title: Control sample- biological rep4


title: F030_S067


title: Mgal_03935_rep2

description:
Transcriptome profiling of Mycoplasma gallisepticum mutant with transposone insertion to  helicase SNF2 GCW_03935 cell culture in exponential growth phase
Tn_03935_2


title: F013_S067


title: L007_S067


title: Mgal_00390_rep1

description:
Transcriptome profiling of Mycoplasma gallisepticum mutant with transposone insertion to RBS of lactate dehydrogenase GCW_00390 cell culture in exponential growth phase
Tn_RBS_00390_1


title: Mgal_03380_rep2

description:
Transcriptome profiling of Mycoplasma gallisepticum mutant with transposone insertion to 5’ UTR of hypothetical protein GCW_03380 cell culture in exponential growth phase
Tn_5UTR_03380_2

source_name: Tn4001opt_mini1 insertion in 5' UTR GCW_03380


title: S067_F012


title: S067_F034


title: Mgal_03380_rep1

description:
Transcriptome profiling of Mycoplasma gallisepticum mutant with transposone insertion to 5’ UTR of hypothetical protein GCW_03380 cell culture in exponential growth phase
Tn_5UTR_03380_1


title: S067_F023


title: Mgal_WT_rep2

description:
Transcriptome profiling of Mycoplasma gallisepticum cell culture in exponential growth phase
C_2

source_name: WT


title: S067_L012


title: Mgal_WT_rep1

description:
Transcriptome profiling of Mycoplasma gallisepticum cell culture in exponential growth phase
C_1


title: WT CML LICs, Biological repeat 2

city: Boston

first: Huafeng

last: Xie

state: MA

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

hyb_protocol: overnight at 45°C

scan_protocol: GeneChip Scanner 3000 7G

data_processing: Data were processed with GenePattern/RMA

source_name: WT CML LICs, 14d post BMT

label_protocol: cDNA is prepared from total RNA using a DNA/RNA chimeric primer and a reverse transcriptase and amplified using SPIA™ amplification. After purification cDNA is fragmented and labeled with Biotin.

growth_protocol: Animals were maintained in the animal facility at Boston Children’s Hospital

extract_protocol: Total RNA was isolated using the RNeasy Micro Plus Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: total BM cells were stained with antibodies and LSK or LICs were sorted directly into RLT Plus buffer summplemented with 1% 2-mercaptoethanol

value: 12 weeks old

value: WT CML LICs


title: WT CML LICs, Biological repeat 3


title: Ezh2 KO CML LICs, Biological repeat 2

source_name: Ezh2 KO CML LICs, 14d post BMT

value: Ezh2 KO CML LICs


title: WT HSC, biological repeat 3

source_name: 12w C57BL BM LSK cells

value: BM LSK


title: WT CML LICs, Biological repeat 1


title: Ezh2 KO CML LICs, Biological repeat 1


title: BMDM_IL-4+IL-10_rep3

status: Public on Aug 17 2016

city: Philadelphia

first: Robert

middle: L

last: Bowman

state: PA

address: 421 Curie Blvd

department: Cancer Biology

institute: University of Pennsylvania School of Medicine

hyb_protocol: 15 μg of cDNA was hybridized for 16 hr to the Affymetrix array as described in the Expression Analysis Technical Manual. GeneChips were washed and stained in the Affymetrix Fluidics Station FS450.

scan_protocol: Affymetrix GeneArray scanner 7G using the GeneChip Command Console version 3.2 as CEL files

data_processing: Feature intensity was extracted by Affymetrix GCOS 1.4. All analysis was completed in R using the Bioconductor suite of packages. Expression values were computed using the robust multi-array average (RMA) method, and then quantile normalized

source_name: BMDM IL-4+IL-10

label_protocol: 75 ng total RNA converted to cRNA using Affymetrix GeneChip®3' IVT Kit and in vitro transcription resulting into biotin-labeled cRNA, fragmented prior to hybridization (Affymetrix Expression Analysis Technical Manual, as described).

growth_protocol: To derive primary bone marrow-derived macrophages (BMDM), bone marrow was harvested from wild-type C57BL/6 mice aged 8 weeks by flushing femurs and tibias with DMEM media using 25-gauge needles. The marrow was passed through a 40 μm strainer and cultured in FEP (Teflon) cell culture bags (American Fluoroseal or PermaLife) with DMEM media containing 10% FBS, supplemented with 10 ng/mL recombinant mouse CSF-1 (R&D Systems). Bone marrow cells were cultured for 7 days, with fresh CSF-1-containing medium replacing old medium every other day.

extract_protocol: Cells were pelleted, washed with PBS, and resuspended in TriZOL.  RNA was isolated following a chloroform extraction, isopropanol precipitation, and ethanol wash.

treatment_protocol: BMDM were isolated after 7 days of CSF-1 treatment. Cells were cultured in suspension in 7 ml Teflon bags (PermaLife) and stimualted for 24 hours with 10 ng/ml of the indicated cytokines in DMEM +10% FBS+ Pen/Strep + CSF-1 10 ng/ml.

value: 8 weeks

value: bone marrow

tag: cell type

value: bone marrow-derived macrophages (BMDMs)

tag: cytokine stimulation


title: BMDM_IL-4+IL-10_rep2

tag: tissue


title: WT HSC, biological repeat 1


title: BMDM_IL-10_rep3

source_name: BMDM IL-10


title: BMDM_IL-4+IL-6_rep5

source_name: BMDM IL-4+IL-6


title: BMDM_Unstimulated_rep5

source_name: BMDM Unstimulated

value: none (unstimulated)


title: BMDM_IL-10_rep1


title: BMDM_IL-4+IL-10_rep1


title: WT HSC, biological repeat 2


title: BMDM_IL-10_rep2


title: BMDM_Unstimulated_rep6


title: BMDM_Unstimulated_rep7


title: BMDM_IL-6_rep3

source_name: BMDM IL-6


title: BMDM_Unstimulated_rep8


title: BMDM_IL-4_rep3

source_name: BMDM IL-4


title: BMDM_IL-6_rep4


title: BMDM_IL-4+IL-6_rep3


title: BMDM_IL-4_rep4


title: BMDM_IL-4+IL-6_rep4


title: BMDM_Unstimulated_rep4


title: BMDM_IL-4_rep5


title: BMDM_IL-4_rep2


title: BMDM_IL-4+IL-6_rep1


title: BMDM_IL-4_rep1


title: BMDM_IL-4+IL-6_rep2


title: BMDM_Unstimulated_rep1


title: BMDM_Unstimulated_rep3


title: BMDM_IL-6_rep2


title: BMDM_Unstimulated_rep2


title: BMDM_IL-6_rep1


title: BMDM_IL-6_rep5


title: 54 [11087]

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

description: PDAC

hyb_protocol: A mixture of fragmented biotinylated cDNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix HG U219 arrays, followed by staining and washing in a GeneChip Fluidics Station 450 (Affymetrix) according to the manufacturer's procedures.

scan_protocol: To assess the raw probe signal intensities, chips were scanned using a GeneChip Scanner 3000 (Affymetrix).

data_processing: Data were normalized using RMA as implemented in the xps package of Bioconductor. Expression values are represented on a log2-scale.

source_name: head of pancreas

label_protocol: RNA concentration and purity were determined spectrophotometrically using the NanoDrop ND-1000 (NanoDrop Technologies), and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Using the NuGEN Ovation Pico WTA System, an amount of 2 ng of total RNA was amplified and converted to cDNA. An amount of 5 ug of cDNA was fragmented and labeled with biotin using the NuGEN Encore Biotin Module.

growth_protocol: Snap-frozen tissue samples were stored in liquid nitrogen and/or at -80C in RNALater (Qiagen) until further use.

extract_protocol: total RNA was extracted using the RNeasy Mini kit (Qiagen) according the manufacturer's instructions. Only samples with an RNA integrity number (RIN) of >7.0 were used.

value: pancreatic tumor

tag: Stage

tag: grouped stage

value: Early


title: 299 [11085]

description: Control

source_name: Control sample

value: non-tumoral pancreatic tissue


title: wt 3

city: Heidelberg

first: Hannah

last: Uckelmann

address: Im Neuenheimer Feld 280

department: Stem Cells and Cancer

institute: German Cancer Research Center (DKFZ)

hyb_protocol: Standard Illumina hybridiation protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: wildtype_hematopoietic stem cells, 4 weeks post transplant

label_protocol: The NuGEN Ovation Pico WTA System (linear isothermal DNA amplification process) is used to generate single-stranded cDNA from small input amounts of 2.5ng RNA. Labeled cRNA were prepared according to Nugene Encore BiotinIL Module.

growth_protocol: wt (CD45.1.2) and Matn4-/- (CD45.2) HSCs (LSKCD150+CD48-) sorted by flow cytometry

extract_protocol: mRNA was isolated using the Arturus RNA isolation kit.

treatment_protocol: Recipient mice (CD45.1) were irradiated with 2x500Rad and transplanted with a 1:1 mixture of wt and Matn4-/- bone marrow (3x10^6 cells).

value: hematopoietic stem cells

tag: gender

value: female

tag: age

value: 12 weeks

value: wildtype


title: Matn4-/- 1

source_name: Matn4-/-_hematopoietic stem cells, 4 weeks post transplant


title: 105

description: PDAC

value: LNM


title: Eutopic Endometrium Sample- Patient 03

city: Ribeirão Preto

first: Flavia

middle: Gaona de Oliveira

last: Gennaro

state: São Paulo

address: Av Bandeirantes, 3900, Depto. Genética, Bloco C

department: Genetics

country: Brazil

institute: USP

description: Women with diagnosis of severe endometriosis and familial history of the disease.

hyb_protocol: The hybridization was performed according Agilent's protocol for a-CGH 2x400K. After hybridization, slides were washed sequential

scan_protocol: Arrays were scanned using an Agilent microarray scanner (Agilent Technologies, Inc), and processed using Agilent’s Feature Extraction software followed manufacturer's instructions.

data_processing: Agilent Feature Extraction Software (Protocol: CGH_107_sep09; Template:021850_D_F_20111015) was used for background subtraction and normalization.

source_name: Eutopic endometrial tissue - Endometriosis Patient

label_protocol: 1ug of gDNA for each sample labeled (test and control) were required. The references were labelled with Cy3-dUTP and endometrium DNA samples were labelled with Cy5-dUTP. The SureTag Complete DNA Labeling kit was used following manufacturer's instructions.

extract_protocol: genomic DNA extracted and purification followed manufacturer's instructions (MasterPure™ DNA Purification Kit- Epicentre, Illumina).

source_name: Commercial DNA Control Promega


title: 96

description: PDAC


title: 299

description: PDAC


title: 98

description: PDAC

source_name: body/tail of pancreas

value: Advanced


title: Normal Endometrium Sample - Control 02

description: Health woman without endometriosis diagnosis neither familial history of the disease.

source_name: Eutopic endometrial tissue - control


title: Eutopic Endometrium Sample- Patient 05


title: Eutopic Endometrium Sample- Patient 02


title: Matn4-/- 2


title: Matn4-/- 3


title: Eutopic Endometrium Sample- Patient 01


title: Eutopic Endometrium Sample- Patient 04

source_name: Eutopic endometrial tissue - EndometriosisPatient


title: Normal Endometrium Sample - Control 05


title: 100

description: PDAC


title: 95

description: PDAC


title: wt 2


title: IFNa 2

source_name: hematopoietic stem cells, 4 weeks post transplant_IFNa

growth_protocol: HSCs (LKCD150+CD48-) sorted by flow cytometry

treatment_protocol: wt mice were treated with PBS or IFNa (5x106U/kg ) for 16h.


title: 99

description: Control


title: wt 1


title: Normal Endometrium Sample - Control 04


title: Normal Endometrium Sample - Control 03


title: IFNa 3


title: Eutopic Endometrium Sample- Patient 06


title: IFNa 1


title: 93

description: PDAC


title: 298 [11077]

description: PDAC


title: Normal Endometrium Sample - Control 01


title: 90

description: PDAC


title: 298

description: Control


title: 295

description: PDAC


title: 88

description: PDAC


title: 129 [11067]

description: Control


title: 297 [11073]

description: PDAC


title: 294 [11066]

description: PDAC


title: 87

description: PDAC


title: 89

description: PDAC


title: 92

description: PDAC


title: 86

description: PDAC


title: 91

description: PDAC


title: PBS 1

source_name: hematopoietic stem cells, 4 weeks post transplant_PBS


title: PBS 3


title: PBS 2


title: 290

description: PDAC


title: 81

description: PDAC


title: 77

description: PDAC


title: 13 [11063]

description: Control


title: 79

description: PDAC


title: 80

description: PDAC


title: 85

description: PDAC


title: 277

description: PDAC


title: 83

description: PDAC


title: 293 [11059]

description: PDAC


title: 289

description: PDAC


title: 74

description: PDAC


title: 271

description: PDAC


title: 70

description: PDAC


title: 297

description: Control


title: 272

description: PDAC


title: 262

description: PDAC


title: 73

description: PDAC


title: 71

description: PDAC


title: 76

description: PDAC


title: 211

description: PDAC


title: 260

description: PDAC


title: 257

description: PDAC


title: 252

description: PDAC


title: 229

description: PDAC


title: 63

description: PDAC


title: 65

description: PDAC


title: 129

description: PDAC


title: 68

description: PDAC


title: 66

description: PDAC


title: 60

description: PDAC


title: 294

description: Control


title: 67

description: PDAC


title: 64

description: PDAC


title: 61

description: PDAC


title: 203

description: PDAC


title: 59

description: PDAC


title: 122

description: Control


title: T15_2

city: Haifa

first: nasra

middle: mohamed

last: yasin

address: Bat Galim haifa- rappaport

department: neuropharmacology

institute: technion

description: replicate 2

hyb_protocol: as described by the manufacturers  (see below)

scan_protocol: The hybridized chip was stained with streptavidin-Cy3 (AmershamTM, GE Healthcare, Little Chalfont, UK) and scanned with an Illumina HiScan. The scanned images were imported into GenomeStudio (Illumina) for extraction and quality control.

data_processing:
Quality measurements for total RNA were performed using TapeStation (Agilent). The RINe values of all samples was >9.5.  The RNA was amplified into biotinylated cRNA by in vitro transcription using the TargetAmp Nano labeling kit for Illumina BeadChips, (Epicentre) with 100 ng of total RNA as input material. Biotinylated cRNAs was purified, fragmented, and subsequently hybridized to an Illumina HumanHT-12 v4 Expression BeadChip according to the Direct Hybridization assay (Illumina Inc.). The hybridized chip was stained with streptavidin-Cy3 (AmershamTM) and scanned with an Illumina HiScan.
The raw gene expression data was exported from GenomeStudio and imported into JMP Genomics V5 software (SAS Institute Inc, Cary, NC). Quality control and analysis in JMP Genomics was done on log2 transformed data, after filtering for non-expressed genes (detection p-value<0.01), and for low variance transcripts across samples (variance <5%). Data Distribution showed that expression between samples were not as uniform as desired, therefore these data were normalized using Loess normalization. The data was analyzed using one-way ANOVA and differently express genes (DEGs) were defined as transcripts that were statistically significant at corrected p-value ≤0.05 using the False Discovery Rate (FDR).   Ingenuity Pathway Analysis (IPA 8.0, Ingenuity® Systems, Redwood City, CA, US) was used to identify statistically significant functional categories in the data set. Gene lists were imported into IPA and mapped to biological functional pathways. Z-score, a statistical method for rescaling and standardizing data, was used to determined enrichment, with Z-scores greater than 2 or smaller than 2 considered significant. The IPA algorithm generates novel networks from a user gene list favoring denser connectivity networks, with low probability to be generated by random chance, and maximization of genes from list, known as focus molecules.

source_name: U1118MG cell line

extract_protocol: Lysates from 3.85 × 10^6 cells were taken for RNA extraction, according to the instructions of the RNeasy® Mini Kit. Amount of obtained RNA was determined from a 1.5 µl sample by NanoDrop™ (Thermo, Rockland, DE). For microarray assay, RNA was diluted to 50 ng/µl. RNA quality was verified in 1 µl of each sample

treatment_protocol: U118MG cells (1.255 × 10^6) were seeded in Petri dishes (i.e. 28.5 × 10^3 cells / cm2) and allowed to proliferate for 3 days in full medium. Experiments for gene expression assayed with microarray typically consisted of three experimental groups and a vehicle control group (n = 3 for each group). Serum deprived medium was applied for 24 hrs, in the experimental groups ending with the inclusion a choice of various PK 11195 exposures i.e. either 15 min , 30 min, or 45 min. Exposure to PK 11195 implies serum deprived medium with 1% alcohol (vehicle) and PK 11195 (25 µM final concentration) for the required time period. 25 µM of PK 11195 is the optimal concentration for these types of experiments with U118MG cells (Kugler W, Veenman L, Shandalov Y, Leschiner S, Spanier I, Lakomek  M, and Gavish M. (2008) Cell Oncol. 30, 435). The cells were collected by trypsinization, washed by centrifugation in phosphate buffered saline (PBS) (400 × g, 5 min), and lysed according to the manufacturer's instructions.    [RLT lysis buffer provided with the RNeasy Mini Kit diluted with β-mercaptoethanol (1 : 100)] Lysates were stored at -70oC

tag: treatment

value: PK 11195 (25 µM) for 15 min exposure


title: T45_1

description: replicate 1

label_protocol: as described by the manufacturers  (see below)

value: PK 11195 (25 µM) for 45 min exposure


title: T45_3

description: replicate 3


title: T45_2

description: replicate 2


title: T30_3

description: replicate 3

value: PK 11195 (25 µM) for 30 min exposure


title: T15_3

description: replicate 3

value: PK 11195 (25 µM) for 15 min  exposure


title: T15_1

description: replicate 1

value: PK 11195 (25 µM ) for 15 min exposure


title: T30_1

description: replicate 1


title: BL_3

description: replicate 3

value: control without treatment


title: BL_2

description: replicate 2


title: 201

description: PDAC


title: T30_2

description: replicate 2


title: 55

description: PDAC


title: 54

description: PDAC


title: 50

description: PDAC


title: 242

description: PDAC


title: 56

description: PDAC


title: 48

description: PDAC


title: BL_1

description: replicate 1


title: 199

description: PDAC


title: 51

description: PDAC


title: 46

description: PDAC


title: 195

description: PDAC


title: 47

description: PDAC


title: 192

description: PDAC


title: 41

description: PDAC


title: 45

description: PDAC


title: WT mLIF 6 hours Replicate 3

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

hyb_protocol: Standard Illumina hybridization protocol

data_processing: IDAT files from BeadStudio were read into the limma package for R using the read.idat function with Illumina manifest file MouseWG-6_V2_0_R3_11278593_A.bgx. Raw intensities were neqc background corrected with offset 16, quantile normalized then log2-transformed.

source_name: Primary calvarial osteoblasts

label_protocol: not provided.

growth_protocol: Cells were grown in osteoblast differentiation media (alpha-minimal essesential media containing 15% heat inactivated fetal bovine serum and 50ng/ml ascorbate) for 17 days.

extract_protocol: RNA was isolated with Trizol

treatment_protocol: Cells with treated with 10ng/ml of human OSM (R&D), mouse OSM (R&D) or human LIF (Chemicon).

tag: background strain

value: osteocyte

tag: genotype

value: Osmr WT

value: mLIF

tag: treatment time

value: 6 hours

tag: replicate

tag: date cells were defrosted

tag: beadchip barcode

tag: beadchip section

value: D


title: WT hOSM 6 hours Replicate 3

value: hOSM

value: A


title: 188

description: PDAC

value: pancreatic tumor


title: WT hOSM 1 hour Replicate 3

value: 1 hour

value: B


title: WT mOSM 6 hours Replicate 3

value: mOSM


title: 40

description: PDAC

value: Early


title: 43

description: PDAC

value: LNM


title: 178

description: PDAC

value: Advanced


title: 119

description: Control

value: non-tumoral pancreatic tissue


title: WT mLIF 1 hour Replicate 3


title: 42

description: PDAC


title: 38

description: PDAC


title: 57

description: PDAC


title: WT control 1 hour Replicate 3

value: control

value: C


title: WT control 6 hours Replicate 3

value: osteocyte

value: E


title: WT mOSM 1 hour Replicate 3

value: Osmr WT


title: KO mLIF 6 hours Replicate 3

value: Osmr KO

value: mLIF

value: 6 hours


title: 37

description: PDAC


title: KO mOSM 6 hours Replicate 3


title: KO hOSM 6 hours Replicate 3

value: hOSM

value: F


title: 206

description: PDAC

value: pancreatic tumor


title: KO control 6 hours Replicate 3

value: D


title: 172

description: PDAC


title: 35

description: PDAC


title: 169

description: PDAC


title: KO mLIF 1 hour Replicate 3

value: 1 hour


title: KO control 1 hour Replicate 3


title: 32

description: PDAC

value: Early


title: 36

description: PDAC


title: 293

description: Control


title: WT hOSM 6 hours Replicate 2


title: 31

description: PDAC

value: LNM


title: 111 [10985]

description: PDAC

value: Advanced


title: WT mLIF 6 hours Replicate 2


title: 30

description: PDAC


title: WT control 6 hours Replicate 2


title: WT mLIF 1 hour Replicate 2

value: B


title: 29

description: PDAC


title: KO mOSM 1 hour Replicate 3

value: mOSM

value: A


title: WT mOSM 6 hours Replicate 2

value: osteocyte


title: 156

description: PDAC


title: 162

description: PDAC


title: WT control 1 hour Replicate 2

value: control


title: 155

description: PDAC


title: KO mOSM 6 hours Replicate 2

value: E


title: 25

description: PDAC


title: 154

description: PDAC


title: KO mLIF 1 hour Replicate 2

value: Osmr KO


title: WT mOSM 1 hour Replicate 2

value: Osmr WT


title: KO control 6 hours Replicate 2

value: 6 hours


title: 27

description: PDAC


title: KO hOSM 1 hour Replicate 3

value: hOSM


title: KO mLIF 6 hours Replicate 2

value: mLIF


title: WT mLIF 6 hours Replicate 1


title: 151

description: PDAC

value: pancreatic tumor


title: KO control 1 hour Replicate 2

value: F


title: 24

description: PDAC


title: 117

description: Control

value: non-tumoral pancreatic tissue


title: KO hOSM 6 hours Replicate 2


title: 19

description: PDAC


title: WT hOSM 1 hour Replicate 2

value: 1 hour


title: KO hOSM 1 hour Replicate 2


title: KO mOSM 1 hour Replicate 2

value: C


title: WT hOSM 6 hours Replicate 1


title: 33

description: PDAC

value: LNM


title: WT mOSM 6 hours Replicate 1

value: D


title: 17

description: PDAC

value: Early


title: 23

description: PDAC

value: Advanced


title: WT control 6 hours Replicate 1

value: osteocyte


title: 13

description: PDAC


title: 16

description: PDAC


title: 14

description: PDAC


title: 148

description: PDAC


title: 204

description: Control