title: MGK131-1

description: Spleen S. suis P1/7 6h Rep 4

value: Female


title: MGK091-1

status: Public on Jun 01 2013

type: RNA

city: Mississauga

first: Claude

last: Lachance

state: Ontario

address: 1329 Meyerside Drive

country: Canada

institute: Bio-Rad

description: Spleen S. suis P1/7 6h Rep 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were first raw-filtered in order to identify and remove probesets that were not detected and then normalised using robust spline normalization with FlexArray v1.6

label: Biotin

molecule: total RNA

organism: Mus musculus

source_name: C57BL/6 TLR2-KO spleen infected with European strain (P1/7) of Streptococcus suis

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

growth_protocol: Bacterial culture was prepared by transferring 10 μl of 1/1,000 dilutions of 8-h cultures into 30 ml of THB, which was incubated for 16 h at 37°C without agitation. Stationary-phase bacteria were washed twice in PBS (pH 7.3). The bacterial pellet was then resuspended and adjusted to a concentration of 5 × 10^8 c.f.u. ml-1.

extract_protocol: RNA was homogenized from RNAlater-stabilized spleen tissus, extracted and DNAse I treated using QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Mice (C57BL/6 and C57BL/6 TLR2-KO) were infected for 6h with 5 x 10^7 CFU of Streptococcus suis strain P1/7.

tag: strain

value: C57BL/6 TLR2-KO

tag: tissue

value: Spleen

tag: gender


title: Untreated Control Replicate 3 of 96h

city: Singapore

first: Choong Yong

last: UNG

address: 14 Science Drive 4

department: Department of Biological Sciences

country: Singapore

institute: National University of Singapore

description: Biological replicate 3 of 7: control at 96 Hr

hyb_protocol: Reference RNA (labelled with Cy3) is co-hybridized with RNA samples extracted either from treated or control fish (labelled with Cy5) on a glass array spotted with Zf_23K_oligo_COMP_v4Apx zebrafish oligo probes.

scan_protocol: The arrays were scanned using the GenePix 4000B microarray scanner (Axon Instruments, USA) and the generated images with their fluorescence signal intensities were analyzed using GenePix Pro 4.0 image analysis software (Axon Instruments, USA).

data_processing: The data were global median normalized. Normalized ratio of means defined by CH1/CH2

organism: Danio rerio

source_name: Male zebrafish liver tissue

label_protocol: For fluorescence labeling of cDNAs, 10 µg of total RNA from the reference and experimental samples were reverse transcribed in the presence of Cy3-dUTP and Cy5-dUTP (Amersham Inc.), respectively. Reference RNA was obtained by pooling equal amount of male and female total RNA extracted from liver tissues of wild-type zebrafish. Labeled cDNA were concentrated, and resuspended in DIG EasyHyb (Roche Applied Science) buffer for hybridization.

growth_protocol: Zebrafish were maintained at room temperature (26°C + 1°C)

extract_protocol: Total RNA of tissue samples were extracted using Trizol reagent (Invitrogen) according to the manufacturers instructions.

treatment_protocol: Male zebrafish were exposed to 0.5, 5, 50 µg/L estradiol for 24 and 96 hours at room temperature.

value: male

tag: sample type

value: Untreated liver tissue

value: liver

tag: treatment

value: untreated

tag: time

source_name: Male and female zebrafish liver tissue

value: male and female


title: MGK088-1

description: Spleen S. suis P1/7 6h Rep 1


title: Untreated Control Replicate 5 of 96h

description: Biological replicate 5 of 7: control at 96 Hr

value: Reference RNA was obtained by pooling equal amount of male and female total RNA extracted from liver tissues of wild-type zebrafish.


title: CD44KO liver_HFD_rep2

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

country: USA

institute: NIEHS

description:
251486837667_1_3
RNA samples from CD44KO mice fed with a HFD.

hyb_protocol: For each sample, 1.65ug of Cy3-labeled cRNAs were fragmented and hybridized for 17 hours in a rotating hybridization oven.

scan_protocol: Slides were washed and then scanned with an Agilent Scanner.

data_processing: Data was obtained using the Agilent Feature Extraction software (v9.5), using the 1-color defaults for all parameters.

source_name: CD44KO mice fed with a HFD for 21 weeks

label_protocol: Starting with 500ng of total RNA, Cy3-labeled cRNA was produced according to the manufacturer's protocol.

extract_protocol: Qiagen RNeasy mini kit.

treatment_protocol: Liver and white adipose tissue (WAT) from WT and CD44KO mice fed with a high-fat diet (HFD; 35% fat) for 21 weeks.

tag: strain/background

tag: genotype/variation

value: CD44 knockout

tag: age

value: 7 months

value: 35% fat diet (high fat)

tag: treatment duration

value: 21 weeks


title: MGK110-1

description: Spleen S. suis P1/7 6h Rep 3

source_name: C57BL/6 spleen infected with European strain (P1/7) of Streptococcus suis


title: CD44KO liver_HFD_rep1

description:
251486838081_1_2
RNA samples from CD44KO mice fed with a HFD.


title: CD44KO liver_HFD_rep3

description:
251486837668_1_3
RNA samples from CD44KO mice fed with a HFD.


title: Untreated Control Replicate 2 of 96h

description: Biological replicate 2 of 7: control at 96 Hr


title: Untreated Control Replicate 4 of 96h

description: Biological replicate 4 of 7: control at 96 Hr


title: Untreated Control Replicate 1 of 96h

description: Biological replicate 1 of 7: control at 96 Hr


title: MGK077-1

description: Spleen S. suis P1/7 6h Rep 1


title: MGK111-1

description: Spleen S. suis P1/7 6h Rep 4


title: leaves_ggt_biological rep2

city: Créteil

first: Ruben

last: Puga-Freitas

address: 61 Avenue du Général de Gaulle

country: France

institute: Université Paris-Est Créteil

description: Gene expression data from plants inoculated with the pathogenic fungus G. graminis

hyb_protocol: Fragmented cRNA was hybridized on Affymetrix GeneChip Wheat Genome array for 16 h at 45°C along with internal hybridization controls. Washing and staining procedures were performed in an Affymetrix Fluidics Station 450.

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

data_processing: Probe-level expression data (CEL files) were produced using GeneChip® Operation Software (GCOS) version 1.4 and data were normalized using the MAS5 algorithm. Quality-control and statistical analyses (background adjustment, normalization, and probe-level summarization of data) used the GC-Robust Multi-Array average algorithm (GC-RMA) from the GeneSpring GX11 Software.

label: biotin

organism: Triticum aestivum

source_name: Wheat leaves, plants inoculated with G. graminis

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

growth_protocol: In a greenhouse experiment, plants were grown in a sandy soil during 52 days. There was 4 levels of treatment (plants only (C), inoculated with Ggt (GGT), inoculated with earthworms (E) or inoculated with earthworms and Ggt (E_GGT)), with 3 plants per treatments.

extract_protocol: RNA was extracted using the RNeasy Plant Mini Kit (Qiagen, France) with an on-column DNase digestion using DNase I (Qiagen, France) according to the manufacturer's instructions.

treatment_protocol: Plants were inoculated or not with Gaeumannomyces graminis var tritici. In treatments with earthworms, two weeks after Ggt inoculation living earthworms were added to the devoted microcosms

value: leaves


title: Wildtype liver_HFD_rep4

description:
251486837667_1_2
RNA samples from WT mice fed with a HFD.

source_name: WT mice fed with a HFD for 21 weeks

value: wildtype


title: Untreated Control Replicate 8 of 24h

description: Biological replicate 8 of 8: control at 24 Hr


title: Wildtype liver_HFD_rep5

description:
251486837668_1_2
RNA samples from WT mice fed with a HFD.


title: Untreated Control Replicate 7 of 24h

description: Biological replicate 7 of 8: control at 24 Hr


title: MGK079-1

description: Spleen S. suis P1/7 6h Rep 2


title: Wildtype liver_HFD_rep3

description:
251486838081_1_1
RNA samples from WT mice fed with a HFD.


title: Wildtype liver_HFD_rep1

description:
251486837668_1_1
RNA samples from WT mice fed with a HFD.


title: Wildtype liver_HFD_rep2

description:
251486837667_1_1
RNA samples from WT mice fed with a HFD.


title: Untreated Control Replicate 4 of 24h

description: Biological replicate 4 of 8: control at 24 Hr


title: SVR, 50 micromolar propranolol, 24h (rep 1)

city: El Paso

first: Brad

middle: Allen

last: Bryan

state: Texas

address: 5001 El Paso Drive

department: Biomedical Sciences

institute: Texas Tech University Health Sciences Center

hyb_protocol: 750 ng of biotinylated aRNA was then briefly heat-denatured and loaded onto Illumina expression arrays to hybridize overnight.

scan_protocol: Illumina ISCAN.

data_processing: Intensity values were transferred to Agilent GeneSpring GX microarray analysis software and data was filtered based on quality of each call.

source_name: 50 micromolar propranolol, 24h

label_protocol: Total RNA was amplified and biotin-labeled using Illumina TotalPrep RNA Amplification Kit (Ambion).

growth_protocol: SVR cells were cultured to 100% confluence in T75 flasks in Dulbecco's modified Eagle's media (DMEM) supplemented with 10% fetal bovine serum (FBS), 80 U/ml penicillin, and 50 micrograms/ml streptomycin C.

extract_protocol: RNA was purified using the Pulink RNA mini kit (Ambion) according to manufacturer's instructions.  Quality control was performed with the Nanodrop and Bioanalyzer.

treatment_protocol: Cells were treated with sham (t=0 hrs) or 50 micromolar propranolol (t=4 & 24 hrs)

tag: cell line

value: SVR

tag: cell type

value: angiosarcoma


title: Untreated Control Replicate 2 of 24h

description: Biological replicate 2 of 8: control at 24 Hr


title: Untreated Control Replicate 3 of 24h

description: Biological replicate 3 of 8: control at 24 Hr


title: SVR, 50 micromolar propranolol, 24h (rep 3)


title: SVR, 50 micromolar propranolol, 24h (rep 2)


title: Untreated Control Replicate 5 of 24h

description: Biological replicate 5 of 8: control at 24 Hr


title: C57_liver_HF_Low_Low_Rep6

city: Palmerston North

first: Helge

last: Dzierzon

address: Bachelar Road

department: Bioinformatics

country: New Zealand

institute: Plant and Food Research Ltd.

description: Tissue Sample ID: BK1877 Tissue: liver Mouse: 53

hyb_protocol: Fluorescently labelled cRNA was hybridized using the Agilent oligonucleotide microarray in situ hybridization plus kit (5184-3568) following the manufacturer’s protocols. Briefly, 750 ng of sample cRNA was mixed with 750 ng of reference cRNA and control targets to ensure correct hybridization onto Agilent Technologies Mouse G41122F – 4x44k 60mer oligonucleotide arrays. After hybridization, the slides were washed in solutions I, II and III  (Agilent Technologies) and air-dried.

scan_protocol: Slides were scanned using an Agilent scanner after an automatic gain and calibration prior to each scan. Spot identification and quantification were performed using Agilent Feature Extraction software version 9.5.

data_processing: Microarray fluorescence signals were normalized using a global loess algorithm in R2.14.1 with the Linear Models for Microarray Data (limma) package in Bioconductor. Differentially expressed genes were determined using an Empirical Bayes modified t-statistic from a linear model of microarray analysis. Genes with a greater than 1.5 fold change and a P value less than 0.01 were considered to be differentially expressed.

source_name: Colon and liver RNA extracts from all mice were pooled in an equimolar proportion and used as the reference sample.

label_protocol: RNA from sample and reference was labelled using the Agilent Low RNA Input Linear Amplification kit (5184-3523) according to the manufacturer’s instructions. Briefly, 500 ng of purified total RNA from each sample was amplified and reverse transcribed in vitro to cDNA using T7-polymerase, which was subsequently labelled with either cyanine 3-CTP (sample pool) or cyanine 5-CTP (reference pool) dyes (10 m M ; PerkinElmer/NEN Life Science (NEL 580, 581), Boston, Mass., USA). A reference design was used. The Nanodrop ND-1000 was used to monitor dye incorporation; sample and reference were between 9 and 22 pmol/g cRNA.

growth_protocol: Female wild type C57BL-6 mice (Animal Resource Centre, Western Australia) were fed a HF-Low diet for 7 days prior to mating with male C57BL-6 mice (Ruakura Small Animal Facility, Hamilton, New Zealand). Once pregnancy was confirmed via the presence of a vaginal plug, males were removed from the mating cages. The breeding dams were maintained on the HF-Low diets during mating, gestation and lactation. Offspring remained with their dams until weaning (c. 28 days of age). At weaning, female offspring were randomly allocated to either the HF-Low diet (n=6; HF-Low-Low) or switched to the HF-Suf diet (n=6; HF-Low-Suf) until 12 weeks of age. Mice were offered 20 g of food pellets twice weekly and had ad libitum access to water. Feed refusals and bodyweight were determined twice weekly. The general health score of the mice was determined daily.

extract_protocol: Genomic DNA, total RNA and protein from whole colon and liver tissue was extracted using an AllPrep® DNA/RNA/Protein mini kit (Qiagen, Cat number 80004). Total RNA was quantified using a NanoDrop ND1000 and RNA quality was determined using an Agilent 2100 Bioanalyser (Agilent Technologies, Palo Alto, CA, USA) to measure the RNA integrity number (RIN). RNA was stored at –85°C until required for microarray analysis.

value: female

value: 12 weeks

value: colon + liver tissue (pooled)

source_name: Liver tissue: Female C57BL/6 mouse fed HF-low diet post-weaning: mother fed HF-low diet during gestation and lactation.

value: Liver

tag: maternal diet

value: High-fat diet with low selenium and folate

tag: offspring diet


title: C57_colon_HF_Low_Low_Rep6

description: Tissue Sample ID: BK1904 Tissue: colon Mouse: 53

source_name: Colon tissue: Female C57BL/6 mouse fed HF-low diet post-weaning: mother fed HF-low diet during gestation and lactation.

value: Colon


title: C57_colon_HF_Low_Suf_Rep6

description: Tissue Sample ID: BK2662 Tissue: colon Mouse: 74

source_name: Colon tissue: Female C57BL/6 mouse fed HF-suf diet post-weaning: mother fed HF-low diet during gestation and lactation.

value: High-fat diet with sufficient selenium and folate


title: SVR, 50 micromolar propranolol, 4h (rep 3)

source_name: 50 micromolar propranolol, 4h


title: SVR, 50 micromolar propranolol, 4h (rep 2)


title: Untreated Control Replicate 1 of 24h

description: Biological replicate 1 of 8: control at 24 Hr

value: male

value: Untreated liver tissue

value: liver

value: untreated

value: male and female


title: C57_liver_HF_Low_Suf_Rep5

description: Tissue Sample ID: BK2597 Tissue: liver Mouse: 73

source_name: Liver tissue: Female C57BL/6 mouse fed HF-suf diet post-weaning: mother fed HF-low diet during gestation and lactation.


title: SVR, 50 micromolar propranolol, 4h (rep 1)


title: SVR, sham, 0h (rep 2)

source_name: sham, 0h


title: SVR, sham, 0h (rep 1)


title: Untreated Control Replicate 6 of 24h

description: Biological replicate 6 of 8: control at 24 Hr

value: Reference RNA was obtained by pooling equal amount of male and female total RNA extracted from liver tissues of wild-type zebrafish.


title: SVR, sham, 0h (rep 3)


title: C57_colon_HF_Low_Low_Rep5

description: Tissue Sample ID: BK1546 Tissue: colon Mouse: 43


title: Raji_shCyclon_rep4

city: Grenoble

first: Anouk

last: Emadali

institute: Institut Albert Bonniot

description: Gene expression data from Raji cells transduced with a sh RNA targeting CYCLON

hyb_protocol: cRNA was hybridized to HG U133 Plus 2.0 microarrays according to manufacturer’s instructions.

scan_protocol: Fluorescence intensities were quantified using the GCOS 1.2 software

data_processing: The data were analyzed with GeneSpring software (v.11.0, Agilent) using default analysis settings and RMA normalization (with no baseline transormation).

organism: Homo sapiens

source_name: Raji_transduced with a sh RNA targeting CYCLON

label_protocol: Biotinylated  cRNA was prepared using the kit GeneChip IVT express according to manufacturer’s instructions.

growth_protocol: Raji cells were cultured in RPMI supplemented with 20 % fœtal bovine serum, sodium pyruvate, non esssential amino acids and penicilllin/streptomycin.

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

treatment_protocol: Stable cell lines have been established using lentiviral transduction of Raji cells with either a control (non-targeting) shRNA sequence or CYCLON shRNA constructs under puromycin selection.

value: Raji

value: Raji Burkitt lymphoma B cells

tag: transduced with

value: CYCLON shRNA constructs


title: Raji_shCyclon_rep2


title: BCG_mouse5_unstim

city: Oxford

first: leanne

last: marsay

address: roosevelt drive

department: Nuffield department

country: United Kingdom

institute: University of Oxford

description:
Sample name: 2.8
splenocytes were stimulated for 12 hours without BCG

data_processing: BeadStudio v2.0 used to generate the raw data (linked as supplementary file on Series record).  Array quality assessment was performed using ArrayQualityMetrics prior to background correction and normalization using quantile normalisation with Bioconductor package limma, neqc function

source_name: Mouse splenocyte

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

growth_protocol: 1.0E6 splenocytes for each sample were cultured for 12 hours at 37 degrees Celcius in RPMI medium with Hepes supplemented with 10% fetal calf serum and 2mM L-glutamine

extract_protocol: RNA was extracted with QIAGEN Rneasy minikit including an on-column Dnase I digestion in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: Female

value: 13 weeks

value: splenocyte

tag: immunization

value: BCG

tag: stimulation


title: C57_liver_HF_Low_Suf_Rep6

description: Tissue Sample ID: BK2633 Tissue: liver Mouse: 74

tag: strain

value: female

value: 12 weeks

value: colon + liver tissue (pooled)

value: Liver


title: Raji_shCyclon_rep1


title: Raji_shCtrl_rep3

description: Gene expression data from Raji cells transduced with a non targeting (Ctrl) sh RNA

source_name: Raji_transduced with a non targeting (Ctrl) sh RNA

value: control (non-targeting) shRNA


title: Raji_shCtrl_rep4


title: Raji_shCyclon_rep3


title: Naïve_mouse1_BCGstim

description:
Sample name: 2.3
splenocytes were stimulated overnight with 1e6 CFU of BCG

value: BCG stimulation


title: C57_liver_HF_Low_Low_Rep5

description: Tissue Sample ID: BK1517 Tissue: liver Mouse: 43

tag: tissue

value: High-fat diet with low selenium and folate


title: BCG_mouse5_BCGstim

description:
Sample name: 2.6
splenocytes were stimulated overnight with 1e6 CFU of BCG

tag: gender


title: C57_liver_HF_Low_Low_Rep4

description: Tissue Sample ID: BK2021 Tissue: liver Mouse: 57


title: Raji_shCtrl_rep2


title: C57_colon_HF_Low_Suf_Rep4

description: Tissue Sample ID: BK2336 Tissue: colon Mouse: 65

value: Colon

value: High-fat diet with sufficient selenium and folate


title: C57_colon_HF_Low_Suf_Rep5

description: Tissue Sample ID: BK2626 Tissue: colon Mouse: 73


title: Naïve_mouse4_BCGstim

description:
Sample name: 2.7
splenocytes were stimulated overnight with 1e6 CFU of BCG


title: Naïve_mouse2_unstim

description:
Sample name: 2.4
splenocytes were stimulated for 12 hours without BCG


title: C57_liver_HF_Low_Suf_Rep4

description: Tissue Sample ID: BK2309 Tissue: liver Mouse: 65


title: BCG_mouse1_BCGstim

description:
Sample name: 2.5
splenocytes were stimulated overnight with 1e6 CFU of BCG


title: C57_colon_HF_Low_Low_Rep4

description: Tissue Sample ID: BK2048 Tissue: colon Mouse: 57


title: C57_liver_HF_Low_Low_Rep3

description: Tissue Sample ID: BK1733 Tissue: liver Mouse: 49


title: Raji_NT_rep3

description: Gene expression data from Raji cells non transduced

source_name: Raji_non transduced

value: none (non-transduced control)


title: C57_colon_HF_Low_Suf_Rep3

description: Tissue Sample ID: BK3560 Tissue: colon Mouse: 99


title: C57_liver_HF_Low_Suf_Rep3

description: Tissue Sample ID: BK3533 Tissue: liver Mouse: 99


title: BCG_mouse1_unstim

description:
Sample name: 1.8
splenocytes were stimulated for 12 hours without BCG


title: C57_colon_HF_Low_Low_Rep3

description: Tissue Sample ID: BK1762 Tissue: colon Mouse: 49


title: Raji_NT_rep4

value: Raji


title: BCG_mouse2_unstim

description:
Sample name: 2.2
splenocytes were stimulated for 12 hours without BCG


title: BCG_mouse3_BCGstim

description:
Sample name: 2.1
splenocytes were stimulated overnight with 1e6 CFU of BCG


title: Naïve_mouse3_BCGstim

description:
Sample name: 1.7
splenocytes were stimulated overnight with 1e6 CFU of BCG


title: Raji_NT_rep2

value: Raji Burkitt lymphoma B cells


title: C57_colon_HF_Low_Low_Rep2

description: Tissue Sample ID: BK1616 Tissue: colon Mouse: 45


title: C57_liver_HF_Low_Suf_Rep2

description: Tissue Sample ID: BK2525 Tissue: liver Mouse: 71


title: BCG_mouse3_unstim

description:
Sample name: 1.5
splenocytes were stimulated for 12 hours without BCG


title: Naïve_mouse4_unstim

description:
Sample name: 1.6
splenocytes were stimulated for 12 hours without BCG


title: macrophages at HIV 10d

city: BOSTON

first: NAYOUNG

last: KIM

state: MA

address: 61 BINNEY

department: MEDICINE

institute: BOSTON CHILDREN'S HOSPITAL

description: Gene expression data from HIVbal 10d

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip human U133A plus 2.0 Affymetrix 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.

source_name: macrophages infected with HIVbal 10 days

label_protocol: Total RNA, 0.1 ug was prepared for hybridization to HG U133 2.0 oligonucleotide array (Affymetrix, Memphis, Tennessee) according to the small sample expression protocol (Affymetrix).  Hybridization was carried out overnight with 1.5 ug of labeled cRNA product, and arrays were scanned on Affymetrix scanners.

growth_protocol: Peripheral blood mononuclear cells were isolated from blood by Ficoll-gradient centrifugation and then monocytes were isolated by negative selection with Monocyte Isolation Kit II (Miltenyi Biotec, Auburn, CA). The monocytes were differentiated into macrophages by culturing them with human recombinant M-CSF for six days. THP-1 cells were differentiated into M2-polarized MDM with PHA.

extract_protocol: The cells were collected in Trizol® (Invitrogen, Carlsbad, CA), which was used to isolate total RNA according to the manufacturer’s instructions. The RNA was treated with 4 U of DNase I (Ambion, Austin, TX) and purified with Trizol® LS.

treatment_protocol: Cells were infected with 5 moi of adeno-lacZ or adeno-Tat for 30 hours or infected with HIVbal or medium alone as a control for 10 days.

value: macrophages differentiated from monocytes

tag: differentiation protocol

value: macrophages differentiated with G-MCSF

tag: differentiation time

value: macrophages differentiated for 7 days

tag: infection

value: HIVbal

tag: infection time

value: 10 days


title: C57_liver_HF_Low_Low_Rep2

description: Tissue Sample ID: BK1589 Tissue: liver Mouse: 45

value: female


title: THP-Mac at tTA control

description: Gene expression data from lacz control

source_name: THP-1 cells infected with adenovirus expressing tTA control for 24 hours

value: macrophages differentiated from THP-1 cells

value: THP-1 derived macrophages differentiated with PMA

value: macrophages differentiated for 3 days

value: adenovirus expressing tTA control

value: 24 hrs


title: THP-Mac at TatHXB2 24 hrs

description: Gene expression data from medium 7d

source_name: THP-1 cells infected with adenovirus expressing TatHXB2 for 24 hours

value: adenovirus expressing TatHXB2


title: BCG_mouse2_BCGstim

description:
Sample name: 1.3
splenocytes were stimulated overnight with 1e6 CFU of BCG

value: Female

value: 13 weeks

value: splenocyte

value: BCG

value: BCG stimulation


title: THP-Mac at TatSF2 24 hrs

description: Gene expression data from Tat

source_name: THP-1 cells infected with adenovirus expressing TatSF2 for 24 hours

value: adenovirus expressing TatSF2


title: C57_colon_HF_Low_Suf_Rep2

description: Tissue Sample ID: BK2554 Tissue: colon Mouse: 71

value: 12 weeks

value: colon + liver tissue (pooled)

value: Colon

value: High-fat diet with low selenium and folate

value: High-fat diet with sufficient selenium and folate


title: C57_colon_HF_Low_Low_Rep1

description: Tissue Sample ID: BK1976 Tissue: colon Mouse: 55

value: female


title: macrophages at medium 10d

description: Gene expression data from medium 10d

source_name: macrophages infected with medium control for 10 days

value: macrophages differentiated from monocytes

value: macrophages differentiated with G-MCSF

value: macrophages differentiated for 7 days

value: medium control

value: 10 days


title: Naïve_mouse3_unstim

description:
Sample name: 1.2
splenocytes were stimulated for 12 hours without BCG

value: Female


title: macrophages at HIV 7d

description: Gene expression data from HIVbal 7d

source_name: macrophages infected with HIVbal 7 days

value: HIVbal

value: 7 days


title: Naïve_mouse2_BCGstim

description:
Sample name: 1.4
splenocytes were stimulated overnight with 1e6 CFU of BCG

value: 13 weeks

value: splenocyte


title: Naïve_mouse1_unstim

description:
Sample name: 1.1
splenocytes were stimulated for 12 hours without BCG


title: Raji_NT_rep1

description: Gene expression data from Raji cells non transduced

value: Raji

value: Raji Burkitt lymphoma B cells

value: none (non-transduced control)


title: C57_liver_HF_Low_Low_Rep1

description: Tissue Sample ID: BK1950 Tissue: liver Mouse: 55

source_name: Colon and liver RNA extracts from all mice were pooled in an equimolar proportion and used as the reference sample.

value: 12 weeks

value: colon + liver tissue (pooled)

value: Liver


title: macrophages at medium 7d

description: Gene expression data from medium 7d

source_name: macrophages infected with medium control for 7 days


title: C57_liver_HF_Low_Suf_Rep1

description: Tissue Sample ID: BK2202 Tissue: liver Mouse: 62

value: female

value: High-fat diet with low selenium and folate

value: High-fat diet with sufficient selenium and folate


title: C57_colon_HF_Low_Suf_Rep1

description: Tissue Sample ID: BK2228 Tissue: colon Mouse: 62

value: Colon


title: 10^2 U/ml IFN-alpha

description: Gene expression data from iDC 10 h after treatment.

data_processing: Values in the raw data below 100, were floored to 100. Expression levels were compared to RNA from uninfected cells and cells infected with Ad-LacZ as a control. Gene up-regulation was examined only for transcripts from Ad-Tat infected cells that were present according to the detection call and down-regulation only for genes that were present in the uninfected and Ad-tTA-infected controls.

source_name: 10^2 U/ml IFN-alpha

label_protocol: Total RNA, 0.1 ug was prepared for hybridization to HG-U133_Plus_2 oligonucleotide array (Affymetrix, Memphis, Tennessee) according to the small sample expression protocol (Affymetrix).  Hybridization was carried out overnight with 1.5 ug of labeled cRNA product, and arrays were scanned on Affymetrix scanners.

growth_protocol: Peripheral blood mononuclear cells were isolated from blood by Ficoll-gradient centrifugation. Monocytes were isolated by negative selection with Monocyte Isolation Kit II (Miltenyi Biotec, Auburn, CA) according to the manufacturer’s instructions. The monocytes were differentiated into immature dendritic cells by culturing them with human recombinant GM-CSF and IL-4 (R&D Systems, Minneapolis, MN) for six days (Bender et al. 1996).

extract_protocol: The cells were collected 0 h, 5 h, 10 h and 20 h post infection. The cells were collected in Trizol® (Invitrogen, Carlsbad, CA), which was used to isolate total RNA according to the manufacturer’s instructions. The RNA was treated with 4 U of DNase I (Ambion, Austin, TX) and purified with Trizol® LS.

treatment_protocol: 10e6 DC cells were infected with 5 plaque-forming units per cell of both Ad-tTA and the Ad-Tat constructs or Ad-LacZ as a control.

value: Immature dendritic cells differentiated from monocytes

tag: treatment

value: 10^2 U/ml IFN-alpha

tag: time (post-treatment)

value: 10 hr


title: TTPA3

city: Baltimore

first: Annan

last: Yang

state: MD

address: 725 N. Wolfe St, Biophysics 203

department: Physiology

institute: Johns Hopkins University

description: replicate 3

data_processing: The data were normalised using vsn normalisation with limma package in R

source_name: keratinocyte harvest from p1 pups

growth_protocol: Keratinocyte media, 37°C, 5% CO2

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

treatment_protocol: TPA treatment (0.2 μM) for 12 h

value: FVBN

tag: genotype/variation

value: Ts

value: keratinocyte


title: 10^2 U/ml IFN-gamma

source_name: 10^2 U/ml IFN-gamma

value: 10^2 U/ml IFN-gamma


title: TTPA2

description: replicate 2


title: L4

city: East Geelong

first: Dragana

last: Stanley

state: Victoria

address: 5 Portarlington Rd

department: AAHL

country: Australia

institute: CSIRO

description: Low AME bird

hyb_protocol: Hybridisation was done overnight (16h) on 42C using NibleGen Hybing Chamber.

scan_protocol: Gene expression signals were captured using a NimbleGen MS200 2 m resolution laser scanner.

data_processing: NimbleScan Software Version 2.5.26 (Roche NimbleGen, Inc) was used to extract the data.  Data was analysed using Bioconductor (Gentleman et al. 2004) and a number of packages: arrayQualityMetrics (Kauffmann et al. 2009) for quality control, preprocessCore (Bolstad 2012) for background correction and normalizing, GeneFilter (Gentleman et al. 2009) for removal of low intensity features and limma (Smyth 2004) was initially used to identify differentially expressed genes. In order to avoid, as far as possible, false positives we used the GeneSelector package as described  by Boulesteix and Slawski (2007). Briefly, selection of differential genes can be highly influenced by the statistical method used, and overlap of genes selected using the same significance value can be quite low (Boulesteix and Slawski 2007). GeneSelector ranks genes based on how well they perform in a selected number of statistical tests and minimises the number of false positives. Ranked lists, based on ordinary t-test, SAM (Chu 2000), limma parametric empirical Bayes (eBayes) testing (Smyth 2004) and fold difference were first generated for each of the criteria. Then the Markov chain model within this package was used to aggregate the ranked lists of all criteria into a list of genes that are significant, independent of the method used.

organism: Gallus gallus

source_name: Low Aparent Metabolisable Energy

label_protocol: Total RNA (3 ug) was reverse transcribed into cDNA using oligo dT20 as per the Invitrogen Superscript III First Strand Synthesis System protocol (Invitrogen Corporation, Carlsbad, CA). The cDNA labeling with Cyanine 3, hybridization and washing was done following NimbleGen Arrays User's Guide protocol without modifications

growth_protocol: At 13 days post-hatch, 96 chickens were transferred in pairs to 48 metabolism cages located in a temperature-controlled room initially kept between 25-27C. Birds were placed in pairs for an initial acclimation period to minimize stress associated with isolation. Birds continued to have free access to food and water prior to, and during, the experimental period. On day 15, birds were placed individually in 96 metabolism cages.  AME values were determined in a classical seven-day energy balance study commencing when birds were 15 days of age. Body weight was recorded at the beginning and end of the seven-day period. The first three days enabled the chickens to adapt to solitary confinement in the metabolism cages. During the following four days, all excreta were collected daily and dried at 80C. Feed intake was recorded during the adaptation and collection phases of the study period. On day 22, all birds were weighed and retained in individual cages until day 25. On day 25 post-hatch birds were killed  by cervical dislocation.  Tissue (1cm segment) from the midpoint of the duodenum was collected, rinsed in phosphate buffered saline and stored in a 5 ml tube containing 2 ml of RNAlater (Ambion, Austin, TX).

extract_protocol: Total RNA was isolated from each duodenal sample using the Meridian total RNA isolation kit (Cartagen Molecular Incorporation, San Carlos, CA) according to the manufacturer's instructions.

treatment_protocol: Birds with extreeme AME values were selected for the experiment. There was a significant difference between top 6 High energy utilising and low energy birds (P=p=7.82e-4).

value: Duodenum


title: TTPA4

description: replicate 4


title: Ad-TatSF2K28,50A

description: Gene expression data from iDC 10 h p.i.

source_name: iDC expressing TatSF2K28,50A

tag: time (hpi)


title: L3

description: Low AME bird


title: TNT2

description: replicate 2

treatment_protocol: No treatment

tag: cell type


title: macrophages at lacZ 30 hrs

description: Gene expression data from lacz control

source_name: macrophages infected with adenovirus expressing LacZ control for 30 hours

value: macrophages differentiated from monocytes

value: macrophages differentiated with G-MCSF

value: macrophages differentiated for 7 days

value: adenovirus expressing LacZ control

value: 30 hrs


title: macrophages at Tat 30 hrs

description: Gene expression data from Tat

source_name: macrophages infected with adenovirus expressing Tat for 30 hours

value: adenovirus expressing Tat


title: TTPA1

description: replicate 1


title: Maize stem, ECB infested biological rep3

city: Gainesville

first: Alisa

last: Huffaker

state: FL

department: Chemistry Research Unit

institute: USDA-ARS CMAVE

description: Gene expression data from ECB infested maize stems

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

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

data_processing: The data were analyzed with ArrayStar 4 software (DNASTAR, Inc.).  All data were preprocessed using Robust MultiArray Analysis and quantile normalization. Annotation was assigned using NetAffx Maize Annotation Files in MAGE-ML XML format, release 31 and CSV format, release 31 (Affymetrix).

organism: Zea mays

source_name: 32 day old var, Golden Queen maize stem, ECB infested

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Affymetrix GeneChip 3# IVT express kit and protocol).

growth_protocol: Maize (Zea mays var. Golden Queen) were grown in 3 gallon pots (4 per pot) under supplemental lighting in a greenhouse (12 h photoperiod) at 24 C: 28 C (night:day) for 32 days.

treatment_protocol: Newly molted 5th Instar ECB larvae were allowed to feed overnight on maize leaf tissue then placed into leaf sheaths where they subsequently tunnelled into stem internodes and continued feeding for 48 hours. The internal non-photosynthetic tissue from developmentally similar internodes was collected from undamaged control plants along with those damaged by ECB after 48 hours. To reduce variation, three (3) individual plants were pooled for each harvested sample.

value: Stem

tag: genotype

value: Var. Golden Queen

tag: age

value: 32 days

value: ECB infested


title: P-4

city: Changchun

first: qin

middle: li

last: hong

state: jilin

address: 5333,xi'an road

department: College of Animal Science and Veterinary Medicine

country: China

institute: Jilin University

description: 18 bulls in our study included 9 bulls of 1 month old (3 samples: S-1; S-2; S-3) and 9 bulls of 24 month old (3 samples: P-2; P-3; P-4); each sample was the pool mixed by total RNA from 3 individuals to enlarge the samples for gene expression difference elimination between the individuals and show the really differential expression genes between different development stages in LM tissue.

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

scan_protocol: according to Affymetrix GeneChip data analysis.

data_processing:
The chips rectified were made by normalization processing using dChip (Affymetrix) software. False discovery rates for the genes were calculated by using t test and P values. Fold changes were calculated based on the unadjusted data’s means. Genes were annotated with NetAffx, and differentially expressed genes were identified using Significance Analysis of Microarrays (SAM). Using the criterion of cutoff
limitation as a fold change≧2 or ≦0.5 and q-value≦5%, differential expression genes were screened and clustered with the Cluster 3.0 software. The selected genes were further analyzed in the context of gene ontology (GO) biological process and KEGG biological pathway using the molecule annotation system 2.0 (MAS 2.0, http://bioinfo.capitalbio.com/mas/) software (CapitalBio, Beijing, China).

organism: Bos taurus

source_name: Longissimus Dorsi muscle tissue of Chinese Red Steppe, stored, -80°C

label_protocol: Amplified and labeled according to Affymetrix GeneChip experiment operation process.

growth_protocol: A total of 18 bulls (9 were 1month old while another 9 were 24 months old) of the same breed (Chinese Red Steppe) were maintained in standard conditions and fed with standard diet.

extract_protocol: Total RNA from muscle samples was extracted using Trizol reagent (Invitrogen, USA) and purified using QIAGEN RNeasy Total RNA Isolation kit (QIAGEN, USA) following manufacturer's instructions.

treatment_protocol: The bulls were humanely killed at the slaughter house of the academy, and fresh longissimus dorsi muscle tissues were obtained during slaughter, immediately frozen in liquid nitrogen and stored at -80°C for microarray analysis.

value: male

value: 24-month old

value: Longissimus Dorsi muscle

tag: breed

value: Chinese Red Steppe


title: L5

description: Low AME bird


title: S-3

value: 1-month old


title: S-2


title: TNT4

description: replicate 4

value: FVBN

value: Ts

value: keratinocyte


title: S-1


title: P-2


title: TNT3

description: replicate 3


title: Ad-TatSF2E86-E92A

description: Gene expression data from iDC 10 h p.i.

source_name: iDC expressing TatSF2E86-E92A

value: Immature dendritic cells differentiated from monocytes

value: 10 hr


title: P-3


title: 10^2 U/ml IFN-beta

source_name: 10^2 U/ml IFN-beta

value: 10^2 U/ml IFN-beta


title: Ad-TatSF2K51A

description: Gene expression data from iDC 10 h p.i.

source_name: iDC expressing TatSF2K51A


title: Ad-TatSF272

description: Gene expression data from iDC 10 h p.i.

source_name: iDC expressing TatSF272


title: WTPA3

description: replicate 3

value: WT


title: Maize stem, ECB infested biological rep1


title: Maize stem, untreated biological rep3

description: Gene expression data from untreated maize stems

source_name: 32 day old var, Golden Queen maize stem, untreated

value: control


title: Maize stem, untreated biological rep2

value: Stem


title: Ad-LacZ

description: Gene expression data from iDC 10 h p.i.

source_name: iDC expressing LacZ

value: Ad-LacZ


title: 0 control

description: Gene expression data from uninfected iDC.

source_name: Uninfected iDC

value: Uninfected


title: Maize stem, untreated biological rep1

value: Var. Golden Queen

value: 32 days


title: WNT4

description: replicate 4


title: H5

description: High AME bird

source_name: High Aparent Metabolisable Energy

value: Duodenum


title: LSEC replicate 4

city: Birmingham

first: Ian

last: Rowe

address: Edgbaston

department: Hepatitis C Virus Research Group

institute: University of Birmingham

description: Technical replicate

hyb_protocol: Hybridisation was performed using an Agilent Gene Expression Hybridization kit as per the manufacturer's instructions.

scan_protocol: Scanned on an Agilent 2505C scanner.  Images were quantified using the Agilent Feature Extraction software v. 10.5.1.1.

data_processing: Agilent Feature Extraction (10.5.1.1) was used for background subtraction.

source_name: LSEC untreated

label_protocol: RNA was labelled using an Agilent Quick Amp Labeling kit according to the manufacturer's instructions.

growth_protocol: LSEC were isolated from diseased human liver and propogated according to standard protocols (Liaskou E, et al Hepatology 2011).  LSEC were cultured on gelatin coated plates for the experiment.

extract_protocol: Total RNA was extracted using Quiagen Rneasy Mini Kit according to the manufacturer's instructions

treatment_protocol: Cells were starved of VEGF for 24 hours and then treated with recombinant VEGF-A for 18 hours at 5% O2.

value: liver sinusoidal endothelial cells

tag: cell passage

source_name: LSEC + VEGF-A 10ng/ml

tag: passage


title: Raji_shCtrl_rep1

description: Gene expression data from Raji cells transduced with a non targeting (Ctrl) sh RNA

source_name: Raji_transduced with a non targeting (Ctrl) sh RNA

tag: cell line

value: Raji

value: Raji Burkitt lymphoma B cells

tag: transduced with

value: control (non-targeting) shRNA


title: WTPA2

description: replicate 2

source_name: keratinocyte harvest from p1 pups

tag: strain

value: FVBN


title: WNT2

description: replicate 2

value: keratinocyte


title: WTPA1

description: replicate 1


title: H2

description: High AME bird

tag: tissue


title: L2

description: Low AME bird

source_name: Low Aparent Metabolisable Energy


title: Ad-TatSF2C25,30,34S 20 h p.i.

description: Gene expression data from iDC 20 h p.i.

source_name: iDC expressing TatSF2C25,30,34S, collected 20 h p.i.

value: Immature dendritic cells differentiated from monocytes

value: 20 hr


title: H4

description: High AME bird


title: WNT3

description: replicate 3


title: Maize stem, ECB infested biological rep2

value: ECB infested


title: Ad-LacZ 20 h p.i.

description: Gene expression data from iDC 20 h p.i.

source_name: iDC expressing LacZ, collected 20 h p.i.


title: H1

description: High AME bird


title: L1

description: Low AME bird


title: H3

description: High AME bird


title: LSEC replicate 3

description: Technical replicate


title: WTPA4

description: replicate 4

value: WT


title: H6

description: High AME bird


title: Ad-TatSF2

description: Gene expression data from iDC 10 h p.i.

source_name: iDC expressing TatSF2

value: 10 hr


title: Ad-TatSF258

description: Gene expression data from iDC 10 h p.i.

source_name: iDC expressing TatSF258


title: SW620 HAS3 silenced, rep2

city: buffalo

first: Dan

last: Wang

state: NY

address: Elm & Carlton Streets

institute: RPCI

hyb_protocol: The labeled probes were mixed with hybridization reagents and hybridized overnight to the HumanRef-8 v3.0 Expression BeadChips.

scan_protocol: Following washing and staining, the BeadChips were imaged using the Illumina BeadArray Reader to measure fluorescence intensity at each probe.

data_processing: BeadChip data files were analyzed with Illumina's GenomeStudio Gene Expression Module (V1.6.0).

source_name: SW620 cells transfected with siRNA to HAS3 incubated for 24 hours

label_protocol: Initially, we converted 250-500 ng total RNA to cDNA, followed by in vitro transcription to generate biotin-labeled cRNA (Illumina TotalPrep RNA Amplification Kit, Ambion Inc., Austin, TX).

extract_protocol: Total RNA was isolated from frozen tissue samples using TRIZOL reagent (Invitrogen).

value: colorectal cancer cells

tag: original tissue source

value: colon

value: transfection of HAS3 siRNA


title: Ad-TatSF2 20 h p.i.

description: Gene expression data from iDC 20 h p.i.

source_name: iDC expressing TatSF2, collected 20 h p.i.

tag: infection


title: SW620 HAS3 silenced, rep1


title: mutant mouse embryonic fibroblast, biological rep 3

city: New York

first: Frank

last: Yeung

state: New York

address: 540 First Ave

institute: Skirball Institute of Biomolecular Medicine

description: Gene expression data from mouse embryonic fibroblasts isolated from 13.5 day C57BL/6 Rap1 knockout embryos, immortalized with SV40LgT, expressing Rap1-I312R

hyb_protocol: Following fragmentation, cRNA were hybridized for GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: The data were analyzed with Bioconductor using normexp background correction and quantiles as normalization method.

source_name: Rap1 mutant mouse embryonic fibroblasts

label_protocol: Biotinylated cRNA were prepared using GeneChip 3’ IVT Express Kit according to manufacturer's protocol

extract_protocol: TRIzol extraction of total RNA followed by purification in Qiagen Rneasy columns

tag: background mouse strain

tag: source

value: mouse embryonic fibroblast

value: Rap1 I312R mutant


title: knockout mouse embryonic fibroblast, biological rep 1

description: Gene expression data from mouse embryonic fibroblasts isolated from 13.5 day C57BL/6 Rap1 knockout embryos, immortalized with SV40LgT

source_name: Rap1 knockout mouse embryonic fibroblasts

value: Rap1 knockout


title: Ad-LacZ 10 h p.i.

description: Gene expression data from iDC 10 h p.i.

source_name: iDC expressing LacZ, collected 10 h p.i.

value: Ad-LacZ


title: TNT1

description: replicate 1

value: Ts


title: Ad-TatHXB2 10 h p.i.

description: Gene expression data from iDC 10 h p.i.

source_name: iDC expressing TatHXB2, collected 10 h p.i.


title: SW620 Y15 treated, rep2

source_name: SW620 cells treated with Y15 and incubated for 24 hours

tag: treatment


title: Ad-TatHXB2 20 h p.i.

description: Gene expression data from iDC 20 h p.i.

source_name: iDC expressing TatHXB2, collected 20 h p.i.


title: wildtype mouse embryonic fibroblast, biological rep 2

description: Gene expression data from mouse embryonic fibroblasts isolated from 13.5 day C57BL/6 wildtype embryos, immortalized with SV40LgT

source_name: Wildtype mouse embryonic fibroblasts

value: wildtype


title: knockout mouse embryonic fibroblast, biological rep 2


title: Ad-TatSF2C25,30,34S 10 h p.i.

description: Gene expression data from iDC 10 h p.i.

source_name: iDC expressing TatSF2C25,30,34S, collected 10 h p.i.


title: WNT1

description: replicate 1

tag: genotype/variation


title: LSEC replicate 1

description: Technical replicate

source_name: LSEC untreated

value: liver sinusoidal endothelial cells

source_name: LSEC + VEGF-A 10ng/ml


title: mutant mouse embryonic fibroblast, biological rep 2


title: SW620 HAS scrambled control, rep2

source_name: SW620 cells transfected with scrambled sequence incubated for 24 hours

value: transfection of scrambled control sequence


title: SW620 HAS scrambled control, rep1


title: LSEC replicate 2

description: Technical replicate


title: SW620 untreated, rep2

source_name: SW620 cells untreated and incubated for 24 hours


title: SW620 untreated, rep1


title: SW620 Y15 treated, rep1


title: knockout mouse embryonic fibroblast, biological rep 3


title: Ad TatSF2A58T 10 h p.i.

description: Gene expression data from iDC 10 h p.i.

source_name: iDC expressing TatSF2A58T, collected 10 h p.i.

value: Ad TatSF2A58T

tag: time (hpi)


title: Ad-TatSF2 10 h p.i.

description: Gene expression data from iDC 10 h p.i.

source_name: iDC expressing TatSF2, collected 10 h p.i.

tag: cell type

value: Immature dendritic cells differentiated from monocytes


title: Ad TatSF2A58T 20 h p.i.

description: Gene expression data from iDC 20 h p.i.

source_name: iDC expressing TatSF2A58T, collected 20 h p.i.

value: 20 hr


title: wildtype mouse embryonic fibroblast, biological rep 3

tag: genotype


title: A6_LEF1

city: Regensburg

first: Katharina

last: Meyer

address: Josef Engert Street 9

department: Statistical Bioinformatics

country: Germany

institute: Institute for Functional Genomics

description: Gene expression data.

hyb_protocol: Following fragmentation, 12.5 μg of cRNA were hybridized for 16 h at 45°C on GeneChip Human Genome U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Gene expression values were obtained by first removing the background and normalizing on probe level using the variance stabilization method by Huber and colleagues. The normalized probe intensities were summarized into gene expression levels by using an additive model fitted by the median polish procedure.

label_protocol: Biotinylated cRNA was prepared from 0,3 µg totalRNA according to the Affymetrix GeneChip  3’ IVT Express Kit manual (Rev. 6)

growth_protocol: complete RPMI

extract_protocol: Qiagen RNA-isolation

treatment_protocol: electroporation of BL2 cells

tag: transfection

value: LEF siRNA

tag: batch


title: mutant mouse embryonic fibroblast, biological rep 1


title: wildtype white adipose tissue, biological rep 3

description: Gene expression data from white adipose tissue from 6-8 week old C57BL/6 wildtype mouse

source_name: Wildtype white adipose tissue

value: white adipose tissue


title: knockout white adipose tissue, biological rep 3

description: Gene expression data from white adipose tissue from 6-8 week old C57BL/6 Rap1 knockout mouse

source_name: Rap1 knockout white adipose tissue


title: A4_LEF1

description: Gene expression data.


title: wildtype mouse embryonic fibroblast, biological rep 1


title: 0-control

source_name: Uninfected iDC

value: Uninfected

value: control


title: knockout liver, biological rep 3

description: Gene expression data from liver from 6-8 week old C57BL/6 Rap1 knockout mouse

source_name: Rap1 knockout liver

value: liver


title: A1_scrb

description: Gene expression data.

value: scrb siRNA


title: knockout white adipose tissue, biological rep 2


title: knockout liver, biological rep 2


title: wildtype white adipose tissue, biological rep 1


title: WC066-400 PBMCs, longitudinal A plasma, visit 4

city: Milwaukee

first: Martin

last: Hessner

state: WI

address: 8701 Watertown Plank Road

department: Pediatrics

institute: Medical College of Wisconsin

hyb_protocol: The GeneChip human genome U133 plus 2.0 array was selected for these studies for its overall comprehensive coverage.

scan_protocol: After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001 and scanned with a 7G Affymetrix GeneChip Scanner.

data_processing: Image data were normalized and analyzed Partek Genomic Suite (v.6.5 (6.11.0321)) to determine signal log ratios.  Each sample was independently analyzed (1 array for each time point on the same patient, 6 arrays in total).  This time serise data was analysis by S.T.E.M. - Short Time-series Expression Miner.

source_name: Healthy control donor PBMCs stimulated with Longitudinal A plasma, visit 4

label_protocol: cRNA was synthesized, labeled, fragmented, and hybridized to an array in accordance to the Affymetrix GeneChip expression analysis technical manual.

growth_protocol: PBMCs from healthy individual control donor WC066-400 were isolated using a Histopaque 1077 gradient (Sigma).

extract_protocol: Total RNA was extracted and amplified using an Affymetrix two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA).

treatment_protocol: Gene expression was accomplished by culturing PBMCs at 37°C in 5% CO2 with 20% of longitudinal T1D plasma.  Cultures were prepared in a Costar 24-well plate (Corning) using 500,000 cells/well and in RPMI 1640 medium supplemented with 100U/ml penicillin and 100ug/ml streptomycin in a total of 500 µl.  After culture (9 hours optimal for cryopreserved PBMCs) total RNA was extracted using TRIzol reagent (Invitrogen Life Technologies).

tag: responder cells

value: healthy control donor WC066-400 PBMCs

tag: stimulated with

value: 20% plasma from a longitudinally monitored sibling of a T1D patient


title: WC066-400 PBMCs, longitudinal A plasma, visit 2

source_name: Healthy control donor PBMCs stimulated with Longitudinal A plasma, visit 2


title: wildtype white adipose tissue, biological rep 2


title: WC066-400 PBMCs, longitudinal A plasma, visit 3

source_name: Healthy control donor PBMCs stimulated with Longitudinal A plasma, visit 3


title: A2_LEF1

description: Gene expression data.

tag: cell line


title: WC066-400 PBMCs, longitudinal A plasma, visit 5

source_name: Healthy control donor PBMCs stimulated with Longitudinal A plasma, visit 5


title: knockout white adipose tissue, biological rep 1

value: Rap1 knockout


title: A3_scrb

description: Gene expression data.


title: A5_scrb

description: Gene expression data.


title: SUM190 genomic DNA

type: genomic

city: Helsinki

first: Henrik

last: Edgren

address: Tukholmankatu 8

country: Finland

institute: Institute for Molecular Medicine, University of Helsinki

hyb_protocol: Labelled tumor and reference samples were combined and hybridized onto the arrays according to manufacturer's (Agilent) instructions. After hybridization, arrays were washed according to manufacturer's instructions.

scan_protocol: Arrays were scanned using a laser scanner from Agilent Technologies. Signal intensities were quantified using the Feature Extraction software from Agilent.

data_processing: Agilent Feature Extraction Software was used for spot quality filtering and normalization.

molecule: genomic DNA

source_name: pooled genomic DNA from healthy female donors

label_protocol: One μg of digested and purified tumor and reference DNA was labeled with Cy5-dUTP and Cy3-dUTP (Perkin-Elmer, Wellesley, MA), respectively, in a random priming reaction using BioPrime DNA Labelling System (Invitrogen, Carlsbad, CA)

growth_protocol: Cell lines were cultured according to recommended conditions.

extract_protocol: Genomic DNA was extracted using TRIzol and purified by chloroform extraction and subsequent ethanol precipitation.

tag: sample type

value: pooled normal female genomic DNA

tag: gender

value: female

source_name: genomic DNA from breast cancer cell line SUM190


title: WC066-400 PBMCs, longitudinal A plasma, visit 6

source_name: Healthy control donor PBMCs stimulated with Longitudinal A plasma, visit 6


title: MCF7 genomic DNA

source_name: genomic DNA from breast cancer cell line MCF7


title: SKBR3 genomic DNA

source_name: genomic DNA from breast cancer cell line SKBR3


title: KPL4 genomic DNA

source_name: genomic DNA from breast cancer cell line KPL4


title: SUM225 genomic DNA

source_name: genomic DNA from breast cancer cell line SUM225


title: HCC1569 genomic DNA

source_name: genomic DNA from breast cancer cell line HCC1569


title: JIMT1 genomic DNA

source_name: genomic DNA from breast cancer cell line JIMT1


title: UACC812 genomic DNA

source_name: genomic DNA from breast cancer cell line UACC812


title: HCC202 genomic DNA

source_name: genomic DNA from breast cancer cell line HCC202


title: wildtype liver, biological rep 3

description: Gene expression data from liver from 6-8 week old C57BL/6 wildtype mouse

source_name: Wildtype liver

value: wildtype


title: HCC1954 genomic DNA

source_name: genomic DNA from breast cancer cell line HCC1954


title: wildtype liver, biological rep 1


title: P3-48hour

city: Dallas

first: Josiah

last: Hawkins

address: 5323 Harry Hines Boulevard

institute: UT Southwestern

description: SAMPLE 17

hyb_protocol: Following fragmentation, 15µg of cRNA were hybridized at 45°C for 16 hr on the GeneChip Mouse Genome 430 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

data_processing: The data were analyzed after uploading to the Genesifter website (Geospiza, Seattle WA). Algorithm: ExpressionStat 5.0

source_name: Neonatal Mouse

label_protocol: Biotinylated cRNA was amplified from 1µg of total RNA using the MessageAmp II-Biotin Enhanced Kit(Ambion) protocol.

growth_protocol: Adult Balb/c mice (at least 6 weeks old) and their pups were bred and maintained under pathogen-free conditions in our vivarium in accordance with the Institutional Animal Care and Use Committee of the University of Texas Southwestern Medical Center.

extract_protocol: Liver was dissected, snap-frozen in liquid nitrogen and stored at -80°C. Samples were homogenized and total RNA was extracted using the the RNeasy Midi Kit(Qiagen) according to the manufacturer's manual. RNA integrity was measured on the Agilent 2100 Bioanalyzer(RIN:9.5).

treatment_protocol: The methods for culturing and counting the Listeria monocytogenes (strain CNL 85/163) had been described in previous publications. The Listeria was injected intraperitoneally using a 1-mL U-100 insulin syringe with a 30 gauge needle. Doses of Listeria monocytogenes used were based on work by our laboratory showing that similar bacterial colony counts were obtained with 4.2 x 105 total Listeria per adult mouse and 150 Listeria per gram for 3 to 5 day old neonatal mice. In neonatal mice, great care was taken to void deep intraperitoneal injection towards the viscera, or across the central abdominal vessels. At specified time points, liver was removed upon animal sacrifice and immediately flash frozen in liquid nitrogen and stored at -80 degrees Centigrade. Three adult mice and three neonatal mice were used at each time point.

tag: strain

value: Balb/c

tag: age

value: neonatal (3 to 5 day old)

tag: injected with

tag: time point

value: 48 hr

tag: tissue


title: wildtype liver, biological rep 2

tag: background mouse strain

tag: source


title: CD138+ plasma cells from patient MM75

city: Bologna

first: Carolina

last: Terragna

address: Via Massarenti, 9

department: Department of Experimental, Diagnostic and Specialty Medicine - DIMES

country: Italy

institute: Institute of Hematology "L.A.Seràgnoli"

description: gene expression profiles of purified plasma cells (PCs) obtained from Multiple Myeloma patients. PCs were purified from bone marrow samples, using CD138 immunomagnetic microbeads. The purity of the positively selected PCs (92%) was assessed by low cytometry. 5 micrograms of total RNA was processed and hybridized to the Affymetrix HG-U133A Plus chip following the manufacturer's instructions. After scanning, the image was processed using Affymetrix MicroArray Suite (MAS) 5.0 software to generate gene expression intensity values.

hyb_protocol: Following fragmentation, 5ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: Affymetrix output (CEL files) was imported into Genespring 7.3 microarray analysis software (Agilent Technologies), in which data files were normalized across chips using RMA and to the 50th percentile, followed by per gene normalization to the median

source_name: CD138+ plasma cells obtained from bone marrow of MM patient

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 30ng total RNA (Two Cycle Kit, Affymetrix).

extract_protocol: Total RNA extraction was performed according to the manufacturer's instructions (Rneasy Mini e micro kit)

tag: stage

value: CD138+ plasma cell

tag: disease state

value: multiple myeloma


title: P6-48hour

description: SAMPLE 18

value: Listeria monocytogenes (strain CNL 85/163)


title: HPAC Non-invasive (Top) [Chip 2]

city: Frederick

first: Lei

last: Sun

address: 1050 Boyles Street

department: Laboratory of Cancer Prevention

institute: Frederick National Laboratory for Cancer Research

description: Input verses methyl collector

hyb_protocol: Samples were applied to Agilent’s 2x244K Human Promoter Tiling Arrays for 40 hours at 65ºC and washed for 5 minutes in wash buffer 1 and then 5 minutes in wash buffer 2.

scan_protocol: The arrays were scanned using a Gene Pix 4000B scanner (Molecular Devices, Sunnyvale, CA) with GenePix Pro software version 6.1 and extracted using Agilent’s Feature Extraction software version 9.5.3.1.

data_processing:
The data was annotated using Agilent’s ChIP Analytics software version 4.0. Normalization was carried out using a blank subtraction model and statistical stringency (p-value) between 0.01-0.05 was applied using a Whitehead Per-Array Neighbourhood Analysis. This analysis allowed for the determination of differentially methylated genes between non-invasive and invasive cells.
Methylated probes appear in the array with a value of 1 in the ISINBOUND Region and un-methylated probes array with a value of 0. Using FileMaker Pro Software (version 9) the full text files were imported and the find option was used in order to query probes that were methylated in the Non-Invasive cells and non-methylated in the Invasive cells.

source_name: Pancreatic Cancer Cell Line

label_protocol: The isolated methylated and non-methylated DNA from each sample (as little as 5 ng) was then amplified in a series of PCR reactions following the mammalian ChIP-on-chip protocol from Agilent. The input DNA was labeled with Cy3-dUTP and the methylated DNA with Cy5-dUTP.

growth_protocol: PANC1 and HPAC cell lines were grown according to methods from ATCC.

extract_protocol: For the isolation of DNA from both non-invasive and invasive cells the DNeasy kit from Qiagen (Valencia, CA) was used and parallel invasion chambers were setup. For non-invading cells, the bottom of the membrane was scrubbed with a cotton swab and cells on top were trypsinized and harvested in 200 µL of PBS followed by the direct addition of lysis buffer or stored at -80ºC. For bottom ‘invading cells’ the top of the membrane was scrubbed with a cotton swab and the membrane was removed and placed directly into lysis buffer or stored at -80ºC until needed.  MethylCollector (Active Motif, Carlsbard, CA) assay was used to isolate methylated and non-methylated fractions of DNA.  The kit utilizes histidine-tagged MeBP2 (methyl-binding protein 2) and magnetic bead separation.

treatment_protocol: 70,000-100,000 cells were seeded in RPMI with nothing else in 24 well matrigel chambers.Cells were migrated toward stem cell media (SCM) for 24 hours containing DMEM/F12 with human supplementation of 10 ng/mL  bFGF, 20 ng/mL EGF, 5 µg/mL insulin, 5 µg/mL transferrin and 5ng/ml sodium selenite along with 0.4% BSA

value: HPAC

tag: phenotype

value: Non-invasive

tag: dna type

value: Non-methylated Genomic DNA

value: Methylated Genomic DNA


title: A1-48hour

description: SAMPLE 13

source_name: Adult mouse

value: adult (>6 weeks old)

value: liver


title: CD138+ plasma cells from patient MM73

tag: cell type


title: P2-48hour

description: SAMPLE 16


title: CD138+ plasma cells from patient MM71


title: WC066-400 PBMCs, longitudinal A plasma, visit 1

source_name: Healthy control donor PBMCs stimulated with Longitudinal A plasma, visit 1

tag: responder cells

value: healthy control donor WC066-400 PBMCs

value: 20% plasma from a longitudinally monitored sibling of a T1D patient


title: A3-48hour

description: SAMPLE 15


title: CD138+ plasma cells from patient MM72


title: CD138+ plasma cells from patient MM76


title: CD138+ plasma cells from patient MM77


title: CD138+ plasma cells from patient MM74


title: RDE_1_inf_3

city: Cambridge

first: Eric

middle: A.

last: Miska

address: Tennis Court Rd

department: Wellcome Trust/Cancer Research UK Gurdon Institute, The Henry We

institute: University of Cambridge

hyb_protocol: labelling, hybridization and scanning was performed by the EMBL microarray service http://www.genecore.embl.de

data_processing: The Bioconductor package was used to generate RMA normalized values for each probe [R ver 2.14 and Bioconductor ver 2.10, package affy].

organism: Caenorhabditis elegans

source_name: C.elegans mixed stage

growth_protocol: C.elegans were grown under standard conditions at 20C The food source used was E. coli strain HB101 (Caenorhabditis Genetics Center, University of Minnesota, Twin Cities, MN, USA). Uninfected animals were picked as L4s.  Virus or control solution was added after 24 hrs and RNA was harvested 4 days later.

extract_protocol: Trizol extraction of RNA

tag: infection

value: Orsay virus


title: HPAC Invasive (Bottom) [Chip 1]

description: Input verses methyl collector

tag: cell line

value: Invasive


title: CD138+ plasma cells from patient MM70


title: A2-48hour

description: SAMPLE 14


title: HPAC Non-invasive (Top) [Chip 1]

description: Input verses methyl collector


title: PANC1 Invasive (Bottom) [Chip 1]

description: Input verses methyl collector


title: PANC1 Invasive (Bottom) [Chip 2]

description: Input verses methyl collector


title: PANC1 Non-invasive (Top) [Chip 2]

description: Input verses methyl collector


title: BT474 genomic DNA

source_name: pooled genomic DNA from healthy female donors

tag: sample type

value: pooled normal female genomic DNA

value: female

source_name: genomic DNA from breast cancer cell line BT474


title: HPAC Invasive (Bottom) [Chip 2]

description: Input verses methyl collector


title: PANC1 Non-invasive (Top) [Chip 1]

description: Input verses methyl collector


title: CD138+ plasma cells from patient MM69


title: RDE_1_1

scan_protocol: labelling, hybridization and scanning was performed by the EMBL microarray service http://www.genecore.embl.de

value: rde-1 ne


title: CD138+ plasma cells from patient MM67


title: A3-24hour

description: SAMPLE 8

value: Balb/c

value: 24 hr


title: CD138+ plasma cells from patient MM66

value: CD138+ plasma cell

value: multiple myeloma


title: RDE_1_inf_2

label_protocol: labelling, hybridization and scanning was performed by the EMBL microarray service http://www.genecore.embl.de


title: CD138+ plasma cells from patient MM78


title: knockout liver, biological rep 1

source_name: Rap1 knockout liver

tag: genotype

value: Rap1 knockout


title: P2-24hour

description: SAMPLE 11

tag: strain

value: neonatal (3 to 5 day old)

value: Listeria monocytogenes (strain CNL 85/163)


title: RDE_1_3


title: RDE_1_2


title: P1-24hour

description: SAMPLE 10

tag: age


title: CD138+ plasma cells from patient MM68


title: CD138+ plasma cells from patient MM65


title: A1-24hour

description: SAMPLE 7

tag: injected with


title: P5-24hour

description: SAMPLE 12

tag: time point


title: A4-24hour

description: SAMPLE 9

tag: tissue


title: JU1580_inf_3

value: JU1580 wild isolate


title: CD138+ plasma cells from patient MM64


title: JU1580_inf_2


title: P2-0hour

description: SAMPLE 5

value: 0 hr


title: M.tbControl_PFD_72hr_rep4

city: Bangalore

first: madavan

last: vasudevan

state: Karnataka

address: Kasturi Nagar

country: India

institute: Theomics International Private Limited

description: Gene expression of exponential M.tuberculosis culture grown for 72 Hrs and labeling using WT and presence of formamide in hybridization

hyb_protocol: The Gene Expression Hybridization Kit (Agilent Technologies, 5188-5279) and associated protocols were used (G4140-90040). To evaluate the effect of formamide on the specificity of annealing of the GC-rich targets, the purified cRNA (600ng) was fragmented with fragmentation blocking mix in the presence or absence of Formamide (7%) by incubating samples at 60°C for 30 minutes. Microarrays were prepared in Agilent Technologies Hybridization Chamber according to manufacturers instructions (G2534-90001). Once loaded into thehybridization chamber, samples were placed in thehybridization oven (Agilent Technologies, G2505-80085) and incubated for 17 hours at 65°C while rotating at setting 10. Following hybridization, samples were washed according to procedure described by Agilent Technologies.

scan_protocol: Microarray slides were scanned at the resolution of 5µmusing Agilent Microarray scanner (G2565CA) with scan control software as per manufacturer’s instructions (G2505-90020). Settings included Agilent HD_GX_1colour (61X21.6mm), TIFF 20 bit, and Photomultiplier tube (PMT) gain 100%. Scanned image displays were analyzed by quantifying the pixel density of each hybridization spot using the Agilent Feature Extraction software (v10.5). Local background signals were subtracted from the data automatically by this software and raw data was obtained.

data_processing: Normalization was done to 50th percentile of each sample and data transformation was done to median of all samples using GeneSpring Gx V 12.0 from Agilent Technologies

organism: Mycobacterium tuberculosis H37Rv

label_protocol: The first priming method (PolyA-dT) involved initial polyadenylation of Mycobacterial RNA folllowed by oligo-dT based amplification and labelling to produce cRNA. Polyadenylation was carried out using Poly (A) polymerase tailing kit (Epicenter Biotechnologies, USA) as per the manufacturer’s instructions. 25 ng of Poly A tailed RNA was amplified and labeled using theoligo-dT based T7 promoter primers included in the Low Input Quick Amp labeling kit(Agilent Technologies, G4140-90040). The Agilent spike-in controls included in the One-Color RNA Spike-In Kit (Agilent Technologies, 5188-5282)were used as control.The second priming method (WT)involved random-priming based amplification and labelling of Mycobacterial RNA. For this, 25 ng of the native non-adenylated total RNA was amplified and labeled using random nucleotide-based T7 promoter primers included in the Low Input Quick Amp WT labeling kit(Agilent Technologies, G4140-90042).

growth_protocol: M. tuberculosis H37Rv was grown in Middlebrook 7H9 (Difco, Becton Dickinson and Co., USA) supplemented with 0.05% Tween 80 and 10% Albumin, Dextrose, Catalase (ADC, Difco,Becton Dickinson and Co., USA) at 37°C, 200rpm, to OD600 of 0.4-0.5.

extract_protocol: The cells were harvested from 25 ml culture of M. tuberculosis grown under different conditions and RNA was isolated using published protocols. The RNA yield (absorbance at 260nm) and purity of the samples was measured by using the Nanodrop 2000c spectrophotometer (Thermo Scientific, USA). Yield of the RNA was calculated from the absorbance of the sample at 260 nm.

treatment_protocol: The exponential phase M.tuberculosis culture was treated with Isoniazid (Sigma Aldrich, USA) at 1ug/ml for 6 hours. Control cultures without drug treatment were also grown. The cells were harvested after 0 hrs, 6 hrs, 24hrs and 72 hrs of growth in presence or absence of drug.

value: M.tuberculosis culture


title: CD138+ plasma cells from patient MM61


title: P3-0hour

description: SAMPLE 6

value: liver


title: M.tbControl_PFD_72hr_rep3


title: RDE_1_inf_1


title: CD138+ plasma cells from patient MM59


title: P1-0hour

description: SAMPLE 4


title: JU1580_2


title: JU1580_inf_1


title: JU1580_1


title: CD138+ plasma cells from patient MM63


title: CD138+ plasma cells from patient MM62


title: A2-0hour

description: SAMPLE 2

value: adult (>6 weeks old)


title: M.tbControl_MFD_24hr_rep2

description: Gene expression of exponential M.tuberculosis culture grown for 24 Hrs and labeling using WT and absence of formamide in hybridization


title: M.tbControl_PFD_24hr_rep1

description: Gene expression of exponential M.tuberculosis culture grown for 24 Hrs and labeling using WT and presence of formamide in hybridization


title: CD138+ plasma cells from patient MM58


title: CD138+ plasma cells from patient MM57


title: N2_inf_3

value: N2 laboratory strain

value: Orsay virus


title: M.tbControl_MFD_72hr_rep2

description: Gene expression of exponential M.tuberculosis culture grown for 72 Hrs and labeling using WT and absence of formamide in hybridization


title: M.tbControl_MFD_72hr_rep1


title: JU1580_3


title: M.tbINH_WT_6hr_rep4

description: Gene expression of exponential M.tuberculosis culture treated with isoniazid and grown for 6hrs labelling using WT


title: N2_inf_2


title: M.tbControl_PFD_24hr_rep2


title: CD138+ plasma cells from patient MM60


title: M.tbINH_WT_6hr_rep3


title: N2_inf_1


title: CD138+ plasma cells from patient MM56


title: M.tbControl_MFD_24hr_rep1


title: A3-0hour

description: SAMPLE 3


title: CD138+ plasma cells from patient MM54


title: M.tbINH_WT_6hr_rep2


title: CD138+ plasma cells from patient MM53


title: CD138+ plasma cells from patient MM55


title: N2_inf_4


title: A1-0hour

description: SAMPLE 1


title: N2_4


title: M.tbControl_WT_6hr_rep4

description: Gene expression of exponential M.tuberculosis culture treated with isoniazid and grown for 6hrs labelling using PolyAdT


title: N2_2


title: CD138+ plasma cells from patient MM52


title: M.tbINH_WT_6hr_rep1


title: N2_1


title: Clonal Extinction Tumor B biol replicate 2

city: Stanford

first: Daniel

last: Corey

state: Ca

address: 265 Campus Drive

institute: Stanford Univeristy

description: Daniel Corey_3-P4_(Mouse430_2).CEL

hyb_protocol: The array were hyb. by using Affymetrix Genechip hybridization Oven 640 and washing labeled using Affymetrix Genechip Fluidics station 450.

scan_protocol: The array was scanned by using Affymetrix Genechip Scanner 3000 7G.

data_processing: Raw CEL files were normalized using the Robust Multichip Average (RMA) method implemented in the affy package of Bioconductor

source_name: Dissociated B16 Mouse Melanoma Tumor Blood Vessels

label_protocol: Labeled using Affymetrix Genechip Fluidics station 450.

growth_protocol: B16 Mouse Melanoma was injected into a multi-color Cre-Reporter Mouse and Blood Vessels and Tumor were dissociated into a single cell suspension two weeks after innoculation

extract_protocol: Samples were processed by using two around amplification method after TRIzol extraction.

tag: tumor

value: Tumor B

tag: tumor endothelial cells

value: CD45-CD31+CD144+ FACS Isolated

tag: clone frequency

value: Clonal Extinction


title: N2_3


title: M.tbControl_WT_6hr_rep2


title: M.tbControl_WT_6hr_rep3


title: M.tbINH_PolyAdT_6hr_rep3

description: Gene expression of exponential M.tuberculosis culture after 6hr labelling using WT


title: Clonal Expansion Tumor B biol replicate 2

description: Daniel Corey_3-P20_(Mouse430_2).CEL

value: Clonal Expansion


title: CD138+ plasma cells from patient MM50

tag: stage

tag: disease state


title: M.tbControl_WT_6hr_rep1


title: M.tbINH_PolyAdT_6hr_rep4


title: M.tbINH_PolyAdT_6hr_rep2


title: Clonal Extinction Tumor A biol replicate 1

description: Daniel Corey_1-P8_(Mouse430_2).CEL

value: Tumor A


title: CD138+ plasma cells from patient MM49

value: CD138+ plasma cell


title: CD138+ plasma cells from patient MM47

value: multiple myeloma


title: M.tbINH_PolyAdT_6hr_rep1


title: CD138+ plasma cells from patient MM51


title: M.tbControl_PolyAdT_6hr_rep4

description: Gene expression of exponential M.tuberculosis culture after 6hr labelling using PolyAdT


title: Clonal Expansion Tumor A biol replicate 1

description: Daniel Corey_1-P4_(Mouse430_2).CEL


title: LPSTZ pancreas, biological rep1

city: Houston

first: Aaron

middle: R

last: Cox

state: TX

address: 1102 Bates Ave.

department: Pediatrics - Endocrinology and Diabetes

institute: Baylor College of Medicine

hyb_protocol: 10 μg of labeled cRNA was hybridized to Affymetrix Mouse 430 2.0 arrays for 16 hours at 45°C as described in the Affymetrix Technical Analysis Manual. GeneChips were stained with Streptavidin-Phycoerythrin, followed by an antibody solution and a second Streptavidin-Phycoerythrin solution, with all liquid handling performed by a GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned with the Affymetrix GeneChip Scanner 3000.

data_processing: Probe level data from the .CEL files were analyzed using Partek Genomics Suite v6.5. Probes were imported and summarized using RMA and ANOVA was used to determine fold changes and p-values.

source_name: pancreas, low protein diet, STZ injected

label_protocol: Biotinylated cRNA was prepared from 10 ug of total RNA as per the Affymetrix GeneChip Technical Analysis Manual.

growth_protocol: Mice were housed in a temperature controlled room with 12 h light:dark cycle. Water and food were given ad libitum.

extract_protocol: Total RNA was extracted and purified using the RNeasy Plus Mini kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Injections were given daily from days 1 to 5 from birth.

value: Balb/C

tag: Sex

value: female

value: pancreas

value: 30 days old

tag: maternal diet

value: Isocaloric low protein diet

tag: treatment

value: streptozotocin


title: M.tbControl_PolyAdT_6hr_rep3

value: M.tuberculosis culture


title: M.tbControl_PolyAdT_6hr_rep2


title: LPSTZ pancreas, biological rep3


title: LPSTZ pancreas, biological rep2


title: M.tbControl_WT_0hr_rep2

description: Gene expression of exponential M.tuberculosis culture after 0hr labelling using WT


title: M.tbControl_PolyAdT_6hr_rep1


title: STZ pancreas, biological rep3

source_name: pancreas, control diet, STZ injected

value: Control diet


title: CD138+ plasma cells from patient MM48

tag: cell type


title: Bj_Indole-3-acetic acid 1mM vs. no treatment_Rep2_dyeswap

city: Arlington

first: Woo-Suk

last: Chang

address: 501 S. Nedderman Dr. , Life Science Building 216

department: Biology

institute: University of Texas at Arlington

hyb_protocol: Both cy3 and cy5 labeled cDNAs to be compared were mixed, dried to completion, and then resuspended in 70 ul of preheated hybridization buffer (nuclease free water:formamide:20X SSC:1% SDS = 4:2.5:2.5:1) at 42 C. After adding 0.7 ul salmon sperm DNA (10 mg/ml) to prevent non-specific binding to the array, the mixture was hybridized at 42 C for 16 to 18 h. Hybridized arrays were washed with 1X SSC, 0.2% SDS at 42 C for 6 min, and, subsequently, with 0.1X SSC, 0.2% SDS at room temperature for 6 min, and twice with 0.1X SSC at room temperature for 3 min.

scan_protocol: The arrays were scanned using an Axon GenePix 4000B scanner (Molecular Devices Corp., Sunnyvale, CA). Signal intensities were analyzed using GenePix Pro 6.0 software (Molecular Devices Corp., Sunnyvale, CA).

data_processing: Signal intensities were normalized for spot and slide abnormalities using spatial lowess. Lowess adjusted data were subsequently analyzed by mixed effect microarray analysis of variance (MAANOVA) (Kerr et al. 2000). The resulting variety-by-gene interaction (VG) values were combined with the residual noise from each spot to obtain the filtered and adjusted expression values (Kerr et al. 2000; Kerr and Churchill 2001). Both lowess and MAANOVA are part of the R/maanova microarray statistical analysis package (http://www.jax.org/staff/churchill/labsite/). Expression values from two technical replicates in each array were combined and averaged. Significant genes were selected based on a 2.0-cut off threshold with a false discovery rate lower than 5%.

organism: Bradyrhizobium diazoefficiens USDA 110

source_name: Indole-3-acetic acid 1 mM

label_protocol: 30 ug of total RNA was used for cDNA synthesis with superscript III reverse transcriptase and random hexamers (Invitrogen Corp.). After digesting the remaining RNA by RNase H (Fermentas), cDNA was purified using a Microcon YM-30 column (Millipore) and concentration was determined using a Nanodrop spectrophotometer (NanoDrop Technologies, Wilmington, DE). Five micrograms of cDNA were used for labeling with either cy3 or cy5 (Armersham) and unincorporated dyes were removed using a Qiaquick PCR purification Kit (Qiagen).

extract_protocol: Standard hot-phenol method

value: Bradyrhizobium japonicum USDA 110

value: Indole-3-acetic acid 1mM for 3 hr

source_name: No Treatment

value: none (control)


title: LP pancreas, biological rep3

source_name: pancreas, low protein diet, sham injected

value: sham


title: Bj_Indole-3-acetic acid 1mM vs. no treatment_Rep2

source_name: Indole-3-acetic acid 1mM treatment


title: M.tbControl_WT_0hr_rep1


title: LP pancreas, biological rep1


title: Bj_Indole-3-acetic acid 1mM vs. no treatment_Rep1_dyeswap


title: control pancreas, biological rep3

source_name: pancreas, control diet, sham injected


title: M.tbControl_PolyAdT_0hr_rep1

description: Gene expression of exponential M.tuberculosis culture after 0hr labelling using PolyAdT


title: Bj_Indole-3-acetic acid 1mM vs. no treatment_Rep3_dyeswap


title: control pancreas, biological rep1


title: Bj_Indole-3-acetic acid 1mM vs. no treatment_Rep1


title: STZ pancreas, biological rep1


title: M.tbControl_PolyAdT_0hr_rep2


title: control pancreas, biological rep2


title: Bj_Indole-3-acetic acid 1mM vs. no treatment_Rep3


title: Phc2 L307R MEF

city: Yokohama

first: Takaho

last: Endo

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

department: IMS

country: Japan

institute: RIKEN

hyb_protocol: Heat the Hybridization Cocktail at 99°C for 5 minutes. Cool to 45°C for 5 minutes. Inject the appropriate amount of the specific sample into the Affymetrix Mouse Genome 430 2.0 array through one of the septa. Place array in 45°C hybridization oven, at 60 rpm, and incubate for 16 hours.

scan_protocol: GeneChip Scaner 3000 was used . The core software was used GCOS for image processing.

data_processing: The summarized probe set data were generated using Expression console. Analyzing algorithm for the data was MAS5 by Affymetrix.

source_name: embryonic fibroblasts

label_protocol: The ds-cDNA derived from total RNA was incubated at 37℃ for 16hr with both IVT Labeling NTP mix and IVT Labeling Enzyme Mix to synthesize Biotin-Labeled cRNA.

growth_protocol: MEFs were cultured in Dulbecco’s minimal essential medium containing 10% fetal calf serum and 1% (w/v) penicillin/streptomycin on gelatin-coated dishes at 37˚C and 5% CO2.

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

value: embryonic day 12.5

tag: passage no.


title: Ramos cell line, replicate 1

status: Public on May 31 2013

city: Pamplona

first: Victor

last: Segura

state: Navarra

address: Avda. Pío XII, 55

department: Unit of Proteomics, Genomics and Bioinformatics

country: Spain

institute: FIMA

description: Gene expression data from Ramos cell line

hyb_protocol: Labeled sense cDNA was hybridized to the Affymetrix HuGene-1_0-st chip according to the the manufacturer protocols and using GeneChip® Hybridization, Wash and Stain Kit.

scan_protocol: Genechips were scanned with the Affymetrix GeneChip® Scanner 3000.

data_processing: The data were normalized with R 2.15 and Bioconductor 2.10 software using RMA algorithm.

source_name: Human B lymphocyte cell line (Burkitt's lymphoma)

label_protocol: The sense cDNA was prepared from 300 ng of total RNA using the Ambion® WT Expression Kit. The sense strand cDNA was then fragmented and biotinylated with the Affymetrix GeneChip® WT Terminal Labeling Kit (PN 900671).

growth_protocol: Cells were grown under standard conditions.

extract_protocol: The cells were harvested with TRIzol Reagent (Invitrogen)  and the RNA was extracted according to the manufacturer's instructions. As a last step of the extraction procedure, the RNA was purified with the RNeasy Mini-kit (Qiagen, Hilden, Germany).

treatment_protocol: No treatment has been applied.

tag: cell line

value: Ramos


title: wild type MEF

tag: genotype

value: wild type


title: Ramos cell line, replicate 2


title: MCF7 cell line, replicate 1

description: Gene expression data from MCF7 cell line

source_name: Human epithelial cell line (breast cancer)


title: CCD18 cell line, replicate 2

description: Gene expression data from CCD18 cell line

source_name: Human fibroblast cell line (colon)


title: CCD18 cell line, replicate 3


title: MCF7 cell line, replicate 3


title: MCF7 cell line, replicate 2


title: 75nm PVP_2

city: Durham

first: William

last: Ward

address: 109 TW Alexander Dr

department: NHEERL

institute: United States EPA

description:
5665167012_K
replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with no background subtraction in Illumina GenomeStudio (V.2011.1).

organism: Rattus norvegicus

source_name: RBEC4_75nm PVP

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep RNA Amplification kit for Illumina arrays

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit with DNase I treatment in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser and quantified by NanoDrop spectrophotometer.

value: Rat blood-brain barrier cells

tag: exposed to

value: 1.0 ppm PVP coated nanosilver particles (75nm)


title: 10nm Citrate_2

description:
5665167012_G
replicate 2

source_name: RBEC4_10nm Citrate

value: 1.0 ppm citrate coated nanosilver particles (10nm)


title: 10nm Citrate_1

description:
5665167012_H
replicate 1


title: 10nm PVP_3

description:
5665167012_I
replicate 3

source_name: RBEC4_10nm PVP

value: 1.0 ppm PVP coated nanosilver particles (10nm)


title: CCD18 cell line, replicate 1


title: 10nm PVP_4

description:
5665167012_J
replicate 4


title: 75nm Citrate_5

description:
5665167004_J
replicate 5

source_name: RBEC4_75nm Citrate

value: 1.0 ppm citrate coated nanosilver particles  (75nm)


title: 10nm Citrate_3

description:
5665167004_K
replicate 3


title: 10nm PVP_5

description:
5665167004_L
replicate 5


title: 75nm Citrate_4

description:
5665167012_B
replicate 4


title: 10nm Citrate_5

description:
5665167012_A
replicate 5


title: 10nm Citrate_4

description:
5665167004_H
replicate 4


title: 75nm PVP_5

description:
5665167004_I
replicate 5


title: Control_1

description:
5665167012_L
replicate 1


title: 75nm Citrate_3

description:
5665167012_F
replicate 3


title: Control_4

description:
5665167012_D
replicate 4


title: 10nm PVP_1

description:
5665167012_E
replicate 1


title: Control_2

description:
5665167012_C
replicate 2


title: Control_3

description:
5665167004_G
replicate 3


title: 10nm PVP_2

description:
5665167004_F
replicate 2


title: 75nm Citrate_1

description:
5665167004_E
replicate 1


title: 75nm PVP_4

description:
5665167004_B
replicate 4


title: 75nm PVP_1

description:
5665167004_A
replicate 1


title: 75nm Citrate_2

description:
5665167004_C
replicate 2


title: NHDF3284 - Ad fem

status: Public on Apr 01 2013

city: Los Angeles

last: Lowry

state: CA

address: 621 Charles Young

institute: UCLA

hyb_protocol: Labeled cRNA was mixed with hybridization mix according to Affymetrix protocol and hybridized in Affymetrix GeneChip hybridization oven 645 at 45C for 16 hours with rotation at 60 rpm

scan_protocol: Scanning was performed on Affymetrix 7G scanner with target intensity 500

data_processing: Cel files were imported into Genespring and RMA normalized.  Probesets not expressed in at least 10% of samples were eliminated

source_name: wildtype fibroblasts

label_protocol: Labeling was performed with Ambion MESSAGEAMP PREMIER kit (cat#: 4383452)

growth_protocol: all grown in standard conditions: hESC/hiPSC (in KO serum replacer, hESC media), FBs (Dmem +10% FBS), NPCs (Dmem, N2, B27, Egf, Fgf)

extract_protocol: Cells were lysed, and run through Stratagene Total RNA isolation kit

value: FBs

tag: genotype/variation

value: wildtype fibroblasts


title: ES_day4, 25-45mer

status: Public on May 18 2013

type: SRA

city: Boston

first: Mark

middle: L

last: Borowsky

address: 185 Cambridge Street

department: Molecular Biology

institute: MGH

library_source: transcriptomic

data_processing: Sequences were aligned to the mouse genome, NCBI Build 37, using the ShortQueryLookup program that is part of the Broad Institute’s Arachne package, with a maximum error tolerance of one with no insertions or deletions.   Alignments to other sequences were performed using BLAST.

source_name: ES cells

extract_protocol: Total RNA was isolated using Trizol from differentiating female ES cells at day 4, size-fractionated (18-24 nt and 25-45 nt), adaptor ligated, reverse transcribed, PCR amplified for 26 cycles, gel purified, and PCR amplified for 10-15 cycles using 454 PCR primers.

tag: developmental stage

value: day 4

tag: gender

value: female


title: H1 p60

source_name: wildtype hESCs

value: hESC

value: wildtype hESCs


title: NHDF17914 - Ad fem


title: HSF1 NPC p1 (1)

source_name: NPCs derived from hiPSCs

value: NPC

value: NPCs derived from hESCs


title: LP pancreas, biological rep2

tag: strain

value: Balb/C

tag: tissue

value: pancreas

tag: age

value: 30 days old

value: Isocaloric low protein diet

value: sham


title: NHDF3535 p5b - Ad fem


title: ES_day4, 18-24mer


title: hiPSC-E NPC p1

source_name: NPCs derived from hESCs

value: NPCs derived from hiPSCs


title: HSF1 p51b

value: hESCs


title: H9 p44


title: 10_231_T_H

city: Aachen

first: Bernd

last: Denecke

state: NRW

address: Pauwelsstrasse 30

department: IZKF Aachen

institute: RWTH Aachen University

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 45° for 5 minutes centrifuge at max speed for 1 minute • Transfer 80μl of hyb solution to each array, then tape holes • Hybridize 16 hours at 45° at 60rpm • Fluidics washing is FS450_00007

scan_protocol: according to Affymetrix protocol - Affymetrix Gene ChIP Scanner 3000 7G

data_processing: normalization method: RMA; raw expression threshold: 150, dabg p: 0.05; expression data format: log2

source_name: Tak1/Caspase8 LPC double knockout mice

label_protocol: Samples were amplified and labelled using the Ambion® WT Expression Kit, combined with the GeneChip® WT Terminal Labeling and Controls Kit according to the manufacturers instructions.

growth_protocol: Liver tissue, excised of 6 week old male mice

extract_protocol: RNA was extracted from snap frozen tissue using the Qiagen RNeasy Kit

value: Tak1/Caspase8 LPC double knockout mice

value: male

value: liver

value: 6 weeks


title: H9  NPC p1

source_name: neural progenitor cell

value: hNPC


title: NHDF3975 - Ad fem

value: FBs

value: wildtype fibroblasts


title: IMR90 - EMB fem


title: NHDF17430 - Ad fem


title: hiPSC E

source_name: wildtype hiPSCs

value: hiPSC

value: wildtype hiPSCs


title: 9_229_T_H


title: 8_221_T_H


title: white_cells_a/alpha

status: Public on Jan 23 2013

city: Foster City

first: Brian

last: Tuch

address: 850 Lincoln Center Dr.

institute: Life Technologies

description:
Strand-specific RNA-Seq.
Strain QMY23 (PMID: 17351132).
Poly(A) RNA.

data_processing:
AB WT Analysis Pipeline.

The reads were aligned to the Candida albicans Assembly 21 (Ca21) genome (from Candida Genome Database [CGD]: www.candidagenome.org) using the alignment algorithm provided by the WT Pipeline v1.2 (Life Technologies) and documented in their manual. The reads were filtered against a database containing rDNA, tRNA, repetitive element, CEN and adapter sequences. Alignments are provided in MAX format. A MAX specification file is available on the Series GSE21291 record.

The WIG files were generated by counting the number of uniquely aligned reads covering each position in the genome. The coverage on the plus and minus strands are provided in the *plus.wig and *minus.wig files, respectively.

Genome_build: Ca21
Supplementary_files_format_and_content: MAX files: alignments. WIG files: Coverage on plus and minus strands.

organism: Candida albicans

source_name: Candida albicans white a/alpha cells

growth_protocol: 23°C; SC medium (PMID: 12073320) with 100 mg/l uridine; log-phase growth (OD600=1).

extract_protocol:
Total RNA was extracted from the yeast cells (Hernday AD, Noble SM, Mitrovich QM, Johnson AD (2010) Genetics and Molecular Biology in Candida albicans. Methods in Enzymology: Elsevier Inc. pp. 737-758).

Two rounds of poly(A) selection with Poly(A)Purist MAG kit (Ambion). SOLiD whole transcriptome (WT) protocol applied to poly(A)-selected RNA.

treatment_protocol: None.

tag: isolate

value: MTLa/MTLalpha

value: white

tag: growth type

value: culture

tag: rna preparation

value: poly(A) RNA selection


title: MC3T3-E1 (control-1)

status: Public on Mar 26 2013

city: Toyama

first: Yoshiaki

last: Tabuchi

state: Toyama

address: 2630 Sugitani

department: Life Science Research Center

institute: University of Toyama

description:
Ctr-1
MC3T3-E1 mock treatment (control-1).
MC3T3-E1 cell line: derived from the calvaria of 0-day-old newborn mice; fibroblast-like morphology; infinite lifespan.

hyb_protocol: After fragmentation, the biotinylated cRNA was hybridized to arrays at 45°C for 16 h. The arrays were washed and stained with streptavidin-phycoerythrin.

scan_protocol: The arrays were scanned with a probe array scanner (Affymetrix).

data_processing: GeneChip Analysis Suite. RMA normalized.

source_name: Mouse preosteoblast MC3T3-E1 cells, mock treated

label_protocol: 500 ng of total RNA was used to synthesize cRNA with a GeneChip 3' IVT Express Kit (Affymetrix).

growth_protocol: The cells were cultured in MEMα supplemented with 10% fetal bovine serum (FBS) at 37˚C in humidified air with 5% CO2.

extract_protocol: Total RNA was extracted from cells using an RNeasy Total RNA Extraction kit (Qiagen), and treated with DNase I (Qiagen) for 15 min at room temperature to remove residual genomic DNA. RNA quality was analyzed using a Bioanalyzer 2100 (Agilent Technologies), producing RIN values between 9.5 and 10.

treatment_protocol: LIPUS treatment was applied by a sonic accelerated gracture-healing system (SAFHS) apparatus (SAFHS 4000J, Teijin Pharma Ltd., Tokyo, Japan). The signal had the SATA (spatial average, temporal average) intensity of 30 mW/cm2, with a frequency of 1.5 MHz in a pulsed-wave mode (0.2 s-burst sine waves repeated at 1.0 kHz). The cells were cultivated in MEMα supplemented with 10% FBS, 0.3 mM L-ascorbic acid and 10 mM β-glycerophosphate at 37˚C for 14 days. After trypsinization, the cells (5 x 10^5 cells) were seeded on 35-mm plastic culture dish (ASAHI GLASS Co., Ltd., Tokyo, Japan) and cultured at 37˚C for 24 h. LIPUS was transmitted through the bottom of the culture dish with standard ultrasound coupling gel (Teijin Pharma Ltd.). Attached cells in the dish with 2 ml of culture medium were sonicated for 20 min at 37˚C in a CO2 incubator. After sonication, cells were incubated at 37˚C in a CO2 incubator for 6 and 24 h. Mock-treated cells served as the control.

value: preosteoblasts

value: mock

tag: time

value: control


title: Normal breast Affymetrix 3

status: Public on Mar 01 2013

city: Bethesda

first: GEO

last: admin

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: The data were analyzed with Partek GS 6.5 and GCRMA as normalization method.

source_name: Normal Breast tissue

label_protocol: 1ng total RNA was used as input for the Pico amplification and 4ug of amplified cDNA was used for Exon Module amplification. cDNA amplification products were fragmented and labeled with biotin using the NuGEN FL module, hybridized to HG Gene 1.0 ST arrays (Affymetrix Inc., Santa Clara, CA, USA) using Affymetrix Hybridization Control Kit. And washed and stained using Affymetrix Wash and Stain kit. All steps were processed following the manufactures suggestions.

extract_protocol: RNA samples for amplification with the Pico kit were isolated from fresh tissues using the RNeasy Micro Kit (Qiagen) including the optional DNase treatment, according to the manufacturer's instructions. Total RNA was quantified using a Nanodrop Spectrophotometer 2000 (Thermo Scientific Inc., Waltham, MA, USA) and the quality confirmed on an Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). RNA amplifications were carried out using Nugen Pico WTA amplification system according to the manufacturersâ€™ suggestions followed by an additional amplification step using Nugen Exon Module.

value: normal breast

tag: histological type

value: Normal

tag: age (y)

tag: grade

tag: site

tag: er   (1= positive, 0=nagative)

tag: pr   (1= positive, 0= negative)

tag: her2  (1=positive, 0=negative)

tag: triple negative (1= yes, 0= no)


title: 4_256_T_R3

source_name: Tak1 LPC-KO/Rip3-/- mice

tag: genotype

value: Tak1 LPC-KO/Rip3-/- mice

value: male


title: MC3T3-E1 LIPUS-24 h 2

description:
US-2
MC3T3-E1 LIPUS + 24h culture at 37˚C-2.
MC3T3-E1 cell line: derived from the calvaria of 0-day-old newborn mice; fibroblast-like morphology; infinite lifespan.

source_name: Mouse preosteoblast MC3T3-E1 cells, LIPUS treated

tag: cell line

tag: cell type

tag: treatment

value: low-intensity pulsed ultrasound (LIPUS)


title: Ramos cell line, replicate 3

source_name: Human B lymphocyte cell line (Burkitt's lymphoma)

value: Ramos


title: Normal breast Affymetrix 1

tag: tissue


title: CMV 2b IPed sRNA from Arabidopsis floral part

status: Public on Jan 18 2013

city: beijing

first: sadia

last: hamera

address: state key lab of plant genomics

institute: chinese academy of sciences

description: CMV 2b IP from 2b transgenic Arabidpsis lines with α-2b antibodies

data_processing: Alignment: Sequence reads were aligned to arabidopsis genome (http://www.arabidopsis.org) using blastn.The small RNAs with perfect genome matches were selected for further analysis

organism: Arabidopsis thaliana

source_name: Inflorescence

growth_protocol: Arabidopsis Col-0 was first transformed with Cucumber Mosaic virus suppressor 2b. T3 lines used for analysis.

extract_protocol: 2b suppressor protein was immuoprecipitated from floral part of arabidopsis transgenic lines with anti 2b antibodies. 2b IP was next subjected to RNA extraction, and resolved on PAGE gel. sRNAs 0f 16-30 nt length were gel purified and ligated to 5′and 3′adapters. After RT-PCR samples were sequenced through Ilumina IG .

value: Inflorescence

tag: antibody

value: Anti 2b IP

tag: background strain


title: MC3T3-E1 LIPUS-24 h 3

description:
US-3
MC3T3-E1 LIPUS + 24h culture at 37˚C-3.
MC3T3-E1 cell line: derived from the calvaria of 0-day-old newborn mice; fibroblast-like morphology; infinite lifespan.

tag: strain