title: SUBJ5_GLIA_EXPER2

city: Bronx

first: Stella

last: Dracheva

state: New York

address: James J. Peters VA Medical Center,130 W Kingsbridge Rd

department: Dept. of Psychiatry

description: FACS-isolated nuclei from postmortem human brain

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: GenomeStudio 2011.1 (Illumina), Methylation v1.9 module

source_name: genomic DNA from nonneuronal cells

extract_protocol:
neuronal and nonneuronal nuclei from human postmortem brain material were isolated by fluorescence-activated sorting, as described in Kozlenkov et.al., (2013), Nucleic Acids Research (accepted for publication on 28-Aug 2013)
genomic DNA was isolated by proteinase K treatment, phenol extraction and ethanol precipitation

value: nonneuronal cells

value: Male

tag: age

value: adult

value: orbitofrontal cortex

value: normal

tag: replicate experiment


title: SUBJ1_GLIA_EXPER2

status: Public on Sep 13 2013

type: genomic

country: USA

institute: Icahn School of Medicine at Mount Sinai

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

label_protocol: Standard Illumina Protocol

tag: cell type

tag: gender

tag: tissue

tag: disease state


title: SUBJ2_GLIA_EXPER2


title: SUBJ5_NEUR_EXPER2

source_name: genomic DNA from neuronal cells

value: neuronal cells


title: Genomic DNA from peripheral blood sample 1

city: New York

first: Andrew

last: Sharp

state: NY

address: Hess CSM Building Floor Floor 8 Room 116

department: Genetics and Genomics

description: Case 4

hyb_protocol: Genome-wide measurement of CpG methylation levels was performed by hybridization of bisulfite-converted DNA from each case to Infinium HumanMethylation450 BeadChips, according to the manufacturer's protocol (Illumina, Inc., San Diego, CA).

scan_protocol: Scanning was performed using an Illumina HiScan Bead Array scanner according to the manufacturer's protocol (Illumina, Inc., San Diego, CA).

data_processing: Array data were processed using the Methylation Module of GenomeStudio v1.8 software using default parameters.

label_protocol: Labelling was performed according to the manufacturer's protocol (Illumina, Inc., San Diego, CA).

extract_protocol: Genomic DNA was isolated from peripheral blood samples from each individual, extracted using a custom salt/ethanol precipitation method.

value: female

value: peripheral blood

value: premature ovarian failure, secondary amennorhea

tag: genotype

value: unbalanced X;11 translocation, 46,X,der(X)t(X;11)(q26;p12)


title: SUBJ4_GLIA_EXPER2


title: SUBJ6_GLIA_EXPER2


title: SUBJ6_NEUR_EXPER2


title: sMPNST_JQ1_2day_rep1

type: RNA

first: Ping

last: Chi

address: 417 East 68th Street

department: Human Oncology and Pathogenesis Program

institute: Memorial Sloan Kettering Cancer Center

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

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

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: sMPNST cells treated with 500 nM JQ1

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: cells grown in DMEM (high glucose, 10% FBS, 1% Pen-strep, 1% Sodium Pyruvate, 1% L-glutamine) medium in 37oC incuabtor

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

treatment_protocol: Cells were plated in the evening. Next day, 1ug/mL  doxycycline was added to induce shRNA expression or JQ1 to final concentration of 500 nM was added

tag: genotype/variation

value: Derived from Nf1-/- P53-/- SKPs

value: spindle cell malignant peripheral nerve sheath tumor cell (SMPNST)

tag: treatment

value: JQ1 treated


title: SUBJ3_GLIA_EXPER2


title: Genomic DNA from peripheral blood sample 7

description:
Case 6B
Sibling of case 6A.

source_name: t(X;20)_Case 6B

value: developmental delay, menstruated at 16 years

value: unbalanced X;20 translocation, 46,X,der(X)t(X;20)(q26.3;q13)


title: sMPNST_shBrd4.552_3day_rep2

source_name: sMPNST cells with Brd4 shRNA induction

value: Brd4 shRNA


title: sMPNST_Vehicle_2day_rep2

source_name: sMPNST cells treated with vehicle (DMSO)

value: Vehicle treated


title: Genomic DNA from peripheral blood sample 6

description:
Case 6A
Sibling of case 6B.

source_name: t(X;20)_Case 6A

value: short stature


title: activated (72h) CD8 T lymphocytes transduced to express Stat5ca  S9

city: MARSEILLE

first: Nathalie

last: AUPHAN-ANEZIN

address: Parc Scientifique de Luminy

country: France

institute: CIML

description: S9-TCRP1A Stat5ca GFP+ eTL 72h

hyb_protocol: Affy-169 : 125.0 ng at 45 degree_C during 17 hours

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

data_processing: Expression console data processing

source_name: S9-TCRP1A Stat5ca GFP+ eTL 72h

label_protocol:
standard Affymetrix protocol
AMBION WT Expression kit-Affy

extract_protocol: standard Affymetrix protocol

tag: amount in (ug)

tag: origin

value: purified CD8 T lymphocytes

value: TCRP1A transgenic Rag-1-/-

tag: genetic background

tag: developmental stage

tag: rin number


title: naive peripheral CD8 T lymphocytes S34

value: naive peripheral CD8 T lymphocytes


title: SUBJ1_NEUR_EXPER2

value: Male

value: adult

value: orbitofrontal cortex

value: normal


title: sMPNST_shBrd4.552_3day_rep3


title: sMPNST_shCONTROL_3day_rep3

source_name: sMPNST cells with control shRNA induction

value: control shRNA


title: sMPNST_shBrd4.552_3day_rep1


title: activated (72h) CD8 T lymphocytes S4

description: S4-TCRP1A eTL 72h

source_name: S4-TCRP1A eTL 72h

value: activated (72h) CD8 T lymphocytes


title: SUBJ6_GLIA_EXPER1

value: nonneuronal cells


title: naive peripheral CD8 T lymphocytes S33


title: sMPNST_shCONTROL_3day_rep1

value: Derived from Nf1-/- P53-/- SKPs

value: spindle cell malignant peripheral nerve sheath tumor cell (SMPNST)


title: sMPNST_Vehicle_2day_rep3


title: Jurkat cells_control_rep1

city: Sendagi, Tokyo

first: Kazuya

last: Yuge

country: Japan

institute: Nippon Medical School

hyb_protocol: 1.65 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 min in a reaction volume of 55 μl containing 2.2 μl of 25x Agilent fragmentation buffer, 11 μl of 10x Agilent blocking agent and 41.8 μl Nuclease-free water following the manufacturers instructions. On completion of the fragmentation reaction, 55 μl of 2x GEx hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent Human GE 4×44 K, v2 Microarray (G4845) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 min at room temperature with Wash Buffer 1 (Agilent) and 1 min with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: The slide was scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x44 K array slides (Scan Area 61x21.6 mm, Scan resolution 5 μm, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 026652_D_F_20110325).

source_name: Jurkat cells, control

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng total RNA using a Low-Input QuickAmp Labeling Kit, One-Color (Agilent Technologies, Santa Clara, CA) according to the manufacturer's instructions, followed by RNAeasy column purification(QIAGEN,Valencia, CA). Dye incorporation, quality and cRNA yield were checked with the NanoDrop 2000 (Thermo Scientific) and Agilent 2100 Bioanalyzer (Agilent).

growth_protocol: Jurkat cells were maintained in RPMI 1640 medium supplemented with 10% exosome-free fetal bovine serum.

extract_protocol: Total RNA was extracted with RNAiso reagent (TaKaRa, Shiga, Japan), followed by clean-up with RNeasy Mini Kits (Qiagen, Valencia, CA, USA) according to the manufacturer’s instructions. The integrity of the total RNA was determined using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: Jurkat cells were transfected with Pre-miR Negative Control #1 (Pre-miR-NC; Applied Biosystems) and Pre-miR-517a at a final concentration of 40 nM using Lipofectamine 2000 (Invitrogen). Pre-miR-transfected cells were harvested 48h after transfection.

tag: cell line

value: Jurkat


title: sMPNST_Vehicle_2day_rep1


title: sMPNST_shCONTROL_3day_rep2


title: NEP Tumor [1886_4647_27149_Nestin-tumor-04_Mouse430+2]

city: Philadelphia

first: Zeng-jie

last: Yang

state: Pennsylvania

address: 333  Cottman Avenue

department: Cancer Biology Program

institute: Fox Chase Cancer Center

description: Tumor origin

hyb_protocol: Affymetrix GeneChip mouse 430 2.0 arrays were hybridized to 5.5ug of biotin labeled cDNA, washed and stained according to Affymetrix protocol.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 (Affymetrix)

data_processing: The data were analyzed using the Affymetrix Gene Expression Console with RMA (Robust Multi-array Average) normalization algorithm.

source_name: Tumor cells from Nestin-CreERT2/Ptch1C/C mice

label_protocol: 100 ng of total RNA were amplified using the Ambion WT Expression Kit and cDNA were biotin labelled using Affymetrix GeneChip WT Terminal Labeling protocol.

growth_protocol: All cells were isolated directly from mouse cerebellum, without any culture or treatment.

extract_protocol: Standard total RNA extraction protocol using Trizol

treatment_protocol: No any treatment was applied to cells prior to RNA extraction.

tag: strain


title: SUBJ2_NEUR_EXPER2

value: neuronal cells


title: NEP Tumor [1886_4647_27148_nestin-tumor-03_Mouse430+2]

description: Tumor origin

value: Tumor cells from Nestin-CreERT2/Ptch1C/C mice


title: SUBJ3_NEUR_EXPER2


title: Jurkat cells_miR-517a_rep1

source_name: Jurkat cells, miR-517a


title: SUBJ4_NEUR_EXPER2


title: SUBJ5_GLIA_EXPER1


title: U937_IFN_rep1

city: London

first: Reiner

last: Schulz

address: 8th floor Guy's Tower

department: Medical & Molecular Genetics

country: United Kingdom

institute: King's College London

description: Sample name: 5385288011_H

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing:
Raw signals, detection p-values, bead numbers, and bead-level standard errors were exported for regular and control probes from GenomeStudio. Data were imported into R using the Bioconductor beadarray and illuminaHumanv4.db packages. Data were background-corrected, quantile-normalised and log2-transformed using the limma implementation of the neqc method (Shi et al. Nucl Acids Res 2010). Data were filtered by probe quality as indicated by illuminaHumanv4PROBEQUALITY: “Bad”, “No match” and control probes were excluded.
Background-correct, quantile-normalised, log2-transformed signals of non-control probes whose probes sequences align with high identity (<=2 mismatches) and specificity to the human reference genome (Barbosa-Morais et al. Nucl Acids Res 2010).

source_name: U937, IFN-treated

label_protocol: Illumina® TotalPrep™ RNA Amplification Kit (Ambion); protocol according to manufacturer instructions (from 500 ng RNA).

growth_protocol: CEM, CEM-SS, Jurkat, U937, THP-1 and primary CD4+ T cells were cultured in RPMI 10% FBS. Primary CD4+ T cells were isolated from PBMCs using total CD4 T cells isolation kit II (Miltenyi) and activated for 24h with IL2 (60 U/mL) and PHA (1 mg/mL) prior to IFN treatment. Monocytes were isolated from PBMCs using CD14 microbeads (Miltenyi) and differentiated into macrophages for 4-6 days in RPMI 10% FBS + 100ng/mL GM-CSF prior to IFN treatment. PMA-treatment of U937 and THP-1 cells (100 ng/mL) was done 24 h prior to IFN treatment. U87-MG and HT1080 were grown in DMEM 10% FBS. For further detail, see Goujon and Malim, Journal of Virology, 2010.

extract_protocol: Qiagen miRNeasy kit; protocol according to manufacturer instructions .

treatment_protocol: 1 to 2 million cells were treated with 1000 U / mL universal type 1 IFN (#11200-1 PBL interferon source) for 24 h prior to RNA extraction, or left untreated.

value: U937 (monocytic cell line)

value: type 1 IFN

tag: donor

tag: replicate

tag: resistance to hiv-1 following ifn treatment

value: permissive


title: SUBJ2_GLIA_EXPER1

tag: cell type

tag: age

tag: replicate experiment


title: U937_IFN_rep2

description: Sample name: 5385288020_I


title: NEP Tumor [1886_4647_27147_Nestin-tumor-02_Mouse430+2]

description: Tumor origin


title: NEP Tumor [1886_4647_27146_Nestin-tumor-01_Mouse430+2]

description: Tumor origin


title: GNP Tumor [1886_4647_27150_Math1-tumor-01_Mouse430+2]

description: Tumor origin

source_name: Tumor cells from Math1-CreERT2/Ptch1C/C mice


title: NSC [1886_4647_27157_NSCs_Mouse430+2]

description: multipotency

source_name: CD133+, Lin- cerebellar progenitors

value: CD133+, Lin- cerebellar progenitors


title: GNP Tumor [1886_4647_27152_Math1-tumor-03_Mouse430+2]

description: Tumor origin

value: Tumor cells from Math1-CreERT2/Ptch1C/C mice


title: GNP Tumor [1886_4647_27153_Math1-tumor-04_Mouse430+2]

description: Tumor origin


title: U937_None_rep2

description: Sample name: 5385288020_J

source_name: U937, untreated

value: untreated


title: U87-MG_None_rep1

description: Sample name: 5398652022_C

source_name: U87-MG, untreated

value: U87-MG (glioblastoma-astrocytoma, epithelial-like cell line)


title: NSC [1886_4647_27158_NSCs_Mouse430+2]

description: multipotency


title: SUBJ4_GLIA_EXPER1

source_name: genomic DNA from nonneuronal cells

tag: gender

value: Male

value: adult

tag: tissue

value: orbitofrontal cortex

tag: disease state


title: SUBJ1_GLIA_EXPER1

value: normal


title: NSC [1886_4647_27159_NSCs-06_Mouse430+2]

description: multipotency


title: U87-MG_None_rep2

description: Sample name: 5398652023_G

tag: treatment


title: U937_None_rep1

description: Sample name: 5385288011_G


title: SUBJ3_GLIA_EXPER1

value: nonneuronal cells


title: NEP [1886_4473_24737_Nestin-04_Mouse430+2]

description: multipotency

source_name: Nestin+ neuronal progenitors

value: Nestin+ neuronal progenitors


title: U87-MG_IFN_rep2

description: Sample name: 5398652023_H

source_name: U87-MG, IFN-treated

value: resistant


title: GNP [1886_4473_24731_Math1-02_Mouse430+2]

description: multipotency

source_name: Math1+ neuronal progenitors

value: Math1+ neuronal progenitors


title: U87-MG_IFN_rep1

description: Sample name: 5398652022_D


title: Total mRNA, group C

first: Sarah

last: Stanley

address: 1230 York Avenue

department: Dept of Molecular Genetics

institute: Rockefeller University

description: polysome RNA

hyb_protocol: standard illumina hybridization protocol

scan_protocol: standard illumina scan protocol

data_processing: data was normalized by quantile normalization using Genespring

source_name: mouse hypothalamus

label_protocol: Amplified cDNA was labeled with Encore BiotinIL kit (Nugen)

extract_protocol: RNA was extracted with Agilent Absolutely RNA nanoprep kit. RNA was amplified and converted to cDNA using Ovation PicoSL WTA System (NuGen, San Carlos, CA)

treatment_protocol: Pooled hypothalami from 10 mice were homogenized, centrifuged and mixed with with streptavidin coated Dynal magnetic beads previously incubated with biotinylated protein L and monoclonal mouse anti-GFP antibody. The homogenate represents the total sample. The homogenate and beads were mixed overnight followed by two washes in high potassium wash buffer then a wash in high potassium wash buffer with DTT, cyclohexamide and RNAse inhibitors. The supernatant represents the IP sample.

tag: antibody

value: control

tag: genotype

value: hypothalamus


title: wt-jb015-k3-b vs. ref1

city: Utrecht

first: Marian

last: Groot Koerkamp

state: Utrecht

address: Heidelberglaan 25

department: Research

country: Netherlands

institute: Princess Maxima Center for Pediatric Oncology

hyb_protocol: Tecan HS4800 hybridization

scan_protocol: Scanning of slides using Agilent G2565BA scanner.

data_processing:
Normalization was done using print-tip LOESS as described in (Yang et al. 2002), by estimating the LOESS curve for all gene probes using no background substraction and a span of 0.4. Probes flagged as absent, or with a (nearly) saturated signal (i.e., > 2^15) in either channel were not considered for the estimation of the LOESS curve. Signals were corrected for dye bias using intrinsic gene-specific dye biases estimated from a set of wild-type hybridizations, as described in Margaritis, Lijnzaad et al., Mol. Sys. Biol. 2009.
A software package for the analysis of gene expression microarray data, especially the use of linear models for analysing designed experiments and the assessment of differential expression. Author(s): Gordon Smyth. The limma R package version 2.12.0 is used. P-values are Benjamini-Hochberg FDR corrected.

organism: Saccharomyces cerevisiae

source_name: wt

label_protocol: All amplification and labeling procedures are performed in 96 wells plates (4titude, Bioke) on a customized Sciclone ALH 3000 Workstation (Caliper LifeSciences), supplemented with a PCR PTC-200 (Bio-Rad Laboratories), SpectraMax 190 spectrofotometer (Molecular Devices), and a magnetic bead-locator (Beckman).

growth_protocol: S. cerevisiae BY4742 deletion mutants and the wild-type strains were cultured in SC Medium (Synthetic Complete; 4gr per 2l Drop out mix 13.42gr per 2l YNB(US biologicals) with 2% D-glucose)under agitation (230rpm), at 30C. The cells were collected at midlog.

extract_protocol: yeast HTP RNA isolation for robot v2.0

tag: genotype/variation

value: wt

source_name: refpool

extract_protocol: yeast RNA isolation for robotic amplification v1.0

value: refpool


title: wt-jb015-k2-b vs. ref1


title: immunoprecipitated mRNA, group C,

description: total RNA

value: anti-GFP


title: THP-1_None_rep1

description: Sample name: 5385288011_C

source_name: THP-1, untreated

value: THP-1 (monocytic cell line)


title: immunoprecipitated mRNA, group B,

description: total RNA


title: GNP [1886_4473_24734_Math1-03_Mouse430+2]

description: multipotency


title: Total mRNA, group B

description: polysome RNA


title: THP-1_None_rep2

description: Sample name: 5385288020_E


title: GNP [1886_4473_24736_Math1-04_Mouse430+2]

description: multipotency


title: NEP [1886_4473_24729_Nestin-01_Mouse430+2]

description: multipotency


title: THP-1_IFN_rep2

description: Sample name: 5385288020_F

source_name: THP-1, IFN-treated

value: type 1 IFN


title: SUBJ2_NEUR_EXPER1

source_name: genomic DNA from neuronal cells

value: neuronal cells


title: immunoprecipitated mRNA, group A,

description: total RNA


title: GNP [1886_4473_24728_Math1-01_Mouse430+2]

description: multipotency


title: SUBJ4_NEUR_EXPER1


title: NEP [1886_4473_24735_Nestin-03_Mouse430+2]

description: multipotency


title: NEP [1886_4473_24732_Nestin-02_Mouse430+2]

description: multipotency


title: GNP Tumor [1886_4647_27151_Math1-tumor-02_Mouse430+2]

description: Tumor origin

value: Tumor cells from Math1-CreERT2/Ptch1C/C mice


title: SUBJ6_NEUR_EXPER1

value: Male


title: SUBJ3_NEUR_EXPER1

value: adult


title: SUBJ5_NEUR_EXPER1

value: orbitofrontal cortex


title: wt-jb015-k1-b vs. ref1


title: THP-1_IFN_rep1

description: Sample name: 5385288011_D


title: InVivoKidney_Recovery Day 29_80 mg/kg gentamycin_male_rep2

city: Shanghai

first: min

last: hong

address: 199 Guoshoujing Rd., Zhangjiang Hi-tech Park

department: general toxicology

country: China

institute: National Shanghai Center for Drug Safety Evaluation and Research

description: Gene expression at Recovery Day 29_80 mg/kg gentamycin_male_rep2

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

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

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

organism: Rattus norvegicus

source_name: Male Kidney 80 mg/kg gentamycin Intramuscular once daily Recovery Day 29 replicate 2

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

extract_protocol: Total RNA was extracted and purified using miRNeasy Mini Kit（Cat#217004, QIAGEN, GmBH, Germany) and mirVanaTM  PARISTM (Cat#AM1556, Ambion, Austin, TX, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US)

treatment_protocol: kidneys from saline-treated or gentamycin-treated rats were collected at necropsy and stored at RNAlater

value: male

value: Sprague Dawley


title: SUBJ1_NEUR_EXPER1

value: normal


title: rpb1-ctrunc-CTD1-26-1-b vs. ref1


title: InVivoKidney_Recovery Day 29_80 mg/kg gentamycin_female_rep2

description: Gene expression at Recovery Day 29_80 mg/kg gentamycin_female_rep2

source_name: Female Kidney 80 mg/kg gentamycin Intramuscular once daily Recovery Day 29 replicate 2

value: female


title: rpb1-ctrunc-CTD1-20-1-b vs. ref1


title: NPC_p5ko_rep2

city: Singapore

first: Julius

last: Müller

address: 61 Biopolis Drive

department: IMCB

country: Singapore

institute: A*Star Singapore

description: replicate 2

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

source_name: Neural progenitor cells

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

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

tag: developmental stage

tag: genetic background

value: mixed C57BL/6 X 129S1/SvlmJ

value: NPC

value: Prmt5 depletion


title: NPC_p5ko_rep4

description: replicate 4


title: Total mRNA, group A

description: polysome RNA

value: control

value: hypothalamus


title: InVivoKidney_Recovery Day 29_80 mg/kg gentamycin_male_rep1

description: Gene expression at Recovery Day 29_80 mg/kg gentamycin_male_rep1

source_name: Male Kidney 80 mg/kg gentamycin Intramuscular once daily Recovery Day 29 replicate 1


title: primary-CD4+-T-cells_None_rep3

description: Sample name: 5398652023_C

source_name: primary CD4+ T cells, untreated

tag: primary cell type

value: primary CD4+ T cells (total CD4+ T cells from blood activated with IL2 / PHA)

value: D

value: untreated


title: wt-jb-15-k1-d vs. ref1

tag: strain

value: wt

value: refpool


title: primary-CD4+-T-cells_IFN_rep2

description: Sample name: 5398652022_L

source_name: primary CD4+ T cells, IFN-treated

value: type 1 IFN

tag: donor

value: C

value: resistant


title: InVivoKidney_Recovery Day 29_80 mg/kg gentamycin_female_rep1

description: Gene expression at Recovery Day 29_80 mg/kg gentamycin_female_rep1

source_name: Female Kidney 80 mg/kg gentamycin Intramuscular once daily Recovery Day 29 replicate 1


title: primary-CD4+-T-cells_None_rep2

description: Sample name: 5398652022_K

tag: replicate


title: rpb1-ctrunc-CTD1-13-1-b vs. ref1


title: NPC_p5ko_rep3

description: replicate 3


title: InVivoKidney_Recovery Day 29_80 mg/kg gentamycin_male_rep3

description: Gene expression at Recovery Day 29_80 mg/kg gentamycin_male_rep3

source_name: Male Kidney 80 mg/kg gentamycin Intramuscular once daily Recovery Day 29 replicate 3

value: male


title: wt-330rpm-1-b vs. ref1


title: primary-CD4+-T-cells_IFN_rep3

description: Sample name: 5398652023_D

tag: resistance to hiv-1 following ifn treatment


title: NPC_wt_rep4

description: replicate 4

tag: cell type


title: InVivoKidney_Recovery Day 29_80 mg/kg gentamycin_female_rep3

description: Gene expression at Recovery Day 29_80 mg/kg gentamycin_female_rep3

source_name: Female Kidney 80 mg/kg gentamycin Intramuscular once daily Recovery Day 29 replicate 3

value: Sprague Dawley


title: primary-CD4+-T-cells_IFN_rep1

description: Sample name: 5385288020_B

value: B


title: InVivoKidney_Day 15_80 mg/kg gentamycin_male_rep2

description: Gene expression at Day 15_80 mg/kg gentamycin_male_rep2

source_name: Male Kidney 80 mg/kg gentamycin Intramuscular once daily Day 15 replicate 2


title: rpb1-ctrunc-CTD1-12-1-b vs. ref1


title: NPC_wt_rep3

description: replicate 3


title: primary-CD4+-T-cells_None_rep1

description: Sample name: 5385288020_A


title: InVivoKidney_Day 15_80 mg/kg gentamycin_male_rep3

description: Gene expression at Day 15_80 mg/kg gentamycin_male_rep3

source_name: Male Kidney 80 mg/kg gentamycin Intramuscular once daily Day 15 replicate 3


title: primary-macrophages_None_rep3

description: Sample name: 5398652023_A

source_name: primary macrophages, untreated

value: primary macrophages (derived from blood monocytes)


title: InVivoKidney_Day 15_80 mg/kg gentamycin_male_rep1

description: Gene expression at Day 15_80 mg/kg gentamycin_male_rep1

source_name: Male Kidney 80 mg/kg gentamycin Intramuscular once daily Day 15 replicate 1


title: primary-macrophages_None_rep2

description: Sample name: 5385288020_C


title: NPC_wt_rep2

description: replicate 2

value: mixed C57BL/6 X 129S1/SvlmJ


title: InVivoKidney_Day 15_80 mg/kg gentamycin_female_rep3

description: Gene expression at Day 15_80 mg/kg gentamycin_female_rep3

source_name: Female Kidney 80 mg/kg gentamycin Intramuscular once daily Day 15 replicate 3

value: female


title: rpb1-ctrunc-CTD1-12+cdk8-del-1-b vs. ref1

source_name: refpool


title: rpb1-ctrunc-CTD1-11-1-b vs. ref1


title: NPC_wt_rep1

description: replicate 1

value: NPC


title: InVivoKidney_Day 15_80 mg/kg gentamycin_female_rep1

description: Gene expression at Day 15_80 mg/kg gentamycin_female_rep1

source_name: Female Kidney 80 mg/kg gentamycin Intramuscular once daily Day 15 replicate 1


title: primary-macrophages_IFN_rep2

description: Sample name: 5385288020_D

source_name: primary macrophages, IFN-treated


title: NailWTSE16.5#3

city: Baltimore

first: Chang-Yi

last: Cui

state: MD

address: 251 Bayview Blvd Suite 100, 10C222

department: NIA

institute: NIH

hyb_protocol: Slides were hybridized according to manufacturers protocol (Two-Color Microarray-Based Genr Expression Analysis Protocol,  Product # G4140-90050, Version 5.0.1, August 2006)

scan_protocol: Slides were scanned with an Agilent DNA Microarray Scanner (model G2505-64120) at 100% and 10% PMT in both channels, with a scan resolution of 5um.

data_processing:
Data are extracted with Agilent Feature Extraction Software.The data were further processed with NIA ANOVA tool utilities.See http://lgsun.grc.nia.nih.gov/ANOVA for details.
The data is normalized with the following method:
(1) Take values from the columns gDyeNormSignal,rDyeNormSignal in the raw files and log-transform them using: log10(max(x,1)). These values will be referenced below as Xgi and Xri where i is array number.
(2) Take average of Xri's for the oligo among 18 arrays in the series:  AverXr = average(Xri).
(3) For each array estimate Yi = Xgi-Xri+AverXr
(4) Round Yi to 4 decimal digits. This is used as the normalized VALUE.
More detailed information with error correction can be found at http://lgsun.grc.nia.nih.gov/ANOVA/help.html#arrayjoin

label_protocol: Total RNA was labeled using Agilents Low RNA Input Fluorescent Linear Amplification kit, according to manufacturers instructions.

extract_protocol: RNA was extracted using Trizol Reagent (Life technologies).

value: mixed sex

tag: age

tag: development stage

value: embryo

value: wild type

tag: individual identifier

source_name: Universal Mouse Reference 129ES Cell

extract_protocol: Total RNA was extracted from cultured cells using a Stratagene Absolutely RNA kit. DNase-treated total RNA samples from 11 cultured cell lines derived from embryo, embryo fibroblast, kidney, liver/hepatocyte, lung/alveolar macrophage, B-lymphocyte, T-lymphocyte (thymus), mammary gland, muscle myoblast, skin, and testis were pooled in equal parts. The resulting URM RNA was mixed with 129ES cell RNA (Lif+) at 2:1 ratio and 2.5ug of mixed RNA was used for labeling in each tube

tag: reference

value: Universal Mouse Reference


title: primary-macrophages_IFN_rep3

description: Sample name: 5398652023_B


title: ref1 vs. wt-330rpm-1-a


title: InVivoKidney_Day 8_80 mg/kg gentamycin_male_rep3

description: Gene expression at Day 8_80 mg/kg gentamycin_male_rep3

source_name: Male Kidney 80 mg/kg gentamycin Intramuscular once daily Day 8 replicate 3

tag: gender


title: PMA-U937_None_rep2

description: Sample name: 5385288020_K

source_name: PMA-U937, untreated

tag: cell line

value: PMA-U937 (PMA-treated monocytic cell line)

tag: treatment

value: untreated


title: NailWTSE18.5#3


title: rpb1-ctrunc-CTD1-11+cdk8-del-1-b vs. ref1

value: refpool


title: InVivoKidney_Day 8_80 mg/kg gentamycin_male_rep1

description: Gene expression at Day 8_80 mg/kg gentamycin_male_rep1

source_name: Male Kidney 80 mg/kg gentamycin Intramuscular once daily Day 8 replicate 1


title: NailFzd6KOSE14.5#3


title: primary-macrophages_IFN_rep1

description: Sample name: 5385288011_B

value: type 1 IFN

value: A


title: NailFzd6KOSE18.5#3


title: ref1 vs. wt-jb015-k2-a

source_name: wt

value: wt


title: InVivoKidney_Day 15_80 mg/kg gentamycin_female_rep2

description: Gene expression at Day 15_80 mg/kg gentamycin_female_rep2

source_name: Female Kidney 80 mg/kg gentamycin Intramuscular once daily Day 15 replicate 2


title: NailFzd6KOSE16.5#3


title: ref1 vs. wt-jb015-k3-a


title: InVivoKidney_Day 8_80 mg/kg gentamycin_male_rep2

description: Gene expression at Day 8_80 mg/kg gentamycin_male_rep2

source_name: Male Kidney 80 mg/kg gentamycin Intramuscular once daily Day 8 replicate 2

value: male


title: ref1 vs. wt-jb015-k1-a


title: PMA-U937_None_rep1

description: Sample name: 5385288011_I


title: InVivoKidney_Day 8_80 mg/kg gentamycin_female_rep3

description: Gene expression at Day 8_80 mg/kg gentamycin_female_rep3

source_name: Female Kidney 80 mg/kg gentamycin Intramuscular once daily Day 8 replicate 3

value: Sprague Dawley


title: NPC_p5ko_rep1

description: replicate 1

source_name: Neural progenitor cells

tag: genotype

value: Prmt5 depletion


title: NailWTSE14.5#3

tag: genotype/variation


title: NailFzd6KOSE18.5#2


title: InVivoKidney_Day 8_80 mg/kg gentamycin_female_rep2

description: Gene expression at Day 8_80 mg/kg gentamycin_female_rep2

source_name: Female Kidney 80 mg/kg gentamycin Intramuscular once daily Day 8 replicate 2


title: PMA-U937_IFN_rep2

description: Sample name: 5385288020_L

source_name: PMA-U937, IFN-treated

value: partially resistant


title: ref1 vs. rpb1-ctrunc-CTD1-26-1-a


title: ref1 vs. rpb1-ctrunc-CTD1-20-1-a


title: InVivoKidney_Day 8_80 mg/kg gentamycin_female_rep1

description: Gene expression at Day 8_80 mg/kg gentamycin_female_rep1

source_name: Female Kidney 80 mg/kg gentamycin Intramuscular once daily Day 8 replicate 1


title: PMA-U937_IFN_rep1

description: Sample name: 5385288011_J


title: InVivoKidney_Day 4_80 mg/kg gentamycin_male_rep3

description: Gene expression at Day 4_80 mg/kg gentamycin_male_rep3

source_name: Male Kidney 80 mg/kg gentamycin Intramuscular once daily Day 4 replicate 3


title: ref1 vs. rpb1-ctrunc-CTD1-13-1-a


title: primary-macrophages_None_rep1

description: Sample name: 5385288011_A

source_name: primary macrophages, untreated

value: primary macrophages (derived from blood monocytes)


title: PMA-THP-1_None_rep1

description: Sample name: 5385288011_E

source_name: PMA-THP-1, untreated

value: PMA-THP-1 (PMA-treated monocytic cell line)


title: PMA-THP-1_IFN_rep2

description: Sample name: 5385288020_H

source_name: PMA-THP-1, IFN-treated

value: resistant


title: ref1 vs. rpb1-ctrunc-CTD1-12-1-a

source_name: refpool


title: PMA-THP-1_None_rep2

description: Sample name: 5385288020_G


title: InVivoKidney_Day 4_80 mg/kg gentamycin_male_rep2

description: Gene expression at Day 4_80 mg/kg gentamycin_male_rep2

source_name: Male Kidney 80 mg/kg gentamycin Intramuscular once daily Day 4 replicate 2


title: ref1 vs. rpb1-ctrunc-CTD1-12+cdk8-del-1-a


title: InVivoKidney_Day 4_80 mg/kg gentamycin_female_rep3

description: Gene expression at Day 4_80 mg/kg gentamycin_female_rep3

source_name: Female Kidney 80 mg/kg gentamycin Intramuscular once daily Day 4 replicate 3

value: female


title: NailFzd6KOSE16.5#1

value: mixed sex

value: embryo

source_name: Universal Mouse Reference 129ES Cell


title: PMA-THP-1_IFN_rep1

description: Sample name: 5385288011_F


title: ref1 vs. rpb1-ctrunc-CTD1-11+cdk8-del-1-a


title: NailWTSE18.5#2

value: wild type

value: Universal Mouse Reference


title: NailFzd6KOSE16.5#2


title: ref1 vs. rpb1-ctrunc-CTD1-11-1-a


title: InVivoKidney_Day 4_80 mg/kg gentamycin_female_rep2

description: Gene expression at Day 4_80 mg/kg gentamycin_female_rep2

source_name: Female Kidney 80 mg/kg gentamycin Intramuscular once daily Day 4 replicate 2


title: NailFzd6KOSE14.5#1


title: InVivoKidney_Day 4_80 mg/kg gentamycin_male_rep1

description: Gene expression at Day 4_80 mg/kg gentamycin_male_rep1

source_name: Male Kidney 80 mg/kg gentamycin Intramuscular once daily Day 4 replicate 1


title: NailFzd6KOSE14.5#2


title: ref1 vs. wt-jb015-k1-c

source_name: wt


title: NailWTSE18.5#1


title: NailWTSE16.5#1


title: Jurkat_None_rep2

description: Sample name: 5398652022_I

source_name: Jurkat, untreated

value: Jurkat (T cell line)

value: Jurkat

value: untreated


title: InVivoKidney_Day 4_80 mg/kg gentamycin_female_rep1

description: Gene expression at Day 4_80 mg/kg gentamycin_female_rep1

source_name: Female Kidney 80 mg/kg gentamycin Intramuscular once daily Day 4 replicate 1


title: Jurkat_None_rep1

description: Sample name: 5385288011_K


title: InVivoKidney_Day 2_80 mg/kg gentamycin_male_rep2

description: Gene expression at Day 2 of 80 mg/kg gentamycin-treated female rats

source_name: Male Kidney 80 mg/kg gentamycin Intramuscular once daily 24 hr replicate 2


title: Jurkat_IFN_rep1

description: Sample name: 5385288011_L

source_name: Jurkat, IFN-treated

value: type 1 IFN

value: permissive


title: HT1080_None_rep2

description: Sample name: 5398652023_E

source_name: HT1080, untreated

value: HT1080 (fibrosarcoma cell line)


title: NailWTSE16.5#2


title: NailFzd6KOSE18.5#1


title: InVivoKidney_Day 2_80 mg/kg gentamycin_male_rep3

source_name: Male Kidney 80 mg/kg gentamycin Intramuscular once daily 24 hr replicate 3

value: male

value: Sprague Dawley


title: Jurkat_IFN_rep2

description: Sample name: 5398652022_J


title: HT1080_None_rep1

description: Sample name: 5398652022_A


title: InVivoKidney_Day 2_80 mg/kg gentamycin_male_rep1

source_name: Male Kidney 80 mg/kg gentamycin Intramuscular once daily 24 hr replicate 1


title: NailWTSE14.5#1


title: NailWTSE14.5#2


title: InVivoKidney_Day 2_80 mg/kg gentamycin_female_rep2

source_name: Female Kidney 80 mg/kg gentamycin Intramuscular once daily 24 hr replicate 2


title: InVivoKidney_Day 2_80 mg/kg gentamycin_female_rep1

source_name: Female Kidney 80 mg/kg gentamycin Intramuscular once daily 24 hr replicate 1


title: siCONTROL_PC-3

city: Nankoku

first: Kenji

last: Tamura

address: Kohasu, Oko-cho

department: Urology

institute: Kochi University

description: Gene expression data in PC-3 cells, control

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 (GeneChip Expression Wash, Stain and Scan User Manual For Cartridge Arrays, P/N 702731 Rev. 2)

scan_protocol: GeneChips were scanned using the Affymetrix GCS3000 scanner.

data_processing: The scanned images were analyzed using the GeneChip operating software version 1.4 (Affymetrix 690036) with Microarray Suite version 5.0 (MAS 5.0). Affymetrix default analysis settings and global scaling was used as normalization method. The trimmed mean target intensity of each array was set to 500.  Differentially expressed genes were extracted using DNA microarray viewer (Kurabo, osaka, Japan)

source_name: PC-3 cell line, control

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250ng total RNA (GeneChipR 3’ IVT Express Kit User Manual, P/N 702646 Rev. 1).

extract_protocol: RNA for microarray analysis was isolated with TRIzol reagent (Life Technologies, Rockville, MD, USA)  and purified with the RNeasy MiniElute kit (QIAGEN, Valencia, CA) according to the manufacturer’s instructions. RNA quality was assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

value: prostate cancer cell line, PC-3


title: HT1080_IFN_rep2

description: Sample name: 5398652023_F

source_name: HT1080, IFN-treated

value: partially resistant


title: HT1080_IFN_rep1

description: Sample name: 5398652022_B


title: siSHISA2_PC-3

description: Gene expression data in PC-3 cells by SHISA2 knockdown

source_name: PC-3 cell line, SHISA2 knockdown


title: InVivoKidney_Day 2_80 mg/kg gentamycin_female_rep3

source_name: Female Kidney 80 mg/kg gentamycin Intramuscular once daily 24 hr replicate 3


title: Aiolos-overexpressing A549 cells Replicate 3

city: Tianjin

first: Zhenyi

last: Ma

address: 22 Qixiangtai Road

department: Biochemistry and Molecular Biology

institute: Tianjin Medical University

description: Biological replicate 3 of 3. Gene expression changes in Aiolos-overexpressing A549 cells versus control vector-expressing A549 cells

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

scan_protocol: Slides were scanned with an Agilent scanner Type C.

data_processing: Images were quantified using Agilent Feature Extraction Software (version 11).

source_name: control vector-expressing A549 cells

label_protocol: 100ng of total RNA was used to produce polyadenylated RNA with polyA polymerase (Ambion, Austin, TX, USA).The products were transcribed to single-stranded DNA witholigo-dT primers. RNA was selectively degraded by RNase H, leaving RNA oligomers as primers for a DNA polymerase to synthesize double-stranded DNA(dsDNA). The dsDNA was purified and served as a template to generate antisense cDNA by cRNA reverse transcription.The fluorescence labeling reactions contained 5× Klenow buffer, dNTP (120 mM dATP, 120 mM dGTP, 120 mM dTTP, and 60 mM dCTP), 40 mM Cy5-dCTP or Cy3-dCTP (GE Healthcare) and Klenow enzyme (TaKaRa, Dalian, China). The reaction was carried out at 37°C for 90 min and stopped by addition of 25 mM EDTA and 0.25% sodium dodecyl sulfate (SDS).

growth_protocol: A549 cells were grown in RPMI1640 medium with 10% FBS, transfected with control vector or Aiolos expression vector.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

value: Human lung adenocarcinoma epithelial cells

source_name: Aiolos-overexpressing A549 cells


title: CEM-SS_None_rep2

description: Sample name: 5398652023_K

source_name: CEM-SS, untreated

value: CEM-SS (T cell line)

value: CEM-SS


title: InVivoKidney_predose_saline_male_rep2

description: Gene expression of saline-treated male rats as pre-dose data

source_name: Male Kidney Saline Intramuscular replicate 2


title: InVivoKidney_predose_saline_male_rep3

source_name: Male Kidney Saline Intramuscular replicate 3


title: HUVECs - V30M TTR, biological rep 4

city: Lisbon

first: Raquel

middle: João

last: Nunes

address: Avenida Prof Egas Moniz

department: Angiogenesis Unit

country: Portugal

institute: Instituto Medicina Molecular

description:
V30M TTR 4
Gene expression data from HUVECs cultured in the presence of V30M TTR

hyb_protocol: The end-labeled, fragmented cDNA was used in a 130-µl hybridization cocktail containing added hybridization controls (GeneAtlas Hybridization, Wash, and Stain Kit for WT Array Strips, Affymetrix) and hybridized on array strips for 20 h at 48°C. Standard post hybridization wash and double-stain protocols (GeneAtlas Hybridization, Wash, and Stain Kit for WT Array Strips, Affymetrix) were used on an Affymetrix GeneAtlas system

scan_protocol: Array strips were scanned on the GeneAtlas system

data_processing: Subsequent analysis was carried out with Chipster 2.3.0. RMA was used to compute expression values for the 6 arrays in this study and based on custom cdf file included in hugene11stv1hsentrezg.db as available from Brainarray database.

source_name: HUVECs_V30M TTR at 4 µM for 3 h

label_protocol: Concentration and purity was determined by spectrophotometry and integrity was confirmed using an Agilent 2100 Bioanalyzer with a RNA 6000 Nano Assay (Agilent Technologies, Palo Alto, CA). RNA was processed for use on Affymetrix (Santa Clara, CA, USA) GeneChip Human Gene 1.1 ST Array Strips, using NuGEN Technologies’ (San Carlos, CA, USA) Ovation PicoSL WTA System V2 and Encore Biotin Module, according to the manufacturer’s protocol. Briefly, 17 ng of total RNA was used in a reverse transcription reaction to obtain first-strand cDNA. After generation and purification of DNA/RNA heteroduplex double strand cDNA, this was subjected to SPIA amplification. Size distribution of purified SPIA cDNA was assessed using an Agilent 2100 Bioanalyzer with a RNA 6000 Nano Assay, followed by fragmentation and end-labeling of 2.5 ug of SPIA cDNA (Encore Biotin Module, NuGEN) and confirmation using a RNA 6000 Nano Assay.

growth_protocol: Primary Human Umbilical Vein Endothelial Cells were cultured in growing endothelial medium (basal EBM-2 medium supplemented with EGM-2 singlequots, BBE and 5% of Fetal Bovine Serum as provided by the manufacturers (Lonza, USA) and used at passage 7.

extract_protocol: Rneasy Micro Kit (Qiagen) was used for the extraction of total RNA according to the manufacturer's instructions.

treatment_protocol: Confluent cells were cultured with WT or V30M TTR proteins at 4 µM for 3 h. Cells were then trypsinized, washed with PBS and the dry pellet was frozen at -80C.

value: Human Umbilical Vein Endothelial Cells (HUVECs)

tag: exposed to

value: V30M TTR at 4 µM for 3 h


title: HUVECs - V30M TTR, biological rep 3

description:
V30M TTR 3
Gene expression data from HUVECs cultured in the presence of V30M TTR


title: Proliferative, biological replicate 2

city: Jacksonville

first: Ed

last: Mougey

state: FL

address: 807 Children's Way

department: Biomedical Research

institute: Nemours Children's Clinic

description: Intentionally left blank

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip U133+ 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

source_name: Human growth plate, proliferative zone chondrocytes

label_protocol: Twenty nanograms of purified total RNA from each of the five growth plate fractions were amplified approximately 1.5 x 10^6 fold in three rounds of T7 polymerase directed linear amplification as described by Baugh, et al. (2001) Quantitative analysis of mRNA amplification by in vitro transcription. Nucleic Acids Res 29: E29. In the final round of amplification, the aRNA was labeled by incorporation of biotinylated CTP and UTP, and the resulting product was purified on a Qiagen RNeasy column. The purified aRNA was quantitated spectrophotometrically. Two micrograms of each aRNA sample was visualized by agarose electrophoresis to confirm the size and quality of the RNA.

growth_protocol: Intentionally left blank

extract_protocol: Populations of cells corresponding to the hypertrophic, prehypertrophic, proliferative, reserve, and perichondrium, were separately isolated by laser microdissection using a Leica AS-LMD microscope. Collection of cells into different fractions was based on cell morphology and position in the growth plate and was accomplished in six steps as follows:  1) the metaphyseal/hypertrophic zone junction with its heterogeneous mixture of cells was microdissected and discarded, removing it from the slide. This eliminated the possibility of metaphyseal contamination of the remaining fractions. 2) The beginning of the hypertrophic zone was identified by locating the position in the growth plate where the chondrocytes had stopped increasing in size. Cells from this point to the metaphyseal junction (now removed), were collected. 3) The beginning of the proliferative zone was identified as the proliferative zone/reserve zone border. Cells from here to where the flattened chondrocytes first start to increase in size were collected. 4) The region between the proliferative and hypertrophic zones was designated as the pre-hypertrophic zone and was microdissected. 5) A region of the reserve zone was collected that was clearly separated from the reserve zone/proliferative zone junction and the secondary ossification center, to avoid contamination. Cells of the groove of Ranvier were not examined in this study. 6) Perichondrium (perichondral ring of La Croix) was collected from the lateral margin(s) of the section and is clearly distinguished from the groove of Ranvier and reserve zone tissue by its fibrous nature. With this approach, landmarks intrinsic to the section allowed collection of the zones in a consistent manner for all sections, however since the columnar region of the growth plate (the proliferative, pre-hypertrophic and hypertrophic zones) is a continuum and has no distinct boundaries, each fraction is enriched for but does not exclusively contain cells of the target zone.  Tissue released from the slide by laser microdissection was collected and stored in Trizol (Invitrogen). For RNA purification, tissue isolates from each fraction were pooled and homogenized for 3 minutes at 25 cps in a Qiagen TissueLyser. Nucleic acids from the tissue lysates were subsequently recovered from the aqueous phase by isopropanol precipitation. The recovered nucleic acids were resuspended, digested with DNAse and proteinase K, and purified by phenol/chloroform extraction and ethanol precipitation. Finally, the resuspended nucleic acids were applied to a Qiagen RNeasy column and purified following the manufacture’s recommendations. Subsequent RNA quantitation was performed by a RiboGreen dye-binding fluorescence assay (Invitrogen).

treatment_protocol: Fluorography in conjunction with a wire guide was used to locate the growth plate. A tissue block (approximately 0.75 x 0.75 x 1.5 cm) containing the growth plate and perichondrium was removed. The recovered tissue block was maintained humidified inside a petri dish on saline-moistened gauze until it was transferred to liquid nitrogen storage. Typically, tissue was recovered 30-60 minutes following tourniquet application and snap-frozen in liquid nitrogen 5-15 minutes after recovery. For sectioning, growth plates were mounted in OCT and sectioned at -20°C in a cryostat. Ten micrometer sections were collected on Leica LMD PEN foil slides, allowed to dry for 1 hr at room temperature, fixed for 5 minutes (-20°C, acetone), dehydrated (1x 95% ethanol, 1x 100% ethanol, both 15 sec.), cleared (1x xylene, 15 sec), maintained over night under vacuum, and finally packaged and stored in a sealed, desiccated container at –70°C.

tag: race

value: Caucasian, Gender:male, Age:13-3/12 years, Tissue:long bone growth plate, Zone:proliferative, Morphology:normal


title: Aiolos-overexpressing A549 cells Replicate 2

description: Biological replicate 2 of 3. Gene expression changes in Aiolos-overexpressing A549 cells versus control vector-expressing A549 cells


title: Perichondrium, biological replicate 2

description: Intentionally left blank

source_name: Human growth plate, perichondrium

value: Caucasian, Gender:male, Age:13-3/12 years, Tissue:long bone growth plate, Zone:perichondrium, Morphology:normal


title: Prehypertrophic, biological replicate 2

description: Intentionally left blank

source_name: Human growth plate, prehypertrophic zone chondrocytes

value: Caucasian, Gender:male, Age:13-3/12 years, Tissue:long bone growth plate, Zone:prehypertrophic, Morphology:normal


title: CEM-SS_IFN_rep1

description: Sample name: 5398652022_H

source_name: CEM-SS, IFN-treated


title: CEM-SS_IFN_rep2

description: Sample name: 5398652023_L


title: Aiolos-overexpressing A549 cells Replicate 1

description: Biological replicate 1 of 3. Gene expression changes in Aiolos-overexpressing A549 cells versus control vector-expressing A549 cells


title: Reserve, biological replicate 2

description: Intentionally left blank

source_name: Human growth plate, reserve zone chondrocytes

value: Caucasian, Gender:male, Age:13-3/12 years, Tissue:long bone growth plate, Zone:reserve, Morphology:normal


title: HUVECs - V30M TTR, biological rep 2

description:
V30M TTR 2
Gene expression data from HUVECs cultured in the presence of V30M TTR


title: Hypertrophic, biological replicate 2

description: Intentionally left blank

source_name: Human growth plate, hypertrophic zone chondrocytes

value: Caucasian, Gender:male, Age:13-3/12 years, Tissue:long bone growth plate, Zone:hypertrophic, Morphology:normal


title: HUVECs - WT TTR, biological rep 4

description:
WT TTR 4
Gene expression data from HUVECs cultured in the presence of WT TTR

source_name: HUVECs_WT TTR at 4 µM for 3 h

value: WT TTR at 4 µM for 3 h


title: InVivoKidney_predose_saline_male_rep1

source_name: Male Kidney Saline Intramuscular replicate 1


title: InVivoKidney_predose_saline_female_rep3

description: Gene expression of saline-treated female rats as pre-dose data

source_name: Female Kidney Saline Intramuscular replicate 3

value: female


title: InVivoKidney_predose_saline_female_rep2

source_name: Female Kidney Saline Intramuscular replicate 2


title: Perichondrium, biological replicate 1

description: Intentionally left blank

value: Caucasian, Gender:female, Age:11-10/12 years, Tissue:long bone growth plate, Zone:perichondrium, Morphology:normal


title: CEM_None_rep2

description: Sample name: 5398652023_I

source_name: CEM, untreated

value: CEM (T cell line)

value: CEM

value: untreated


title: Reserve, biological replicate 1

description: Intentionally left blank

value: Caucasian, Gender:female, Age:11-10/12 years, Tissue:long bone growth plate, Zone:reserve, Morphology:normal


title: Prehypertrophic, biological replicate 1

description: Intentionally left blank

value: Caucasian, Gender:female, Age:11-10/12 years, Tissue:long bone growth plate, Zone:prehypertrophic, Morphology:normal


title: CEM_None_rep1

description: Sample name: 5398652022_E


title: CEM_IFN_rep2

description: Sample name: 5398652023_J

source_name: CEM, IFN-treated

value: type 1 IFN

value: permissive


title: Proliferative, biological replicate 1

description: Intentionally left blank

value: Caucasian, Gender:female, Age:11-10/12 years, Tissue:long bone growth plate, Zone:proliferative, Morphology:normal


title: HUVECs - WT TTR, biological rep 3

description:
WT TTR 3
Gene expression data from HUVECs cultured in the presence of WT TTR

value: Human Umbilical Vein Endothelial Cells (HUVECs)


title: InVivoKidney_predose_saline_female_rep1

source_name: Female Kidney Saline Intramuscular replicate 1

value: Sprague Dawley


title: HUVECs - WT TTR, biological rep 1

description:
WT TTR 1
Gene expression data from HUVECs cultured in the presence of WT TTR


title: CEM_IFN_rep1

description: Sample name: 5398652022_F


title: CD34+ cells 100nM prostaglandin treated 2hr 37deg

status: Public on Sep 12 2013

city: San Diego

first: Dave

last: Robbins

state: CA

address: 3535 General Atomics Court Ste. 200

institute: Fate Therapeutics

description: CD34+ cells 100nM dmPGE2 treated 2hr 37 deg C in StemSpan-SFEM.

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

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

data_processing: Probe intensities were normalized according to a log-scale robust multi-array analysis (RMA) method in Expression Console (Affymetrix).

source_name: Pre-isolated cryopreserved UCB CD34+ cells, 100nM dmPGE2 treated 2hr 37 deg C in StemSpan-SFEM

label_protocol: Biotinylated cRNA were prepared using the Message Amp II kit two-round protocol from 100 ng total RNA.

extract_protocol: Total RNA was isolated post incubation with the PicoPure RNA Isolation kit.

treatment_protocol: UCB CD34+ cells were treated with 0.1, 1, 10, 50, or 100uM 16,16-dimethyl Prostaglandin E2 (or vehicle) for 2 hours at 25 or 37 deg C in StemSpan-SFEM.

tag: tissue

value: umbilical cord blood

value: CD34+ cells

value: 100nM dmPGE2

tag: treatment temperature

value: 37 deg C

tag: treatment duration


title: CD34+ cells 50uM prostaglandin treated 2hr 25deg

description: CD34+ cells 50uM dmPGE2 treated 2hr 25 deg C in StemSpan-SFEM.

source_name: Pre-isolated cryopreserved UCB CD34+ cells, 50uM dmPGE2 treated 2hr 25 deg C in StemSpan-SFEM

value: 50uM dmPGE2

value: 25 deg C


title: Hypertrophic, biological replicate 1

description: Intentionally left blank

value: Caucasian, Gender:female, Age:11-10/12 years, Tissue:long bone growth plate, Zone:hypertrophic, Morphology:normal


title: CD34+ cell 60min dmPGE2-60min Vehicle treated 37deg

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

data_processing: Probe intensities were normalized according to a log-scale robust multi-array analysis (RMA) method in Expression Console (Affymetrix)

source_name: Pre-isolated cryopreserved UCB CD34+ cells

label_protocol: Biotinylated cRNA were prepared using the Message Amp II kit two-round protocol from 100 ng total RNA

extract_protocol: Total RNA was isolated post incubation with the PicoPure RNA Isolation kit

treatment_protocol: UCB CD34+ cells were treated for a portion of the 120 minute treatment (5, 15, 30, 60 or 120 minutes) with 10uM 16,16-dimethyl Prostaglandin E2 and compared to a 120 min. vehicle treated sample

value: 60min 10uM dmPGE2-60min Vehicle treated 37deg


title: CD34+ cells 10uM prostaglandin treated 2hr 25deg

description: CD34+ cells 10uM dmPGE2 treated 2hr 25 deg C in StemSpan-SFEM.

source_name: Pre-isolated cryopreserved UCB CD34+ cells, 10uM dmPGE2 treated 2hr 25 deg C in StemSpan-SFEM

value: 10uM dmPGE2


title: CD34+ cells 10uM prostaglandin treated 2hr 37deg

description: CD34+ cells 10uM dmPGE2 treated 2hr 37 deg C in StemSpan-SFEM.

source_name: Pre-isolated cryopreserved UCB CD34+ cells, 10uM dmPGE2 treated 2hr 37 deg C in StemSpan-SFEM


title: CD34+ cells vehicle treated 2hr 25deg

description: CD34+ cells Vehicle treated 2hr 25 deg C in StemSpan-SFEM.

source_name: Pre-isolated cryopreserved UCB CD34+ cells, vehicle treated 2hr 25 deg C in StemSpan-SFEM

value: vehicle


title: CD34+ cells vehicle treated 2hr 37deg

description: CD34+ cells Vehicle treated 2hr 37 deg C in StemSpan-SFEM.

source_name: Pre-isolated cryopreserved UCB CD34+ cells, vehicle treated 2hr 37 deg C in StemSpan-SFEM


title: CD34+ cells 100uM prostaglandin treated 2hr 37deg

description: CD34+ cells 100uM dmPGE2 treated 2hr 37 deg C in StemSpan-SFEM.

source_name: Pre-isolated cryopreserved UCB CD34+ cells, 100uM dmPGE2 treated 2hr 37 deg C in StemSpan-SFEM

value: 100uM dmPGE2


title: CD34+ cells 1uM prostaglandin treated 2hr 37deg

description: CD34+ cells 1uM dmPGE2 treated 2hr 37 deg C in StemSpan-SFEM.

source_name: Pre-isolated cryopreserved UCB CD34+ cells, 1uM dmPGE2 treated 2hr 37 deg C in StemSpan-SFEM

value: 1uM dmPGE2


title: CD34+ cell 15min dmPGE2-105min Vehicle treated 37deg

value: 15min 10uM dmPGE2-105min Vehicle treated 37deg


title: CD34+ cell 5min dmPGE2-115min Vehicle treated 37deg

value: 5min 10uM dmPGE2-115min Vehicle treated 37deg


title: CD34+ cell 120min dmPGE2

description: CD34+ cell 120min dmPGE2

value: 120min 10uM dmPGE2


title: CD34+ cells 100uM prostaglandin treated 2hr 4deg

source_name: Pre-isolated cryopreserved UCB CD34+ cells 100uM dmPGE2 treated 2hr 4 deg C in StemSpan-SFEM

treatment_protocol: UCB CD34+ cells were treated with 10, 50, or 100uM 16,16-dimethyl Prostaglandin E2 (or vehicle) for 2 hours at 4 deg C in SS


title: CD34+ cells 10uM prostaglandin treated 2hr 4deg

source_name: Pre-isolated cryopreserved UCB CD34+ cells 10uM dmPGE2 treated 2hr 4 deg C in StemSpan-SFEM


title: CD34+ cells vehicle treated 2hr 4deg

description: CD34+ cells vehicle treated 2hr 4deg

source_name: Pre-isolated cryopreserved UCB CD34+ cells vehicle treated 2hr 4 deg C in StemSpan-SFEM


title: CD34+ cells 100uM prostaglandin treated 2hr 25deg

description: CD34+ cells 100uM dmPGE2 treated 2hr 25 deg C in StemSpan-SFEM.

source_name: Pre-isolated cryopreserved UCB CD34+ cells, 100uM dmPGE2 treated 2hr 25 deg C in StemSpan-SFEM


title: CD34+ cell 30min dmPGE2-90min Vehicle treated 37deg

value: 30min 10uM dmPGE2-90min Vehicle treated 37deg


title: CD34+ cell 120min Vehicle

description: CD34+ cell 120min Vehicle

value: 120min Vehicle


title: CD34+ cells vehicle treated 2hr 37deg in LMD/HAS

source_name: Pre-isolated cryopreserved UCB CD34+ cells vehicle treated 2hr 37 deg C in LMD/HAS

treatment_protocol: UCB CD34+ cells were treated with 10uM 16,16-dimethyl Prostaglandin E2 for 2 hours at varying temperatures in SS or LMD/HAS

value: umbilical cord blood


title: CD34+ cells vehicle treated 2hr 37deg in SS (1)

source_name: Pre-isolated cryopreserved UCB CD34+ cells vehicle treated 2hr 37 deg C in StemSpan-SFEM


title: CD34+ cells 50uM prostaglandin treated 2hr 4deg

source_name: Pre-isolated cryopreserved UCB CD34+ cells 50uM dmPGE2 treated 2hr 4 deg C in StemSpan-SFEM


title: CD34+ cells vehicle treated 2hr 37deg in SS (2)


title: CD34+ cells prostaglandin treated 2hr 37deg in SS (2)

source_name: Pre-isolated cryopreserved UCB CD34+ cells 10uM dmPGE2 treated 2hr 37 deg C in StemSpan-SFEM


title: CD34+ cells prostaglandin treated 2hr 37deg in SS (1)


title: CD34+ cells vehicle treated 2hr 4deg in SS


title: CD34+ cells prostaglandin treated 2hr 25deg in SS

source_name: Pre-isolated cryopreserved UCB CD34+ cells 10uM dmPGE2 treated 2hr 25 deg C in StemSpan-SFEM


title: CD34+ cells vehicle treated 2hr 25deg in SS

source_name: Pre-isolated cryopreserved UCB CD34+ cells vehicle treated 2hr 25 deg C in StemSpan-SFEM


title: CD34+ cells prostaglandin treated 2hr 4deg in SS


title: CD34+ cells prostaglandin treated 2hr 37deg in LMD/HAS

source_name: Pre-isolated cryopreserved UCB CD34+ cells 10uM dmPGE2 treated 2hr 37 deg C in LMD/HAS


title: a549-3d-treated-2

city: Charlottesville

first: Marcin

middle: Piotr

last: Cieslik

state: VA

address: 400 Stribling Ave Ext

institute: University of Virginia

scan_protocol: Laser GeneArray scanner

data_processing: the data was analyzed using limma 3.6.9 and GCRMA using all 8 arrays

label_protocol: biotin label, sample preparation according to manufacturer protocols: http://www.affymetrix.com/support/index.affx on the left choose Technical Documentation

growth_protocol: NSCLC lines A549 were obtained from ATCC and maintained as 2D cultures in DMEM (CellGro), 10% FBS (Invitrogen) and penicillin/streptomycin (Invitrogen). For 3D cultures, cells were grown to approximately 80% confluency, trypsinized, resuspended in DMEM/10% FBS and pipeted onto the underside of a sterile 10 cm tissue-culture plate lid and incubated for 48 hours to facilitate cellular aggregation and spheroid formation.

extract_protocol: RNA was isolated as specified using the RNEasy mini-prep kit (Qiagen).  The RNA was eluted into RNase-free water.  After isolation, 10% of the sample was run on a 0.8% agarose gel to ensure RNA integrity.  The remaining RNA was quantified, and 500 ng was submitted for microarray analysis per sample.  Sample preparation according to manufacturer protocols: http://www.affymetrix.com/support/index.affx on the left choose Technical Documentation

treatment_protocol: 2D and 3D cultures were subjet to two treatment rounds of 10 ng/mL TNF and 2 ng/mL TGF treatment and incubation for 48 hours each.

tag: culture

tag: treated twice with

value: 10 ng/mL TNF and 2 ng/mL TGF for 48hr each


title: a549-3d-treated-1

hyb_protocol: according to manufacturer protocols: http://www.affymetrix.com/support/index.affx on the left choose Technical Documentation


title: a549-3d-control-2


title: a549-3d-control-1


title: a549-2d-treated-1


title: a549-2d-control-2


title: a549-2d-treated-2


title: a549-2d-control-1


title: CEM-SS_None_rep1

description: Sample name: 5398652022_G

source_name: CEM-SS, untreated

value: CEM-SS (T cell line)

tag: donor

value: CEM-SS

tag: replicate

tag: resistance to hiv-1 following ifn treatment

value: untreated


title: K96243_Zn2+ML_2 (Cy5)

first: Wen Fong

last: Ooi

address: 60 Biopolis Street, Genome, #02-01

institute: Genome Institute of Singapore

description: SAMPLE 332

hyb_protocol: Microarray hybridizations were performed at 65°C in a MAUI hybridization station (BioMicro Systems, USA) for 17hrs.

scan_protocol: The slides were washed, dried in a centrifuge at 600rpm for 4mins, and scanned on an Axon Genepix 4000B scanner (Molecular Devices, USA) at a resolution of 5 microns

data_processing: The raw data (.pair file) was subjected to Lowess within-chip normalization as implemented in GeneSpring GX11 , and cross-chip median normalization using R, .

organism: Burkholderia pseudomallei K96243

source_name: Burkholderia pseudomallei K96243 wild type

label_protocol: Sample cDNAs were labeled with Cy3 (Cy3-ULS, Kreatech Diagnostics, USA) and a universal hybridization reference (K9LBS) was similarly labeled with Cy5.

growth_protocol: Reference sample used (Cy5) is common to all - Bacteria subjected to growth in LB. Harvested at stationary phase (OD600 = 2.0).

extract_protocol: Bacterial cells in liquid cultures were isolated by centrifugation at 3500rpm at 4°C for 15mins, washed with 1xDPBS, and re-pelleted. Cell pellets were mixed with 4-8ml TRIZOL reagent (Invitrogen, USA) and maintained at room temperature for 10mins. For bacterial cells on plate cultures, bacterial colonies were harvested using sterile inoculation loops directly into 4ml TRIZOL. One-tenth the volume of 1-bromo-3-chloro-propane (Sigma, USA) was then added, and the entire mixture vortexed for 15s. The mixture was incubated at room temperature for 3mins and centrifuged at 9,000rpm at 4°C for 30mins. The aqueous phase was transferred to a fresh tube containing an equal volume of isopropanol, mixed well, and maintained at room temperature for 10mins. The tube was then centrifuged at 9,000rpm at 4°C for 30mins to obtain the total RNA pellet. The pellet was washed with 1ml 75% ethanol, dried at room temperature for 5mins, and resuspended in 30ul of RNase-free water. Bp-infected RAW264.7 cells were lysed with TRIZOL and both murine and bacterial total RNAs were extracted using a PureLink RNA mini kit (Invitrogen, USA). Bp-infected murine lungs from infected BALB/c mice were treated with 2ml TRIZOL, homogenized using a Polytron homogenizer (maximum speed, two bursts 10–15s each), and processed for RNA extraction. Extracted RNAs were treated with DNase I (DNA-free; Ambion, USA) to remove contaminating genomic DNA, according to the manufacturer’s instructions.

treatment_protocol: RNA samples were further enriched for bacterial mRNAs using a MICROBExpress kit (Ambion, USA) to deplete bacterial 16S and 23S rRNAs, according to the manufacturer’s instructions. For RNA samples comprising both bacterial and mammalian RNAs, bacterial RNAs were separated from mammalian 18S and 28S rRNAs using a MICROBEnrich kit (Ambion, USA), according to the manufacturer’s instructions. The MICROBEnrich kit uses a Capture Oligo Mix of capture oligonucleotides homologous to mammalian 18S and 28S rRNAs. After processing, bacterial mRNA samples were quantified by spectrophotometry, and electrophoresed in TAE/formamide agarose gels to assess overall mRNA quality and integrity.

value: wild type

tag: infection

value: Not applicable

tag: condition


title: K96243_Zn2+ML_2 (Cy3)

description: SAMPLE 331

value: Bacteria subjected to growth in TSBDC with 200uM Zinc sulfate heptahydrate. Harvested at log phase.


title: K96243_UV1hrref_2 (Cy3)

description: SAMPLE 327

value: Bacteria grown to log phase and exposed to fluorescent light for 1hr in BioSafety Cabinet.


title: K96243_Zn2+ML_1 (Cy5)

description: SAMPLE 330

value: Bacteria subjected to growth in LB. Harvested at stationary phase (OD600 = 2.0).


title: AL30_04C16hr_1 (Cy3)

description: SAMPLE 1

source_name: Burkholderia pseudomallei K96243 rpoE mutant

value: rpoE mutant

value: Bacteria grown to log phase, pelleted and resuspended in cold LB medium for 16 hours


title: K96243_Zn2+ML_1 (Cy3)

description: SAMPLE 329


title: K96243_UV1hrref_2 (Cy5)

description: SAMPLE 328


title: K96243_UV1hr_2 (Cy5)

description: SAMPLE 324


title: K96243_UV1hrref_1 (Cy3)

description: SAMPLE 325


title: K96243_UV1hrref_1 (Cy5)

description: SAMPLE 326


title: K96243_UV1hr_1 (Cy5)

description: SAMPLE 322


title: K96243_UV1hr_2 (Cy3)

description: SAMPLE 323

value: Bacteria grown to log phase and exposed to UV for 1hr in BioSafety Cabinet.


title: K96243_UV1hr_1 (Cy3)

description: SAMPLE 321


title: K96243_UV10minsref_2 (Cy5)

description: SAMPLE 320


title: K96243_TaurineML_2 (Cy5)

description: SAMPLE 312


title: K96243_UV10minsref_2 (Cy3)

description: SAMPLE 319

value: Bacteria grown to log phase and exposed to fluorescent light for 10mins in BioSafety Cabinet.


title: K96243_Revived_1 (Cy5)

description: SAMPLE 302


title: K96243_UV10mins_1 (Cy5)

description: SAMPLE 314


title: K96243_UV10mins_1 (Cy3)

description: SAMPLE 313

value: Bacteria grown to log phase and exposed to UV for 10mins in BioSafety Cabinet.


title: K96243_TaurineML_2 (Cy3)

description: SAMPLE 311

value: Bacteria grown to log phase in modified M63 medium with Taurine and harvested.


title: K96243_UV10mins_2 (Cy5)

description: SAMPLE 316


title: K96243_UV10mins_2 (Cy3)

description: SAMPLE 315


title: K96243_UV10minsref_1 (Cy3)

description: SAMPLE 317


title: K96243_Revived_2 (Cy5)

description: SAMPLE 304


title: K96243_UV10minsref_1 (Cy5)

description: SAMPLE 318


title: K96243_Revived_1 (Cy3)

description: SAMPLE 301

value: Bacteria grown to log phase in LB, pelleted and incubated in oven (desiccation) for 24 hrs then revived in 5ml H2O for 15mins (37C, 150rpm)


title: K96243_Revived_2 (Cy3)

description: SAMPLE 303


title: K96243_TaurineES_2 (Cy5)

description: SAMPLE 308


title: K96243_pH7_2 (Cy3)

description: SAMPLE 295

value: Bacteria grown to log phase, pelleted and resuspended in 1XPBS (pH 7.0)


title: K96243_TaurineML_1 (Cy5)

description: SAMPLE 310


title: K96243_TaurineES_2 (Cy3)

description: SAMPLE 307

value: Bacteria grown to stationary phase in modified M63 medium with Taurine and harvested.


title: K96243_Plate_1 (Cy3)

description: SAMPLE 297

value: Bacteria grown to log phase in LB, pelleted and resuspended. 10^7 cfu/ml plated out (lawn) on LA and grown simultaneously.


title: K96243_pH7_2 (Cy5)

description: SAMPLE 296


title: K96243_TaurineES_1 (Cy3)

description: SAMPLE 305


title: K96243_TaurineML_1 (Cy3)

description: SAMPLE 309


title: K96243_Plate_1 (Cy5)

description: SAMPLE 298


title: K96243_Plate_2 (Cy3)

description: SAMPLE 299


title: LB+glycerol, biological rep2

city: Hyderabad

first: kotakonda

last: Arunasri

state: Andhra Pradesh

address: Habsiguda

country: India

institute: Centre for Cellular and Molecular biology

description:
PSP effect E2
Gene expression data of E.coli in LB + glycerol medium

hyb_protocol: The DNA micro array chips were hybridized with the labelled cDNA using the Affymetrix protocol (www.affymetrix.com).

scan_protocol: Microarray slides were then scanned using Affymetrix 428 Array Scanner and GCOS software to obtain images of the chips and further processed to get intensity cell files for the probe sets.

data_processing: The  intensity cell files were then imported, normalized for background correction (used RMA for normalization)and data analysed using Gene Spring 11.5 software.

organism: Escherichia coli

source_name: E.coli, grown in LB+glycerol to 0.8OD

label_protocol: The cDNA was fragmented with DNAse 1 (Promega Corporation, Madison, USA) and then labeled with biotin at the 3’ end using the labeling reagent from Affymetrix (CA, USA) and Terminal transferase enzyme (Promega).

growth_protocol: Escherichia coli was grown aerobically in Luria-Bertani (LB) broth and LB + glycerol at 30°C in an incubator shaker at 150 r.p.m.

extract_protocol: RNA was isolated from the culture by using the Qiagen RNeasy mini-prep kit.cDNA was synthesized using 5-10 µg/ml of RNA and the first strand cDNA synthesis kit from Invitrogen (Invitrogen Bioservices India Pvt. Ltd., Bangalore).

treatment_protocol: To study gene expression,  28 days old E.coli cells were grown in the presence of LB broth and LB broth supplemented with 10% v/v glycerol.

tag: growth protocol

value: grown in LB+glycerol to 0.8OD


title: K96243_pH7_1 (Cy5)

description: SAMPLE 294


title: LB+glycerol, biological rep1

description:
PSP effect E1
Gene expression data of E.coli in LB + glycerol medium


title: LB, biological rep3

description:
PSP effect C3
Gene expression data of E.coli in LB medium

source_name: E.coli, grown in LB to 0.8OD

value: grown in LB to 0.8OD


title: K96243_pH4_1 (Cy5)

description: SAMPLE 290

value: wild type


title: K96243_Plate_2 (Cy5)

description: SAMPLE 300

value: Not applicable


title: K96243_pH4_2 (Cy3)

description: SAMPLE 291

value: Bacteria grown to log phase, pelleted and resuspended in 1XPBS (pH 4.0)


title: K96243_TaurineES_1 (Cy5)

description: SAMPLE 306


title: LB, biological rep2

description:
PSP effect C2
Gene expression data of E.coli in LB medium


title: K96243_Pb2+24hrs_2 (Cy5)

description: SAMPLE 288


title: K96243_Pb2+24hrs_2 (Cy3)

description: SAMPLE 287

value: Bacteria subjected to growth in TSBDC with 200uM Lead(II) carbonate. Harvested at stationary phase.


title: K96243_pH4_1 (Cy3)

description: SAMPLE 289


title: K96243_Pb2+24hrs_1 (Cy5)

description: SAMPLE 286

value: Bacteria subjected to growth in LB. Harvested at stationary phase (OD600 = 2.0).


title: LB+glycerol, biological rep3

description:
PSP effect E3
Gene expression data of E.coli in LB + glycerol medium


title: K96243_Pb2+24hrs_1 (Cy3)

description: SAMPLE 285


title: K96243_OsmRef_2 (Cy5)

description: SAMPLE 284


title: K96243_OsmRef_2 (Cy3)

description: SAMPLE 283

value: Bacteria grown to log phase, pelleted and resuspended in LB.


title: K96243_pH7_1 (Cy3)

description: SAMPLE 293


title: K96243_pH4_2 (Cy5)

description: SAMPLE 292


title: LB, biological rep1

description:
PSP effect C1
Gene expression data of E.coli in LB medium


title: K96243_OsmRef_1 (Cy5)

description: SAMPLE 282


title: K96243_Ni2.24hrs_2 (Cy3)

description: SAMPLE 279

value: Bacteria subjected to growth in TSBDC with Nickel (II) sulfate hexahydrate. Harvested at stationary phase.


title: K96243_OsmRef_1 (Cy3)

description: SAMPLE 281


title: K96243_Na2SO4ML_1 (Cy5)

description: SAMPLE 274


title: shCypB2

city: ROCHESTER

first: Richard

middle: J

last: Bram

state: MN

address: 200 First Street SW

department: Pediatric and Adolescent Medicine

institute: Mayo Clinic

description: U251 shRNA against CypB, biological replicate B

hyb_protocol: standard as recommended by illumina

scan_protocol: standard as recommended by illumina

data_processing: Fastlo [1] normalization was used to preprocess the data. In the quality control step, the Principal Components Analysis (PCA) graph and the hierarchical clustering plot (based on Pearson’s dissimilarity) showed a plate effect, which was removed later using Partek’s batch removal tool[2]. 1. J. E. Eckel, C. Gennings, T. M. Therneau, L. D. Burgoon, D. R. Boverhof, and T. R. Zacharewski. Normalization of two-channel microarray experiments: a semiparametric approach. Bioinformatics (2005) 21(7): 1078-1083.    2. Removing Batch Effects in Partek. Partek® software On-line Help, version 6.5, build 6.10.0915. Copyright © 2010 Partek Inc., St. Louis, MO, USA.

source_name: human glioblastoma cell line

label_protocol: standard as recommended by illumina

growth_protocol: U251 GBM cells were grown in DMEM with 10% FBS

extract_protocol: Total RNA was isolated using the miRNeasy RNA isolation kit from Qiagen

treatment_protocol: U251 GBM cells were transduced with the lentiviral shRNA (shCON or shCypB) for 5 days before total RNA extraction. The pLKO1.5 vectors (shCON encoding non-target control sequence and shCypB to target CypB gene) were used to generate lentiviral particles.

tag: cell line

tag: transduction

value: stably expressing shRNA against cyclophilin B


title: K96243_Na2SO4ML_2 (Cy3)

description: SAMPLE 275

value: Bacteria grown to log phase in modified M63 medium with Na2SO4 as reference.


title: shCON3

description: U251 shRNA-Control, biological replicateC

value: stably expressing non-target control shRNA


title: shCypB3

description: U251 shRNA against CypB, biological replicate C


title: K96243_Na2SO4ES_2 (Cy5)

description: SAMPLE 272


title: shCypB1

description: U251 shRNA against CypB, biological replicate A


title: shCON2

description: U251 shRNA-Control, biological replicate B


title: K96243_Mn2+ML_2 (Cy5)

description: SAMPLE 268


title: K96243_Mn2+ML_2 (Cy3)

description: SAMPLE 267

value: Bacteria subjected to growth in TSBDC with 200uM Manganese chloride tetrahydrate. Harvested at log phase.


title: shCON1

description: U251 shRNA-Control, biological replicate A


title: K96243_Na2SO4ML_1 (Cy3)

description: SAMPLE 273


title: K96243_Mn2+ML_1 (Cy3)

description: SAMPLE 265


title: K96243_Na2SO4ML_2 (Cy5)

description: SAMPLE 276


title: K96243_MHB_4 (Cy3)

description: SAMPLE 263

value: Bacteria grown to log phase in MHB (5hr, 200rpm), pelleted and resuspended in fresh MHB.


title: K96243_Ni2.24hrs_2 (Cy5)

description: SAMPLE 280


title: K96243_Na2SO4ES_1 (Cy5)

description: SAMPLE 270


title: K96243_MHB_2 (Cy3)

description: SAMPLE 259


title: K96243_MHB_2 (Cy5)

description: SAMPLE 260


title: K96243_Ni2.24hrs_1 (Cy5)

description: SAMPLE 278


title: K96243_MHB_4 (Cy5)

description: SAMPLE 264


title: K96243_Na2SO4ES_1 (Cy3)

description: SAMPLE 269

value: Bacteria grown to stationary phase in modified M63 medium with Na2SO4 as reference.


title: K96243_Mn2+ML_1 (Cy5)

description: SAMPLE 266


title: K96243_MHB_3 (Cy3)

description: SAMPLE 261


title: K96243_MHB_3 (Cy5)

description: SAMPLE 262


title: K96243_Na2SO4ES_2 (Cy3)

description: SAMPLE 271


title: K96243_Ni2.24hrs_1 (Cy3)

description: SAMPLE 277


title: K96243_Mg2+ML_2 (Cy5)

description: SAMPLE 256


title: K96243_Mg2+ML_2 (Cy3)

description: SAMPLE 255

value: Bacteria subjected to growth in TSBDC with 200uM Magnesium sulfate heptahydrate. Harvested at log phase.


title: K96243_Mg2+ML_1 (Cy5)

description: SAMPLE 254


title: K96243_LBS_2 (Cy3)

description: SAMPLE 251


title: K96243_LBS_2 (Cy5)

description: SAMPLE 252


title: K96243_MHB_1 (Cy3)

description: SAMPLE 257


title: K96243_LBML_3 (Cy5)

description: SAMPLE 248


title: K96243_LBS_1 (Cy3)

description: SAMPLE 249


title: K96243_Mg2+ML_1 (Cy3)

description: SAMPLE 253


title: K96243_LBML_1 (Cy5)

description: SAMPLE 244


title: K96243_LBS_1 (Cy5)

description: SAMPLE 250


title: K96243_LBML_3 (Cy3)

description: SAMPLE 247

value: Bacteria subjected to growth in LB. Harvested at log phase (OD600 = 0.8).


title: K96243_MHB_1 (Cy5)

description: SAMPLE 258


title: K96243_LBML_2 (Cy3)

description: SAMPLE 245


title: K96243_LBML_2 (Cy5)

description: SAMPLE 246


title: K96243_LBES_1 (Cy5)

description: SAMPLE 238


title: K96243_Insulin_2 (Cy5)

description: SAMPLE 236


title: K96243_LBES_2 (Cy3)

description: SAMPLE 239

value: Bacteria subjected to growth in LB. Harvested at early-stationary phase (OD600 = 1.8).


title: K96243_LBES_3 (Cy3)

description: SAMPLE 241


title: K96243_LBES_3 (Cy5)

description: SAMPLE 242


title: K96243_H2O2ref_1 (Cy3)

description: SAMPLE 231

value: Bacteria grown in LB, reference condition for hydrogen peroxide perturbation.


title: K96243_Insulin_1 (Cy3)

description: SAMPLE 233

value: wild type

value: Bacteria grown to log phase in 1XTSBDC and exposed to PBS with 11U/ml human insulin for 16hrs.


title: K96243_Insulin_1 (Cy5)

description: SAMPLE 234

value: Not applicable


title: K96243_LBML_1 (Cy3)

description: SAMPLE 243


title: K96243_H2O24hrref_1 (Cy3)

description: SAMPLE 227

value: Bacteria grown to log phase in LB, pelleted and resuspended in fresh LB.


title: K96243_H2O24hrref_1 (Cy5)

description: SAMPLE 228

value: Bacteria subjected to growth in LB. Harvested at stationary phase (OD600 = 2.0).


title: K96243_H2O2ref_1 (Cy5)

description: SAMPLE 232


title: K96243_LBES_1 (Cy3)

description: SAMPLE 237


title: K96243_H2O24hrref_2 (Cy5)

description: SAMPLE 230


title: K96243_Insulin_2 (Cy3)

description: SAMPLE 235


title: K96243_H2O24hrref_2 (Cy3)

description: SAMPLE 229


title: K96243_LBES_2 (Cy5)

description: SAMPLE 240


title: K96243_H2O1hrref_2 (Cy5)

description: SAMPLE 220


title: K96243_H2O210mins_1 (Cy3)

description: SAMPLE 221

value: Bacteria grown in LB with hydrogen peroxide treatment for 10mins.


title: K96243_H2O1hrref_2 (Cy3)

description: SAMPLE 219


title: K96243_H2O24hr_1 (Cy5)

description: SAMPLE 224


title: K96243_H2O24hr_1 (Cy3)

description: SAMPLE 223

value: Bacteria grown to log phase in LB, pelleted, washed with dH2O and resuspended in sterile deionized water.


title: K96243_H2O1hrref_1 (Cy5)

description: SAMPLE 218


title: K96243_Fe3+ML_1 (Cy5)

description: SAMPLE 210


title: K96243_H2O1hr_1 (Cy3)

description: SAMPLE 213


title: K96243_H2O24hr_2 (Cy3)

description: SAMPLE 225


title: K96243_H2O210mins_1 (Cy5)

description: SAMPLE 222


title: K96243_Fe3+ML_2 (Cy3)

description: SAMPLE 211

value: Bacteria subjected to growth in TSBDC with 200uM Fe(III) chloride hexahydrate. Harvested at log phase.


title: K96243_H2O24hr_2 (Cy5)

description: SAMPLE 226


title: K96243_H2O1hr_2 (Cy5)

description: SAMPLE 216


title: K96243_Fe3+24hrs_2 (Cy3)

description: SAMPLE 207

value: Bacteria subjected to growth in TSBDC with 200uM Fe(III) chloride hexahydrate. Harvested at stationary phase.


title: OBWT_FE_1 with array type rose from Affymetrix

city: evry

first: stephanie

last: huguet

address: 2 rue gaston cremieux

institute: inra

description:
rosa chinensis  mutant (no) - dev.stage (boyes et al. plant cell 2001): flowering complete,gra f1 1 (granulosa cells collected at the f1 stage)
- Study of rose perfume by comparing a wild-tpe rose with one in which the expression of a scent gene has been altered.

hyb_protocol: labelled extract quantity: 10ug

scan_protocol: GCOS, Biotin:pmt voltage 570nm,650V,laser power 1

data_processing: The data were normalized with the gcrma algorithm (Irizarry et al., 2003), available in the Bioconductor package (Gentleman and Carey, 2002).

label: Biotin

organism: Rosa chinensis

label_protocol: labelling Biotin indirect, amplification=yes, ssDNA 5.5 ug.

growth_protocol: petal - Species: Rosa chinensis cv. Old Blush

treatment_protocol: Name:GENE-DISRUPTION - nothing - gene disruption,nothing:.

tag: cultivar

value: Rosa chinensis cv. Old Blush

value: petal

tag: treatment

value: control


title: K96243_H2O1hr_2 (Cy3)

description: SAMPLE 215

tag: genotype/variation


title: K96243_Fe3+ML_1 (Cy3)

description: SAMPLE 209


title: K96243_H2O1hrref_1 (Cy3)

description: SAMPLE 217


title: K96243_Fe3+24hrs_1 (Cy5)

description: SAMPLE 206


title: K96243_Fe3+24hrs_2 (Cy5)

description: SAMPLE 208


title: OBWT_BJO_2 with array type rose from Affymetrix


title: K96243_H2O1hr_1 (Cy5)

description: SAMPLE 214


title: K96243_Des24hrs_1 (Cy3)

description: SAMPLE 197

value: Bacteria grown to log phase in LB, pelleted and incubated in oven (desiccation) for 24 hrs.


title: K96243_Des24hrs_2 (Cy3)

description: SAMPLE 199


title: K96243_Fe3+24hrs_1 (Cy3)

description: SAMPLE 205


title: K96243_Fe3+ML_2 (Cy5)

description: SAMPLE 212


title: OBWT_FE_2 with array type rose from Affymetrix


title: K96243_Des24hrs_1 (Cy5)

description: SAMPLE 198


title: K96243_Des24hrs_2 (Cy5)

description: SAMPLE 200


title: K96243_Cu2+ML_2 (Cy3)

description: SAMPLE 195

value: Bacteria subjected to growth in TSBDC with 200uM Copper (II) sulfate pentahydrate. Harvested at log phase.


title: OBRNAI_BJO_2 with array type rose from Affymetrix

value: RhDiF1 RNAi


title: OBWT_BJO_1 with array type rose from Affymetrix


title: K96243_DesRef_1 (Cy5)

description: SAMPLE 202


title: K96243_DesRef_1 (Cy3)

description: SAMPLE 201

value: Bacteria grown to log phase in LB, pelleted and kept wet in dH2O for 24 hrs (not resuspended!)


title: K96243_Cu2+ML_1 (Cy3)

description: SAMPLE 193


title: K96243_Cu2+ML_2 (Cy5)

description: SAMPLE 196


title: OBRNAI_FE_2 with array type rose from Affymetrix


title: K96243_DesRef_2 (Cy3)

description: SAMPLE 203


title: K96243_DesRef_2 (Cy5)

description: SAMPLE 204


title: K96243_Chlamp_2 (Cy5)

description: SAMPLE 192


title: OBRNAI_FE_1 with array type rose from Affymetrix


title: OBRNAI_BJO_1 with array type rose from Affymetrix


title: K96243_Chlamp_2 (Cy3)

description: SAMPLE 191

value: Bacteria grown to log phase in MHB (5hr, 200rpm), pelleted and resuspended in MHB + antibiotics.


title: K96243_Chlamp_1 (Cy5)

description: SAMPLE 190

value: wild type


title: K96243_Cu2+ML_1 (Cy5)

description: SAMPLE 194


title: K96243_ChemRef_2 (Cy3)

description: SAMPLE 187

value: Bacteria grown to log phase, pelleted, resuspended and continued incubation in fresh LB.


title: K96243_Chlamp_1 (Cy3)

description: SAMPLE 189

value: Not applicable


title: K96243_CDMML_2 (Cy5)

description: SAMPLE 178


title: K96243_ChemRef_1 (Cy5)

description: SAMPLE 186


title: K96243_ChemRef_1 (Cy3)

description: SAMPLE 185


title: K96243_CDMML_2 (Cy3)

description: SAMPLE 177

value: Bacteria subjected to growth in CDM. Harvested at log phase (OD600 = 0.2).


title: K96243_ChemRef_2 (Cy5)

description: SAMPLE 188

value: Bacteria subjected to growth in LB. Harvested at stationary phase (OD600 = 2.0).


title: K96243_Ceft_2 (Cy5)

description: SAMPLE 184


title: K96243_Ceft_1 (Cy5)

description: SAMPLE 182


title: K96243_Ceft_1 (Cy3)

description: SAMPLE 181


title: K96243_Ca2+ML_2 (Cy5)

description: SAMPLE 164


title: K96243_Cd2+24hrs_2 (Cy3)

description: SAMPLE 167

value: Bacteria subjected to growth in TSBDC with 200uM Cadmium (II) sulfate hydrate. Harvested at stationary phase.


title: K96243_Ceft_2 (Cy3)

description: SAMPLE 183


title: K96243_Bleach_2 (Cy5)

description: SAMPLE 160


title: K96243_Cd2+24hrs_1 (Cy5)

description: SAMPLE 166


title: K96243_CDMML_3 (Cy5)

description: SAMPLE 180


title: K96243_CDMES_2 (Cy3)

description: SAMPLE 171

value: Bacteria subjected to growth in CDM. Harvested at early-stationary phase (OD600 = 0.5).


title: K96243_Cd2+24hrs_1 (Cy3)

description: SAMPLE 165


title: K96243_CDMES_1 (Cy3)

description: SAMPLE 169


title: K96243_Ca2+ML_1 (Cy5)

description: SAMPLE 162


title: K96243_CDMES_2 (Cy5)

description: SAMPLE 172


title: K96243_Bleach_1 (Cy3)

description: SAMPLE 157

value: Bacteria grown to log phase, pelleted, resuspended and incubated in LB with 0.01% bleach (11% sodium hypochloride).


title: K96243_Ca2+ML_1 (Cy3)

description: SAMPLE 161

value: Bacteria subjected to growth in TSBDC with 200uM Calcium chloride dihydrate. Harvested at log phase.


title: K96243_Bleach_2 (Cy3)

description: SAMPLE 159


title: K96243_CDMML_1 (Cy5)

description: SAMPLE 176


title: K96243_Ca2+ML_2 (Cy3)

description: SAMPLE 163


title: K96243_Cd2+24hrs_2 (Cy5)

description: SAMPLE 168


title: K96243_BALBcLungs_2 (Cy5)

description: SAMPLE 156


title: K96243_CDMML_3 (Cy3)

description: SAMPLE 179


title: K96243_CDMML_1 (Cy3)

description: SAMPLE 175


title: K96243_Bleach_1 (Cy5)

description: SAMPLE 158


title: K96243_CDMES_1 (Cy5)

description: SAMPLE 170


title: K96243_BALBcLungs_1 (Cy3)

description: SAMPLE 153

value: Bp-infected murine lungs

value: BALBc mice infected with 1000CFU bacteria. Lungs harvested 3 days post-infection.


title: K96243_CDMES_3 (Cy3)

description: SAMPLE 173


title: K96243_Anaer2wks_1 (Cy5)

description: SAMPLE 150


title: K96243_CDMES_3 (Cy5)

description: SAMPLE 174


title: K96243_Anaer2wks_2 (Cy3)

description: SAMPLE 151

value: Bacteria grown to log phase in LB,  transfer to 50ml TPP tubes into anaerobic jar and incubated at 37C for 2 weeks.


title: K96243_Anaer1wk_2 (Cy3)

description: SAMPLE 147

value: Bacteria grown to log phase in LB,  transfer to 50ml TPP tubes into anaerobic jar and incubated at 37C for 1 week.


title: K96243_BALBcLungs_1 (Cy5)

description: SAMPLE 154


title: K96243_Anaer1wk_1 (Cy3)

description: SAMPLE 145


title: K96243_Al3+24hrs_1 (Cy5)

description: SAMPLE 142


title: K96243_Anaer2wks_2 (Cy5)

description: SAMPLE 152


title: K96243_Anaer1wk_2 (Cy5)

description: SAMPLE 148


title: K96243_BALBcLungs_2 (Cy3)

description: SAMPLE 155


title: K96243_Al3+24hrs_1 (Cy3)

description: SAMPLE 141

value: Bacteria subjected to growth in TSBDC with 200uM Aluminium (III) chloride hexahydrate. Harvested at stationary phase.


title: K96243_Al3+24hrs_2 (Cy5)

description: SAMPLE 144


title: K96243_Al3+24hrs_2 (Cy3)

description: SAMPLE 143


title: K96243_Aer2wks_2 (Cy5)

description: SAMPLE 140


title: K96243_Anaer1wk_1 (Cy5)

description: SAMPLE 146


title: K96243_42C30mins_2 (Cy3)

description: SAMPLE 131

value: Bacteria grown to log phase, pelleted and resuspended in heated LB medium for 30 minutes


title: K96243_Aer2wks_1 (Cy5)

description: SAMPLE 138


title: K96243_Aer1wk_1 (Cy5)

description: SAMPLE 134


title: K96243_Aer1wk_2 (Cy5)

description: SAMPLE 136


title: K96243_Aer1wk_2 (Cy3)

description: SAMPLE 135

value: Bacteria grown to log phase in LB, transfer to 50ml TPP tubes, continue incubation under static conditions for 1 week.


title: K96243_42C30mins_1 (Cy5)

description: SAMPLE 130


title: K96243_42C16hrs_1 (Cy5)

description: SAMPLE 126


title: K96243_37C30mins_2 (Cy5)

description: SAMPLE 124


title: K96243_Anaer2wks_1 (Cy3)

description: SAMPLE 149


title: K96243_Aer2wks_2 (Cy3)

description: SAMPLE 139

value: Bacteria grown to log phase in LB, transfer to 50ml TPP tubes, continue incubation under static conditions for 2 weeks.


title: K96243_Aer2wks_1 (Cy3)

description: SAMPLE 137

value: wild type


title: K96243_42C30mins_1 (Cy3)

description: SAMPLE 129


title: K96243_42C30mins_2 (Cy5)

description: SAMPLE 132


title: K96243_Aer1wk_1 (Cy3)

description: SAMPLE 133


title: K96243_42C16hrs_2 (Cy5)

description: SAMPLE 128


title: K96243_37C30mins_2 (Cy3)

description: SAMPLE 123

value: Bacteria grown to log phase, pelleted and resuspended in warmed LB medium for 30 minutes


title: K96243_30NHS_2 (Cy3)

description: SAMPLE 115

value: Not applicable

value: Bacteria grown to log phase in 1XTSBDC and exposed to PBS with 30% human serum for 16hrs.


title: K96243_37C16hrs_2 (Cy5)

description: SAMPLE 120

value: Bacteria subjected to growth in LB. Harvested at stationary phase (OD600 = 2.0).


title: K96243_42C16hrs_2 (Cy3)

description: SAMPLE 127

value: Bacteria grown to log phase, pelleted and resuspended in heated LB medium for 16 hours


title: K96243_37C30mins_1 (Cy3)

description: SAMPLE 121


title: K96243_30NHS_1 (Cy5)

description: SAMPLE 114


title: K96243_37C30mins_1 (Cy5)

description: SAMPLE 122


title: K96243_37C16hrs_1 (Cy5)

description: SAMPLE 118


title: K96243_37C16hrs_2 (Cy3)

description: SAMPLE 119

value: Bacteria grown to log phase, pelleted and resuspended in warmed LB medium for 16 hours.


title: K96243_2MSorb_2 (Cy3)

description: SAMPLE 111

value: Bacteria grown to log phase, pelleted and resuspended in LB with 2M Sorbitol


title: K96243_30NHS_2 (Cy5)

description: SAMPLE 116


title: K96243_37C16hrs_1 (Cy3)

description: SAMPLE 117


title: K96243_2MSorb_1 (Cy3)

description: SAMPLE 109


title: K96243_2MSorb_1 (Cy5)

description: SAMPLE 110


title: K96243_2MSorb_2 (Cy5)

description: SAMPLE 112


title: K96243_30NHS_1 (Cy3)

description: SAMPLE 113


title: K96243_28C30mins_2 (Cy5)

description: SAMPLE 104


title: water column DNA_ETSP_Station 26_260m

type: mixed

city: Princeton

first: Xuefeng

last: Peng

state: NJ

address: Guyot Hall

department: Geosciences

institute: Princeton University

description: DNA extracted from sterivex filter used to create 2 targets to run on duplicate arrays

hyb_protocol: Samples were hybridized to duplicate arrays by overnight incubation at 64°C and washed.

scan_protocol: The arrays were scanned with a laser scanner (Molecular Devices 4200) Images were analyzed with Gene Pix Pro 6.0 software (Molecular Devices)

data_processing: Quality control was employed to remove noise by eliminating features 1) in which the Cy3 signal was not at least twice the value of the control probes, and 2) in which the Cy3/Cy5 could not pass a Z test to find out the outlier values. The Z test was performed by calculating Zi = ri/(s/square root of 3), i = 1, 2, or 3, where ri represents Cy3/Cy5, s the standard deviation of the triplicate Cy3/Cy5 values. A feature is considered as an outlier if the Z is greater than 1.9 (CI = 80%).

molecule: other

organism: synthetic construct

source_name: Universal Internal Standard + 70-mer

label_protocol: Hybridization targets were prepared by digesting environmental DNA  with a four cutter restriction enzyme. The digested environmental DNA were labeled with amino-allyl-dUTP (Ambion) during linear amplification using random octamers and a Klenow polymerase (Applied Biosystems). The reaction contained 3.96 mM d(AGC)TP, 0.44 mM dTTP, and 4.84 mM dUaa and was amplified for 3 h at 37°C. The Klenow product was purified and conjugated with Cy3. The Cy3-labelled target (1000 ng) was combined with 2x hybridization buffer (1x final concentration; Agilent) and 0.25 pmol of a Cy5-labelled complementary 20-mer standard oligonucleotide and incubated at 95°C for 5 min before being cooled to room temperature.

extract_protocol: DNA was extracted from the filters using the PureGene DNA kit (Gentra, Minneapolis, MN) or the AllPrep DNA/RNA Mini Kit (Qiagen Sciences, Maryland, USA) with slight modifications (as in Ward 2008).

tag: sample type

value: Universal Internal Standard + 70-mer

organism: marine metagenome

source_name: Total DNA from water colum

tag: location

value: Eastern Tropical South Pacific Station 26

tag: depth


title: K96243_2MNaCl_1 (Cy3)

description: SAMPLE 105

value: Bacteria grown to log phase, pelleted and resuspended in LB with 2M NaCl


title: water column DNA_ETSP_Station 26_20m


title: K96243_2MNaCl_2 (Cy3)

description: SAMPLE 107


title: K96243_2MNaCl_1 (Cy5)

description: SAMPLE 106


title: water column DNA_ETSP_Station 31_55m


title: water column DNA_ETSP_Station 32_200m


title: water column DNA_ETSP_Station 24_20m

value: Eastern Tropical South Pacific Station 24


title: water column DNA_ETSP_Station 24_260m


title: K96243_2MNaCl_2 (Cy5)

description: SAMPLE 108


title: K96243_28C30mins_1 (Cy3)

description: SAMPLE 101

value: Bacteria grown to log phase, pelleted and resuspended in room temp LB medium for 30 minutes


title: water column DNA_ETSP_Station 20_20m

value: Eastern Tropical South Pacific Station 20


title: K96243_28C16hrs_1 (Cy3)

description: SAMPLE 97

value: Bacteria grown to log phase, pelleted and resuspended in room temp LB medium for 16 hours


title: K96243_1XTSBDCML_1 (Cy5)

description: SAMPLE 94


title: K96243_28C30mins_1 (Cy5)

description: SAMPLE 102


title: K96243_28C16hrs_1 (Cy5)

description: SAMPLE 98


title: K96243_1XTSBDCML_2 (Cy3)

description: SAMPLE 95

value: Bacteria subjected to growth in TSBDC. Harvested at log phase (OD600 = 0.8, 5 1/2hrs).


title: water column DNA_ETSP_Station 20_260m


title: K96243_28C16hrs_2 (Cy3)

description: SAMPLE 99


title: water column DNA_ETSP_Station 12_260m

value: Eastern Tropical South Pacific Station 12


title: water column DNA_ETSP_Station 12_20m


title: water column DNA_ETSP_Station 19_20m

value: Eastern Tropical South Pacific Station 19


title: water column DNA_ETSP_Station 14_260m

value: Eastern Tropical South Pacific Station 14


title: K96243_28C16hrs_2 (Cy5)

description: SAMPLE 100

value: wild type

value: Not applicable


title: water column DNA_ETSP_Station 14_20m


title: K96243_1XTSBDCML_2 (Cy5)

description: SAMPLE 96

value: Bacteria subjected to growth in LB. Harvested at stationary phase (OD600 = 2.0).


title: K96243_28C30mins_2 (Cy3)

description: SAMPLE 103


title: K96243_1XTSBDC24hrs_2 (Cy3)

description: SAMPLE 91

value: Bacteria subjected to growth in TSBDC. Harvested at stationary phase (24hr).


title: K96243_1XTSBDC24hrs_2 (Cy5)

description: SAMPLE 92


title: water column DNA_Arabian Sea_Station 3_110m

value: Arabian Sea Station 3


title: K96243_1XDPBS16hrs_2 (Cy5)

description: SAMPLE 88


title: K96243_1XDPBS16hrs_1 (Cy5)

description: SAMPLE 86


title: K96243_1XTSBDC24hrs_1 (Cy3)

description: SAMPLE 89


title: K96243_42C16hrs_1 (Cy3)

description: SAMPLE 125

value: Bacteria grown to log phase, pelleted and resuspended in heated LB medium for 16 hours.


title: K96243_1XTSBDCML_1 (Cy3)

description: SAMPLE 93


title: water column DNA_Arabian Sea_Station 3_10m

value: Universal Internal Standard + 70-mer


title: water column DNA_Arabian Sea_Station 2_200m

value: Arabian Sea Station 2


title: water column DNA_Arabian Sea_Station 2_10m


title: water column DNA_Arabian Sea_Station 1_175m

value: Arabian Sea Station 1


title: water column DNA_Arabian Sea_Station 2_150m


title: water column DNA_Arabian Sea_Station 1_150m


title: K96243_1XTSBDC24hrs_1 (Cy5)

description: SAMPLE 90


title: water column DNA_ETSP_Station 19_260m


title: water column DNA_Arabian Sea_Station 1_102m


title: K96243_1XDPBS16hrs_1 (Cy3)

description: SAMPLE 85

value: Bacteria grown to log phase in 1XTSBDC and exposed to 1XPBS for 16hrs.


title: K96243_04C30mins_2 (Cy3)

description: SAMPLE 83

value: Bacteria grown to log phase, pelleted and resuspended in cold LB medium for 30 minutes.


title: water column DNA_Arabian Sea_Station 1_60m


title: K96243_04C30mins_1 (Cy5)

description: SAMPLE 82


title: K96243_04C16hrs_2 (Cy5)

description: SAMPLE 80


title: water column DNA_Arabian Sea_Station 1_10m


title: K96243_04C16hrs_2 (Cy3)

description: SAMPLE 79

value: Bacteria grown to log phase, pelleted and resuspended in cold LB medium for 16 hours


title: K96243_04C30mins_1 (Cy3)

description: SAMPLE 81


title: K96243_1XDPBS16hrs_2 (Cy3)

description: SAMPLE 87


title: Bp22_VirAGRAW_1 (Cy5)

description: SAMPLE 74


title: Bp22_VirAGRAW_2 (Cy3)

description: SAMPLE 75

organism: Burkholderia pseudomallei Bp22

source_name: Burkholderia pseudomallei Bp22 virAG mutant

value: virAG mutant

value: Bp-infected RAW264.7 cell line

value: Extracellular bacteria killed by 250ug/ml kanamycin 2 hrs p.i.  Infected cells lysed for intracellular bacteria harvest after 5 hrs.


title: K96243_04C16hrs_1 (Cy5)

description: SAMPLE 78


title: K96243_04C30mins_2 (Cy5)

description: SAMPLE 84


title: water column DNA_Arabian Sea_Station 3_150m


title: Bp22_VirAGRAW_2 (Cy5)

description: SAMPLE 76


title: K96243_04C16hrs_1 (Cy3)

description: SAMPLE 77


title: Bp22_RAW_2 (Cy5)

description: SAMPLE 72