title: Human_normal_sample_Healthy-6

status: Public on Feb 28 2017

type: RNA

city: Ann Arbor

first: Weichen

last: Zhou

state: Michigan

address: 800 fuller St. 26

country: USA

institute: Fudan University

description:
Gene expression data from liver tissue of healthy patients.
Liver tissue cRNA

hyb_protocol: not provided

scan_protocol: not provided

data_processing: CEL files were performed by Affymetrix Expression Console. Probe set signals were normalized and summarized by the robust multi-array average (RMA) algorithm to adjust different batch effects. All samples passed quality control and were then annotated.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Healthy liver

label_protocol: not provided

extract_protocol: All samples were obtained by liver biopsy and blood sampling, and liver tissues were preserved at -80℃. Liver tissue cRNA was extracted and processed by GeneChip Human Genome U133 Plus 2.0 Arrays.

tag: tissue

value: liver

tag: alt

value: NON

tag: ast

tag: hbv-dna


title: Human_normal_sample_Healthy-2


title: Human_normal_sample_Healthy-5


title: Human_normal_sample_Healthy-3


title: Human_normal_sample_Healthy-1


title: Human_normal_sample_Healthy-4


title: brain stem control/experimental repl. 5

city: Cleveland

first: Yibayiri

middle: Osee

last: Sanogo

state: OH

address: 9500 S Euclid Ave

department: Genomics Core

institute: Cleveland Clinic Foundation

description:
Navarro river, CA, USA
5BS

hyb_protocol: Samples representing individual brain parts were labeled using either Cy3 or Cy5 dyes and competitively hybridized to the arrays. We used a balanced design in the microarray experiment and controlled for dye effect by performing dye swaps. For hybridization, 900 ng cRNA of samples from control and experimental groups labeled with different dyes were mixed, fragmented and hybridized onto an Agilent 4×44K oligonucleotide microarray

scan_protocol: The microarray slides were scanned on an Axon 4000B scanner (Molecular Devices Corporation, Sunnyvale, CA, USA) and expression feature were extracted using GenePix Pro 6.0 software (Molecular Devices)

data_processing: As preprocessing methods of gene expression intensities, we used within array loess normalization, background-corrected using normepr method. For the between array normalization, we used the Aquantile method.

organism: Gasterosteus aculeatus

source_name: control fish

label_protocol: The samples were labeled using the Agilent Two-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) following the manufacturer’s instructions.

growth_protocol: The fish were maintained in our laboratory in 104L tanks under 8:16h light/dark photoperiod during the winter period. An average of 10% of the water in the tanks was recycled each day. The adult fish were fed ad libitum with a mixture of bloodworms, serpula and mysis

extract_protocol: Each fish brain parts was individually dissected and placed immediately on ice in 500ml of TRIzol® Reagent (Invitrogen, Carlsbad, CA). Total RNA was isolated immediately from individual brains using TRIzol® Reagent according to the manufacturer’s recommendation followed by on column purification with RNeasy kit (QIAGEN GmbH, Hilden, Germany).

treatment_protocol: Fish in the control and experimental groups were paired and matched by size. The behavior of the fish was video-recordedand later scored for courtship behavior.

value: brain regions

tag: developmental stage

value: Adult

tag: Sex

value: Male

tag: sample group

value: control

value: brain stem

source_name: experimental fish selected for aggressive behavior

value: presented a female on their territory


title: Human_HBV_sample_Hep-0880

description: Gene expression data from liver tissue of HBV infected patients

source_name: positive HBsAg or serum HBV-DNA


title: brain stem control/experimental repl. 6

description:
Navarro river, CA, USA
6BS


title: Human_HBV_sample_Hep-0879


title: Human_HBV_sample_Hep-0898


title: CD11cCrexTGFßRKO Cre- Replicate 3

city: Edinburgh

first: Anika

last: Schridde

address: 47 Little France Crescent

country: United Kingdom

institute: University of Edinburgh

hyb_protocol: cRNA fragmentation, hybridization and washing steps were carried-out as recommended in the ‘One-Color Microarray-Based Gene Expression Analysis Protocol V5.7’, except that 300ng of each fluorescently labelled cRNA population were used for hybridization.

scan_protocol: Slides were scanned on the Agilent Micro Array Scanner G2565CA (pixel resolution 3 µm, bit depth 20).

data_processing: Data extraction was performed with the ‘Feature Extraction Software V10.7.3.1’ using the extraction protocol file ‘GE1_107_Sep09.xml’. Processed intensity values of the green channel, ‘gProcessedSignal’ (gPS) were normalized by global linear scaling: All gPS values of one sample were multiplied by an array-specific scaling factor. This factor was calculated by dividing a ‘reference 75th Percentile value’ (set as 1500 for the whole series) by the 75th Percentile value of the particular Microarray to be normalized (‘Array I’ in the formula shown below). Accordingly, normalized gPS values for all samples (microarray data sets) were calculated by the following formula:   normalized gPSArray i = gPSArray i  x (1500 / 75th PercentileArray i)  Measurements of on-chip replicates (quadruplicates) were averaged using the geometric mean of normalized gPS values to retrieve one resulting value per probe and sample. Single Features were excluded from averaging, if they i) were manually flagged, ii) were identified as Outliers by the Feature Extraction Software, iii) lay outside the interval of ‘1.42 x interquartile range‘ regarding the normalized gPS distribution of the respective on-chip replicate population, or, iv) showed a coefficient of variation of pixel intensities per Feature that exceeded 0.5.

organism: Mus musculus

source_name: colonic lamina propria

label_protocol: 10-20 ng of total RNA were used to prepare aminoallyl-UTP-modified (aaUTP) cRNA (Amino Allyl MessageAmp™ II Kit; #AM1753; Life Technologies) as directed by the company (applying one-round of amplification). Prior to the reverse transcription reaction, 1µl of a 1:100000 dilution of Agilent’s ‘One-Color spike-in Kit stock solution’ (#5188-5282, Agilent Technologies) was added to each single sample. The labeling of aaUTP-cRNA was performed by use of Cy3 Post-Labelling Reactive Dye (#1027-8754; Fisher Scientific).

extract_protocol: RNA was prepared using the Rneasy Micro Kit (Qiagen) following the manufacturer's recommendations.

tag: strain

value: colon

tag: age

value: 7 weeks

tag: gender

value: female


title: CD11cCrexTGFßRKO Cre+ Replicate 3


title: M2 polarized macrophage, biological rep1

city: shanghai

first: Jian-Yang

last: Ao

state: State...

address: fenglin 180#, Xuhui district,shanghai

country: China

description:
Gene expression data from  PMA differentiated-THP-1 macrophages
M(IL4)a

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 4.0 (Affymetrix, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software12.6.1 (Agilent technologies, Santa Clara, CA, US).

source_name: M2 polarized macrophage

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3' IVT PLUS Reagent Kit (Cat#902416, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: Human monocyte THP-1 cells obtained from American Type Culture Collection were cultured in RPMI 1640 (Invitrogen, Carlsbad, CA) containing 10% FBS and supplemented with 10 mM Hepes (Gibco BRL).

extract_protocol: Total RNA was extracted and purified using miRNeasy Mini Kit（Cat#217004, QIAGEN, GmBH, Germany) following the manufacturer’s instructions.

treatment_protocol: THP-1 was differentiated into macrophages by 24-h incubation with 160 nM phorbol 12-myristate 13-acetate (PMA; Sigma, St. Louis, MO) followed by 24-h incubation in RPMI medium. Macrophages were further polarized to M1 macrophages by incubation with 20 ng/ml of IFN-γ (R&D Systems, MN, USA) and 10 pg/ml of LPS (Sigma). M2 polarization of macrophages was obtained by incubation with 20 ng/ml of IL-4 (R&D Systems)

tag: source cell type

value: Human monocyte THP-1 cells

tag: cell type

value: PMA differentiated-THP-1 macrophages

tag: stimulated with

tag: cell subtype

value: M2 polarized macrophage


title: M1 polarized macrophage, biological rep3

description:
Gene expression data from  PMA differentiated-THP-1 macrophages
M(LPS+IFNγ)c

source_name: M1 polarized macrophage

value: 20 ng ml(-1) IFNγ + 10 pg ml(-1) LPS

value: M1 polarized macrophage


title: M2 polarized macrophage, biological rep3

description:
Gene expression data from  PMA differentiated-THP-1 macrophages
M(IL4)c


title: M2 polarized macrophage, biological rep2

description:
Gene expression data from  PMA differentiated-THP-1 macrophages
M(IL4)b


title: M1 polarized macrophage, biological rep1

description:
Gene expression data from  PMA differentiated-THP-1 macrophages
M(LPS+IFNγ)a


title: M1 polarized macrophage, biological rep2

description:
Gene expression data from  PMA differentiated-THP-1 macrophages
M(LPS+IFNγ)b


title: Human_HBV_sample_Hep-0878


title: brain stem control/experimental repl. 3

description:
Navarro river, CA, USA
3BS


title: brain stem control/experimental repl. 4

description:
Navarro river, CA, USA
4BS


title: brain stem control/experimental repl. 2

description:
Navarro river, CA, USA
2BS


title: CD11cCrexTGFßRKO Cre- Replicate 2


title: brain stem control/experimental repl. 1

description:
Navarro river, CA, USA
1BS


title: Human_HBV_sample_Hep-0863


title: CD11cCrexTGFßRKO Cre+ Replicate 2


title: CD11cCrexTGFßRKO Cre+ Replicate 1


title: Human_HBV_sample_Hep-0876


title: cerebellum control/experimental repl. 3

description:
Navarro river, CA, USA
3C

value: cerebellum


title: cerebellum control/experimental repl. 5

description:
Navarro river, CA, USA
5C


title: cerebellum control/experimental repl. 4

description:
Navarro river, CA, USA
4C


title: cerebellum control/experimental repl. 6

description:
Navarro river, CA, USA
6C


title: CD11cCrexTGFßRKO Cre- Replicate 1


title: Human_HBV_sample_Hep-0862

value: liver


title: cerebellum control/experimental repl. 1

description:
Navarro river, CA, USA
1C


title: diencephalon control/experimental repl. 5

description:
Navarro river, CA, USA
5D

value: diencephalon


title: cerebellum control/experimental repl. 2

description:
Navarro river, CA, USA
2C

value: brain regions


title: Human_HBV_sample_Hep-0859

value: NON


title: Human_HBV_sample_Hep-0858


title: telencephalon control/experimental repl. 6

description:
Navarro river, CA, USA
6T

value: Adult

value: Male

value: telencephalon


title: telencephalon control/experimental repl. 3

description:
Navarro river, CA, USA
3T

value: control

value: presented a female on their territory


title: Human_HBV_sample_Hep-0855


title: diencephalon control/experimental repl. 1

description:
Navarro river, CA, USA
1D


title: diencephalon control/experimental repl. 2

description:
Navarro river, CA, USA
2D


title: Human_HBV_sample_Hep-0851


title: diencephalon control/experimental repl. 3

description:
Navarro river, CA, USA
3D


title: diencephalon control/experimental repl. 4

description:
Navarro river, CA, USA
4D


title: diencephalon control/experimental repl. 6

description:
Navarro river, CA, USA
6D


title: telencephalon control/experimental repl. 4

description:
Navarro river, CA, USA
4T


title: Human_HBV_sample_Hep-0846


title: telencephalon control/experimental repl. 5

description:
Navarro river, CA, USA
5T


title: telencephalon control/experimental repl. 2

description:
Navarro river, CA, USA
2T


title: telencephalon control/experimental repl. 1

description:
Navarro river, CA, USA
1T


title: Human_HBV_sample_Hep-0815


title: Human_HBV_sample_Hep-0816


title: Human_HBV_sample_Hep-0811


title: Human_HBV_sample_Hep-0813


title: 1054T

city: Guangzhou

first: Dong-liang

last: Chen

address: No.651 Dong Feng East Road

institute: Sun Yat-sen University Cancer Center

hyb_protocol: and the cDNA was then labeled and hybridized to the LncRNA Expression Microarray (Arraystar 8x60Kv3.0, Rockville, USA) according to the manufacturer’s protocol.

scan_protocol: After hybridization, the arrays were washed, and the slides were scanned with a Agilent Microarray Scanner (Agilent p/n G2565BA).

data_processing:
Data were extrated using Agilent Feature Extraction Software, the procedure is as following:
1) Open the Agilent Feature Extraction (FE) software; 2) Add the images (.tif) to be extracted to the FE Project; 3) Set FE Project Properties; 4) Check the Extraction Set Configuration; 5) Save the FE Project (.fep) by selecting File > Save As and browse for desired location; 6) Select Project > Start Extracting and export data to txt

source_name: colorectal cancer tissue

label_protocol: Standard agilent protocol

extract_protocol: Total RNA was extracted using Trizol reagent (Invitrogen, Carlsbad, CA) according to the manufacturer’s instructions.

tag: tissue/phenotype

value: colorectal cancer with liver metastasis


title: 1051T

value: male

value: colorectal cancer without liver metastasis


title: 1057T

value: female


title: 1043T


title: 1049T


title: 1019T


title: Human_HBV_sample_Hep-0799


title: 1033T


title: Human_HBV_sample_Hep-0794


title: 939T


title: 933T


city: Baltimore

first: Luigi

last: Marchionni

state: MD

address: 1550 Orleans St., CRB2, Room 1M52

department: Oncology

institute: Johns Hopkins University

description: Hybridization for patient S_11-243 - Tumor

hyb_protocol: Hybridization were performed according to the Agilent miRNA Microarray Protocol (Agilent Technologies, Santa Clara, CA). Briefly, the labeled RNA samples were concentrated in a Vacuum Concentrator and prepared for hybridization by adding nuclease-free water, Hyb Spike-In solution, 10X GE Blocking Agent and 2X Hi-RPM Hybridization Buffer. 45 microliter of hybridization solution was dispensed into the gasket slide and assembled to the Agilent SurePrint G3 Human miRNA 8X60K, V16.0 Microarrays and then rotated at 20 rpm for 20 hours at 55 degrees Celsius.

scan_protocol: After hybridization, all slides were washed using Agilent Gene Expression Wash Buffers 1(at room temperature) and 2 ( at 37 degrees Celsius). The slides were immediately scanned on a Agilent Technologies G4900DA SureScan scanner at 3 micrometer resolution.

data_processing: Data were acquired with Agilent Feature Extraction 9.5.3.1 software for miRNA microarray, generating both probe-level signal intensities from all probes and summarized expression levels for each miRNA. The AgiMicroRna Bioconductor package was used to pre-process the raw data. First control, undetected probes, and outliers were filtered, then gene level expression summaries were obtained after normalization at the probe level using the RMA algorithm and quantile-normalization across samples.

source_name: Hybridization for  Clear cell papillary renal cell carcinoma sample: S_11-243_Tumor

label_protocol: The miRNA Microarray System with miRNA Complete Labeling and hybridization Kit (Agilent Technologies) was used according to manufacturer′s protocols. The Agilent microRNA Spike-In Kit was used to measure labeling and hybridization efficiency. Briefly, 150ng total RNA was dephosphorylated at 37 degrees Celsius for 30 min with calf intestinal phosphatase and denatured by using 100% DMSO at 100 degrees Celsius for 7 minutes. Samples were labeled with pCp-Cy3 using T4 ligase by incubation at 16 degrees Celsius for 2 hour.

extract_protocol: Representative formalin fixed paraffin embedded (FFPE) tissue samples were selected for RNA preparation. The FFPE blocks were cored with a sterile 16-gauge needle, and tumor areas showing at least 50% neoplastic cellularity were selected microscopically to enrich for neoplastic cells. Total RNA was extracted using the RecoverAll Total Nucleic Acid Isolation kit (Ambion Inc., Austin, TX, USA) per manufacturer’s protocol. RNA quality was evaluated using Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA). All analyzed samples showed 28S to 18S ratio > 1.2, an RNA Integrity Number (RIN) > 8, and detectable microRNAs.

tag: disease status

value: Tumor

tag: patient


title: Human_HBV_sample_HeP-0781

tag: tissue


title: 1009T


description: Hybridization for patient S_11-243 - Normal

source_name: Hybridization for  Clear cell papillary renal cell carcinoma sample: S_11-243_Normal

value: Normal


title: Untreated ECF delta 7 labeled with 555 vs induced Strain labeled with 647

city: Ithaca

first: Ahmed

last: Gaballa

state: NY

address: 370 Wing Hall, Cornell Univ

institute: Cornell University

description: uninduced delta7555 induced647

hyb_protocol: Equal amounts (100-150 pmol) of labeled cDNA were combined plus hybridization buffer (2X = 50% form amide, 10X SSC, 0.1% SDS). cDNA mix was denatured at 95oC and hybridized 16-18 hours at 42oC to DNA microarray slides which had been prehybridized for at least 30 min at 42oC in 1% bovine serum albumin, 5X SSC (1X SSC is 0.15 M NaCl and 0.015 M sodium citrate), 0.1% sodium dodecyl sulfate (SDS), washed in water and dried. Following hybridization the slides were washed sequentially in: 2X SSC + 0.1% SDS for 5 min at 42oC, 2X SSC + 0.1% SDS for 5 min at room temperature, 2X SSC for 5 min at room temperature, 0.2X SSC for 5 min at room temperature, and finally dipped in water and spun until dry.

scan_protocol: Arrays were scanned using a GenePixTM 4000B array scanner (Axon Instruments, Inc.). Raw data files were produced from the scanned images using the GenePix Pro 4.0 software package (GPR files).

data_processing: Red/green fluorescence intensity values were normalized using the GenePix Pro 4.0 software package such that the ratio of medians of all features was equal to 1

label: Alexa Fluor 555

organism: Bacillus subtilis

source_name: Untreated delta 7

label_protocol: Total RNA were then treated with Turbo-DNAse (Thermo Fisher Scientific) to remove any possible DNA contamination, and then reverse transcribed using SuperScript™ Indirect cDNA Labeling System (Thermo Fisher Scientific) into cDNA. cDNA was aliquoted and labelled with either fluorescent dye 555 or dye 647, and hybridized to microarray slides containing 60 nt oligonucleotides for each coding region according to laboratory protocol.

extract_protocol: Total RNA was extracted using RNeasy kit from independent replicate cultures using the manufacturer recommendations.

treatment_protocol: The wild type and delta 7 expressing Pspac-sigV strains were grown separately in liquid LB medium to OD600 ~0.6. IPTG was added to one half of the cultures and RNA was isolated after 20 minutes of further incubation.

tag: genotype/variation

value: lacking all 7 ECF sigma factor

tag: induced with

value: none (untreated)

label: Alexa Fluor 647

source_name: IPTG induced

value: IPTG for 20min


title: 1014T


title: Untreated WT labeled with 555 vs induced Strain labelled with 647

description: uninduced WT555 induced647

source_name: Untreated WT

value: wild type


title: Human_HBV_sample_Hep-0783

value: liver

tag: alt

tag: ast

tag: hbv-dna


title: Human_HBV_sample_Hep-0784


title: 951T


title: 946T


title: 920T


title: 930T


description: Hybridization for patient S_11-82070 - Normal

source_name: Hybridization for  Clear cell papillary renal cell carcinoma sample: S_11-82070_Normal


description: Hybridization for patient S_11-82070 - Tumor

source_name: Hybridization for  Clear cell papillary renal cell carcinoma sample: S_11-82070_Tumor


title: Human_HBV_sample_HeP-0782

value: NON


title: sk_TSA2

city: Xi'an

first: Ting

last: Wang

address: Changlexilu Road

department: Biochemistry and Molecular Biology

institute: the Fourth Military Medical University

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

scan_protocol: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images.

data_processing:
Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 1 out of 6 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis.
Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering. Hierarchical Clustering and combined analysis were performed using homemade scripts.

label_protocol: Sample labeling were 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 (Arraystar Flash RNA Labeling Kit, Arraystar). 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: Three cases of TSA treated and untreated SKBR3 cells were prepared for the extraction of total RNA.RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

treatment_protocol: Gene expression in human breast cancer cell SKBR3 was measured at 24 hours after treated with 330nM TSA. Three independent experiments were performed at each time using different donors for each experiment.

value: Breast cancer

tag: cell line

tag: treatment

value: 330nM TSA treated for 24 hours.


title: sk_TSA3


title: sk_TSA1


title: sk_control3

value: pbs


description: Hybridization for patient S_12-41240 - Tumor

source_name: Hybridization for  Clear cell papillary renal cell carcinoma sample: S_12-41240_Tumor


title: Human_HBV_sample_Hep-0779


title: Human_HBV_sample_Hep-0877


description: Hybridization for patient S_12-36332 - Tumor

source_name: Hybridization for  Clear cell papillary renal cell carcinoma sample: S_12-36332_Tumor


description: Hybridization for patient S_12-36332 - Normal

source_name: Hybridization for  Clear cell papillary renal cell carcinoma sample: S_12-36332_Normal


description: Hybridization for patient S_12-41240 - Normal

source_name: Hybridization for  Clear cell papillary renal cell carcinoma sample: S_12-41240_Normal


title: sk_control2


title: Human_HBV_sample_Hep-0776


title: Human_HBV_sample_Hep-0773


title: Human_HBV_sample_Hep-0777


title: Human_HBV_sample_Hep-0775


title: Human_HBV_sample_Hep-0770


title: Dexamethasone_F30

city: Linkoping

first: Neil

last: Lagali

address: sandbacksgatan 7

department: Ophthalmology

country: Sweden

institute: linkoping University

hyb_protocol: Following fragmentation, 200µl of the prepared hybridisation cocktail was hybridized into GeneChip Rat Genome 230 2.0 (64-format) Array, and incubated for 16hr at 45ºC, and at 60 rpm (GeneChip® WT PLUS Reagent Kit, P/N 703174 Rev. 2, Affymetrix Inc).

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

data_processing: Hybridisation of the Poly-A spike-in controls were verified, and gride alignment was checked. Robust Multi-array Average (RMA) was used for background correction, normalisation and computation of probe-set level expression using Expression Console™ Software 1.4.1 (Affymetrix)

organism: Rattus norvegicus

source_name: R. norvegicus albino-right eye sutured eye_dexamethasone

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

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

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

treatment_protocol: Suture-Induced inflammatory corneal neovascularization model in rats was used. Two sutures were placed temporally into the cornea at a distance of 1.5mm from the limbus. Opnol (Dexamethasone 1 mg/ml), Rat specific anti-VEGF 20 mg/ml and Goat IgG 20 mg/ml, were given as topical eyedrops, over a period of two days. Four eyedrops were given perday, and a total of 8 eyedrops per treament were given.

tag: strain

value: wistar

tag: age

value: sutured cornea

tag: treated with

value: dexamethasone


title: Control sample 4

description: Cont 4

source_name: R. norvegicus albino non sutured eye_no treatment

tag: gender

value: male

value: non-sutured cornea


title: Human_HBV_sample_Hep-0774

source_name: positive HBsAg or serum HBV-DNA


title: Control sample 2

description: Cont 2R


title: Control sample 1

description: Cont 1


title: Human_HBV_sample_Hep-0768


title: Human_HBV_sample_Hep-0769


title: Dexamethasone_F27


title: sk_control1


title: Control sample 3

description: Cont 3


title: Human_HBV_sample_Hep-0767


title: Control basal cells_D4 post wound_ Biological replicate3

city: Bruxelles

first: Cedric

last: Blanpain

address: route de Lennik, 808

country: Belgium

institute: Université Libre De Bruxelles

description:
Gene expression data from basal cells of the interfollicular epidermis
Control_3

hyb_protocol: Affymetrix MG-430 PM array strips were hybridized with 8 mg of labeled cDNA, washed, stained and scanned according to the protocol described in GeneAtlas 3’IVT express kit User Manual.

scan_protocol: Arrays were scanned with GeneAtlasImaging station scanner (Affymetrix, Santa Clara, CA)

data_processing: Normalized expression signals were calculated from Affymetrix CEL files using RMA algorithm (Irizarry et al., 2003)

label: Biotin

source_name: Control basal cells, D4 post wound

label_protocol: cDNA was labeled using GeneChip Mapping 250K Nsp Assay Kit (Affymetrix; catalog # 900766), according to manufacturer's instructions.

growth_protocol: Mouse colonies were maintained in a certified animal facility in accordance with the European guidelines.

extract_protocol: RNA isolation and cDNA amplification was performed as described by Gonzalez-Roca et al. (2010).In brief, 300 cells were sorted into lysis buffer and RNA was purified using magnetic beads (RNAClean XP beads, Agencourt).RNA was reverse transcribed and cDNA was amplified using Whole Transcriptome Amplification chemistry (WTA2, Sigma Aldrich). For monitoring amplification, SYBR Green was added to the reaction; it was stopped after 25 cycles when SYBR Green signal reached a plateau. cDNA was purified using Genelute PCR Clean-Up kit (Sigma Aldrich).

treatment_protocol: To separate epidermis from dermis, the samples were incubated in HBSS (Gibco) 0,25% trypsin  (Gibco) at 37°C.Epidermis was then incubated on a rocking plate (100 rpm) at room temperature for 5 min. Basal cells were mechanically separated from the epidermis by flushing 10 times under the epidermis. Epidermis was then incubated on a rocking plate (100 rpm) at room temperature for 5 min. Basal cells were mechanically separated from the epidermis by flushing 10 times under the epidermis. Tissues were then cut in pieces of 1 mm2 with scalpel and trypsin was neutralized by adding DMEM medium (Gibco) supplemented with 2% Chelex Fetal Calf Serum (FCS). Samples were filtrated on 70 and 40µm filter (Falcon). Cells were incubated in 2% FCS/PBS with primary antibodies for 30 min on ice, protected from the light, with shaking every 10 min. Immunostaining for isolating basal IFE and infundibulum cells was performed using FITC-conugated anti-α6-integrin (clone GoH3; BD biosciences). CD34 staining was used to exclude bulge cells from the sorted cells (clone RAM34; BD Biosciences).Cells were then gated with PE-coniugated-anti--α5-integrin (clone 5H10-27; BD biosciences). Primary antibodies were washed with 2% FCS/PBS and cells incubated for 30 min in APC conjugated streptavidin (BD Biosciences), on ice, with shaking every 10 min. Living epidermal cells were gated by forward scatter, side scatter and negative staining for Hoechst dye. Basal cells from the interfollicular epidermis were targeted using CD34 negative and α6 integrin positive gating. Fluorescence-activated cell sorting analysis was performed using FACSAria I at high pressure (70 psi) and FACSDiva software (BD Biosciences).

value: Wounded tail interfollicular epidermis

tag: time point

value: D4 post wound

tag: region

value: Control (a region far from the wounded area)

tag: cell type

value: basal cells


title: Dexamethasone_F26


title: Human_HBV_sample_Hep-0763


title: Human_HBV_sample_Hep-0759


title: Proliferative hub basal cells_D4 post wound_ITGA5negative_Biological replicate3

description:
Gene expression data from basal cells of the interfollicular epidermis
ProliferativeHub_ITGA5neg_3

source_name: Proliferative hub basal cells, D4 post wound, ITGA5negative

value: Proliferative hub


title: Control basal cells_D4 post wound_ Biological replicate2

description:
Gene expression data from basal cells of the interfollicular epidermis
Control_2


title: Dexamethasone_F25


title: Anti-IgG_F23

source_name: R. norvegicus albino-right eye sutured eye_anti-IgG antibody

value: anti-IgG antibody


title: Control basal cells_D4 post wound_ Biological replicate1

description:
Gene expression data from basal cells of the interfollicular epidermis
Control_1


title: Human_HBV_sample_Hep-0762

description: Gene expression data from liver tissue of HBV infected patients


title: Anti-IgG_F22


title: Human_HBV_sample_Hep-0758


title: Anti-IgG_F19


title: Human_HBV_sample_Hep-0327


title: Anti-VEGF_F2

source_name: R. norvegicus albino-right eye sutured eye_anti-VEGFA antibody

value: anti-VEGFA antibody


title: Anti-VEGF_F1x


title: Proliferative hub basal cells_D4 post wound_ITGA5negative_Biological replicate1

description:
Gene expression data from basal cells of the interfollicular epidermis
ProliferativeHub_ITGA5neg_1


title: Human_HBV_sample_Hep-0757

value: liver


title: Human_HBV_sample_Hep-0326


title: Human_HBV_sample_Hep-0325

value: NON


title: Human_HBV_sample_Hep-0754


title: Proliferative hub basal cells_D4 post wound_ITGA5negative_Biological replicate2

description:
Gene expression data from basal cells of the interfollicular epidermis
ProliferativeHub_ITGA5neg_2


title: Anti-VEGF_F7


title: Anti-IgG_F17


title: Leading edge basal cells_ D4 post wound_ITGA5positive_Biological replicate3

description:
Gene expression data from basal cells of the interfollicular epidermis
LeadingEdge_ITGA5pos_3

source_name: Leading edge basal cells, D4 post wound, ITGA5positive

value: Leading edge


title: Anti-VEGF_F6


title: Leading edge basal cells_ D4 post wound_ITGA5positive_Biological replicate1

description:
Gene expression data from basal cells of the interfollicular epidermis
LeadingEdge_ITGA5pos_1


title: Human_HBV_sample_Hep-0818


title: Liver_WildType_Female_Vehicle_rep4

city: Research Triangle Park

first: Christopher

last: Corton

state: NC

address: 109 TW Alexander Dr.

institute: US-EPA

hyb_protocol: Hybridization and washing were carried out according to the manufacturer's recommendations

scan_protocol: Scanning (Affymetrix Gene Atlas) was performed according to the manufacturer's recommendations

data_processing: Gene expression results were analyzed in Partek Genomic Suite by standard methods using Robust Multichip Average (RMA) normalization.

source_name: Female_Liver, Wild type, 0 mg/kg Vehicle

label_protocol: Procedures for labeling (Affymetrix GeneChip 3’-IVT Plus kit) was carried out according to the manufacturer's recommendations

extract_protocol: Liver RNA was isolated using a modified guanidinium isothiocyanate method (TRIzol®, Invitrogen) and was further purified using silica membrane spin columns (RNeasy®, Qiagen, Valencia, CA).  RNA integrity was assessed by the RNA 6000 LabChip® kit using a 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

treatment_protocol: Livers were excised, weighed, diced, and snap frozen for RNA extraction and stored at -80oC.

tag: genotype

value: Wild type

value: 8-10 weeks

tag: Sex

value: Female

tag: vehicle

value: Corn Oil

tag: dose

value: 0 mg/kg

tag: route

value: Intraperitoneal Injection

tag: number of doses

tag: sample time

value: 48 hours post dose


title: Leading edge basal cells_ D4 post wound_ITGA5positive_Biological replicate2

description:
Gene expression data from basal cells of the interfollicular epidermis
LeadingEdge_ITGA5pos_2

tag: tissue

value: Wounded tail interfollicular epidermis


title: Liver_WildType_Female_Vehicle_rep3


title: ALL_patient_108 [HG-U133A]

city: Munich

first: Tobias

last: Herold

address: Marchioninistr. 15

department: Department of Internal Medicine III

country: Germany

institute: University Hospital Grosshadern, Ludwig-Maximilians-University (LMU)

description: Sample name: ALK_ALL_Ph_040372_12_PZ

hyb_protocol: Sample hybridisation was performed for 16 hours according to standard Affymetrix protocols.

scan_protocol: Samples were scanned using an Affymetrix GeneChip scanner.

data_processing: Normalization was performed using the Robust Multichip Average (RMA) method. Quality control consisted of visual inspection of the array image for artifacts, assessment of RNA degradation plots, and inspection of rank-vs.-residual plots after normalization and probe set summarization.

source_name: bone marrow mononuclear cells, Ph-positive ALL

label_protocol: Biotin labeling of antisense cRNA was performed according to standard Affymetrix protocols.

extract_protocol: Mononuclear cells from bone marrow (BM) were enriched by Ficoll gradient centrifugation. Total RNA was isolated using the RNeasy Mini Kit (Qiagen, Hilden, Germany). cDNA preparation and in vitro transcription were performed according to standard Affymetrix protocols.

treatment_protocol: Pretreatment bone marrow mononuclear cells from patients with newly diagnosed acute lymphoblastic leukemia (ALL).

value: adult

value: bone marrow mononuclear cells

tag: disease state

value: acute lymphoblastic leukemia (ALL)

tag: all type

value: Ph-positive


title: Liver_WildType_Female_Vehicle_rep1

tag: strain


title: Human_HBV_sample_Hep-0324

tag: alt

tag: ast

tag: hbv-dna


title: Human_HBV_sample_Hep-0319


title: Liver_WildType_Female_TCPOBOP_rep4

source_name: Female_Liver, Wild type, 3 mg/kg TCPOBOP

tag: age

tag: chemical

value: 3 mg/kg


title: ALL_patient_109 [HG-U133A]

description: Sample name: ALK_ALL_Ph_040718_18_PZ

tag: cell type


title: Liver_WildType_Female_TCPOBOP_rep3

tag: genotype


title: Human_HBV_sample_Hep-0323


title: Liver_WildType_Female_Vehicle_rep2

tag: Sex


title: Liver_WildType_Female_TCPOBOP_rep1

tag: vehicle


title: Human_HBV_sample_Hep-0315


title: Liver_WildType_Female_TCPOBOP_rep2

tag: dose


title: ALL_patient_106 [HG-U133A]

description: Sample name: ALK_ALL_Ph_034837_92_PZ


title: ALL_patient_107 [HG-U133A]

description: Sample name: ALK_ALL_Ph_040367_48_PZ


title: Liver_Cyp2b9/10/13-null_Female_Vehicle_rep3

source_name: Female_Liver, Cyp2b9/10/13-null, 0 mg/kg Vehicle

tag: route


title: ALL_patient_101 [HG-U133A]

description: Sample name: ALK_ALL_Ph_024972_31_PZ


title: ALL_patient_105 [HG-U133A]

description: Sample name: ALK_ALL_Ph_034794_91_PZ


title: ALL_patient_102 [HG-U133A]

description: Sample name: ALK_ALL_Ph_031058_1_PZ


title: Human_HBV_sample_Hep-0311


title: Human_HBV_sample_Hep-0321


title: Human_HBV_sample_Hep-0314


title: ALL_patient_103 [HG-U133A]

description: Sample name: ALK_ALL_Ph_031163_29_PZ


title: Human_HBV_sample_Hep-0309


title: ALL_patient_104 [HG-U133A]

description: Sample name: ALK_ALL_Ph_033157_2_PZ


title: Liver_Cyp2b9/10/13-null_Female_Vehicle_rep2

tag: number of doses


title: Liver_Cyp2b9/10/13-null_Female_Vehicle_rep4

tag: sample time


title: Liver_Cyp2b9/10/13-null_Female_Vehicle_rep1


title: Human_HBV_sample_Hep-0313

tag: tissue


title: Human_HBV_sample_Hep-0305


title: ALL_patient_100 [HG-U133A]

description: Sample name: ALK_ALL_Ph_023168_46_PZ

tag: disease state


title: Liver_Cyp2b9/10/13-null_Female_TCPOBOP_rep4

source_name: Female_Liver, Cyp2b9/10/13-null, 3 mg/kg TCPOBOP


title: ALL_patient_95 [HG-U133A]

description: Sample name: ALK_ALL_Ph_022204_15_PZ

tag: all type


title: ALL_patient_98 [HG-U133A]

description: Sample name: ALK_ALL_Ph_022644_37_PZ


title: ALL_patient_99 [HG-U133A]

description: Sample name: ALK_ALL_Ph_023121_28_PZ


title: Liver_Cyp2b9/10/13-null_Female_TCPOBOP_rep3

tag: strain


title: ALL_patient_94 [HG-U133A]

description: Sample name: ALK_ALL_Ph_021896_4_PZ


title: Human_HBV_sample_Hep-0293

tag: alt


title: Human_HBV_sample_Hep-0304

tag: ast


title: ALL_patient_97 [HG-U133A]

description: Sample name: ALK_ALL_Ph_022497_23_PZ


title: Liver_WildType_Male_Vehicle_rep4

source_name: Male_Liver, Wild type, 0 mg/kg Vehicle

value: Male


title: Human_HBV_sample_Hep-0290

value: liver

tag: hbv-dna


title: Liver_Cyp2b9/10/13-null_Female_TCPOBOP_rep2

tag: age


title: Human_HBV_sample_Hep-0303


title: ALL_patient_93 [HG-U133A]

description: Sample name: ALK_ALL_Ph_020898_24_PZ


title: Human_HBV_sample_Hep-0295


title: Liver_WildType_Male_Vehicle_rep3


title: Human_HBV_sample_Hep-0288

value: NON


title: ALL_patient_96 [HG-U133A]

description: Sample name: ALK_ALL_Ph_022302_16_PZ


title: Liver_WildType_Male_Vehicle_rep1


title: Human_HBV_sample_Hep-0281


title: Human_HBV_sample_Hep-0284


title: ALL_patient_91 [HG-U133A]

description: Sample name: ALK_ALL_Ph_020208_89_PZ


title: ALL_patient_92 [HG-U133A]

description: Sample name: ALK_ALL_Ph_020607_32_PZ


title: ALL_patient_90 [HG-U133A]

description: Sample name: ALK_ALL_Ph_020132_26_PZ


title: Liver_WildType_Male_TCPOBOP_rep4

source_name: Male_Liver, Wild type, 3 mg/kg TCPOBOP

tag: chemical


title: Liver_Cyp2b9/10/13-null_Female_TCPOBOP_rep1


title: Liver_WildType_Male_Vehicle_rep2


title: Human_HBV_sample_Hep-0280


title: Liver_WildType_Male_TCPOBOP_rep3


title: Human_HBV_sample_Hep-0287


title: Human_HBV_sample_Hep-0278


title: ALL_patient_89 [HG-U133A]

description: Sample name: ALK_ALL_Ph_015394_42_PZ

tag: cell type


title: ALL_patient_87 [HG-U133A]

description: Sample name: ALK_ALL_Ph_014319_43_PZ


title: ALL_patient_85 [HG-U133A]

description: Sample name: ALK_ALL_Ph_014066_27_PZ


title: Human_HBV_sample_Hep-0274


title: ALL_patient_84 [HG-U133A]

description: Sample name: ALK_ALL_Ph_012553_3_PZ


title: ALL_patient_86 [HG-U133A]

description: Sample name: ALK_ALL_Ph_014069_53_PZ


title: ALL_patient_88 [HG-U133A]

description: Sample name: ALK_ALL_Ph_014810_60_PZ


title: Liver_WildType_Male_TCPOBOP_rep1

tag: genotype


title: Human_HBV_sample_Hep-0235


title: Liver_Cyp2b9/10/13-null_Male_Vehicle_rep2

source_name: Male_Liver, Cyp2b9/10/13-null, 0 mg/kg Vehicle

tag: Sex


title: ALL_patient_83 [HG-U133A]

description: Sample name: ALK_ALL_Ph_012076_12_PZ


title: Human_HBV_sample_Hep-0273


title: Human_HBV_sample_Hep-0234


title: Human_HBV_sample_Hep-0217


title: Human_HBV_sample_Hep-0219


title: ALL_patient_82 [HG-U133A]

description: Sample name: ALK_ALL_Ph_011910_5_PZ


title: Human_HBV_sample_Hep-0216


title: ALL_patient_80 [HG-U133A]

description: Sample name: ALK_ALL_Ph_010823_30_PZ


title: Human_HBV_sample_Hep-0272


title: Human_HBV_sample_Hep-0214


title: Liver_Cyp2b9/10/13-null_Male_TCPOBOP_rep1

source_name: Male_Liver, Cyp2b9/10/13-null, 3 mg/kg TCPOBOP

tag: vehicle


title: Liver_Cyp2b9/10/13-null_Male_Vehicle_rep4

tag: dose


title: Liver_Cyp2b9/10/13-null_Male_TCPOBOP_rep4

tag: route


title: Human_HBV_sample_Hep-0220


title: Liver_Cyp2b9/10/13-null_Male_TCPOBOP_rep3

tag: number of doses


title: Liver_Cyp2b9/10/13-null_Male_Vehicle_rep3

tag: sample time


title: Liver_WildType_Male_TCPOBOP_rep2


title: Liver_Cyp2b9/10/13-null_Male_Vehicle_rep1


title: ALL_patient_81 [HG-U133A]

description: Sample name: ALK_ALL_Ph_011568_10_PZ


title: ALL_patient_77 [HG-U133A]

description: Sample name: ALK_ALL_MLL_035987_70_PZ

source_name: bone marrow mononuclear cells, MLL-positive ALL

value: MLL-positive


title: Human_HBV_sample_Hep-0213

tag: tissue


title: Control basal cells_D7 post wound_ Biological rep2

description:
Gene expression data from basal cells of the interfollicular epidermis
Control_D7_2

source_name: Control basal cells_D7 post wound

treatment_protocol: To separate epidermis from dermis, the samples were incubated in HBSS (Gibco) 0,25% trypsin  (Gibco) at 37°C.Epidermis was then incubated on a rocking plate (100 rpm) at room temperature for 5 min. Basal cells were mechanically separated from the epidermis by flushing 10 times under the epidermis. Epidermis was then incubated on a rocking plate (100 rpm) at room temperature for 5 min. Basal cells were mechanically separated from the epidermis by flushing 10 times under the epidermis. Tissues were then cut in pieces of 1 mm2 with scalpel and trypsin was neutralized by adding DMEM medium (Gibco) supplemented with 2% Chelex Fetal Calf Serum (FCS). Samples were filtrated on 70 and 40µm filter (Falcon). Cells were incubated in 2% FCS/PBS with primary antibodies for 30 min on ice, protected from the light, with shaking every 10 min. Immunostaining for isolating basal IFE and infundibulum cells was performed using PE-conjugated anti-α6-integrin (clone GoH3; BD biosciences). CD34 staining was used to exclude bulge cells from the sorted cells (clone RAM34; BD Biosciences). Primary antibodies were washed with 2% FCS/PBS and cells incubated for 30 min in APC conjugated streptavidin (BD Biosciences), on ice, with shaking every 10 min. Living epidermal cells were gated by forward scatter, side scatter and negative staining for Hoechst dye. Basal cells from the interfollicular epidermis were targeted using CD34 negative and α6 integrin positive gating. Fluorescence-activated cell sorting analysis was performed using FACSAria I at high pressure (70 psi) and FACSDiva software (BD Biosciences).

tag: strain background

tag: time point

value: D7 post wound

value: Wounded tail inetrfollicular epidermis

value: Control basal cells


title: Proliferative hub basal cells_D7 post wound_Biological rep1

description:
Gene expression data from basal cells of the interfollicular epidermis
ProliferativeHub_D7_1

value: Proliferative hub basal cells


title: ALL_patient_76 [HG-U133A]

description: Sample name: ALK_ALL_MLL_035349_15_PZ

tag: disease state

tag: all type


title: ALL_patient_75 [HG-U133A]

description: Sample name: ALK_ALL_MLL_030470_71_PZ


title: Liver_Cyp2b9/10/13-null_Male_TCPOBOP_rep2

tag: strain

value: 8-10 weeks

value: Corn Oil


title: Human_HBV_sample_Hep-0210

source_name: positive HBsAg or serum HBV-DNA

tag: alt

tag: ast

tag: hbv-dna


title: ALL_patient_74 [HG-U133A]

description: Sample name: ALK_ALL_MLL_030123_72_PZ

tag: age

tag: cell type


title: Human_HBV_sample_Hep-0206


title: Human_HBV_sample_Hep-0211


title: Human_HBV_sample_Hep-0208


title: Leading edge basal cells_ D7 post wound_Biological rep2

description:
Gene expression data from basal cells of the interfollicular epidermis
LeadingEdge_D7_2

source_name: Leading edge basal cells_D7 post wound

value: Leading edge basal cells


title: Control basal cells_D7 post wound_ Biological rep1

description:
Gene expression data from basal cells of the interfollicular epidermis
Control_D7_1


title: Proliferative hub basal cells_D7 post wound_Biological rep2

description:
Gene expression data from basal cells of the interfollicular epidermis
ProliferativeHub_D7_2


title: Human_HBV_sample_Hep-0204


title: ALL_patient_73 [HG-U133A]

description: Sample name: ALK_ALL_MLL_024733_69_PZ


title: ALL_patient_72 [HG-U133A]

description: Sample name: ALK_ALL_MLL_021932_79_PZ


title: Leading edge basal cells_ D7 post wound_Biological rep1

description:
Gene expression data from basal cells of the interfollicular epidermis
LeadingEdge_D7_1


title: Control basal cells_D4 post wound_ Biological rep2

description:
Gene expression data from basal cells of the interfollicular epidermis
Control_D4_2

source_name: Control basal cells_D4 post wound

value: D4 post wound


title: ALL_patient_70 [HG-U133A]

description: Sample name: ALK_ALL_hype_991773_41_PZ

source_name: bone marrow mononuclear cells, B-other ALL

value: adult

value: B-other


title: Human_HBV_sample_Hep-0197


title: Control basal cells_D4 post wound_ Biological rep1

description:
Gene expression data from basal cells of the interfollicular epidermis
Control_D4_1


title: ALL_patient_71 [HG-U133A]

description: Sample name: ALK_ALL_MLL_013575_66_PZ

value: bone marrow mononuclear cells

value: acute lymphoblastic leukemia (ALL)


title: ALL_patient_79 [HG-U133A]

description: Sample name: ALK_ALL_Ph_002136_26_PZ

value: Ph-positive


title: Human_HBV_sample_Hep-0191


title: ALL_patient_69 [HG-U133A]

description: Sample name: ALK_ALL_BN_035602_35_PZ

source_name: bone marrow mononuclear cells, Ph-like ALL

value: Ph-like


title: Human_HBV_sample_Hep-0201

value: liver


title: Proliferative hub basal cells_D4 post wound_Biological rep2

description:
Gene expression data from basal cells of the interfollicular epidermis
ProliferativeHub_D4_2


title: Leading edge basal cells_ D4 post wound_Biological rep2

description:
Gene expression data from basal cells of the interfollicular epidermis
LeadingEdge_D4_2

source_name: Leading edge basal cells_D4 post wound


title: Human_HBV_sample_Hep-0126


title: Human_HBV_sample_Hep-0118

value: NON


title: Human_HBV_sample_Hep-0127


title: Human_HBV_sample_Hep-0129


title: ALL_patient_67 [HG-U133A]

description: Sample name: ALK_ALL_BN_032229_14_PZ


title: Proliferative hub basal cells_D4 post wound_Biological rep1

description:
Gene expression data from basal cells of the interfollicular epidermis
ProliferativeHub_D4_1


title: R_Leaf at PDR, biological replicate 2

city: TOKAT

first: KUBILAY

last: YILDIRIM

address: TASLICIFTLIK

department: BIOENGINEERING

country: Turkey

institute: GAZIOSMANPASA UNIVERSITY

description: Resistant Black poplar leaves under post drought rewatering condition

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

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

data_processing: The data were analyzed with Robust Multiarray Analysis (RMA) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

organism: Populus nigra

source_name: leaves at 100% re_ field capacity

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: one year old black poplar seedling were cultivated in pots and subjected to a well-watered period by watering the pots up to field capacity (FC).

extract_protocol: Leaves collected at each watering regimes were utilized for total RNA isolation as described in Chang et al. (1993) with minor modifications as described in Le-Provost et al (2007).

treatment_protocol: the pots were weighted and let to transpire until the soil water contents (SWC) of the pots were decreased to %75 field capacity. At this level, the pots were weighted daily and the transpired water was replenished to keep the SWC of the pot at 75% FC for one week. The same procedure was adapted when the SWC of the pots was decreased 50 %, 25 % and 5% of FC. Lastly drought stressed plants were irrigated again to FC for three weeks

value: leaf

value: one year old seedling

tag: genotype

value: Drought Resistant


title: ALL_patient_66 [HG-U133A]

description: Sample name: ALK_ALL_BN_031375_22_PZ


title: Human_HBV_sample_Hep-0114

description: Gene expression data from liver tissue of HBV infected patients


title: ALL_patient_68 [HG-U133A]

description: Sample name: ALK_ALL_BN_033417_3_PZ


title: Leading edge basal cells_ D4 post wound_Biological rep1

description:
Gene expression data from basal cells of the interfollicular epidermis
LeadingEdge_D4_1

value: Wounded tail inetrfollicular epidermis


title: Human_HBV_sample_Hep-0113


title: ALL_patient_65 [HG-U133A]

description: Sample name: ALK_ALL_BN_024934_79_PZ


title: ALL_patient_64 [HG-U133A]

description: Sample name: ALK_ALL_BN_023445_42_PZ


title: R_Leaf at PDR, biological replicate 1

description: Resistant Black poplar leaves under severe drought condition


title: R_Leaf at SD, biological replicate 2

source_name: leaves at 5% field capacity


title: R_Leaf at SD, biological replicate 1

description: Resistant Black poplar leaves under moderate drought condition


title: ALL_patient_63 [HG-U133A]

description: Sample name: ALK_ALL_BN_023106_9_PZ


title: ALL_patient_62 [HG-U133A]

description: Sample name: ALK_ALL_BN_022243_23_PZ


title: Human_HBV_sample_Hep-0110


title: Human_HBV_sample_Hep-0102


title: ALL_patient_61 [HG-U133A]

description: Sample name: ALK_ALL_BN_022019_5_PZ


title: R_Leaf at MD, biological replicate 1

description: Resistant Black poplar leaves under well watered condition

source_name: leaves at 25% field capacity


title: Human_HBV_sample_Hep-0111


title: Human_HBV_sample_Hep-0117


title: R_Leaf at WWP, biological replicate 1

description: Sensitive Black poplar leaves under post drought rewatering condition

source_name: leaves at 100% field capacity


title: S_Leaf at PDR, biological replicate 2

value: Drought Sensitive


title: ALL_patient_60 [HG-U133A]

description: Sample name: ALK_ALL_BN_020186_88_PZ


title: Human_HBV_sample_Hep-0104


title: R_Leaf at WWP, biological replicate 2


title: R_Leaf at MD, biological replicate 2


title: Human_HBV_sample_Hep-0112


title: S_Leaf at PDR, biological replicate 1


title: ALL_patient_58 [HG-U133A]

description: Sample name: ALK_ALL_BA_040735_16_PZ


title: ALL_patient_56 [HG-U133A]

description: Sample name: ALK_ALL_BA_034658_90_PZ


title: Human_HBV_sample_Hep-0086


title: ALL_patient_57 [HG-U133A]

description: Sample name: ALK_ALL_BA_035276_34_PZ


title: S_Leaf at SD, biological replicate 1

description: Sensitive Black poplar leaves under severe drought condition


title: ALL_patient_54 [HG-U133A]

description: Sample name: ALK_ALL_BA_033676_8_PZ


title: Human_HBV_sample_Hep-0076


title: ALL_patient_59 [HG-U133A]

description: Sample name: ALK_ALL_BN_015539_84_PZ


title: ALL_patient_53 [HG-U133A]

description: Sample name: ALK_ALL_BA_033113_28_PZ


title: S_Leaf at MD, biological replicate 2

description: Sensitive Black poplar leaves under moderate drought condition


title: ALL_patient_52 [HG-U133A]

description: Sample name: ALK_ALL_BA_022422_17_PZ


title: Human_HBV_sample_Hep-0074


title: S_Leaf at WWP, biological replicate 1

description: Sensitive Black poplar leaves under well watered condition


title: ALL_patient_55 [HG-U133A]

description: Sample name: ALK_ALL_BA_034603_8_PZ


title: ALL_patient_78 [HG-U133A]

description: Sample name: ALK_ALL_MLL_040731_15_PZ

value: MLL-positive


title: ALL_patient_50 [HG-U133A]

description: Sample name: ALK_ALL_BA_021402_11_PZ


title: Human_HBV_sample_Hep-0101


title: Human_HBV_sample_Hep-0075


title: Human_HBV_sample_Hep-0072


title: Human_HBV_sample_Hep-0073


title: ALL_patient_51 [HG-U133A]

description: Sample name: ALK_ALL_BA_021833_24_PZ


title: S_Leaf at MD, biological replicate 1


title: Human_HBV_sample_Hep-0071


title: S_Leaf at SD, biological replicate 2


title: MR_Leaf at PDR, biological replicate 2

description: Moderate Resistant Black poplar leaves under post drought rewatering condition

value: Moderate Drought Resistant


title: Human_HBV_sample_Hep-0069


title: MR_Leaf at PDR, biological replicate 1


title: MR_Leaf at SD, biological replicate 2

description: Moderate Resistant Black poplar leaves under severe drought condition


title: S_Leaf at WWP, biological replicate 2


title: ALL_patient_48 [HG-U133A]

description: Sample name: ALK_ALL_BA_020704_18_PZ


title: ALL_patient_49 [HG-U133A]

description: Sample name: ALK_ALL_BA_021091_16_PZ


title: Human_HBV_sample_Hep-0067


title: Human_HBV_sample_Hep-0068


title: ALL_patient_44 [HG-U133A]

description: Sample name: ALK_ALL_B_036348_28_PZ


title: ALL_patient_46 [HG-U133A]

description: Sample name: ALK_ALL_BA_013739_8_PZ


title: Human_HBV_sample_Hep-0061


title: Human_HBV_sample_Hep-0040


title: Human_HBV_sample_Hep-0059


title: ALL_patient_45 [HG-U133A]

description: Sample name: ALK_ALL_BA_000875_34_PZ


title: ALL_patient_42 [HG-U133A]

description: Sample name: ALK_ALL_411_990613_12_PZ


title: ALL_patient_43 [HG-U133A]

description: Sample name: ALK_ALL_411_991533_18_PZ


title: Human_HBV_sample_Hep-0039


title: MR_Leaf at MD, biological replicate 1

description: Moderate Resistant Black poplar leaves under moderate drought condition


title: ALL_patient_108 [HG-U133B]

description: Sample name: ALK_ALL_Ph_040372_12_PZ

source_name: bone marrow mononuclear cells, Ph-positive ALL


title: ALL_patient_40 [HG-U133A]

description: Sample name: ALK_ALL_411_023231_3_PZ


title: ALL_patient_41 [HG-U133A]

description: Sample name: ALK_ALL_411_024086_30_PZ


title: ALL_patient_109 [HG-U133B]

description: Sample name: ALK_ALL_Ph_040718_18_PZ


title: ALL_patient_47 [HG-U133A]

description: Sample name: ALK_ALL_BA_014872_56_PZ


title: Human_HBV_sample_Hep-0036


title: MR_Leaf at SD, biological replicate 1


title: MR_Leaf at WWP, biological replicate 2

description: Moderate Resistant Black poplar leaves under well watered condition


title: Human_HBV_sample_Hep-0031


title: Human_HBV_sample_Hep-0032


title: ALL_patient_39 [HG-U133A]

description: Sample name: ALK_ALL_411_021957_29_PZ


title: ALL_patient_107 [HG-U133B]

description: Sample name: ALK_ALL_Ph_040367_48_PZ


title: Human_HBV_sample_Hep-0030


title: MR_Leaf at WWP, biological replicate 1


title: MR_Leaf at MD, biological replicate 2


title: ALL_patient_36 [HG-U133A]

description: Sample name: ALK_ALL_411_013713_3_PZ


title: ALL_patient_104 [HG-U133B]

description: Sample name: ALK_ALL_Ph_033157_2_PZ


title: ALL_patient_38 [HG-U133A]

description: Sample name: ALK_ALL_411_020895_8_PZ


title: ALL_patient_103 [HG-U133B]

description: Sample name: ALK_ALL_Ph_031163_29_PZ


title: Human_HBV_sample_Hep-0025


title: ALL_patient_102 [HG-U133B]

description: Sample name: ALK_ALL_Ph_031058_1_PZ


title: ALL_patient_105 [HG-U133B]

description: Sample name: ALK_ALL_Ph_034794_91_PZ


title: ALL_patient_106 [HG-U133B]

description: Sample name: ALK_ALL_Ph_034837_92_PZ


title: Human_HBV_sample_Hep-0024


title: ALL_patient_35 [HG-U133A]

description: Sample name: ALK_ALL_411_012176_23_PZ


title: Human_HBV_sample_Hep-0006


title: ALL_patient_32 [HG-U133A]

description: Sample name: ALK_ALL_411_002127_15_PZ


title: ALL_patient_31 [HG-U133A]

description: Sample name: ALK_ALL_411_000555_13_PZ


title: ALL_patient_99 [HG-U133B]

description: Sample name: ALK_ALL_Ph_023121_28_PZ


title: ALL_patient_33 [HG-U133A]

description: Sample name: ALK_ALL_411_011227_21_PZ


title: Human_HBV_sample_Hep-0026


title: Human_HBV_sample_Hep-0007


title: Human_HBV_sample_Hep-0003


title: ALL_patient_100 [HG-U133B]

description: Sample name: ALK_ALL_Ph_023168_46_PZ


title: ALL_patient_34 [HG-U133A]

description: Sample name: ALK_ALL_411_012074_11_PZ


title: Human_HBV_sample_Hep-0002


title: Human_HBV_sample_Hep-0004


title: ALL_patient_29 [HG-U133A]

description: Sample name: ALK_ALL_119_020834_39_PZ


title: ALL_patient_101 [HG-U133B]

description: Sample name: ALK_ALL_Ph_024972_31_PZ


title: ALL_patient_96 [HG-U133B]

description: Sample name: ALK_ALL_Ph_022302_16_PZ


title: ALL_patient_30 [HG-U133A]

description: Sample name: ALK_ALL_119_030184_46_PZ


title: ALL_patient_97 [HG-U133B]

description: Sample name: ALK_ALL_Ph_022497_23_PZ


title: ALL_patient_95 [HG-U133B]

description: Sample name: ALK_ALL_Ph_022204_15_PZ


title: ALL_patient_98 [HG-U133B]

description: Sample name: ALK_ALL_Ph_022644_37_PZ


title: ALL_patient_37 [HG-U133A]

description: Sample name: ALK_ALL_411_014921_28_PZ


title: ALL_patient_28 [HG-U133A]

description: Sample name: ALK_ALL_1119_013742_7_PZ


title: ALL_patient_91 [HG-U133B]

description: Sample name: ALK_ALL_Ph_020208_89_PZ


title: ALL_patient_26 [HG-U133A]

description: Sample name: AHW_ALL_Ph_035793_73_PZ


title: ALL_patient_27 [HG-U133A]

description: Sample name: AHW_ALL_Ph_035841_75_PZ


title: ALL_patient_94 [HG-U133B]

description: Sample name: ALK_ALL_Ph_021896_4_PZ


title: ALL_patient_92 [HG-U133B]

description: Sample name: ALK_ALL_Ph_020607_32_PZ


title: ALL_patient_93 [HG-U133B]

description: Sample name: ALK_ALL_Ph_020898_24_PZ


title: ALL_patient_25 [HG-U133A]

description: Sample name: AHW_ALL_Ph_035655_63_PZ


title: ALL_patient_90 [HG-U133B]

description: Sample name: ALK_ALL_Ph_020132_26_PZ


title: ALL_patient_23 [HG-U133A]

description: Sample name: AHW_ALL_Ph_032805_17_PZ


title: ALL_patient_88 [HG-U133B]

description: Sample name: ALK_ALL_Ph_014810_60_PZ


title: ALL_patient_89 [HG-U133B]

description: Sample name: ALK_ALL_Ph_015394_42_PZ


title: ALL_patient_21 [HG-U133A]

description: Sample name: AHW_ALL_Ph_032522_48_PZ


title: ALL_patient_20 [HG-U133A]

description: Sample name: AHW_ALL_Ph_031549_14_PZ


title: ALL_patient_86 [HG-U133B]

description: Sample name: ALK_ALL_Ph_014069_53_PZ


title: ALL_patient_19 [HG-U133A]

description: Sample name: AHW_ALL_Ph_030031_32_PZ


title: ALL_patient_87 [HG-U133B]

description: Sample name: ALK_ALL_Ph_014319_43_PZ


title: ALL_patient_85 [HG-U133B]

description: Sample name: ALK_ALL_Ph_014066_27_PZ


title: ALL_patient_17 [HG-U133A]

description: Sample name: AHW_ALL_Ph_021890_6_PZ


title: ALL_patient_82 [HG-U133B]

description: Sample name: ALK_ALL_Ph_011910_5_PZ


title: ALL_patient_14 [HG-U133A]

description: Sample name: AHW_ALL_MLL_035404_54_PZ


title: ALL_patient_83 [HG-U133B]

description: Sample name: ALK_ALL_Ph_012076_12_PZ


title: ALL_patient_15 [HG-U133A]

description: Sample name: AHW_ALL_MLL_035442_56_PZ


title: ALL_patient_84 [HG-U133B]

description: Sample name: ALK_ALL_Ph_012553_3_PZ


title: ALL_patient_81 [HG-U133B]

description: Sample name: ALK_ALL_Ph_011568_10_PZ


title: ALL_patient_18 [HG-U133A]

description: Sample name: AHW_ALL_Ph_024890_108_PZ


title: ALL_patient_22 [HG-U133A]

description: Sample name: AHW_ALL_Ph_032683_15_PZ


title: ALL_patient_80 [HG-U133B]

description: Sample name: ALK_ALL_Ph_010823_30_PZ


title: ALL_patient_24 [HG-U133A]

description: Sample name: AHW_ALL_Ph_033050_97_PZ


title: ALL_patient_16 [HG-U133A]

description: Sample name: AHW_ALL_MLL_036187_80_PZ


title: ALL_patient_79 [HG-U133B]

description: Sample name: ALK_ALL_Ph_002136_26_PZ


title: ALL_patient_76 [HG-U133B]

description: Sample name: ALK_ALL_MLL_035349_15_PZ


title: ALL_patient_11 [HG-U133A]

description: Sample name: AHW_ALL_BN_032462_73_PZ


title: ALL_patient_13 [HG-U133A]

description: Sample name: AHW_ALL_MLL_031351_13_PZ


title: ALL_patient_10 [HG-U133A]

description: Sample name: AHW_ALL_BN_022495_7_PZ


title: ALL_patient_75 [HG-U133B]

description: Sample name: ALK_ALL_MLL_030470_71_PZ


title: ALL_patient_12 [HG-U133A]

description: Sample name: AHW_ALL_MLL_024687_10_PZ


title: ALL_patient_74 [HG-U133B]

description: Sample name: ALK_ALL_MLL_030123_72_PZ


title: ALL_patient_9 [HG-U133A]

description: Sample name: AHW_ALL_BN_021234_5_PZ


title: ALL_patient_73 [HG-U133B]

description: Sample name: ALK_ALL_MLL_024733_69_PZ


title: ALL_patient_6 [HG-U133A]

description: Sample name: AHW_ALL_BA_030703_59_PZ


title: ALL_patient_5 [HG-U133A]

description: Sample name: AHW_ALL_BA_030638_12_PZ


title: ALL_patient_72 [HG-U133B]

description: Sample name: ALK_ALL_MLL_021932_79_PZ


title: ALL_patient_70 [HG-U133B]

description: Sample name: ALK_ALL_hype_991773_41_PZ


title: ALL_patient_7 [HG-U133A]

description: Sample name: AHW_ALL_BA_032751_71_PZ


title: ALL_patient_71 [HG-U133B]

description: Sample name: ALK_ALL_MLL_013575_66_PZ


title: ALL_patient_8 [HG-U133A]

description: Sample name: AHW_ALL_BA_035608_60_PZ


title: ALL_patient_4 [HG-U133A]

description: Sample name: AHW_ALL_BA_025919_13_PZ


title: ALL_patient_78 [HG-U133B]

description: Sample name: ALK_ALL_MLL_040731_15_PZ


title: ALL_patient_77 [HG-U133B]

description: Sample name: ALK_ALL_MLL_035987_70_PZ


title: ALL_patient_2 [HG-U133A]

description: Sample name: AHW_ALL_1221_032511_23_PZ


title: ALL_patient_68 [HG-U133B]

description: Sample name: ALK_ALL_BN_033417_3_PZ


title: ALL_patient_66 [HG-U133B]

description: Sample name: ALK_ALL_BN_031375_22_PZ


title: ALL_patient_3 [HG-U133A]

description: Sample name: AHW_ALL_BA_025903_51_PZ


title: ALL_patient_1 [HG-U133A]

description: Sample name: AHW_ALL_119_031965_38_PZ


title: ALL_patient_69 [HG-U133B]

description: Sample name: ALK_ALL_BN_035602_35_PZ


title: ALL_patient_65 [HG-U133B]

description: Sample name: ALK_ALL_BN_024934_79_PZ


title: ALL_patient_67 [HG-U133B]

description: Sample name: ALK_ALL_BN_032229_14_PZ


title: ALL_patient_64 [HG-U133B]

description: Sample name: ALK_ALL_BN_023445_42_PZ


title: B5_CRY_3B7N_rep2

city: Yokohama

first: Wen Dee

last: Ong

state: Kanagawa

address: 1-7-22 Suehiro-cho

department: Biomass Engineering

country: Japan

institute: RIKEN

description:
description
Gene expression of 4d blue light irradiated cry1cry2 seedlings in 3-bromo-7-nitroindazole treatment

hyb_protocol: 1.65 μg of purified Cy3-labelled cRNA were fragmented in reaction mixture containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent at 60°C for 30 min in a reaction volume of 55 mL. After incubation, the reaction was immediately stopped with addition of 55 mL 2X GEx Hybridization Buffer HI-RPM. Preapared cRNAs were lay on slides and microarray chip was incubated in oven at 65°C for 17 hours with rotation. 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 scanned after washing using the Agilent DNA Microarray Scanner (G2505B) with one color scan setting for 1x44k array slides

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Arabidopsis thaliana

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1 ug RNA using Agilent One-Color Microarray Quick-Amp Labeling kit according to the manufacturer's instructions. Cy3-labeled cRNA was purification using Qiagen RNAeasy column purification. Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Seeds of Arabidopsis thaliana were sterilized with sodium hypochlorite solution and EtOH and washed with sterilized water. Sterilized seed were sown on medium comprised of 0.5x MS salt mixture, MES, 1x Gamborg’s vitamin mixture, respective chemical (added below 50°C) and 0.8 % (w/v) agar (pH 5.8) and incubated in the dark at 4˚C for 3 days. Subsequently, the seeds were incubated under continuous blue light for 4 days. 4-day-old seedlings were harvested and frozen in liquid nitrogen immediately.

extract_protocol: Total RNAs were extracted using RNeasy Plant Mini RNA kit (Qiagen, USA) according to the manufacturer’s instructions.in brief, 0.2 g of frozen tissues was grinded using mortar and pestle and bind and total RNA was allowed to bind to RNeasy Mini Spin columns and further followed by washing by buffer and finally eluted using RNase-free water. Eluted RNAs was then treated with of RNase-free DNase I (Takara, Japan) and extracted with phenol:chloroform.

treatment_protocol: Seeds sown on medium with respective chemical treatment at 15 µM were kept at 4°C in dark for 3 days followed by continuous blue light irrradiation for 4 days at intensity of 5 µmol m-2s-1.

tag: developmental stage

value: seedlings


title: B5_CRY_3B7N_rep3


title: B5_CRY_3B7N_rep1


title: ALL_patient_63 [HG-U133B]

description: Sample name: ALK_ALL_BN_023106_9_PZ


title: ALL_patient_61 [HG-U133B]

description: Sample name: ALK_ALL_BN_022019_5_PZ


title: ALL_patient_57 [HG-U133B]

description: Sample name: ALK_ALL_BA_035276_34_PZ


title: ALL_patient_62 [HG-U133B]

description: Sample name: ALK_ALL_BN_022243_23_PZ


title: B5_CRY_DMSO_rep2

description:
description
Gene expression of 4d blue light irradiated cry1cry2 seedlings in dimethyl sulfoxide treatment

source_name: chemical treatment: Dimethyl sulfoxide


title: B5_CRY_DMSO_rep1


title: ALL_patient_56 [HG-U133B]

description: Sample name: ALK_ALL_BA_034658_90_PZ


title: B5_WT_DMSO_rep3

description:
description
Gene expression of 4d blue light irradiated WT Col-0 seedlings in dimethyl sulfoxide treatment

value: wild type Col-0


title: B5_WT_3B7N_rep3

description:
description
Gene expression of 4d blue light irradiated WT Col-0 seedlings in 3-bromo-7-nitroindazole treatment


title: ALL_patient_54 [HG-U133B]

description: Sample name: ALK_ALL_BA_033676_8_PZ

value: adult


title: B5_WT_3B7N_rep1


title: ALL_patient_53 [HG-U133B]

description: Sample name: ALK_ALL_BA_033113_28_PZ


title: B5_WT_3B7N_rep2


title: ALL_patient_60 [HG-U133B]

description: Sample name: ALK_ALL_BN_020186_88_PZ


title: B5_WT_DMSO_rep2


title: ALL_patient_55 [HG-U133B]

description: Sample name: ALK_ALL_BA_034603_8_PZ


title: ALL_patient_59 [HG-U133B]

description: Sample name: ALK_ALL_BN_015539_84_PZ

value: B-other


title: ALL_patient_52 [HG-U133B]

description: Sample name: ALK_ALL_BA_022422_17_PZ

value: bone marrow mononuclear cells


title: B5_WT_DMSO_rep1


title: B10_WT_3B7N_rep3

description:
10 µmol m-2s-1
Gene expression 4d blue light irradiated WT Col-0 seedlings in 3-bromo-7-nitroindazole treatment

treatment_protocol: Seeds sown on medium with respective chemical treatment at 2.5 µM were kept at 4°C in dark for 3 days followed by continuous blue light irrradiation for 4 days.

value: wild type

tag: cultivar


title: B10_WT_7NIT_rep3

description:
10 µmol m-2s-1
Gene expression 4d blue light irradiated WT Col-0 seedlings in 7-nitroindazole treatment

source_name: chemical treatment: 7-nitroindazole


title: B10_WT_3B7N_rep1


title: ALL_patient_51 [HG-U133B]

description: Sample name: ALK_ALL_BA_021833_24_PZ

value: acute lymphoblastic leukemia (ALL)


title: ALL_patient_58 [HG-U133B]

description: Sample name: ALK_ALL_BA_040735_16_PZ


title: B10_WT_7NIT_rep1


title: B10_WT_7NIT_rep2


title: ALL_patient_50 [HG-U133B]

description: Sample name: ALK_ALL_BA_021402_11_PZ


title: ALL_patient_47 [HG-U133B]

description: Sample name: ALK_ALL_BA_014872_56_PZ

value: Ph-like


title: ALL_patient_49 [HG-U133B]

description: Sample name: ALK_ALL_BA_021091_16_PZ


title: ALL_patient_48 [HG-U133B]

description: Sample name: ALK_ALL_BA_020704_18_PZ


title: ALL_patient_46 [HG-U133B]

description: Sample name: ALK_ALL_BA_013739_8_PZ


title: ALL_patient_44 [HG-U133B]

description: Sample name: ALK_ALL_B_036348_28_PZ


title: B10_WT_3BRO_rep2

description:
10 µmol m-2s-1
Gene expression 4d blue light irradiated WTCol-0 seedlings in 3-bromoindazole treatment

source_name: chemical treatment: 3-bromoindazole


title: B10_WT_3BRO_rep1


title: B10_WT_3BRO_rep3


title: B10_WT_DMSO_rep2

description:
10 µmol m-2s-1
Gene expression 4d blue light irradiated WT Col-0 seedlings in DMSO treatment

source_name: chemical treatment: Dimethyl sulfoxide (DMSO)


title: ALL_patient_42 [HG-U133B]

description: Sample name: ALK_ALL_411_990613_12_PZ

source_name: bone marrow mononuclear cells, MLL-positive ALL


title: ALL_patient_45 [HG-U133B]

description: Sample name: ALK_ALL_BA_000875_34_PZ


title: B10_WT_DMSO_rep3


title: ALL_patient_43 [HG-U133B]

description: Sample name: ALK_ALL_411_991533_18_PZ


title: B10_WT_DMSO_rep1

description:
blue light: 10 µmol m-2s-1
Gene expression 4d blue light irradiated WT Col-0 seedlings in DMSO treatment


title: ALL_patient_40 [HG-U133B]

description: Sample name: ALK_ALL_411_023231_3_PZ


title: ALL_patient_39 [HG-U133B]

description: Sample name: ALK_ALL_411_021957_29_PZ


title: ALL_patient_41 [HG-U133B]

description: Sample name: ALK_ALL_411_024086_30_PZ


title: MP replicate 3

city: Davis

first: Patricia

last: Baldrich Gonzalez

state: CA

address: 451 Health Sciences Dr., Davis, CA 95616

department: Genome Center

institute: University of California - Davis

hyb_protocol: After fragmentation, 1650 ng of labeled cRNA from each sample was hybridized in in situ hybridization oven (Agilent) for 17 h at 65ºC and washed during 1 min at rt in Gene Expression Wash Buffer 1 (Agilent) and 1 min at 37 ºC with Gene Expression Wahs buffer 2 (Agilent).

scan_protocol: Scanned on an Agilent G2539A scanner at 5um resolution and 100%PMT The intensity data of each individual hybridization were extracted and the quality was assessed with the Feature Extraction software 10.7 (Agilent).

data_processing: Raw data was corrected for background noise using the normexp method. Quantile normalization was applied to assure comparability across samples.

source_name: MIM Infected

label_protocol: 100ng of total RNA from each sample were amplified by Oligo-dT-T7 reverse transcription and labeled by in vitro transcription with T7 RNA polymerase in the presence of Cy3-CTP using the LowInputQuick Amp Labeling kit  (Agilent) and purified using RNAeasy columns (Qiagen, Hilden, Germany)

extract_protocol: Total RNAs were prepared with Qiagen Rneasy minikit according to manufacturer’s protocol

tag: genotype/variation

value: Leaf

tag: Stage

value: 36 days-old plants


title: MS replicate 3

source_name: MIM Control


title: MS replicate 2


title: ALL_patient_38 [HG-U133B]

description: Sample name: ALK_ALL_411_020895_8_PZ


title: MP replicate 2


title: MP replicate 1


title: MS replicate 1


title: ALL_patient_36 [HG-U133B]

description: Sample name: ALK_ALL_411_013713_3_PZ


title: ALL_patient_37 [HG-U133B]

description: Sample name: ALK_ALL_411_014921_28_PZ


title: SP replicate 3

source_name: WT Infected

value: Wild type


title: SP replicate 2


title: ALL_patient_35 [HG-U133B]

description: Sample name: ALK_ALL_411_012176_23_PZ


title: ALL_patient_28 [HG-U133B]

description: Sample name: ALK_ALL_1119_013742_7_PZ


title: ALL_patient_32 [HG-U133B]

description: Sample name: ALK_ALL_411_002127_15_PZ


title: ALL_patient_29 [HG-U133B]

description: Sample name: ALK_ALL_119_020834_39_PZ


title: ALL_patient_31 [HG-U133B]

description: Sample name: ALK_ALL_411_000555_13_PZ


title: SP replicate 1


title: SS replicate 1

source_name: WT Control


title: ALL_patient_33 [HG-U133B]

description: Sample name: ALK_ALL_411_011227_21_PZ


title: ALL_patient_30 [HG-U133B]

description: Sample name: ALK_ALL_119_030184_46_PZ

source_name: bone marrow mononuclear cells, B-other ALL


title: treated-TAM, biological rep2

description:
Gene expression data from PLX3397 treated orthotopic hepatoma.
M(IL4)b

source_name: treated-TAM

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip2 WT Terminal  Labeling Kit and Controls Kit(Cat#901524, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: TAMs were obtained from orthotopically implanted hepa1-6 tumors in C57BL/6 mice.

treatment_protocol: TAMs were sorted using FACS according to the protocol listed at http://www.immgen.org. vehicle-TAM and treated-TAM  were processed in Trizol within 4 h after sorting and then analyzed by using whole-mouse genome Affymetrix Mouse Gene 1.0 ST Arrays.

value: liver;  orthotopically implanted hepa1-6 tumors

value: tumor associated macrophages (TAM)

tag: treated with


title: treated-TAM, biological rep3

description:
Gene expression data from PLX3397 treated orthotopic hepatoma.
M(IL4)c

tag: tissue


title: ALL_patient_34 [HG-U133B]

description: Sample name: ALK_ALL_411_012074_11_PZ


title: ALL_patient_27 [HG-U133B]

description: Sample name: AHW_ALL_Ph_035841_75_PZ

value: Ph-positive


title: SS replicate 3


title: ALL_patient_26 [HG-U133B]

description: Sample name: AHW_ALL_Ph_035793_73_PZ


title: SS replicate 2


title: ALL_patient_25 [HG-U133B]

description: Sample name: AHW_ALL_Ph_035655_63_PZ


title: treated-TAM, biological rep1

description:
Gene expression data from PLX3397 treated orthotopic hepatoma.
M(IL4)a


title: B5_CRY_DMSO_rep3


title: ALL_patient_21 [HG-U133B]

description: Sample name: AHW_ALL_Ph_032522_48_PZ


title: vehicle-TAM, biological rep3

description:
Gene expression data from vehicle orthotopic hepatoma.
M(LPS+IFNγ)c

source_name: vehicle-TAM

value: vehicle


title: vehicle-TAM, biological rep2

description:
Gene expression data from vehicle orthotopic hepatoma.
M(LPS+IFNγ)b


title: ALL_patient_24 [HG-U133B]

description: Sample name: AHW_ALL_Ph_033050_97_PZ


title: ALL_patient_22 [HG-U133B]

description: Sample name: AHW_ALL_Ph_032683_15_PZ


title: M(CSF2) cells, biological rep3

source_name: M(CSF2) cells

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip2 WT Terminal Labeling Kit and Controls Kit(Cat#901524, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: M(CSF1) and M(CSF2) cells were obtained from bone marrow of C57BL/6 mice.

treatment_protocol: M(CSF1) and M(CSF2) cells analyzed by using whole-mouse genome Affymetrix Mouse Gene 1.0 ST Arrays.

value: bone marrow

value: bone marrow derived macrophages (BMDMs)

tag: induced with

value: 7 days to obtain M(CSF2)


title: ALL_patient_23 [HG-U133B]

description: Sample name: AHW_ALL_Ph_032805_17_PZ


title: M(CSF2) cells, biological rep2


title: vehicle-TAM, biological rep1

description:
Gene expression data from vehicle orthotopic hepatoma.
M(LPS+IFNγ)a


title: M(CSF2) cells, biological rep1


title: ALL_patient_20 [HG-U133B]

description: Sample name: AHW_ALL_Ph_031549_14_PZ


title: ALL_patient_17 [HG-U133B]

description: Sample name: AHW_ALL_Ph_021890_6_PZ


title: ALL_patient_18 [HG-U133B]

description: Sample name: AHW_ALL_Ph_024890_108_PZ


title: ALL_patient_19 [HG-U133B]

description: Sample name: AHW_ALL_Ph_030031_32_PZ


title: M(CSF1) cells, biological rep1

source_name: M(CSF1) cells

value: 7 days to obtain M(CSF1)


title: M(CSF1) cells, biological rep2


title: M(CSF1) cells, biological rep3


title: ALL_patient_15 [HG-U133B]

description: Sample name: AHW_ALL_MLL_035442_56_PZ

value: adult

value: MLL-positive


title: ALL_patient_16 [HG-U133B]

description: Sample name: AHW_ALL_MLL_036187_80_PZ

value: bone marrow mononuclear cells


title: ALL_patient_13 [HG-U133B]

description: Sample name: AHW_ALL_MLL_031351_13_PZ


title: ALL_patient_11 [HG-U133B]

description: Sample name: AHW_ALL_BN_032462_73_PZ

source_name: bone marrow mononuclear cells, Ph-like ALL


title: NUP98-HOXA9 delFG1 no2

city: Chuo-ku

first: Yutaka

last: Shima

state: Tokyo

address: 5-1-1 Tsukiji

department: Division of Hematological Malignancy

institute: National Cancer Center

hyb_protocol: Labeled cDNA were hybridized on GeneChip Mouse Gene 1.0 ST Array. Arrays were washed and stained in the GeneChip Fluidics Station 450 (Affimetrix).

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

data_processing: The data were analyzed with GeneChip Command Console Software. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v11.5.1 software package (Agilent Technologies)

source_name: NUP98-HOXA9 delFG1 no2

label_protocol: Using the GeneChip WT Terminal Labeling Kit (Affimetrix), fragmented single-stranded DNA was labeled.

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (Qiagen).


title: NUP98-HOXA9 no2

source_name: NUP98-HOXA9 no2


title: ALL_patient_9 [HG-U133B]

description: Sample name: AHW_ALL_BN_021234_5_PZ

value: B-other


title: empty vector no2

source_name: empty vector no2


title: ALL_patient_8 [HG-U133B]

description: Sample name: AHW_ALL_BA_035608_60_PZ

value: acute lymphoblastic leukemia (ALL)


title: NUP98-HOXA9 delFG2 no2

source_name: NUP98-HOXA9 delFG2 no2


title: ALL_patient_10 [HG-U133B]

description: Sample name: AHW_ALL_BN_022495_7_PZ


title: ALL_patient_12 [HG-U133B]

description: Sample name: AHW_ALL_MLL_024687_10_PZ


title: ALL_patient_14 [HG-U133B]

description: Sample name: AHW_ALL_MLL_035404_54_PZ


title: ALL_patient_7 [HG-U133B]

description: Sample name: AHW_ALL_BA_032751_71_PZ


title: P4 Macrophage CD11b+ CX3CR1hi Ly6C- MHCII+ F4/80hi CD11clow Replicate 3

description: Gene expression data from P4 subsets isolated from the colonic lamina propria

hyb_protocol: Following fragmentation and end-labeling, 2 μg of cDNAs were hybridized for 16 hours at 45°C on Affymetrix GeneChip Mouse Gene 1.0 ST arrays. The chips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G at a resolution of 0.7 µm.

data_processing: The data were RMA normalized by using the OMICS Software from Qlucore.

source_name: 6-12 week old mouse

label_protocol: 4 to 20 ng of  RNA from each sample was used to synthesize biotinylated probes, using the NuGEN Ovation Pico WTA System V2 Kit followed by the NuGEN Encore Biotin Module Kit, according to NuGEN recommendations, with appropriate quality control to ensure full length synthesis according to standard Affymetrix protocols.

extract_protocol: Total RNA was extracted from sorted cell subsets with the Qiagen RNeasy Micro Kit, according to the manufacturer protocol

value: Colon

tag: gender

value: Female


title: NUP98-HOXA9 no1

source_name: NUP98-HOXA9 no1


title: NUP98-HOXA9 delFG1 no1

source_name: NUP98-HOXA9 delFG1 no1


title: P2 Monocyte CD11b+ CX3CR1int Ly6Chitolow MHCII+  Replicate 3

description: Gene expression data from P2 subsets isolated from the colonic lamina propria


title: P3 Macrophage CD11b+ CX3CR1int Ly6C- MHCII+ F4/80hi CD11clow  Replicate 3

description: Gene expression data from P3 subsets isolated from the colonic lamina propria


title: B10_WT_3B7N_rep2

value: seedlings

value: wild type


title: NUP98-HOXA9 delFG2 no1

source_name: NUP98-HOXA9 delFG2 no1


title: ALL_patient_5 [HG-U133B]

description: Sample name: AHW_ALL_BA_030638_12_PZ

tag: disease state


title: ALL_patient_4 [HG-U133B]

description: Sample name: AHW_ALL_BA_025919_13_PZ

tag: all type

value: Ph-like


title: P4 Macrophage CD11b+ CX3CR1hi Ly6C- MHCII+ F4/80hi CD11clow Replicate 2

tag: strain


title: ALL_patient_6 [HG-U133B]

description: Sample name: AHW_ALL_BA_030703_59_PZ


title: ALL_patient_2 [HG-U133B]

description: Sample name: AHW_ALL_1221_032511_23_PZ


title: empty vector no1

source_name: empty vector no1


title: P3 Macrophage CD11b+ CX3CR1int Ly6C- MHCII+ F4/80hi CD11clow  Replicate 2


title: P1 Monocyte CD11b+ CX3CR1int Ly6Chi MHCII-  Replicate 2

description: Gene expression data from P1 subsets isolated from the colonic lamina propria


title: P4 Macrophage CD11b+ CX3CR1hi Ly6C- MHCII+ F4/80hi CD11clow Replicate 1


title: P3 Macrophage CD11b+ CX3CR1int Ly6C- MHCII+ F4/80hi CD11clow  Replicate 1


title: P2 Monocyte CD11b+ CX3CR1int Ly6Chitolow MHCII+  Replicate 1


title: ALL_patient_3 [HG-U133B]

description: Sample name: AHW_ALL_BA_025903_51_PZ


title: P1 Monocyte CD11b+ CX3CR1int Ly6Chi MHCII-  Replicate 3


title: ALL_patient_1 [HG-U133B]

description: Sample name: AHW_ALL_119_031965_38_PZ


title: MK546_plus_alpha3_and_alpha9_1

city: Rensselaer

first: Sridar

middle: V

last: Chittur

address: One Discovery Drive, CRC 342G

department: Center for Functional Genomics

institute: SUNY-University at Albany

hyb_protocol: Standard Affymetrix WT protocol

scan_protocol: Standard Affymetrix protocol for GCS30007G scanner

data_processing:
CHP files generated with Affymetrix Expression Console using Core probeset
PLIER expression value derived from Expression Console software; core-exon analysis

label_protocol: Standard Affymetrix WT protocol starting with 1ug total RNA and incuding riboreduction

growth_protocol: MK546 cells derived from α3-null neonatal mice were immortalized by SV40 large T antigen expression. All keratinocytes were maintained at 33 degrees C, 8% CO2, on plates coated with 30 μg/ml denatured rat tail collagen.  Cells were grown in Eagle's Minimum Essential Medium (EMEM) supplemented with 4% FBS from which Ca2+ had been chelated, 0.05 mM CaCl2, 0.4 μg/ml hydrocortisone, 5 μg/ml insulin, 10 units/ml interferon-γ, 10 ng/ml EGF, 100 units/ml penicillin, and 100 μg/ml streptomycin.

extract_protocol: Total cellular RNA was isolated from MK cells using the RNeasy Plus isolation kit (Qiagen, Valencia, CA), and quality was confirmed on an Agilent Bioanalyzer.

treatment_protocol: MK546 cells were engineered to express human alpha3 by stable transfection and/or human alpha9 by stable retroviral transduction.

tag: cell line

value: keratinocyte cell line MK546

tag: integrin a3 status

value: rescued with human a3 and a9


title: MK546_plus_alpha3_and_alpha9_2


title: MK546_plus_alpha9_2

value: rescued with human a9


title: P2 Monocyte CD11b+ CX3CR1int Ly6Chitolow MHCII+  Replicate 2


title: P1 Monocyte CD11b+ CX3CR1int Ly6Chi MHCII-  Replicate 1


title: UCD4 E2+P4, replicate 2

city: Aurora

first: Jessica

last: Finlay-Schultz

state: CO

department: Pathology

institute: University of Colorado Denver Anschutz Medical Campus

description: Human breast cancer samples xenografted in NSG mice

hyb_protocol: Following fragmentation, 3.5 ug of cDNA were hybridized for 20 hr at 48C on HuGene 1.1ST Array strip. GeneStrips were washed and stained in the Affymetrix Gene Atlas fluidics station.

scan_protocol: GeneStrips were scanned using the Gene Atlas imaging station

data_processing: The data were analyzed with Partek using RMA as normalization method.

source_name: xenograft: UCD4

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 500ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Tumors were partitioned into 10 mm^3 pieces and placed into recipient NSG mice under various hormone conditons as in Kabos et al Breast Cancer Res Treat 2012 (PMID 22821401)

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

treatment_protocol: Mice were treated using silastic pellets as described in Sartorius et al, Breast Cancer Res Treat 2003 (PMID 12846413)

value: breast tumor xenograft

tag: treatment

value: estradiol and progesterone


title: UCD4 E2+P4, replicate 3


title: UCD4 E2+MPA, replicate 3

value: estradiol and medroxyprogesterone acetate


title: MK546_plus_alpha9_1


title: UCD4 E2+P4, replicate 1


title: MK546_a3null_1 (re-analysis)


title: UCD4 E2+MPA, replicate 2


title: MK546_3a rescue2 (re-analysis)

source_name: MK546_3a rescue

value: rescued with human a3


title: UCD4 placebo, replicate 3

value: placebo


title: UCD4 placebo, replicate 2


title: UCD4 E2+MPA, replicate 1


title: MK546_3a rescue1 (re-analysis)


title: UCD4 E2, replicate 3

value: estradiol


title: MK546_a3null_2 (re-analysis)


title: MDA-MB-468 Parental 1 N=4

city: Montreal

first: Elaheh

last: Ahmadzadeh

state: Please select

address: 3220 Ridgewood, apt 319

country: Canada

institute: McGill University

hyb_protocol: Labeled cRNA was hybridized onto SurePrint G3 Human GE 8X60K microarrays (Agilent Technologies) at 65 °C for 17h in a rotating Agilent hybridization oven.

scan_protocol: Following hybridization, arrays were washed and scanned using the Agilent Scanner G2505B.

data_processing: Microarray data were extracted and visualized using the Feature Extraction Software v8.1. (Agilent), default parameters  (protocol GE1-v1_91 and Grid: 012391_D_20060331) was used to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: MDA-MB-468 Cell line_Parental

label_protocol: Cy3 labeled cRNA was prepared from 100ng RNA using the One-Color Low Input Quick Amp labeling kit (Agilent Technologies). The amplified labeled cRNA was purified using the RNeasy Mini Kit (Qiagen, Canada) assessed for dye incorporation and cRNA yield using the NanoDrop™ Spectrophotometer (ND-1000.)

growth_protocol: Parental and resistant cells were seeded at a density of 1x106 per well in 6 well-plates and incubated without drug for 24 hours

extract_protocol: Cells were harvested and total RNA from parental and resistant cell lines were extracted simultaneously using the AllPrep DNA/RNA Mini kit (Qiagen, Canada). The quality of RNA was determined with the NanoDrop™ spectrophotometer (ND-1000) (Wilmington, DE, USA). All RNA samples with A260/A280 ratio higher than 1.8 and DNA with A260/A280 ratio higher than 2 were selected for further analysis. The RNA integrity number (RIN) was measured with a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). RNA with RIN higher than 8 qualified forgene expression profiling.

value: Breast Cancer Cell Line

value: none (parental)


title: MDA-MB-436 Resistant 4 N=4

source_name: MDA-MB-436 Cell line_Resistant

value: Paclitaxel


title: MDA-MB-468 Resistant 2 N=4

source_name: MDA-MB-468 Cell line_Resistant


title: UCD4 placebo, replicate 1


title: MDA-MB-468 Resistant 3 N=4


title: UCD4 E2, replicate 2


title: UCD4 E2, replicate 1


title: MDA-MB-436 Resistant 3 N=4


title: MDA-MB-468 Parental 3 N=4


title: MDA-MB-468 Parental 2 N=4


title: MDA-MB-436 Resistant 2 N=4


title: MDA-MB-468 Resistant 1 N=4


title: MDA-MB-231 Resistant 1 N=4

source_name: MDA-MB-231 Cell line_Resistant


title: MDA-MB-436 Parental 4 N=4

source_name: MDA-MB-436 Cell line_Parental


title: MDA-MB-436 Resistant 1 N=4


title: MDA-MB-436 Parental 2 N=4


title: MDA-MB-231 Resistant 2 N=4


title: MDA-MB-231 Parental 4 N=4

source_name: MDA-MB-231 Cell line_Parental


title: MDA-MB-231 Parental 2 N=4


title: MDA-MB-231 Resistant 4 N=4


title: MDA-MB-231 Parental 1 N=4


title: SUM149 Resistant 2 N=4

source_name: SUM149 Cell line_Resistant


title: MDA-MB-436 Parental 3 N=4


title: MDA-MB-436 Parental 1 N=4


title: MDA-MB-231 Resistant 3 N=4


title: S4 Ca 12h

city: Würzburg

first: Kristin

last: Czakai

address: Josef-Schneider-Straße 2

department: Department of Internal Medicine II

institute: University Hospital of Würzburg

hyb_protocol: Standard Affymetrix GeneTitan Hyb protocol.

scan_protocol: Standard Affymetrix GeneTitan Scan protocol.

data_processing: RMA normalisation using Agilent GeneSpring version 13.1.

source_name: DC 12h + C. albicans wild type

label_protocol: Standard 3'-Assay Labeling for Affymetrix Plates.

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were separated from leucocyte concentrate blood of healthy donors (University Hospital Würzburg, transfusion medicine, Germany) by Ficoll-Hypaque density gradient centrifugation (Biochrom AG, Berlin, Germany). Human monocytes were isolated from PBMCs by magnetic-associated cell sorting (MACS) using paramagnetic microbeads conjugated to monoclonal anti-human CD14 antibodies (Miltenyi, Bergisch Gladbach, Germany). Wild-type C. albicans SC5314 was maintained on YPD agar. For experiments, colonies were transferred to M199 medium (PAA), pH 4 and cultured at 30°C to stationary phase. Germ tubes were induced by culturing in M199 medium, pH 8 for one hour at 37°C. Germ tubes were inactivated by washing them in phosphate-buffered saline (PBS) and followed by incubation in PBS containing 0.1% thimerosal (Sigma-Aldrich) for one hour at 37°C with shaking. Afterwards, germ tubes were washed 5 times and then re-suspended in RPMI-1640. Killing was confirmed by plating potential CFU on YPD (2% D-glucose, 1% peptone, 5% yeast extract, Roth) agar plates. A. fumigatus was cultivated on beer mesh plates at 37°C. After 3 days, conidia were detached by adding sterile water and singularized by a 40 µm cell strainer. Swelling and germination were achieved by incubation in RPMI 1640 medium with refocabin at room temperature and 37°C, respectively. Germ tubes and conidia were inactivated by incubation in 100% Ethanol for 45°min.

extract_protocol: Qiagen RNA-Isolation Kit (miRNeasy Mini).

treatment_protocol: Differentiation of monocytes into immature DCs (moDCs) was achieved by cultivating cells in RPMI 1640 medium (Invitrogen, Karlsruhe, Germany) supplemented with 100 mg/ml Refobacin (Merck, Darmstadt, Germany), 10% fetal calf serum (FCS, Sigma-Aldrich, Taufkirchen, Germany), 100 ng/ml recombinant human granulocyte-macrophage colony-stimulating factor (Leukine, Novartis, Basel, Switzerland) and 10 ng/ml interleukin-4 (Miltenyi Biotec, Germany). Cultures were fed with fresh medium and cytokines every other day. After culturing for 6 days at 37°C and 5% CO2, moDCs were collected and 1x10^6 cells were resuspended in 1 ml complete medium. moDCs were stimulated with 1x10^6 Aspergillus fumigatus germ tubes, 1x10^6 Candida albicans wild type or LPS (1 µg/ml) for 12h.

tag: donor

tag: donor disease state

value: healthy

value: monocyte-derived dendritic cells (moDCs)

value: Candida albicans wild type (SC5314)

tag: treatment duration


title: SUM149 Resistant 3 N=4

tag: cell type


title: MDA-MB-231 Parental 3 N=4


title: S4 LPS 12h

source_name: DC 12h + LPS

value: lipopolysaccharide (LPS)


title: SUM149 Resistant 4 N=4


title: SUM149 Resistant 1 N=4


title: SUM149 Parental 4 N=4

source_name: SUM149 Cell line_Parental


title: S4 Af 12h

source_name: DC 12h + A. fumigatus germ tubes

value: Aspergillus fumigatus (ATCC 46645) germ tubes


title: SUM149 Parental 1 N=4


title: S2 Af 12h


title: SUM149 Parental 3 N=4


title: S3 LPS 12h


title: S3 Af 12h


title: S2 Ca 12h


title: S3 Control 12h

source_name: DC 12h negative control


title: S2 LPS 12h


title: S1 LPS 12h


title: S4 Control 12h


title: S2 Control 12h


title: S1 Af 12h


title: SUM149 Parental 2 N=4


title: piglet_pig milk replacer with 0.6g/L lactoferrin_rep11

city: Beijing

first: yujie

last: shi

address: No.5 building No.5 Road Dijin

institute: Nestle research center- Beijing hub

description:
S5P06_H0015
Gene expression data from piglet hippocampus of control pig milk replacer with 0.6g/L lactoferrin

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45˚C on Affymetrix Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneArray Scanner G3000 7G system.

data_processing: The data were analyzed with Expression console software (1.1) using Robust Multichip Average(RMA) as normalization method.

organism: Sus scrofa

source_name: piglet hippocampus_pig milk replacer with 0.6g/L lactoferrin

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: Three-day-old male domestic piglets (Sus scrofa, Landrace×Large White cross) were purchased from a commercial piggery in Xiamen City, China and randomly placed in the 3 groups. All animals were kept in the temperature-controlled environment with a 12-h light (08:00~20:00) and a 12-h dark (20:00~08:00) cycle. The home pens contained a “nest” (a rubber tire covered with a clean towel), a heat lamp over the nest and an identical woody toy hang in the home pen. All facilities (including home pens and behavior room) were monitored for 24-h. The feeding time was fixed as 8:00, 13:00, 18:00, 22:30, with an extra 50mL milk/pig supplied at the last feeding.

extract_protocol: The extraction of total RNA was performed using Agencourt RNAdvance tissue kit according to the manufacturer's instructions.

treatment_protocol: Pig hippocampus samples were collected after sacrifice and immediately stored in liquid nitrogen tank until RNA extraction.

tag: breed

value: Domestic pig (Landrace×Large White)

value: male

tag: age

value: postnatal day 38 (piglet)

tag: feeding group

value: Hippocampus


title: piglet_pig milk replacer with 1.2g/L lactoferrin_rep11

description:
S4P16_H0037
Gene expression data from piglet hippocampus of control pig milk replacer with 1.2g/L lactoferrin

source_name: piglet hippocampus_pig milk replacer with 1.2g/L lactoferrin


title: piglet_pig milk replacer with 1.2g/L lactoferrin_rep12

description:
S5P09_H0011
Gene expression data from piglet hippocampus of control pig milk replacer with 1.2g/L lactoferrin


title: piglet_pig milk replacer_rep10

description:
S4P14_H0035
Gene expression data from piglet hippocampus of control pig milk replacer

source_name: piglet hippocampus_contrl milk replacer

value: contrl milk replacer


title: piglet_pig milk replacer with 0.6g/L lactoferrin_rep8

description:
S4P05_H0028
Gene expression data from piglet hippocampus of control pig milk replacer with 0.6g/L lactoferrin


title: piglet_pig milk replacer with 0.6g/L lactoferrin_rep9

description:
S4P06_H0029
Gene expression data from piglet hippocampus of control pig milk replacer with 0.6g/L lactoferrin


title: piglet_pig milk replacer with 0.6g/L lactoferrin_rep10

description:
S4P12_H0033
Gene expression data from piglet hippocampus of control pig milk replacer with 0.6g/L lactoferrin


title: piglet_pig milk replacer_rep12

description:
S5P04_H0021
Gene expression data from piglet hippocampus of control pig milk replacer


title: piglet_pig milk replacer with 1.2g/L lactoferrin_rep8

description:
S3P16_H0065
Gene expression data from piglet hippocampus of control pig milk replacer with 1.2g/L lactoferrin


title: piglet_pig milk replacer with 1.2g/L lactoferrin_rep9

description:
S4P02_H0026
Gene expression data from piglet hippocampus of control pig milk replacer with 1.2g/L lactoferrin


title: piglet_pig milk replacer with 0.6g/L lactoferrin_rep12

description:
S5P12_H0023
Gene expression data from piglet hippocampus of control pig milk replacer with 0.6g/L lactoferrin


title: piglet_pig milk replacer_rep11

description:
S5P03_H0020
Gene expression data from piglet hippocampus of control pig milk replacer


title: piglet_pig milk replacer_rep9

description:
S4P13_H0034
Gene expression data from piglet hippocampus of control pig milk replacer


title: piglet_pig milk replacer_rep8

description:
S4P04_H0027
Gene expression data from piglet hippocampus of control pig milk replacer


title: S1 Ca 12h


title: S1 Control 12h


title: piglet_pig milk replacer with 1.2g/L lactoferrin_rep10

description:
S4P15_H0036
Gene expression data from piglet hippocampus of control pig milk replacer with 1.2g/L lactoferrin


title: piglet_pig milk replacer_rep5

description:
S3P04_H0057
Gene expression data from piglet hippocampus of control pig milk replacer


title: piglet_pig milk replacer_rep4

description:
S2P12_H0053
Gene expression data from piglet hippocampus of control pig milk replacer


title: piglet_pig milk replacer with 0.6g/L lactoferrin_rep6

description:
S3P11_H0040
Gene expression data from piglet hippocampus of control pig milk replacer with 0.6g/L lactoferrin


title: piglet_pig milk replacer with 1.2g/L lactoferrin_rep6

description:
S2P10_H0051
Gene expression data from piglet hippocampus of control pig milk replacer with 1.2g/L lactoferrin


title: piglet_pig milk replacer with 0.6g/L lactoferrin_rep7

description:
S3P12_H0062
Gene expression data from piglet hippocampus of control pig milk replacer with 0.6g/L lactoferrin


title: piglet_pig milk replacer_rep6

description:
S3P13_H0041
Gene expression data from piglet hippocampus of control pig milk replacer


title: piglet_pig milk replacer with 1.2g/L lactoferrin_rep7

description:
S3P15_H0064
Gene expression data from piglet hippocampus of control pig milk replacer with 1.2g/L lactoferrin


title: piglet_pig milk replacer_rep7

description:
S3P14_H0063
Gene expression data from piglet hippocampus of control pig milk replacer


title: piglet_pig milk replacer with 1.2g/L lactoferrin_rep3

description:
S2P07_H0048
Gene expression data from piglet hippocampus of control pig milk replacer with 1.2g/L lactoferrin


title: piglet_pig milk replacer with 1.2g/L lactoferrin_rep4

description:
S2P08_H0049
Gene expression data from piglet hippocampus of control pig milk replacer with 1.2g/L lactoferrin