title: BMSCs osteogenic differention from 188 KO mice, biological rep1

city: Changsha

first: Xianghang

last: Luo

state: Hunan

address: 139# Middle Renmin Road, Changsha, Hunan 410011, PR China

institute: Institute of Endocrinology & Metabolism, The Second Xiangya Hospital of Central South University, Changsha, Hunan, PR China.

description: Gene expression data from BMSCs osteogenic differention from 188KO mice

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Mouse Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing:
RMA (Robust Multi-array Average) was used to perform the data  normalization.  PCA (Principal component analysis) in Partek Genomics Suite  was used to performed the cluster analysis of different samples. ANOVA  (Analysis of variance) was used to identify the differential expression  genes
affymetrix-algorithm-name = rma-gene-default
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.2.0.20

source_name: BMSCs from 188KO mice undergoing osteogenic differention

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

growth_protocol: BMSCs from WT and 188KO mice were cultured in 6-well plates at 2.5 × 10^6 cells/well with osteogenic induction medium (α-MEM containing 10% fetal calf serum (FCS), 100nM dexamethasone, 10Mm beta-glycerophosphate, and 0.05mM L-ascorbic acid-2-phosphate)

extract_protocol: Extraction of total RNA was performed using QIAGEN RNA extraction mini kit

treatment_protocol: Culture medium was changed every second day.

tag: strain background

value: 6months old

value: 188 knockout

value: Bone marrow

value: Bone marrow stromal cells (BMSCs)


title: uninfected_4_rep

status: Public on Dec 02 2014

type: RNA

city: Singapore

first: jinmiao

last: chen

address: 8A Biomedical Grove, #04-06 Immunos

country: Singapore

institute: Singapore Immunology Network

hyb_protocol: 750ng of labelled cRNAs were hybridized to the Illumina mouse arrays for 16 hours at 58°C and the arrays were washed and stained according to the Illumina Wash Protocol

scan_protocol: The mouse chips were scanned using BeadArray Scanner 500GX and the images were analyzed using GenomeStudio Gene Expression v 1.9.0

data_processing: The data were normalised using quantile normalisation with R package lumi.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: uninfected

label_protocol: Biotinylated cRNA was prepared according to the Epicentre TargetAmp Nano-g Biotin-aRNA Labelling kit for Illumina system.

extract_protocol: RNA extraction was performed according to the miRVana miRNA isolation kit. Total RNA integrity was assessed by Agilent Bioanalyzer.

treatment_protocol: Mycobacterium tuberculosis infected mouse were treated with 500 mg/Kg of metformin starting day 7 post-infection for 30 days.

tag: infection

tag: strain

tag: tissue

value: lung


title: day 30, infected + metformin treated_1

source_name: day 30, infected + metformin treated

value: Mycobacterium tuberculosis


title: BMSCs osteogenic differention from 188 KO mice, biological rep3

country: China

tag: age

tag: genotype

tag: cell type


title: BMSCs osteogenic differention from 188 KO mice, biological rep2


title: day 30, infected_3

source_name: day 30, infected


title: day 30, infected_2


title: BMSCs adipogenic differention from WT mice, biological rep3

description: Gene expression data from BMSCs adipogenic differention from WT mice

source_name: BMSCs from WT mice undergoing adipogenic differention

growth_protocol: BMSCs from WT and 188KO mice were cultured in 6-well plates at 2.5 × 10^6 cells/well with adipogenesis induction medium (α-MEM containing 10% fetal calf serum (FCS), 0.5 mM 3-isobutyl-1-methylxanthine, 5 μg/ml insulin and 1 μM dexamethasone)

value: wild type


title: BMSCs osteogenic differention from WT mice, biological rep1

description: Gene expression data from BMSCs osteogenic differention from WT mice

source_name: BMSCs from WT mice undergoing osteogenic differention


title: uninfected_2


title: BMSCs adipogenic differention from 188 KO mice, biological rep3

description: Gene expression data from BMSCs adipogenic differention from 188KO mice

source_name: BMSCs from 188KO mice undergoing adipogenic differention


title: BMSCs adipogenic differention from WT mice, biological rep2


title: BMSCs adipogenic differention from 188 KO mice, biological rep2


title: BMSCs adipogenic differention from 188 KO mice, biological rep1


title: BMSCs adipogenic differention from WT mice, biological rep1


title: BMSCs osteogenic differention from WT mice, biological rep3


title: day 30, infected_2_rep


title: day 30, infected + metformin treated_2


title: BMSCs osteogenic differention from WT mice, biological rep2


title: Muscone 120512 MP

city: Lexington

first: Tim

last: McClintock

state: KY

address: 780 Rose St.

department: Physiology

country: USA

institute: University of Kentucky

description:
mRNA abundance data from FACS sample
MP_120512

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Mouse GeneChip 1.0 ST arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using an Affymetrix GCS3000 7G Scanner

data_processing: The data were analyzed with Affymetrix Gene Expression Console sofware using default analysis settings and global scaling as normalization method.

source_name: GFP positive_Muscone

growth_protocol: S100a5-tauGFP mice were housed in standard laboratory conditions

extract_protocol: Dissociated olfactory mucosal cells were separated by FACS; total RNA was isolated using the Qiagen RNeasy Micro kit

treatment_protocol: For odor stimulation, mice were individually housed in a custom olfactometer for 26 hrs in clean air, then 14 hrs of intermittent volatile odorant exposure, 10 sec of exposure every  5 min.

tag: genotype/variation

value: S100a5-tauGFP mice

value: adult olfactory epithelium cells

tag: gfp status

value: GFP positive

tag: stimulated with

value: Muscone (ordorant)


title: Muscone 120512 CP

description:
mRNA abundance data from FACS sample
CP_120512

source_name: GFP positive_vehicle

value: vehicle (control)


title: Muscone 120512 CN

description:
mRNA abundance data from FACS sample
CN2_120512

source_name: GFP negative_vehicle

value: GFP negative


title: Subject 7 - 4h post-meal

city: Leiden

first: Bruno

last: Guigas

address: P.O.Box 9600, Postzone L40-Q

department: Parasitology

country: Netherlands

institute: Leiden University Medical Center

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol using Illumina’s Genomestudio v.2011.1

data_processing: The data were normalised using quantile normalisation with the lumi package version 2.4.0 in R

organism: Homo sapiens

source_name: Human skeletal muscle

label_protocol: Biotinylated cRNA were prepared using the Illumina TotalPrep-96 RNA Amplification kit

extract_protocol: Total RNA was isolated from skeletal muscle biopsies (~25-30 mg) using the phenol-chloroform extraction method (Tripure RNA Isolation reagent, Roche, Germany), treated with the TurboDNAse kit according to manufacturer protocol (TurboDNAse, Life Technologies, The Netherlands) and quantified by NanoDrop (ND1000, Thermo Scientific, The Netherlands). The quality and integrity of RNA was tested using 2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany) and all the samples had a RIN score >8.

value: Skeletal muscle (musculus vastus lateralis)

tag: gender

value: Male

tag: post-meal time

tag: individual

value: Subject 7


title: Muscone 120512 MN

description:
mRNA abundance data from FACS sample
MN2_120512

source_name: GFP negative_Muscone


title: Muscone 100413 MP

description:
mRNA abundance data from FACS sample
MP815_100413


title: Muscone 100413 CP

description:
mRNA abundance data from FACS sample
CP815_100413


title: Diabetes Myotubes 6

city: Newcastle

first: Mark

last: Walker

address: Framlington Place

department: Institute of Cellular Medicine

country: United Kingdom

institute: Newcastle University

description: Gene expression myotubes

hyb_protocol: Hybridisation took place at 45oC for 16h in a GeneChip Hybridization Oven 640 (Affymetrix). Gene chips were washed and stained in a GeneChip Fluidics station 400 (Affymetrix).

scan_protocol: Arrays were scanned in a GeneChip Scanner 3000.

data_processing: Data were analysed using GeneSpring GX (Affymetrix) and normalised by RMA.

label: Biotin

source_name: Diabetes myotubes

label_protocol: Biotinylated cRNA was produced as per the manufacturer's instructions.

growth_protocol: Myoblasts were grown in Ham's F10 media containing 20% FBS, 2% chick embryo extract. Myotubes were differentiated in MEM containing 2% FBS.

extract_protocol: RNA was extracted using Trizol as per the manufacturer's instructions.

treatment_protocol: No treatment

tag: disease states

value: Diabetic

value: myotubes


title: Diabetes Myotubes 5

description: Gene expression myotubes


title: Diabetes Myotubes 4

description: Gene expression myotubes


title: Muscone 100413 MN

description:
mRNA abundance data from FACS sample
MN2815_100413


title: Diabetes Myotubes 1

description: Gene expression myotubes


title: Muscone 100113 MP

description:
mRNA abundance data from FACS sample
MP88_100113


title: Muscone 100413 CN

description:
mRNA abundance data from FACS sample
CN1815_100413


title: Muscone 100113 MN

description:
mRNA abundance data from FACS sample
MN288_100113


title: Muscone 100113 CN

description:
mRNA abundance data from FACS sample
CN288_100113


title: Diabetes Myotubes 2

description: Gene expression myotubes


title: Diabetes Myotubes 3

description: Gene expression myotubes


title: Muscone 062513 MP

description:
mRNA abundance data from FACS sample
MP_062513


title: Muscone 100113 CP

description:
mRNA abundance data from FACS sample
CP88_100113


title: Eugenol 110912 EP

description:
mRNA abundance data from FACS sample
EP_110912

source_name: GFP positive_Eugenol

value: Eugenol (ordorant)


title: Control Myotubes 4

description: Gene expression myotubes

source_name: Control myotubes

value: Control


title: Muscone 062513 MN

description:
mRNA abundance data from FACS sample
MN2_062513


title: Eugenol 110912 EN

description:
mRNA abundance data from FACS sample
EN1_110912

source_name: GFP negative_Eugenol


title: Eugenol 110912 CP

description:
mRNA abundance data from FACS sample
CP_110912


title: Muscone 062513 CN

description:
mRNA abundance data from FACS sample
CN2_062513


title: Control Myotubes 5

description: Gene expression myotubes


title: Eugenol 090512 EN

description:
mRNA abundance data from FACS sample
EN_090512


title: Eugenol 040512 EP

description:
mRNA abundance data from FACS sample
Epos_040512


title: Eugenol 110912 CN

description:
mRNA abundance data from FACS sample
CN1_110912


title: Eugenol 090512 EP

description:
mRNA abundance data from FACS sample
EP_090512


title: Muscone 062513 CP

description:
mRNA abundance data from FACS sample
CP_062513


title: Eugenol 090512 CP

description:
mRNA abundance data from FACS sample
CP_090512


title: Control Myotubes 1

description: Gene expression myotubes


title: Eugenol 090512 CN

description:
mRNA abundance data from FACS sample
CN_090512


title: Diabetes Myoblasts 6

description: Gene expression myoblasts

source_name: Diabetes myoblasts

value: myoblasts


title: Control Myotubes 2

description: Gene expression myotubes


title: Eugenol 040512 CP

description:
mRNA abundance data from FACS sample
Apos_04051


title: Eugenol 040512 CN

description:
mRNA abundance data from FACS sample
Aneg2_040512


title: Eugenol 022113 CP

description:
mRNA abundance data from FACS sample
CP_02211


title: Eugenol 040512 EN

description:
mRNA abundance data from FACS sample
Eneg2_040512


title: Diabetes Myoblasts 4

description: Gene expression myoblasts


title: Eugenol 022113 EN

description:
mRNA abundance data from FACS sample
EN1_02211


title: Diabetes Myoblasts 5

description: Gene expression myoblasts


title: Eugenol 022113 EP

description:
mRNA abundance data from FACS sample
EP_022113


title: Diabetes Myoblasts 1

description: Gene expression myoblasts


title: Eugenol 022113 CN

description:
mRNA abundance data from FACS sample
CN1_022113


title: Diabetes Myoblasts2

description: Gene expression myoblasts


title: Diabetes Myoblasts 3

description: Gene expression myoblasts


title: Control Myoblasts 5

description: Gene expression myoblasts

source_name: Control myoblasts


title: Liver at 168h after sham operation, technical rep2

city: Xinxiang

first: Cunshuan

last: Xu

address: No. 46, Construction East Road

institute: Henan Normal University

description: Gene expression data from hepatocyte at termination phase after sham operation

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45℃ on Rat Genome 230 2.0 array. GeneChips were washed and stained in the Affymetrix GeneChip® Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 (Affymetrix Inc., Santa Clara, CA, USA).

data_processing:
The data were analyzed with Affymetrix GCOS 2.0 software using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
When P value is < 0.05, it means that the gene is present (P), when < 0.065, means marginal (M), and when > 0.065, means marked absent (A). On the other hand, the normalized signal values in PH to that in control were used to calculate the relative value, that is, ratio value of gene expression abundance. When ratio value is ≥ 3, it means that gene expression change was significantly up-regulated, when ≤ 0.33, means significantly down-regulated, and when 0.33-2.99, means biologically insignificant. To minimize the technical errors from microarray analysis, each sample was tested at least three times using Rat Genome 230 2.0 microarray, and the average value was considered as a reliable value (Wang and Xu, 2010).

organism: Rattus norvegicus

source_name: Liver at 168h after sham operation

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (GeneChip In Vitro Transcript Labeling Kit, ENZO Biochemical, New York, USA).

extract_protocol: Total RNA was extracted according to the manual of Trizol reagent (Invitrogen Corporation, Carlsbad, California, USA) and purified following the RNeasy mini protocol (Qiagen, Inc, Valencia, CA, USA).

treatment_protocol: After the operations were done, the rats at corresponding recovery time points were anaesthetized, and the intrahepatic blood was removed by hepatic portal vein infusion firstly, then the liver tissues from the middle part of the right lobe of the liver were collected in RNase-free tubes and stored at﹣80℃ until use.

tag: treatment

value: sham operation

tag: time

value: 168h after sham operation

value: Liver

value: Sprague-Dawley (SD) rat


title: Liver at 168h after sham operation, technical rep1


title: day 30, infected_1

value: Mycobacterium tuberculosis

value: lung


title: Control Myoblasts 3

description: Gene expression myoblasts


title: Control Myoblasts 4

description: Gene expression myoblasts


title: Liver at  120h after sham operation, technical rep2

source_name: Liver at 120h after sham operation

value: 120h after sham operation


title: Regenerating liver at 168h after PH,technical rep3

description: Gene expression data from hepatocyte at termination phase of liver regeneration after partial hepatectomy.

source_name: Regenerating liver at 168h after partial hepatectomy

value: partial hepatectomy

value: 168h after partial hepatectomy


title: Regenerating liver at  120h after PH,technical rep3

source_name: Regenerating liver at 120h after partial hepatectomy

value: 120h after partial hepatectomy


title: Regenerating liver at 72h after PH,technical rep3

source_name: Regenerating liver at 72h after partial hepatectomy

value: 72h after partial hepatectomy


title: Control Myoblasts 2

description: Gene expression myoblasts


title: Regenerating liver at 168h after PH,technical rep1


title: Regenerating liver at 168h after PH,technical rep2


title: Regenerating liver at 72h after PH,technical rep2


title: Liver at 72h after sham operation, technical rep3

source_name: Liver at 72h after sham operation

value: 72h after sham operation


title: Regenerating liver at  120h after PH,technical rep2


title: Liver at 120h after sham operation, technical rep1


title: Liver at 168h after sham operation, technical rep3


title: Liver at  120h after sham operation, technical rep3


title: Regenerating liver at  120h after PH,technical rep1


title: Control Myoblasts 1

description: Gene expression myoblasts


title: Regenerating liver at 36h after PH,technical rep3

description: Gene expression data from hepatocyte at proliferation phase of liver regeneration after partial hepatectomy.

source_name: Regenerating liver at 36h after partial hepatectomy

value: 36h after partial hepatectomy


title: Liver at 72h after sham operation, technical rep2


title: Liver at 72h after sham operation, technical rep1


title: Control Myotubes 6

description: Gene expression myotubes

value: myotubes


title: Regenerating liver at 72h after PH,technical rep1


title: Control Myoblasts 6

description: Gene expression myoblasts


title: OSCC 2

city: Turku

first: Kristiina

last: Heikinheimo

address: Lemminkäisenkatu 2

department: Department of Oral and Maxillofacial Surgery

country: Finland

institute: University of Turku

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Standard Affymetrix scanning protocol

data_processing: The data were preprocessed using GC-RMA normalization (with affy R/Bioconductor package)

source_name: control

label_protocol: Standard Affymetrix One-Cycle Target Labeling protocol

extract_protocol: Standard RNA extraction protocol using the RNeasy Total RNA kit

tag: tissue type

value: control


title: Liver at 24h after sham operation, technical rep3

description: Gene expression data from hepatocyte at priming phase after sham operation

source_name: Liver at 24h after sham operation

value: 24h after sham operation


title: Liver at 36h after sham operation, technical rep3

source_name: Liver at 36h after sham operation

value: 36h after sham operation


title: normal gingiva 2


title: Liver at 30h after sham operation, technical rep1

source_name: Liver at 30h after sham operation

value: sham operation

value: 30h after sham operation


title: gingiva sulcus epithelium


title: Liver at 30h after sham operation, technical rep3

value: Liver


title: KCOT 11

source_name: sporadic keratocystic odontogenic tumour


title: Regenerating liver at 24h after PH,technical rep3

source_name: Regenerating liver at 24h after partial hepatectomy

value: 24h after partial hepatectomy

value: Sprague-Dawley (SD) rat


title: Regenerating liver at 36h after PH,technical rep1


title: Regenerating liver at 24h after PH,technical rep1


title: Liver at 36h after sham operation, technical rep1


title: Regenerating liver at 30h after PH,technical rep3

source_name: Regenerating liver at 30h after partial hepatectomy

value: 30h after partial hepatectomy


title: floor of mouth


title: amel fibro-odontoma


title: Regenerating liver at 30h after PH,technical rep1


title: Liver at 24h after sham operation, technical rep1


title: KCOT 12

value: sporadic keratocystic odontogenic tumour


title: Regenerating liver at 30h after PH,technical rep2

value: partial hepatectomy


title: Regenerating liver at 24h after PH,technical rep2


title: Regenerating liver at 36h after PH,technical rep2


title: Regenerating liver at 12h after PH,technical rep2

source_name: Regenerating liver at 12h after partial hepatectomy

value: 12h after partial hepatectomy


title: KCOT 9


title: Regenerating liver at 12h after PH,technical rep3


title: OSCC 1


title: Liver at 36h after sham operation, technical rep2


title: normal gingiva 1


title: Liver at 24h after sham operation, technical rep2


title: KCOT 10


title: Regenerating liver at 12h after PH,technical rep1


title: Liver at 30h after sham operation, technical rep2


title: KCOT 8


title: KCOT 7


title: Liver at 12h after sham operation, technical rep2

source_name: Liver at 12h after sham operation

value: 12h after sham operation


title: Regenerating liver at 6h after PH,technical rep3

source_name: Regenerating liver at 6h after partial hepatectomy

value: 6h after partial hepatectomy


title: Liver at 12h after sham operation, technical rep3


title: Liver at 12h after sham operation, technical rep1


title: Regenerating liver at 6h after PH,technical rep2


title: KCOT 5


title: KCOT 4


title: Liver at 6h after sham operation, technical rep1

source_name: Liver at 6h after sham operation

value: 6h after sham operation


title: Regenerating liver at 2h after PH,technical rep3

description: Gene expression data from hepatocyte at priming phase of liver regeneration after partial hepatectomy.

source_name: Regenerating liver at 2h after partial hepatectomy

value: 2h after partial hepatectomy


title: Liver at 6h after sham operation, technical rep2


title: Liver at 6h after sham operation, technical rep3


title: Liver at 2h after sham operation, technical rep3 (2)

source_name: Liver at 2h after sham operation

value: 2h after sham operation


title: KCOT 3


title: Regenerating liver at 6h after PH,technical rep1


title: KCOT 6


title: KCOT (NBCCS)

value: control


title: Liver at 2h after sham operation, technical rep2 (2)


title: KCOT 2


title: Liver at 2h after sham operation, technical rep1 (2)


title: Regenerating liver at 2h after PH,technical rep2


title: Regenerating liver at 2h after PH,technical rep1


title: KCOT 1


title: 0003670062|KE Contact Eczema

city: Bonn

first: Joerg

last: Wenzel

address: Sigmund Freud Str 25

department: Dermatology

country: Germany

institute: University of Bonn

hyb_protocol: The fluorescently labeled samples were hybridized overnight to topic-defined PIQOR (TM) Skin 2.0 Microarrays Human Antisense using the GeneTAC hybridisation station (Genomics Solutions).

scan_protocol: Image capture and signal quantification of hybridized PIQOR ™Skin 2.0 microarrays were done with the ScanArrayLite4000 Microarray Scanner (Packard-Biosciences) and ImaGene software Version 5.0 (BioDiscovery, Los Angeles, CA, USA).

data_processing: Signals were analysed with the PIQOR Analyzer software (Miltenyi Biotec, Bergisch Gladbach, Germany). The PIQOR Analyzer allows automated data processing of the raw data text files (_1b = Cy3 channel and _2b = Cy5 channel) derived from the ImaGene software. This includes background subtraction to obtain the net signal intensity, data normalization, and calculation of the Cy5/Cy3 ratios. Subsequently, the mean of the ratios of the four corresponding spots representing the same cDNA was computed. The ratios were normalized using the LOWESS method. As an additional quality filtering step, only genes were taken into account for the calculation of the Cy5/Cy3 ratio that have at least in one channel a signal intensity that was at least 2-fold higher than the mean background

source_name: Common skin reference

label_protocol: Samples were labeled with FluoroLinkk Cy3/Cy5-dCTP (100 µg total RNA per sample, Amersham Pharmacia Biotech, Freiburg, Germany).

extract_protocol: Isolation of total RNA from skin excision biopsies was performed using TriReagent (Sigma, St Louis, MO) and the NucleoSpin 96 RNA Kit (Macherey & Nagel, Dueren, Germany). RNA was quantified by photometrical measurement, and the integrity was checked using a 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

value: whole skin biopsy

tag: sample type

value: skin biopsies from pool of 160 patients with skin disorders and healthy donors

source_name: skin disease

value: Contact Eczema


title: 0003660055|KE Contact Eczema


title: 0003690008|KE Contact Eczema


title: 0003830047|KE Contact Eczema


title: 0003660054|KE Contact Eczema


title: 0003670059|KE Contact Eczema


title: Regenerating liver at 0h after PH, technical rep3 (2)

description: Gene expression data from normal hepatocyte.

source_name: Regenerating liver at 0h after partial hepatectomy

value: 0h after partial hepatectomy


title: amel 14

source_name: conventional intraosseous ameloblastom

value: conventional intraosseous ameloblastom


title: amel 15


title: 0003670060|KE Contact Eczema


title: 0003670061|KE Contact Eczema


title: 0003660053|KE Contact Eczema


title: 0003690173|KE Contact Eczema


title: amel 13


title: 0003670008|KE Contact Eczema


title: 0003830154|PS Psoriasis Vulgaris

value: Psoriasis Vulgaris


title: 0004040072|PS Psoriasis Vulgaris


title: 0003830163|PS Psoriasis Vulgaris


title: Regenerating liver at 0h after PH, technical rep2 (2)

value: Liver

value: Sprague-Dawley (SD) rat


title: 0003830146|PS Psoriasis Vulgaris


title: 0003830161|PS Psoriasis Vulgaris


title: Regenerating liver at 0h after PH, technical rep1 (2)


title: amel 12


title: 0003830069|PS Psoriasis Vulgaris


title: 0003830067|PS Psoriasis Vulgaris


title: 0003830065|PS Psoriasis Vulgaris


title: 0003830090|PS Psoriasis Vulgaris


title: 0003830062|PS Psoriasis Vulgaris


title: amel 8


title: 0003830003|PS Psoriasis Vulgaris


title: 0003830060|PS Psoriasis Vulgaris


title: 0003830088|PS Psoriasis Vulgaris


title: 0003830089|PS Psoriasis Vulgaris


title: 0003830072|PS Psoriasis Vulgaris


title: 0003830016|PS Psoriasis Vulgaris


title: 0003830058|PS Psoriasis Vulgaris


title: amel 10


title: amel 3


title: amel 9


title: amel 11


title: amel 7


title: amel 4


title: 0003690145|PS Psoriasis Vulgaris


title: amel 5


title: amel 6


title: amel 1


title: MPM tumor_Short_FFPE72

city: Zürich

first: Michaela

middle: B

last: Kirschner

address: Rämisstr. 100

department: Division of Thoracic Surgery

country: Switzerland

institute: University Hospital Zürich

description:
MicroRNA expression data from MPM tumors
FFPE72_MBK

hyb_protocol: Labeled RNA was hybridized for 22h at 55°C on Agilent Unrestricted AMADID miRNA 8x15k-AMADID:021827 miRNA arrays. hybridized arrays were washed and stored in nitrogen gas for scanning within 48h.

scan_protocol: MicroRNA arrays were scanned using the Agilent C Microarray Scanner (at 2µm resolution)

data_processing: Data were feature extracted using the Agilent Feature Extraction Software FE10.5. Raw txt data files were imported into GeneSpring v12. Probes detected in at least 100% in 1 out of 2 conditions (long or short survival) were included. Data processing involved thresholding to 1, log2 transformation and normalization to the 90th percentile without baseline transformation.

source_name: MPM tumor after EPP

label_protocol: Cy3 labeled RNA was prepared from 100ng total RNA using Agilent miRNA System with miRNA Complete Labeling and Hyb Kit according to the manufacturer's protocol

extract_protocol: Prior to RNA isolation, tumor sections were laser-capture microdissected using the PALM System (Zeiss) to enrich for tumor cell content. Samples were deparaffinised in Xylene followed by extrcation of total RNA using the RNeasy  FFPE Mini Kit according to the manufacturer's instructions.

tag: disease state

value: malignant pleural mesothelioma

tag: survival

value: Short


title: 0003690146|PS Psoriasis Vulgaris

tag: tissue


title: MPM tumor_Long_FFPE75

description:
MicroRNA expression data from MPM tumors
FFPE75_MBK

value: Long


title: MPM tumor_Long_FFPE69

description:
MicroRNA expression data from MPM tumors
FFPE69_MBK


title: MPM tumor_Short_FFPE54

description:
MicroRNA expression data from MPM tumors
FFPE54_MBK


title: MPM tumor_Short_FFPE52

description:
MicroRNA expression data from MPM tumors
FFPE52_MBK


title: MPM tumor_Short_FFPE46

description:
MicroRNA expression data from MPM tumors
FFPE46_MBK


title: MPM tumor_Long_FFPE50

description:
MicroRNA expression data from MPM tumors
FFPE50_MBK


title: 0003690132|PS Psoriasis Vulgaris


title: 0003690131|PS Psoriasis Vulgaris


title: 0003840012|PS Psoriasis Vulgaris


title: 0003690154|PS Psoriasis Vulgaris


title: 0003690150|PS Psoriasis Vulgaris


title: 0003830124|LI Lichen Planus

value: Lichen Planus


title: 0003690018|PS Psoriasis Vulgaris


title: 0003690217|PS Psoriasis Vulgaris


title: 0003830023|PS Psoriasis Vulgaris


title: 0003690155|PS Psoriasis Vulgaris


title: 0003830014|PS Psoriasis Vulgaris


title: 0003690195|LI Lichen Planus


title: 0003830026|PS Psoriasis Vulgaris


title: 0003690048|LI Lichen Planus


title: MPM tumor_Short_FFPE44

description:
MicroRNA expression data from MPM tumors
FFPE44_MBK


title: 0003830087|LI Lichen Planus


title: MPM tumor_Long_FFPE39

description:
MicroRNA expression data from MPM tumors
FFPE39_MBK


title: 0004040006|LI Lichen Planus


title: 0003690047|LI Lichen Planus


title: 0003690040|LI Lichen Planus


title: 0003690042|LI Lichen Planus


title: 0003690041|LI Lichen Planus


title: MPM tumor_Long_FFPE35

description:
MicroRNA expression data from MPM tumors
FFPE35_MBK


title: MPM tumor_Long_FFPE45

description:
MicroRNA expression data from MPM tumors
FFPE45_MBK


title: MPM tumor_Short_FFPE34

description:
MicroRNA expression data from MPM tumors
FFPE34_MBK


title: MPM tumor_Short_FFPE19

description:
MicroRNA expression data from MPM tumors
FFPE19_MBK


title: MPM tumor_Short_FFPE36

description:
MicroRNA expression data from MPM tumors
FFPE36_MBK


title: MPM tumor_Long_FFPE7

description:
MicroRNA expression data from MPM tumors
FFPE7_MBK


title: 0003690156|LI Lichen Planus


title: 0003690046|LI Lichen Planus


title: 0004040105|LI Lichen Planus


title: 0003660047|LI Lichen Planus


title: 0003690161|LI Lichen Planus


title: 0004040071|LI Lichen Planus


title: MPM tumor_Long_FFPE2

description:
MicroRNA expression data from MPM tumors
FFPE2_MBK


title: 0003690044|LI Lichen Planus


title: 0003670075|LI Lichen Planus


title: 0003690163|LI Lichen Planus


title: 0003690045|LI Lichen Planus


title: 0003690043|LI Lichen Planus


title: 0003690166|LI Lichen Planus


title: 0004040150|LI Lichen Planus


title: 0003670073|LI Lichen Planus


title: 0003670045|LI Lichen Planus


title: 0003670072|LI Lichen Planus


title: 0003670046|LI Lichen Planus


title: 0003670044|LI Lichen Planus


title: 0003670048|LI Lichen Planus


title: Male_liver_furan_8 mg-kg-day_90 days_replicate 3

city: Jefferson

first: Volodymyr

last: Tryndyak

address: 3900 NCTR Rd

department: Division of Biochemical Toxicology

institute: US-FDA National Center for Toxicological Research

description: Gene expression in the livers of male Fisher 344 rats treated with 8 mg/kg/day furan for 90 days

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Rat GE Oligo Microarrays (G4853A-028279) 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 (G2505B) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. The raw data were normalized using ArrayTrack software (USFDA National Center for Toxicological Research, Jefferson, AR).

source_name: Male, liver, furan, 8 mg/kg/day, 90 days, replicate 3

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

extract_protocol: Total RNA was extracted from liver tissue using RNeasy Mini kits (Qiagen, Valencia, CA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-2000C spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Male Fisher 344 (F344) rats were treated by gavage 5 days per week with 8 mg furan/kg body weight (bw)/day for 90 days. Experimental and control rats were euthanized by exsanguination following deep isoflurane anesthesia 24 hours after the last treatment. The liver was snap-frozen immediately in liquid nitrogen and stored at −80 °C for subsequent analyses.

tag: strain

value: Fisher 344

value: liver

value: Male

tag: age

value: 18 weeks


title: 0003660049|LI Lichen Planus


title: Male_liver_furan_8 mg-kg-day_90 days_replicate 2

source_name: Male, liver, furan, 8 mg/kg/day, 90 days, replicate 2


title: 0004040151|AD Atopic Dermatitis

value: Atopic Dermatitis


title: 0003830094|AD Atopic Dermatitis

value: whole skin biopsy


title: 0003690205|AD Atopic Dermatitis

value: skin biopsies from pool of 160 patients with skin disorders and healthy donors


title: Male_liver_furan_8 mg-kg-day_90 days_replicate 4

source_name: Male, liver, furan, 8 mg/kg/day, 90 days, replicate 4


title: 0003670039|AD Atopic Dermatitis


title: Male_liver_furan_8 mg-kg-day_90 days_replicate 1

source_name: Male, liver, furan, 8 mg/kg/day, 90 days, replicate 1


title: 0003670038|AD Atopic Dermatitis


title: Blood_schizophrenia 15

city: Wuxi

first: Fuquan

last: Zhang

address: 156 Qianrong Rd

institute: Wuxi mental health center

description: early onset schizophrenia < 18 years

hyb_protocol: 1. Prepare the hybridization mix in a PCR tube according to the table below:  Components Amount(ul)  Labeled sample 12.5  2×Hybridization buffer 90  Nuclease-free Buffer 77.5  Total 180    2. Incubate at 95°C for 2 min. During the incubation the target preparation should be protected from light.  3. Leave on ice for at least 2 min. and up to 15min. Briefly spin the reaction after ice incubation.  4. Take cover slide out of the package.         5. Carefully laid the miRCURYTM Array on top of the assembly of cover slide and spacer, where the printed side of array should be facing toward the cover slide, to form a hybridization assembly. The printed side of array is on the side of the label.         6. Insert the hybridization assembly into a (3.1 x 9cm) heat-shrank hybridization (hyb.) bag. Sample loading side of the hybridization assembly should face the opening side of film bag. Lower the assembly to the end of the bag (Assembly viewed from the other side).         7. Clip the bag with a clipper “securely” from the opening end. Immerse the assembly to the rim of the slide in 95℃ hot water swiftly (approximately 2~5 sec). Do not dip the assembly too far into the water to avoid water leaking into the assembly. The hyb. bag will shrink and tightly wrap around the assembly.     8. Remove the assembly from water and wipe off the water from the assembly. Trim off the excess film from the top of the assembly. Keep the assembly in a 50℃ oven for at least 10 minutes.         9. Load the180ul target hybridization mix into the assembly through the sample loading opening. Fill up the hybridization space with 1X Hybridization buffer till the liquid level reaches to approximately 5 mm (0.5cm) away from the top rim.     10. Cut the second Hyb. Bag to approximately one-half of its original length.         11. Keep the assembly vertical and slip on the shortened hyb. bag from step 11 all the way until the assembly reaches the end of the hyb. bag.         12. Use a pair of forceps to hold onto the top of the assembly. Immerse the entire assembly into 95℃ hot water with the assembly in upright position.             13. Place the hybridization assembly into a 56℃ oven and set it on a rotator. Remember to rotate the assembly at 2 rotations per minute (RPM) for overnight.     14. After hybridization, disassembled the hybridization assembly, and wash the slides at 56℃ for 2min. using Wash buffer A.  15. Wash briefly at room temperature in Wash buffer B.  16. Wash for 2min. at room temperature in Wash buffer B.  17. Wash for 2min. at room temperature in Wash buffer C.  18. Wash briefly in water.  19. Dry the slides by centrifugation for 5 min. at 200* g(1000rpm). Scan slides immediately after drying.

scan_protocol: Scanning is performed with the Axon GenePix 4000B microarray scanner. GenePix pro V6.0 is used to read the raw intensity of the image.

data_processing: a) The intensity of green signal is calculated after background subtraction and four Replicated spots of each probe on the same slide have been averaged.  b) We use Median Normalization Method to obtain “Normalized Data”, Normalized Data= (Foreground-Background)¬/¬median, the median is 50 percent quantile of microRNA intensity which is larger than 50 in all samples after background correction.  c) After normalization, the statistical significance of differentially expressed miRNA was analyzed by T-test.

source_name: schizophrenia patient

label_protocol: miRCURYTM Array Power Labeling kit (Cat #208032-A, Exiqon)

growth_protocol: Lyse cells directly in a culture dish by adding 1 ml of TRIzol Reagent to a 3.5 cm diameter dish, and passing the cell lysate several times through a pipette. The amount of TRIzol Reagent added is based on the area of the culture dish (1 ml per 10 cm2) and not on the number of cells present.Pellet cells by centrifugation. Lyse cells in TRIzol Reagent by repetitive pipetting. Use 1 ml of the reagent per 5-10 × 106 of animal, plant or yeast cells, or per 1 × 107 bacterial cells. Washing cells before addition of TRIzol Reagent should be avoided as this increases the possibility of mRNA degradation. Disruption of some yeast and bacterial cells may require the use of a homogenizer.

extract_protocol: Total RNA was harvested using TRIzol (Invitrogen) and miRNeasy mini kit (QIAGEN) according to manufacturer’s instructions.

treatment_protocol: Buffer RPE is supplied as a concentrate. Before using for the first time, add 4 volumes of ethanol (96–100%) as indicated on the bottle to obtain a working solution.

value: peripheral blood mononuclear cells


title: Blood_schizophrenia 14

description: early onset schizophrenia < 18 years


title: 0003690055|AD Atopic Dermatitis


title: 0003670037|AD Atopic Dermatitis


title: 0003840095|AD Atopic Dermatitis


title: Blood_schizophrenia 13

description: early onset schizophrenia < 18 years


title: 0003670035|AD Atopic Dermatitis


title: Blood_schizophrenia 12

description: early onset schizophrenia < 18 years


title: Blood_schizophrenia 11

description: early onset schizophrenia < 18 years


title: 0003830093|AD Atopic Dermatitis


title: 0003660048|LI Lichen Planus


title: Male_liver_control_replicate 3

description: Gene expression in the livers of control male Fisher 344 rats

source_name: Male, liver, control, replicate 3


title: Male_liver_control_replicate 4

source_name: Male, liver, control, replicate 4


title: 0003670036|AD Atopic Dermatitis


title: 0003830113|AD Atopic Dermatitis


title: 0003660002|AD Atopic Dermatitis


title: Blood_schizophrenia 10

description: early onset schizophrenia < 18 years


title: Blood_schizophrenia 9

description: early onset schizophrenia < 18 years


title: Male_liver_control_replicate 1

source_name: Male, liver, control, replicate 1


title: 0003690165|AD Atopic Dermatitis


title: 0003660043|AD Atopic Dermatitis


title: 0003690052|AD Atopic Dermatitis


title: 0003670032|AD Atopic Dermatitis


title: Blood_schizophrenia 8

description: early onset schizophrenia < 18 years


title: 0003660001|AD Atopic Dermatitis


title: 0003660006|AD Atopic Dermatitis


title: Blood_schizophrenia 5

description: early onset schizophrenia < 18 years


title: 0003830099|AD Atopic Dermatitis


title: Male_liver_control_replicate 2

source_name: Male, liver, control, replicate 2


title: Blood_schizophrenia 6

description: early onset schizophrenia < 18 years


title: 0003690054|AD Atopic Dermatitis


title: 0003670033|AD Atopic Dermatitis


title: 0003670001|AD Atopic Dermatitis


title: 0003660095|AD Atopic Dermatitis


title: 0003690168|AD Atopic Dermatitis


title: 0003840094|AD Atopic Dermatitis


title: 0003660005|AD Atopic Dermatitis


title: Blood_schizophrenia 2

description: early onset schizophrenia < 18 years


title: Blood_schizophrenia 3

description: early onset schizophrenia < 18 years


title: Blood_schizophrenia 7

description: early onset schizophrenia < 18 years


title: 0004040021|KO Control

value: Control


title: Blood_schizophrenia 1

description: early onset schizophrenia < 18 years


title: 0003690053|AD Atopic Dermatitis


title: 0004040027|KO Control


title: 0003670031|AD Atopic Dermatitis


title: 0004040031|KO Control


title: Blood_control 15

description: Healthy controls < 18 years

source_name: healthy control


title: 0004040138|KO Control


title: 0004040060|KO Control


title: 0004040008|KO Control


title: 0003670014|KO Control


title: 0003660063|KO Control


title: 0004040133|KO Control


title: 0003660056|KO Control


title: 0003840041|KO Control


title: 0003670047|KO Control


title: 0003660007|KO Control


title: 0003840042|KO Control


title: Blood_control 9

description: Healthy controls < 18 years


title: Blood_control 10

description: Healthy controls < 18 years


title: Blood_control 12

description: Healthy controls < 18 years


title: Blood_control 14

description: Healthy controls < 18 years


title: Blood_control 8

description: Healthy controls < 18 years


title: Blood_control 7

description: Healthy controls < 18 years


title: 0003840040|KO Control


title: 0004040131|KO Control


title: 0004040064|KO Control


title: 0004040065|KO Control


title: Blood_control 6

description: Healthy controls < 18 years


title: 0003660061|KO Control


title: Blood_control 13

description: Healthy controls < 18 years


title: Blood_control 11

description: Healthy controls < 18 years


title: amel 2

value: conventional intraosseous ameloblastom


title: 0003670043|KO Control


title: 0003670054|KO Control


title: 0003670042|KO Control


title: 0003670050|KO Control


title: 0004040155|KO Control


title: 0003830159|KO Control


title: 0004040070|KO Control


title: Blood_control 2

description: Healthy controls < 18 years


title: Blood_control 4

description: Healthy controls < 18 years


title: Blood_control 3

description: Healthy controls < 18 years


title: Blood_control 1

description: Healthy controls < 18 years


title: 0003670053|KO Control


title: Blood_control 5

description: Healthy controls < 18 years


title: 0003670013|KO Control


title: 0004040095|KO Control


title: 0003690029|KE Contact Eczema

value: Contact Eczema


title: 0003690118|KE Contact Eczema


title: 0003690206|KE Contact Eczema


title: FetalLiverCD34_differentiated_rep11

type: genomic

city: Montreal

first: Guillaume

last: Lettre

state: Québec

address: 5000 rue Bélanger

country: Canada

institute: Montreal Heart Institute

hyb_protocol: Illumina HumanMethylation450 BeadChip Protocol

scan_protocol: BeadChips were imaged using iScan using recommended Illumina scanner settings

data_processing: GenomeStudio 2011.1 software and R version 3.0.0. Quality control was performed using the R package minfi V1.6.0. Beta-values were normalized using ARRm V1.1.0 . Probes targeting regions containing SNP were removed from the analysis. A total of 402,819 CpGs was left for analysis.

label: Cy3, Cy5

molecule: genomic DNA

source_name: Erythroblast differentiated from human fetal liver CD34+ hematopoietic stem cells

growth_protocol: Fetal and adult erythroblasts were generated from CD34+ hematopoietic stem cells using a two-phase serum-free culture as described previously (Sankaran VG et al. Science 2008).

extract_protocol: Genomic DNA was extracted using the Gentra Puregene Cell Kit (Qiagen), followed by an additional alcohol precipitation step to obtain highly purified DNA. DNA bisulfite conversion was performed using the EZ DNA Methylation Gold Kit (Zymo).

tag: developmental stage

value: fetal

value: Fetal Liver


title: 0003690162|KE Contact Eczema


title: 0003690089|KE Contact Eczema


title: Blood_schizophrenia 4

description: early onset schizophrenia < 18 years


title: FetalLiverCD34_differentiated_rep10

label_protocol: Illumina HumanMethylation450 BeadChip Protocol


title: FetalLiverCD34_differentiated_rep6


title: FetalLiverCD34_differentiated_rep3


title: 0003660003|AD Atopic Dermatitis


title: BM PMN_KO_LPS 3h

city: shanghai

last: Shen

address: 145 Shan Dong Middle Road

institute: Shanghai Institute of Rheumatology

description: Gene expression data from mouse bone marrow neutrophils stimulation with LPS

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

source_name: miR-125a knockout mice,bone marrow neutrophils,LPS stimulation,3 hours

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3’IVT Express Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: Neutrophils were isolated from mouse bone marrow by using the Neutrophil Isolation Kit (Miltenyi Biotec) and cultured in 10%FBS RPMI 1640 medium.

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA 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: stimulation without or  with LPS for 3 hours

value: 8 weeks

tag: genotype

tag: cell type

value: bone marrow neutrophils


title: FetalLiverCD34_differentiated_rep9


title: FetalLiverCD34_differentiated_rep5


title: 0003660014|KE Contact Eczema

source_name: Common skin reference


title: 0003830079|KE Contact Eczema

source_name: skin disease


title: FetalLiverCD34_differentiated_rep4


title: 0004040104|KE Contact Eczema


title: BM PMN_WT_LPS 3h

source_name: wild type mice,bone marrow neutrophils,LPS stimulation,3 hours


title: 0003670010|KE Contact Eczema


title: FetalLiverCD34_differentiated_rep8


title: 0003830158|KO Control


title: FetalLiverCD34_differentiated_rep1


title: FetalLiverCD34_differentiated_rep7


title: 0003670009|KE Contact Eczema


title: BoneMarrowCD34_differentiated_rep11

source_name: Erythroblast differentiated from human bone marrow CD34+ hematopoietic stem cells

value: adult

value: Bone marrow


title: KN6+Lig+ [US22502680_251486820448_S01_GE2-v5_95_Feb07_1_3]

city: philadelphia

first: suraj

last: peri

state: PA

address: 333 cottman ave

department: biostatistics and bioinformatics

institute: Fox chase cancer center

hyb_protocol: Amplified RNA hybridized to Agilent whole mouse genome, 4x44K array slides (catalog #G4846A) overnight.

scan_protocol: Slides were washed and scanned at 5μm resolution on Agilent scanner 2505B.

data_processing:
Images were quantified using Agilent Feature Extraction Software (version 9.5.1.1).
Agilent Feature Extraction Software (v 9.5.1.1) was used for background subtraction and LOWESS normalization.

label: Alexa 555

label_protocol: Amplified RNA was labeled with either Alexa Flour 555 or 647 (Invitrogen catalog# A32755)

growth_protocol: Microarray analysis as performed on RNA from the following flowcytometrically isolated cell populations: 1) KN6 Tg Rag2-/- Lig+ DN4 (Lig+); 2) KN6 Tg Rag2-/- Lig- DN4(Lig-); and 3) non-Tg Rag2-/- DN3(KN6-DN3 control samples).

extract_protocol: RNA was extracted using Qiagen RNeasy, (Catalog # 74104) Antisense RNA was amplified using Agilent’s Amino Allyl MessageAMp aRNA Amplification kit (catalog #AM1753)

value: BALB/c

value: Experimental

label: Alexa 647


title: 0003690027|KE Contact Eczema


title: BM PMN_KO_LPS 0h

source_name: miR-125a knockout mice,bone marrow neutrophils,without LPS stimulation


title: KN6+Lig- [US22502680_251486820447_S01_GE2-v5_95_Feb07_1_2]


title: 0003830048|KE Contact Eczema


title: 0003690039|KE Contact Eczema


title: BoneMarrowCD34_differentiated_rep6


title: BM PMN_WT_LPS 0h

source_name: wild type mice,bone marrow neutrophils,without LPS stimulation


title: 0003830049|KE Contact Eczema


title: KN6+Lig+ [US22502680_251486814364_S01_GE2-v5_95_Feb07_1_1]


title: BoneMarrowCD34_differentiated_rep8


title: KN6+Lig- [US22502680_251486814365_S01_GE2-v5_95_Feb07_1_3]


title: 0003690011|KE Contact Eczema


title: KN6+Lig- [US22502680_251486814364_S01_GE2-v5_95_Feb07_1_3]


title: FetalLiverCD34_differentiated_rep2


title: 0003690028|KE Contact Eczema


title: 0003830050|KE Contact Eczema


title: KN6+Lig+ [US22502680_251486820447_S01_GE2-v5_95_Feb07_1_1]


title: FetalLiverCD34_differentiated_rep0


title: tetO:HAL3 vhs3/WT_100µg/mlDOX_Rep1

city: Cerdanyola del Vallès

first: David

last: Canadell

address: IBB, Campus UAB

country: Spain

institute: UAB

description: Biological replicate 1 of 2. Dye-swapping

hyb_protocol: Prehybridizations of the DNA microarrays were carried out at 42ºC for 1 h in a solution containing 5x SSC, 0.1% SDS, 1% bovine serum albumin. For hybridization, dried Cy3-and Cy5-labelled probes were resuspended in 35 microl of hybridization solution (50% formamide, 5x SSC, 0.1% SDS) each and mixed. Five microg of salmon sperm DNA was added to the mix before denaturation for 3 min at 95ºC. DNA microarrays were hybridized in an ArrayBooster hybridization station (Sunergia Group) for 14 h at 42ºC.

scan_protocol: The scanner ScanArray 4000 (Packard) was used to obtain the Cy3 and Cy5 images with a resolution of 10 microm.

data_processing: The fluorescent intensity of the spots was measured and processed using the GenePix Pro 6.0 software (Molecular Devices). Spots with a diameter smaller than 120 microm were not considered for further analysis.  The duplicated genes values have been merged (mean).

organism: Saccharomyces cerevisiae

source_name: tetO:HAL3 vhs3 mutant strain in synthetic complete medium 15 h 100µg/ml doxycycline

label_protocol: Fluorescent labeled cDNA was prepared from 8 microg of purified total RNA by the indirect dUTP-labeling method using the CyScribe post-labeling kit (GE Healthcare) and oligo(dT) as a primer.

growth_protocol: Grown at 28ºC in synthetic complete medium for 15 h in the presence of 100 µg/ml of doxycycline. Cells were harvested by centrifugation and washed with cold water. Dried cell pellet was kept at -80ºC until RNA purification.

extract_protocol: Total RNA purification using the Ambion RiboPure™-Yeast Total RNA Isolation Kit

treatment_protocol: Synthetic complete medium during 15 h in the presence of 100 µg/ml of doxycycline

value: JA100 genetic background

value: tetO:HAL3 vhs3::URA3

source_name: Wild type strain in synthetic complete medium 15 h 100µg/ml doxycycline

value: Wild type Strain


title: WT/tetO:HAL3 vhs3_100µg/mlDOX_Rep2

description: Biological replicate 2 of 2


title: BoneMarrowCD34_differentiated_rep7


title: WT/tetO:HAL3 vhs3_100µg/mlDOX_Rep1


title: 0003830078|KE Contact Eczema

value: whole skin biopsy


title: BreastCancer_EndocrineResistant_Biopsy_R98_microRNA

status: Public on Dec 01 2014

city: Cambridge

first: Alexey

middle: A

last: Larionov

state: Cambridgeshire

address: Box 238, Lv 6 Addenbrooke's Treatment Centre, Cambridge BioMedical Campus

department: School of Clinical Medicine

institute: The University of Cambridge

hyb_protocol: Standard Illumina hybridisation protocol recommended for the chip

scan_protocol: Standard Illumina scanning protocol

data_processing: Raw data were exported from Genome Studio; then data were normalised using default settings of lumiExpresso() function from lumi R-package.

source_name: Clinical biopsy of breast cancer taken at the time of endocrine resistance

label_protocol: Standard Illumina labelling protocol recommended for the chip

extract_protocol: RNA was extracted using miRNEasy Qiagen kits. Quality control was performed with NanoDrop and Agilent Bioanalyser.

value: Clinical biopsy of breast cancer

tag: molecule subtype

value: microRNA


title: 0003690093|KE Contact Eczema

value: skin biopsies from pool of 160 patients with skin disorders and healthy donors


title: BoneMarrowCD34_differentiated_rep0


title: BoneMarrowCD34_differentiated_rep4


title: BoneMarrowCD34_differentiated_rep5


title: KN6+Lig+ [US22502680_251486814365_S01_GE2-v5_95_Feb07_1_1]

value: Control


title: BoneMarrowCD34_differentiated_rep1


title: BreastCancer_EndocrineResistant_Biopsy_R97_microRNA


title: BoneMarrowCD34_differentiated_rep9


title: BoneMarrowCD34_differentiated_rep10


title: BoneMarrowCD34_differentiated_rep2


title: BreastCancer_EndocrineResistant_Biopsy_R86_microRNA


title: BoneMarrowCD34_differentiated_rep3


title: BreastCancer_EndocrineResistant_Biopsy_R51_microRNA


title: BreastCancer_EndocrineResistant_Biopsy_R64_microRNA


title: BreastCancer_EndocrineResistant_Biopsy_R75_microRNA


title: BreastCancer_EndocrineResistant_Biopsy_R06_microRNA


title: BreastCancer_EndocrineResistant_Biopsy_R45_microRNA


title: BreastCancer_EndocrineResistant_Biopsy_R79_microRNA


title: BreastCancer_EndocrineResistant_Biopsy_R77_microRNA


title: Aortic root from 129, rep3

city: Chapel Hill

first: Yukako

last: Kayashima

state: NC

address: 701 Brinkhous-Bullitt Building

institute: University of North Carolina at Chapel Hill

description: Gene expression data of aortic arch pooled from 6 mice

hyb_protocol: The Beckman Coulter Biomek FXP Laboratory Automation Workstation with the Target Express set up was used to prepare the samples with these two kits. Fragmented and labeled cDNA was used to prepare a hybridization cocktail with the Affymetrix GeneTitan Hybridization Wash and Stain Kit for WT Arrays. Hybridization, washing, staining.

scan_protocol: Scanning of the Affymetrix array plate was carried out using the Affymetrix GeneTitan MC Instrument.

data_processing: Affymetrix Expression Console Software was used for basic data analysis and quality control.

source_name: Mouse aortic root

label_protocol: Total RNA (250 ng) was used to synthesize fragmented and labeled sense-strand cDNA and hybridize onto Affymetrix arrays. The Affymetrix HT WT User Manual was followed to prepare the samples. Briefly, the WT Expression HT Kit for Robotics (Ambion) was used to generate sense-strand cDNA from total RNA.  Following synthesis of sense-strand cDNA, the cDNA was fragmented and labeled with the Affymetrix GeneChip HT Terminal Labeling Kit.

growth_protocol: Wild type DBA2/J, C57BL/6 and 129S6/SvEvTac mice mice were fed with a regular chow.

extract_protocol: Tissues from 4-6 mice were pooled and total RNA was extracted using an RNeasy Mini Kit (QIAGEN), according to manufacturer’s protocol. RNA quality was assessed by an Agilent Bioanalyzer.

treatment_protocol: Aortic were dissected from 2- to 5-month-old male mice.

tag: gender

value: male

value: aortic root


title: Aortic arch from 129, rep2

description: Gene expression data of aortic arch pooled from 5 mice

source_name: Mouse aortic arch

value: aortic arch


title: Aortic arch from 129, rep3


title: Aortic root from 129, rep1


title: Aortic arch from 129, rep1


title: BreastCancer_EndocrineResistant_Biopsy_R46_microRNA


title: BreastCancer_EndocrineResistant_Biopsy_R40_microRNA


title: BreastCancer_EndocrineResistant_Biopsy_R54_microRNA


title: BreastCancer_EndocrineResistant_Biopsy_R32_microRNA


title: Aortic arch from B6, rep2


title: Aortic arch from B6, rep3


title: BreastCancer_EndocrineResistant_Biopsy_R02_microRNA


title: BreastCancer_EndocrineResistant_Biopsy_R07_microRNA


title: BreastCancer_EndocrineResistant_Biopsy_R59_microRNA


title: BreastCancer_EndocrineResistant_Biopsy_R88_microRNA


title: BreastCancer_EndocrineResistant_Biopsy_R89_microRNA


title: Aortic arch from B6, rep1

description: Gene expression data of aortic arch pooled from 4 mice


title: BreastCancer_EndocrineResistant_Biopsy_R92_microRNA


title: BreastCancer_EndocrineResistant_Biopsy_R83_microRNA


title: BreastCancer_EndocrineResistant_Biopsy_R31_microRNA


title: BreastCancer_EndocrineResistant_Biopsy_R13_microRNA


title: BreastCancer_EndocrineResistant_Biopsy_R47_microRNA


title: BreastCancer_EndocrineResistant_Biopsy_R78_microRNA


title: BreastCancer_EndocrineResistant_Biopsy_R67_microRNA


title: Aortic arch from DBA, rep3


title: Aortic arch from DBA, rep1


title: Aortic arch from DBA, rep2


title: B6-Female Macrophages

description: Gene expression data of peritoneal macrophages pooled from three mice.

source_name: Peritoneal macrophages isolated from C57BL/6 female mice

growth_protocol: Wild type 129S6/SvEvTac and C57BL/6 mice mice were fed with a regular chow.

extract_protocol: Total RNA was extracted by RNeasy kit (Qiagen) according to the manufacturer's instructions.  Equal amounts of RNA from three mice in each group were pooled.

treatment_protocol: Three mice per group (malesand females of each strain) were treated with 1 ml 4 % thioglycolate medium by intra-peritoneal injection and sacrificed 4 days after injection followed by intra-peritoneal lavage with 10 ml PBS. Macrophages were plated at in 100 mm plates and cultured overnight in DMEM supplemented with 10% FBS.

value: female

value: peritoneal macrophage


title: 129-Male Macrophages

source_name: Peritoneal macrophages isolated from 129S6/SvEvTac male mice


title: B6-Male Macrophages

source_name: Peritoneal macrophages isolated from C57BL/6 male mice


title: BreastCancer_EndocrineResistant_Biopsy_R34_microRNA


title: BreastCancer_EndocrineResistant_Biopsy_R43_microRNA


title: BreastCancer_EndocrineResistant_Biopsy_R42_microRNA


title: Patient exosome 253118110900_S01_2_3

city: Heidelberg

first: Shijing

last: Yue

address: Im Neuenheimer Feld 365

department: Tumor cell biology

institute: University hospital Heidelberg

description:
microRNA
Cy3 reactions were combined and purified using Microcon YM-30 Filters (Amicon), before loading onto the arrays and assembled in hybridization chambers according to manufacturer’s protocol.

hyb_protocol: Hybridizations consisting of 25 μl hybridization solution (50% formamide,  5xSSC, 0.1% SDS) and 10 μl labeled DNA were denatured at 95 ºC for five minutes in a MJ Research Tetrad and pre-annealed at 37 oC for 30 min. The solution was loaded on the arrays and hybridized under a coverslip at 42 ºC for 14 to16 hours in a 5xSSC and formamide moisturized hybridization oven.

scan_protocol: The microarray slides were scanned using an Agilent Scanner or GenePix (Axon/Molecular Devices) scanner.

data_processing: Feature Extraction (FE) 9.5.3 supports extraction of one-color .tif images of Agilent microarrays scanned on Agilent Scanner or GenePix (Axon/Molecular Devices) scanner

source_name: Patient serum

label_protocol: Samples were labeled with Cy3-duTP using the Megaprime DNA labeling kit (Amersham Bioscience) and incubated for 2 hours at 37C

extract_protocol: MicroRNA was extracted from exosomes and exosomes depleted serum using the miRNeasy Mini Kit (Qiagen, Germany) according to the manufacturer’s instructions

value: serum


title: BreastCancer_EndocrineResistant_Biopsy_R82_microRNA


title: 129-Female Macrophages

source_name: Peritoneal macrophages isolated from 129S6/SvEvTac female mice


title: Patient exosome 253118110900_S01_2_4


title: Patient serum 253118110900_S01_1_4


title: Normal_Prostate_HSPH0261

city: Boston

first: Kathryn

last: Penney

address: 181 Longwood Ave

department: Medicine

institute: Brigham and Women's Hospital

hyb_protocol: Not provided

scan_protocol: Not provided

data_processing: For the expression profiles generated, we regressed out technical variables including mRNA concentration, age of the block, batch (96-well plate), percent of the probes on the array detectable above the background, log transformed average background signal, and the median of the perfect match probes for each probe intensity of the raw data. The residuals were then shifted to have the original mean expression values and normalized using the RMA method. We mapped gene names to Affymetrix transcript cluster IDs using the NetAffx annotations as implemented in Bioconductor annotation package pd.hugene.1.0.st.v1; this resulted in 20,254 unique named genes.  As gene names were used in the final analysis, this is what we have included in the sample tables.

source_name: FFPE normal prostate

label_protocol: Not provided

extract_protocol: Not provided


title: Berries skin_uv_1hour_rep2

city: Nagoya

first: Mami

last: Suzuki

state: Aichi

address: Chikusa hurocho

department: Graduate School of Bioagricultural Sciences

country: Japan

institute: Nagoya University

description: This sample is berries skins of Vitis vinifera L. harvested at the vine yard. It is the second of three wild-type biological replicates used in this experiment, each from separate clusters.

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

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

data_processing: The raw data (call file) were then analyzed using the Subio platform (Subio, Japan). After removal of noise signals less than 3,000, the triplicate data were standardized by Global normalization method.

organism: Vitis vinifera

source_name: Berries skin, UV 1 hour

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

extract_protocol: Total RNA was extracted from berry skins according to the Hot Borate method ( Wan CY and Wilkins TA 1994). Obtained RNA was further purified using the RNeasy Plant Mini Kit (QIAGEN, Hilden, Germany). RNA quality and quantity were determined using a spectrophotometer (ND-1000, Thermo Fisher Scientific, USA) and a Bioanalyzer (Bioanalyzer 2100, Agilent, USA).

treatment_protocol: Berry clusters were irradiated using a UV-C lamp (253.7 nm, GL-15, TOSHIBA, Japan) from a distance of 50 cm for 1 hour (UV). Control samples (dark) were covered with box and placed next to the sample of UV irradiation.

tag: cultivar

value: Pinot Noir

value: berries skin

value: UV 1 hour


title: BreastCancer_EndocrineResistant_Biopsy_R53_microRNA


title: Berries skin_dark_1hour_rep3

description: This sample is berries skins of Vitis vinifera L. harvested at the vine yard. It is the third of three wild-type biological replicates used in this experiment, each from separate clusters.

source_name: Berries skin, Dark 1 hour

value: control (dark 1hour)


title: BreastCancer_EndocrineResistant_Biopsy_R44_microRNA


title: Berries skin_uv_1hour_rep3


title: ChIP_Rpb3_IP

city: Burjassot

first: Jose

middle: E.

last: Perez-Ortin

state: Valencia

address: Dr. Moliner 50

department: Bioquimica y Biologia Molecular

institute: Universitat de Valencia

hyb_protocol: For BioGRO samples, we followed the instructions of the GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Manual (part # 701880), starting from Chapter 5: Hybridization, using the GeneChip® Hybridization, Wash and Stain Kit. For ChIP samples, we followed the Affymetrix® Chromatin Immunoprecipitation Assay Protocol (PN 702238).

scan_protocol: For BioGRO samples, we followed the instructions of the GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Manual (part # 701880), scanning the array as described in Chapter 7: Scanning. For ChIP samples, we followed the Affymetrix® Chromatin Immunoprecipitation Assay Protocol (PN 702238), scanning the arrays as described in Chapter 5: Scan.

data_processing:
Raw .CEL images were processed with Tiling Analysis Software (TAS, Affymetrix) with the signal detection parameters set by default. BioGRO samples where normalized against a reference genomic DNA hybridized on the same Affymetrix tiling arrays (ArrayExpress E-TABM-590). The ChIP (IP) sample was normalized against its respective Input sample (Input).
The resulting files were obtained with Tiling Analysis Software (TAS, Affymetrix) with the signal detection parameters set by default. BioGRO samples where normalized against a reference genomic DNA hybridized on the same Affymetrix tiling arrays (ArrayExpress E-TABM-590). The ChIP (IP) sample was normalized against its respective Input sample (Input).

source_name: Yeast cells grown in YPD to exponential phase

label_protocol: For BioGRO samples, labeling of nascent RNAs was achieved by incorporating Bio-11-UTP (Ambion) to the nascent chains in vivo by run-on. For ChIP samples, we followed Affymetrix® Chromatin Immunoprecipitation Assay Protocol (PN 702238).

growth_protocol: All yeast strains where grown in standard conditions (YPD medium, 30 ºC). For each sample we used an aliquot of 100 mL cells grown to mid exponetial phase (DO600 = 0.55).

extract_protocol: For BioGRO samples, RNA extraction was done using the “MasterPure Yeast RNA Purification Kit” (Epicentre), following manufacturer’s instructions. Once extracted, genomic DNA was removed digesting with 2 µL of RNase-free DNase I (Roche) for 30 min at 37 °C. The purified RNA was resuspended in 32 µL of water and spectrophotometrically quantified. For ChIP samples, we followed the Affymetrix® Chromatin Immunoprecipitation Assay Protocol (PN 702238).

treatment_protocol: For BioGRO samples, cells were collected by centrifugation and frozen in liquid nitrogen. Frozen pellets were transferred immediately to -20 °C. After at least 3 h, cells were thawed on ice and permeabilized with 10 mL of a 0.5% sarkosyl solution. Once permeabilized, cells were treated with RNase A (Roche). RNase trimming was achieved by incubating the cells with 32 µL of RNase A (10 mg/mL) dissolved in 3.2 mL of Sarkosyl 0.5% in agitation for 10 min at 30 °C. In order to remove the RNase, cells were washed three times with 50 mL 0.5% sarkosyl, and then transferred to an eppendorf tube. Cells  were resuspended in 115 µL of water plus 5 µL of RNase OUT (Invitrogen) to protect the integrity of nascent RNAs from any residual RNase that might be present. Run-on reactions where performed as described (Jordán-Pla et al., 2014). For ChIP samples we followed the Affymetrix® Chromatin Immunoprecipitation Assay Protocol (PN 702238).

value: WT strain:BY4741 (SC288 background)

tag: antibody

value: Anti-POLR2C antibody [1Y26 (1Y27)]-ChIP Grade

tag: antibody manufacturer

value: Abcam

tag: antibody catalog number


title: Berries skin_dark_1hour_rep2

tag: treatment


title: ChIP_Rpb3_Input

value: none (input)


title: Healthy serum 253118110900_S01_1_2

source_name: Healthy serum


title: Patient serum 253118110900_S01_1_3


title: Berries skin_uv_1hour_rep1

description: This sample is berries skins of Vitis vinifera L. harvested at the vine yard. It is the first of three wild-type biological replicates used in this experiment, each from separate clusters.


title: BioGRO_Dst1

value: dst1 delta strain:BQS409 (BY4741 derived)


title: Healthy exosome 253118110900_S01_2_2


title: BioGRO_Isw2

value: isw2 delta strain:YOR304W (BY4741 derived)


title: BreastCancer_EndocrineResistant_Biopsy_R80_microRNA

value: Clinical biopsy of breast cancer

value: microRNA


title: Healthy serum 253118110900_S01_1_1


title: BreastCancer_EndocrineResistant_Biopsy_R76_microRNA


title: Berries skin_dark_1hour_rep1


title: BioGRO_WT

value: WT strain:BQS252 (SC288 background)


title: BioGRO_Rpb4

value: rpb4 delta strain:BQS408 (BY4741 derived)


title: Healthy exosome 253118110900_S01_2_1


title: BreastCancer_EndocrineResistant_Biopsy_R74_microRNA


title: BreastCancer_EndocrineResistant_Biopsy_R73_microRNA


title: BreastCancer_EndocrineResistant_Biopsy_R81_microRNA


title: BreastCancer_EndocrineResistant_Biopsy_R71_microRNA


title: BreastCancer_EndocrineResistant_Biopsy_R70_microRNA


title: BreastCancer_EndocrineResistant_Biopsy_R72_microRNA


title: Aortic root from 129, rep2

value: male

value: aortic root


title: BreastCancer_EndocrineResistant_Biopsy_R65_microRNA


title: BreastCancer_EndocrineResistant_Biopsy_R69_microRNA


title: BreastCancer_EndocrineResistant_Biopsy_R60_microRNA


title: BreastCancer_EndocrineResistant_Biopsy_R56_microRNA


title: BreastCancer_EndocrineResistant_Biopsy_R62_microRNA


title: BreastCancer_EndocrineResistant_Biopsy_R68_microRNA


title: Normal_Prostate_HSPH0231


title: BreastCancer_EndocrineResistant_Biopsy_R41_microRNA


title: Normal_Prostate_HSPH0225


title: Control siRNA vs N-Myc siRNA

city: Randwick, Sydney

first: Tao

last: Liu

state: NSW

address: Lowy Cancer Research Centre UNSW

country: Australia

institute: Children's Cancer Institute Australia

description: NCode™ Human Non-coding RNA Microarray

hyb_protocol: Labeled cDNA samples were hybridized to NCode™ Human Non-coding RNA Microarrays at the Ramaciotti Centre for Gene Function Analysis at the University of New South Wales, Australia, following Life Technologies instructions.

scan_protocol: Micorarray slides were scanned at the Ramaciotti Centre for Gene Function Analysis at the University of New South Wales, following manufacturers instructions

data_processing: standard Agilent protocol

source_name: neuroblastoma cells

label_protocol: Samples were labelled with Cy3 or Cy5 during cDNA synthesis following manufacturer's instructions at the Ramaciotti Centre for Gene Function Analysis at the University of New South Wales, Sydney, NSW, Australia.

growth_protocol: BE(2)-C cells were maintained in Dulbecco's Modified Eagle Medium supplemented with 10% fetal calf serum.

extract_protocol: Total RNA was extracted by using Qiagen RNAeasy kit and genomic DNA was removed.

treatment_protocol: Cells were transfected with a mixture of siRNA and Lipofectamine2000 (Invitrogen) transfection reagent for 30 hours.

tag: cell line

value: control

value: N-Myc siRNA


title: Macrophage Donor 4 day 12 [35 Hy5TM]

city: Chicago

first: Jezrom

middle: Bokcaerin

last: Self-Fordham

state: IL

address: 801 S Paulina

department: Periodontics

institute: UIC

description: The samples were labeled using the miRCURY LNATM microRNA Hi-Power Labeling Kit, Hy3TM/Hy5TM and hybridized on the miRCURY LNATM microRNA Array (7th Gen)

hyb_protocol: Hybridisation was performed by Exiqon.

scan_protocol: Scanning was performed by Exiqon.

data_processing:
Data normalization was performed using Quantile normalization by Exiqon.
Fold change (Normalized Reads)
Expression analysis (ANOVA for Time - Macrophages)
Expression analysis (ANOVA for Time – Macrophages, excluding monocytes)
Expression analysis (ANOVA for Time - Osteoclasts)
Expression analysis (ANOVA for Time – Osteoclasts, excluding monocytes)
Expression analysis for Mac_1 vs. Ost_1
Expression analysis for Mac_3 vs. Ost_3
Expression analysis for Mac_6 vs. Ost_6
Expression analysis for Mac_12 vs. Ost_12

source_name: Monocyte-derived macrophages & Monocyte-derived osteoclasts

label_protocol: 250ng of total RNA was used as input for miRCURY LNATM microRNA Hi-Power Labeling Kit. Labelling was performed on an automated Tecan hybridization station.

growth_protocol: CD14+ monocytes were cultured at 4×106 cells/ml in: (A, osteoclasts) RPMI 1640 medium supplemented with 10% FBS, 2 mmol/L L-glutamine, penicillin (100 U/ml), streptomycin (100 μg/ml), 33ng/ml M-CSF, 100ng/ml sRANKL, or (B, macrophages) RPMI 1640 medium supplemented with 10% FBS, 2 mmol/L L-glutamine, penicillin (100 U/ml), streptomycin (100 μg/ml), 33ng/ml M-CSF. Media was replenished every 72 hours.

extract_protocol: Total RNA was isolated using the miRNeasy kit (Qiagen) following manufacturer’s protocol. The RNA was quantitated using the NanoDrop (Thermo Scientific) and integrity assessed using the 2100 Bioanalyzer.

treatment_protocol: Cells were left untreated.

value: Macrophage

tag: donor

tag: time point

value: day 12


title: Osteoclast Donor 4 day 12 [36 Hy5TM]

source_name: Monocyte-derived osteoclasts

value: Osteoclast


title: Osteoclast Donor 3 day 12 [34 Hy5TM]


title: HCC replicate 12

city: Vassilika Vouton, Herakleion

first: Iannis

last: Talianidis

state: Crete

address: 100 N. Plastira Str

department: Institute of Molecular Biology and Biotechnology

country: Greece

institute: Foundation for Research and Technology - Hellas

hyb_protocol: Following clean-up and quantification, equal volumes of the corresponding Cyanine-5- and Cyanine-3-labeled samples were mixed. Mouse Cot-1 DNA® (Life Technologies) was added to block repetitive sequences and these combined samples were pre-hybridized in-tube before two-color-based hybridization (Oligo aCGH Hybridization Kit, Agilent Technologies). All 12 combinations of experimental and reference sample were hybridized at 67°C for 40 hrs on separate Agilent SurePrint G3 Mouse Genome CGH 4x180K Microarrays (AMADID 027411). Afterwards, microarrays were washed with increasing stringency using Oligo aCGH Wash Buffers (Agilent Technologies) followed by drying with acetonitrile (SIGMA).

scan_protocol: Fluorescent signal intensities were detected with Scan Control A.8.4.1 software (Agilent Technologies) on the Agilent DNA Microarray Scanner.

data_processing: Probe features were extracted from the images using Feature Extraction 10.7.3.1 software (Agilent Technologies) and imported to the Agilent Genomic Workbench 7.0 software for subsequent analysis. Normalization was performed using the algorithms implemented in AGF. Centralization was applied with the following options: Diploid Peak: on, Legacy: on, Threshold: 6, Bin size: 10. GC correction was also applied with the following options: Window Size: 2kb. Intra-array replicate probes were combined. Chromosomal aberrations were called using the AMD-2 algorithm with threshold 6 and a 0.4 log ratio threshold for amplifications and -0.3 for deletions, supported by at least three array probes in the aberrant genomic region.

source_name: normal liver

label_protocol: The SureTag Complete DNA Labeling Kit (Agilent Technologies) was used to differentially label the digested gDNA samples with fluorescently labeled nucleotides according to manufacturer's instructions. Cyanine-5 dUTP was used for the 12 cancerous samples, whereas Cyanine-3 dUTP was used for the 12 aliquots of the reference sample.

extract_protocol: For liver genomic DNA extraction the proteinase K/phenol-chloroform extraction was used. The tissues were lysed in a lysis buffer (50mM Tris pH=8, 400mM NaCl, 100mM EDTA, 0,5%SDS and proteinase K) overnight at 55C. After saturated NaCl was added, mixed well and centrifuged at 12000x for 5 min. In the supernatant equal volume of a mixture of phenol:chloroform:isoamyl alcohol (25:24:1) was added, mixed and centrifuged. The supernatant contained liver genomic DNA was precipitated using ethanol. Finally the liver genomic DNA was resuspended in TE (10mM Tris, 1mM EDTA).

value: 8 months

source_name: cancerous liver


title: HCC replicate 8


title: Osteoclast Donor 2 day 12 [31 Hy5TM]


title: Monocyte Donor 3 day 0 [32 Hy5TM]

source_name: Monocyte

value: Monocyte

value: day 0


title: BreastCancer_EndocrineResistant_Biopsy_R33_microRNA

source_name: Clinical biopsy of breast cancer taken at the time of endocrine resistance


title: BreastCancer_EndocrineResistant_Biopsy_R35_microRNA


title: HCC replicate 11


title: Normal adjacent breast tissue [67]

city: Houston

first: Liuqing

last: Yang

state: Texas

address: 1515 Holcombe Blvd.

department: Molecular and Cellular Oncology

institute: The University of Texas MD Anderson Cancer Center

description: LncRNA expression in normal adjacent breast tissue of patient 1

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.0 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 2 out of 4 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs were identified through Fold Change filtering between two samples. Hierarchical Clustering was performed using the Agilent GeneSpring GX software (version 12.0). GO analysis and Pathway analysis were performed in the standard enrichment computation method.

source_name: Breast tissue, fresh frozen

label_protocol: Sample labeling was performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method. The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: RNA was extracted from human breast cancers and their matched adjacent normal tissues using the TRIzol® Plus RNA Purification Kit (Life Technologies, Grand Island NY) following the manufacturer's recommendations. RNA quantity and quality were measured by NanoDrop ND-2000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

value: Breast

value: Female


title: HCC replicate 5


title: HCC replicate 3


title: Infiltrating Ductal Carcinima of breast [67]

description: LncRNA expression in breast cancer tissue of patient 2


title: HCC replicate 4


title: Normal adjacent breast tissue [73]


title: Infiltrating Ductal Carcinima of breast [73]

description: LncRNA expression in breast cancer tissue of patient 1


title: HCC replicate 6


title: Macrophage Donor 3 day 12 [33 Hy5TM]


title: Macrophage Donor 2 day 12 [30 Hy5TM]


title: HCC replicate 1


title: HCC replicate 2


title: Macrophage Donor 1 day 12 [28 Hy5TM]


title: HCC replicate 10


title: Osteoclast Donor 3 day 1 [25 Hy5TM]

value: day 1


title: Macrophage Donor 3 day 1 [23 Hy5TM]


title: Osteoclast Donor 4 day 1 [27 Hy5TM]


title: Monocyte Donor 2 day 0 [24 Hy5TM]


title: Macrophage Donor 4 day 1 [26 Hy5TM]


title: Osteoclast Donor 2 day 1 [22 Hy5TM]


title: HCC replicate 9


title: HCC replicate 7


title: Osteoclast Donor 1 day 12 [29 Hy5TM]


title: Macrophage Donor 2 day 1 [21 Hy5TM]


title: BreastCancer_EndocrineResistant_Biopsy_R29_microRNA

value: Clinical biopsy of breast cancer


title: Osteoclast Donor 1 day 1 [20 Hy5TM]


title: BreastCancer_EndocrineResistant_Biopsy_R15_microRNA

value: microRNA


title: BreastCancer_EndocrineResistant_Biopsy_R18_microRNA


title: BreastCancer_EndocrineResistant_Biopsy_R08_microRNA


title: Macrophage Donor 1 day 1 [19 Hy5TM]


title: BreastCancer_EndocrineResistant_Biopsy_R14_microRNA


title: Monocyte Donor 1 day 0 [17 Hy5TM]


title: Monocyte Donor 4 day 0 [18 Hy5TM]


title: BreastCancer_EndocrineResistant_Biopsy_R01_microRNA


title: Macrophage Donor 4 day 3 [14 Hy5TM]

value: day 3


title: Osteoclast Donor 4 day 3 [15 Hy5TM]


title: Macrophage Donor 3 day 6 [13 Hy5TM]

value: day 6


title: Osteoclast Donor 3 day 3 [12 Hy5TM]


title: Macrophage Donor 3 day 3 [11 Hy5TM]


title: Osteoclast Donor 2 day 3 [9 Hy5TM]


title: Macrophage Donor 2 day 6 [10 Hy5TM]


title: Macrophage Donor 1 day 6 [7 Hy5TM]


title: Macrophage Donor 1 day 3 [5 Hy5TM]

source_name: Monocyte-derived macrophages


title: Macrophage Donor 2 day 3 [8 Hy5TM]


title: Osteoclast Donor 1 day 3 [6 Hy5TM]


title: Osteoclast Donor 4 day 6 [4 Hy5TM]


title: Osteoclast Donor 1 day 6 [1 Hy5TM]


title: Osteoclast Donor 2 day 6 [2 Hy5TM]


title: Osteoclast Donor 3 day 6 [3 Hy5TM]


title: Osteoclast Donor 4 day 12 [36 Hy3TM]


title: Osteoclast Donor 3 day 12 [34 Hy3TM]


title: Macrophage Donor 4 day 12 [35 Hy3TM]


title: Osteoclast Donor 2 day 12 [31 Hy3TM]


title: Macrophage Donor 3 day 12 [33 Hy3TM]


title: Osteoclast Donor 1 day 12 [29 Hy3TM]


title: Macrophage Donor 4 day 6 [16 Hy5TM]


title: Macrophage Donor 2 day 12 [30 Hy3TM]


title: Macrophage Donor 1 day 12 [28 Hy3TM]


title: Macrophage Donor 4 day 1 [26 Hy3TM]


title: Osteoclast Donor 4 day 1 [27 Hy3TM]


title: Normal_Prostate_HSPH0195


title: Osteoclast Donor 3 day 1 [25 Hy3TM]


title: Osteoclast Donor 2 day 1 [22 Hy3TM]


title: Osteoclast Donor 1 day 1 [20 Hy3TM]


title: Monocyte Donor 2 day 0 [24 Hy3TM]


title: Monocyte Donor 4 day 0 [18 Hy3TM]


title: Macrophage Donor 1 day 1 [19 Hy3TM]


title: Osteoclast Donor 4 day 3 [15 Hy3TM]


title: Macrophage Donor 4 day 3 [14 Hy3TM]


title: Macrophage Donor 3 day 6 [13 Hy3TM]


title: Osteoclast Donor 3 day 3 [12 Hy3TM]


title: Monocyte Donor 3 day 0 [32 Hy3TM]


title: Macrophage Donor 2 day 6 [10 Hy3TM]


title: Macrophage Donor 3 day 3 [11 Hy3TM]


title: Macrophage Donor 4 day 6 [16 Hy3TM]


title: Osteoclast Donor 2 day 3 [9 Hy3TM]


title: Osteoclast Donor 1 day 3 [6 Hy3TM]


title: Macrophage Donor 1 day 6 [7 Hy3TM]


title: Macrophage Donor 1 day 3 [5 Hy3TM]


title: Osteoclast Donor 4 day 6 [4 Hy3TM]


title: Osteoclast Donor 3 day 6 [3 Hy3TM]


title: Osteoclast Donor 1 day 6 [1 Hy3TM]


title: Macrophage Donor 3 day 1 [23 Hy3TM]


title: Macrophage Donor 2 day 1 [21 Hy3TM]


title: DC Donor 7 day 7 [45 Hy5TM]

data_processing:
Data normalization was performed using Quantile normalization by Exiqon.
Quantile normalized signal
Fold change (Normalized Reads)
Expression analysis (ANOVA for Time - dendritic cells)
Expression analysis (ANOVA for Time - macrophages)
Expression analysis for DC_1h vs. Monocyte
Expression analysis for MP_1h vs. Monocyte

source_name: DC Donor 7 day 7

growth_protocol: CD14+ monocytes were cultured at 3×106 cells/ml in either (a) RPMI 1640 medium supplemented with 10% FBS, 2 mmol/L L-glutamine, penicillin (100 U/ml), streptomycin (100 μg/ml), 1000U/ml IL-4, 500U/ml GM-CSF; or (b) DMEM medium supplemented with 10% FBS, 2 mmol/L L-glutamine, penicillin (100 U/ml), streptomycin (100 μg/ml), gentamicin (50ng/ml), 100ng/ml M-CSF. Media was replenished every 48 hours.

value: DC


title: DC Donor 7 day 3 [43 Hy5TM]

source_name: DC Donor 7 day 3


title: DC Donor 7 day 1 [42 Hy5TM]

source_name: DC Donor 7 day 1


title: DC Donor 7 day 5 [44 Hy5TM]

source_name: DC Donor 7 day 5


title: Monocyte Donor 1 day 0 [17 Hy3TM]


title: DC Donor 7 4 hour [40 Hy5TM]

source_name: DC Donor 7 4 hour

value: 4 hour


title: Macrophage Donor 7 day 7 [38 Hy5TM]

source_name: Macrophage Donor 7 day 7


title: Macrophage Donor 7 day 5 [37 Hy5TM]

source_name: Macrophage Donor 7 day 5


title: Macrophage Donor 7 day 1 [35 Hy5TM]

source_name: Macrophage Donor 7 day 1


title: Macrophage Donor 7 1 hour [32 Hy5TM]

source_name: Macrophage Donor 7 1 hour

value: 1 hour


title: Monocyte Donor 7 [31 Hy5TM]

source_name: Monocyte Donor 7


title: Macrophage Donor 7 12 hour [34 Hy5TM]

source_name: Macrophage Donor 7 12 hour

value: 12 hour


title: DC Donor 6 day 7 [30 Hy5TM]

source_name: DC Donor 6 day 7


title: DC Donor 6 day 1 [27 Hy5TM]

source_name: DC Donor 6 day 1


title: DC Donor 6 day 5 [29 Hy5TM]

source_name: DC Donor 6 day 5


title: DC Donor 7 12 hour [41 Hy5TM]

source_name: DC Donor 7 12 hour


title: DC Donor 6 day 3 [28 Hy5TM]

source_name: DC Donor 6 day 3


title: DC Donor 6 4 hour [25 Hy5TM]

source_name: DC Donor 6 4 hour


title: DC Donor 6 12 hour [26 Hy5TM]

source_name: DC Donor 6 12 hour


title: Osteoclast Donor 2 day 6 [2 Hy3TM]

source_name: Monocyte-derived osteoclasts


title: BreastCancer_EndocrineResistant_Biopsy_R48_microRNA

source_name: Clinical biopsy of breast cancer taken at the time of endocrine resistance


title: DC Donor 7 1 hour [39 Hy5TM]

source_name: DC Donor 7 1 hour


title: DC Donor 6 1 hour [24 Hy5TM]

source_name: DC Donor 6 1 hour


title: Macrophage Donor 6 day 7 [23 Hy5TM]

source_name: Macrophage Donor 6 day 7

value: Macrophage


title: Macrophage Donor 6 day 5 [22 Hy5TM]

source_name: Macrophage Donor 6 day 5


title: Macrophage Donor 7 day 3 [36 Hy5TM]

source_name: Macrophage Donor 7 day 3


title: Macrophage Donor 7 4 hour [33 Hy5TM]

source_name: Macrophage Donor 7 4 hour


title: Macrophage Donor 6 day 3 [21 Hy5TM]

source_name: Macrophage Donor 6 day 3


title: Macrophage Donor 2 day 3 [8 Hy3TM]

source_name: Monocyte-derived macrophages & Monocyte-derived osteoclasts


title: Macrophage Donor 6 day 1 [20 Hy5TM]

source_name: Macrophage Donor 6 day 1


title: Macrophage Donor 6 12 hour [19 Hy5TM]

source_name: Macrophage Donor 6 12 hour


title: Macrophage Donor 6 1 hour [17 Hy5TM]

source_name: Macrophage Donor 6 1 hour


title: DC Donor 5 day 7 [15 Hy5TM]

source_name: DC Donor 5 day 7


title: Macrophage Donor 6 4 hour [18 Hy5TM]

source_name: Macrophage Donor 6 4 hour


title: Monocyte Donor 6 [16 Hy5TM]

source_name: Monocyte Donor 6


title: DC Donor 5 day 5 [14 Hy5TM]

source_name: DC Donor 5 day 5


title: Normal_Prostate_HSPH0147

source_name: FFPE normal prostate


title: C4WK-IR (SPRET/EiJ)

city: Berkeley

first: Antoine

middle: M

last: Snijders

state: CA

address: 1 Cyclotron Road

institute: Lawrence Berkeley National Laboratory

hyb_protocol: Hybridizations performed commercially by Ambry Genetics

data_processing: Data normalization was performed with GeneSpring GX12.5 (Agilent Technologies). Signal intensities for each probe were normalized to the 75th percentile without baseline transformation.

source_name: mammary gland 4 weeks post 10 cGy X-ray

growth_protocol: BALB/c and SPRET/EiJ mice were purchased from Jackson Laboratory, housed four per cage under a 12 hr light and 12 hr dark cycle, and fed with Lab Diet 5008 chow and water ad libitum.

extract_protocol: Total RNA was isolated by homogenizing the frozen tissue in Trizol reagent (Invitrogen) followed by phase separation using chloroform. RNA was further purified utilizing the RNeasy mini kit (Qiagen; 74104) and DNA was removed using RNase-free DNase (Qiagen; 79254).

treatment_protocol: The mice were irradiated whole body at 8-9 weeks of age to 10cGy dose using a Precision X-ray Inc RAD320 320 kVp X-ray machine

value: SPRET/EiJ

tag: Sex

value: female

tag: age exposure

value: 8-9 wks

tag: exposure

value: 10 cGy X-ray

tag: time after exposure

value: 4 weeks

value: mammary gland


title: DC Donor 5 day 1 [12 Hy5TM]

source_name: DC Donor 5 day 1


title: C4WK-SHAM (SPRET/EiJ)

scan_protocol: Hybridizations performed commercially by Ambry Genetics

source_name: mammary gland 4 weeks post sham

tag: strain

value: Sham

tag: tissue


title: B4WK-SHAM (SPRET/EiJ)

label_protocol: Hybridizations performed commercially by Ambry Genetics


title: A4WK-IR (SPRET/EiJ)


title: DC Donor 5 4 hour [10 Hy5TM]

source_name: DC Donor 5 4 hour

tag: cell type


title: DC Donor 5 12 hour [11 Hy5TM]

source_name: DC Donor 5 12 hour


title: C8WK-IR

source_name: mammary gland 8 weeks post 10 cGy X-ray

value: BALB/c

value: 8 weeks


title: A4WK-SHAM (SPRET/EiJ)


title: B8WK-IR


title: DC Donor 5 1 hour [9 Hy5TM]

source_name: DC Donor 5 1 hour


title: A8WK-IR


title: B8WK-SHAM

source_name: mammary gland 8 weeks post sham


title: C8WK-SHAM


title: C4WK-IR


title: Macrophage Donor 5 day 7 [8 Hy5TM]

source_name: Macrophage Donor 5 day 7


title: B4WK-IR (SPRET/EiJ)


title: Macrophage Donor 5 day 5 [7 Hy5TM]

source_name: Macrophage Donor 5 day 5


title: DC Donor 5 day 3 [13 Hy5TM]

source_name: DC Donor 5 day 3


title: Macrophage Donor 5 day 3 [6 Hy5TM]

source_name: Macrophage Donor 5 day 3


title: Macrophage Donor 5 day 1 [5 Hy5TM]

source_name: Macrophage Donor 5 day 1


title: Macrophage Donor 5 4 hour [3 Hy5TM]

source_name: Macrophage Donor 5 4 hour


title: A8WK-SHAM


title: A4WK-IR


title: Monocyte Donor 5 [1 Hy5TM]

source_name: Monocyte Donor 5

value: Monocyte


title: Macrophage Donor 5 1 hour [2 Hy5TM]

source_name: Macrophage Donor 5 1 hour


title: C4WK-SHAM


title: DC Donor 7 day 7 [45 Hy3TM]

source_name: DC Donor 7 day 7


title: Macrophage Donor 5 12 hour [4 Hy5TM]

source_name: Macrophage Donor 5 12 hour


title: C2WK-SHAM

source_name: mammary gland 2 weeks post sham

value: 2 weeks


title: DC Donor 7 day 5 [44 Hy3TM]

source_name: DC Donor 7 day 5


title: A4WK-SHAM

source_name: mammary gland 4 weeks post sham


title: DC Donor 7 day 1 [42 Hy3TM]

source_name: DC Donor 7 day 1


title: B4WK-SHAM


title: DC Donor 7 1 hour [39 Hy3TM]

source_name: DC Donor 7 1 hour


title: Macrophage Donor 7 day 1 [35 Hy3TM]

source_name: Macrophage Donor 7 day 1


title: Macrophage Donor 7 day 5 [37 Hy3TM]

source_name: Macrophage Donor 7 day 5


title: Macrophage Donor 7 4 hour [33 Hy3TM]

source_name: Macrophage Donor 7 4 hour


title: Macrophage Donor 7 12 hour [34 Hy3TM]

source_name: Macrophage Donor 7 12 hour


title: Macrophage Donor 7 day 3 [36 Hy3TM]

source_name: Macrophage Donor 7 day 3


title: Macrophage Donor 7 1 hour [32 Hy3TM]

source_name: Macrophage Donor 7 1 hour


title: DC Donor 6 day 7 [30 Hy3TM]

source_name: DC Donor 6 day 7


title: DC Donor 6 day 5 [29 Hy3TM]

source_name: DC Donor 6 day 5


title: DC Donor 7 day 3 [43 Hy3TM]

source_name: DC Donor 7 day 3


title: Monocyte Donor 7 [31 Hy3TM]

source_name: Monocyte Donor 7


title: DC Donor 7 12 hour [41 Hy3TM]

source_name: DC Donor 7 12 hour


title: Normal_Prostate_HSPH0123

source_name: FFPE normal prostate


title: DC Donor 6 day 3 [28 Hy3TM]

source_name: DC Donor 6 day 3


title: DC Donor 7 4 hour [40 Hy3TM]

source_name: DC Donor 7 4 hour


title: DC Donor 6 day 1 [27 Hy3TM]

source_name: DC Donor 6 day 1


title: Normal_Prostate_HSPH0127


title: DC Donor 6 4 hour [25 Hy3TM]

source_name: DC Donor 6 4 hour


title: A2WK-SHAM

source_name: mammary gland 2 weeks post sham


title: DC Donor 6 1 hour [24 Hy3TM]

source_name: DC Donor 6 1 hour


title: B2WK-SHAM


title: B4WK-IR

source_name: mammary gland 4 weeks post 10 cGy X-ray


title: B2WK-IR

source_name: mammary gland 2 weeks post 10 cGy X-ray


title: C2WK-IR


title: Macrophage Donor 6 day 7 [23 Hy3TM]

source_name: Macrophage Donor 6 day 7


title: Macrophage Donor 6 day 3 [21 Hy3TM]

source_name: Macrophage Donor 6 day 3


title: Macrophage Donor 6 day 1 [20 Hy3TM]

source_name: Macrophage Donor 6 day 1


title: Macrophage Donor 6 day 5 [22 Hy3TM]

source_name: Macrophage Donor 6 day 5


title: Macrophage Donor 6 12 hour [19 Hy3TM]

source_name: Macrophage Donor 6 12 hour


title: A2WK-IR


title: Day4os_11426_2

city: San Diego

first: Ricardo

last: Zayas

address: 5500 Campanile Dr.

department: Biology

institute: San Diego State University

description:
raw data file: Day4os_11426.pair
Following amputation of one side of the head, planarians were allowed to regenerate for four days and then tissue was collected from the non-regenerating side of the head and pooled from around 300 animals to form the second of 2 independent biological replicates for this sample type.  These data are from the second of 2 technical replicates for this biological sample obtained from the same array.

hyb_protocol: Hybridization was performed by the VMRF GeneChip Microarray Core at University of California-San Diego following standard operating procedures laid out in the Nimblegen Array User's Guide for gene expression analysis.

scan_protocol: Scanning was performed by the VMRF GeneChip Microarray Core at University of California-San Diego following standard operating procedures laid out in the Nimblegen Array User's Guide for gene expression analysis.

data_processing: The raw data (.pair files) were processed with RMA (Robust Multi-Array Analysis), quantile normalization and background correction using Nimblescan software  (Roche NimbleGen, Inc.).  Replicates were normalized first within sample type, and then all samples were normalized together.

organism: Schmidtea mediterranea

source_name: non-regenerating side of head, day 4 regenerates

label_protocol: Labeling was performed by the VMRF GeneChip Microarray Core at University of California-San Diego following standard operating procedures laid out in the Nimblegen Array User's Guide for gene expression analysis.

growth_protocol: Asexual Schmidtea mediterranea of the CIW4 strain were maintained in Montjuïc salts and fed pureed calf liver.  Animals were starved for one week prior to use in experiments.

extract_protocol: Total RNA was extracted with Trizol reagent (Invitrogen), treated with Turbo DNA-free DNase (Ambion), then further purified using the Qiagen RNeasy MinElute Cleanup kit.  cDNA was synthesized with the SuperScript Double-Stranded cDNA Synthesis kit (Invitrogen).

treatment_protocol: Control samples were collected from the heads of intact (non-regenerating) planarians.  All other samples were collected from either the blastema or non-regenerating half of the head on day 2, 3 or 4 following removal of one side of the head.

value: asexual CIW4

tag: developmental stage

value: adult

value: half-head amputation

tag: time (regeneration stage)

value: day 4 after half-head amputation

value: non-regenerating side of head


title: Macrophage Donor 6 1 hour [17 Hy3TM]

source_name: Macrophage Donor 6 1 hour

value: Macrophage

value: 1 hour


title: Macrophage Donor 6 4 hour [18 Hy3TM]

source_name: Macrophage Donor 6 4 hour

value: 4 hour


title: DC Donor 5 day 7 [15 Hy3TM]

source_name: DC Donor 5 day 7

value: DC


title: DC Donor 5 day 5 [14 Hy3TM]

source_name: DC Donor 5 day 5


title: DC Donor 6 12 hour [26 Hy3TM]

source_name: DC Donor 6 12 hour

value: 12 hour


title: DC Donor 5 day 3 [13 Hy3TM]

source_name: DC Donor 5 day 3


title: DC Donor 5 day 1 [12 Hy3TM]

source_name: DC Donor 5 day 1


title: Macrophage Donor 7 day 7 [38 Hy3TM]

source_name: Macrophage Donor 7 day 7


title: Day4os_11426_1

description:
raw data file: Day4os_11426.pair
Following amputation of one side of the head, planarians were allowed to regenerate for four days and then tissue was collected from the non-regenerating side of the head and pooled from around 300 animals to form the second of 2 independent biological replicates for this sample type.  These data are from the first of 2 technical replicates for this biological sample obtained from the same array.


title: DC Donor 5 12 hour [11 Hy3TM]

source_name: DC Donor 5 12 hour


title: DC Donor 5 4 hour [10 Hy3TM]

source_name: DC Donor 5 4 hour


title: Day4os_9003_2

description:
raw data file: Day4os_9003.pair
Following amputation of one side of the head, planarians were allowed to regenerate for four days and then tissue was collected from the non-regenerating side of the head and pooled from around 300 animals to form the first of 2 independent biological replicates for this sample type.  These data are from the second of 2 technical replicates for this biological sample obtained from the same array.


title: DC Donor 5 1 hour [9 Hy3TM]

source_name: DC Donor 5 1 hour


title: Day4os_9003_1

description:
raw data file: Day4os_9003.pair
Following amputation of one side of the head, planarians were allowed to regenerate for four days and then tissue was collected from the non-regenerating side of the head and pooled from around 300 animals to form the first of 2 independent biological replicates for this sample type.  These data are from the first of 2 technical replicates for this biological sample obtained from the same array.


title: Macrophage Donor 5 day 7 [8 Hy3TM]

source_name: Macrophage Donor 5 day 7


title: Macrophage Donor 5 day 5 [7 Hy3TM]

source_name: Macrophage Donor 5 day 5


title: Monocyte Donor 6 [16 Hy3TM]

source_name: Monocyte Donor 6


title: Macrophage Donor 5 day 3 [6 Hy3TM]

source_name: Macrophage Donor 5 day 3


title: Macrophage Donor 5 day 1 [5 Hy3TM]

source_name: Macrophage Donor 5 day 1


title: Macrophage Donor 5 4 hour [3 Hy3TM]

source_name: Macrophage Donor 5 4 hour


title: Macrophage Donor 5 12 hour [4 Hy3TM]

source_name: Macrophage Donor 5 12 hour


title: Day3os_11424_1

description:
raw data file: Day3os_11424.pair
Following amputation of one side of the head, planarians were allowed to regenerate for three days and then tissue was collected from the non-regenerating side of the head and pooled from around 300 animals to form the second of 2 independent biological replicates for this sample type.  These data are from the first of 2 technical replicates for this biological sample obtained from the same array.

source_name: non-regenerating side of head, day 3 regenerates

value: day 3 after half-head amputation