title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_227

description: Group HSS

source_name: High School Students_Fecal


title: Tularensis monoclonal Tularensis_2

status: Public on Jan 16 2014

type: protein

city: Tempe

first: Phillip

last: Stafford

state: Arizona

address: 727 E. Tyler St.

department: Biodesign Institute

country: USA

institute: Arizona State University

description:
Alexa-647 conjugated Streptavidin tertiary
Tularensis_2

hyb_protocol: Antibodies were incubated with the peptide microarrays for 1 hour at room temperature according to Stafford et al. (Stafford, Halperin, Legutki, Magee, Galgiani, Johnston, Physical characterization of the Immunosignaturing Effect, MCP 11(4), 2012).

scan_protocol: Scanning was done on an Innopsys Innoscan 910 at 10um resolution, high laser power, 70% PMT, autofocus ON, 545nm.

data_processing: Median normalization per slide was done, and any negative values were adjusted to 0.01.

label: biotinylated anti-mouse IgG

molecule: protein

organism: Mus musculus

source_name: Tularensis

label_protocol: Alexafluor 647-labeled Streptavidin was used to detect biotinylated anti-mouse secondary antibody.

tag: antibody

value: Tularensis monoclonal


title: Hu_Anhui01_pCalu3_7h_4

type: RNA

city: Seattle

first: Michael

last: Katze

state: WA

address: Rosen Building 960 Republican St.

department: Microbiology

institute: University of Washington

hyb_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for all processing steps, including Cy3-cDNA probe preparation, hybridization and array washing.

scan_protocol: Dry slides were scanned on an Agilent DNA microarray scanner (Model G2505B) using the XDR setting.

data_processing: After control probes filtering : 58,717 probes including 8118 duplicated probes 3. After SUMMARIZATION OF non-CTRL PROBES: 50,599 probes 4. Filtering of probes: we require that the probes pass the following QC in at least 100% samples of 1 infected time-point: gIsFound, gIsWellAboveBG, gIsSaturated: no probe was excluded based on that criteria, gIsFeatNonUnifOL, and gIsFeatPopnOL. Probes passing qc: 29,382 probes only.

molecule: total RNA

organism: Homo sapiens

source_name: Human, virus, polarized calu-3 cells, timepoint, replicate

label_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for the Cy3-cDNA probe preparation, followed by RNeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: The human bronchial epithelial cell line Calu-3 was originally derived from subbronchial epithelium of a lung adenocarcinoma (ATCC) and cells were grown in Eagle's minimal essential medium (MEM) supplemented with 2 mM l-glutamine, 1 mM sodium pyruvate, 0.1 mM nonessential amino acids, 1.5 g/liter sodium bicarbonate, and 10% fetal bovine serum. Calu-3 cells (5 × 105) were seeded onto Corning 24-mm-diameter semipermeable membrane inserts with a 0.4-μm pore size (Corning, NY) and cultured for 1 week with the addition of fresh culture medium every 2 to 3 days.  Confluent monolayers of polarized Calu-3 achieving stable transepithelial resistance were infected apically at a MOI of 1. After a 1-hour incubation, monolayers were washed to remove nonadherent virus and 2 ml of MEM-BSA was added to both apical and basolateral reservoirs of cells and left for the duration of the experiment.

extract_protocol: All Trizol lysates were processed simultaneously: they were phase-separated, and RNA was isolated from the aqueous phase (diluted 2 fold with RLT buffer) using Qiagen RNeasy Mini columns and the manufacturer’s recommended protocol (Qiagen Inc., Valencia, CA). RNA quality was assessed on an Agilent 2100 Bioanalyzer using the nanochip format, and only intact RNA was used for microarray analyses.

tag: cell line

value: polarized Calu3 cells

tag: infection

tag: time


title: CHI7

city: Sydney

first: daniel

last: murray

address: cnr West and Boundary Streets

country: Australia

institute: Kirby Institute

description: MicroRNA profile of monocytes

hyb_protocol: Cy3 labelled RNA was hybridized to the slide overnight in rotating incubator at 37 degrees celsius

scan_protocol: Scanning was performed using an agilent G2505B scanner

data_processing: Data was uploaded to CaArray by the Peter Wills Bioinformatics centre at the Garvan Institute before it was analyzed on the online bioinformatics program Genepattern. Data was first filtered for miRNA expressed in more than 4 patients across all patient groups before being run on the Limma and Comparative Marker Selection Modules which determine statistical difference while accounting for multiple testing.

source_name: miRNA extracted from monocytes

label_protocol: 100ng total RNA used, dephosphorylated and labelled with Cy3 as per manufacturer's recommendations

extract_protocol: Monocytes were extracted from PBMCs by positive selection using MACS CD14 magnetic beads and separation columns (Miltenyi Biotec, Cologne area, Germany. RNA was then extracted using a miRNeasy mini kit (Qiagen, Hilden, Germany)

tag: cell type

value: Monocytes

tag: disease status

value: Chronic HIV patient


title: Tularensis monoclonal Tularensis_1

description:
Alexa-647 conjugated Streptavidin tertiary
Tularensis_1


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_225

type: genomic

city: Beijing

first: Yongfei

last: Hu

address: NO.1 West Beichen Road, Chaoyang District

department: CAS key Laboratory of Pathogenic Microbiology and Immunology

country: China

institute: Institute of Microbiology, Chinese Academy of Sciences

description: Group HSS

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

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

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

molecule: genomic DNA

organism: human gut metagenome

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

growth_protocol: All fecal samples were collected from healthy volunteers in Hangzhou,China. All the volunteers were required not to take any antibiotic agent in the past three months.

extract_protocol: DNA from gut microbiomes was extracted directly from each fecal sample using QIAamp DNA stool mini kit according to the manufacturer’s suggested protocol.

treatment_protocol: All the fecal samples were stored in -80°C ultra low temperature refrigerator before DNA extracton.

tag: gender

value: Femal

tag: age

tag: molecule type

value: Metagenomic DNA


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_226

description: Group HSS


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_224

description: Group HSS


title: Treponema monoclonal Treponema_2

description:
Alexa-647 conjugated Streptavidin tertiary
Treponema_2

source_name: Treponema

value: Treponema monoclonal


title: LTNP6

description: MicroRNA profile of monocytes

value: Long-term nonprogressor


title: CHI6

description: MicroRNA profile of monocytes


title: Treponema monoclonal Treponema_1

description:
Alexa-647 conjugated Streptavidin tertiary
Treponema_1


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_223

description: Group HSS


title: LTNP5

description: MicroRNA profile of monocytes


title: Toxoplasma monoclonal Toxoplasma_2

description:
Alexa-647 conjugated Streptavidin tertiary
Toxoplasma_2

source_name: Toxoplasma

value: Toxoplasma monoclonal


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_228

description: Group HSS


title: Hu_Anhui01_pCalu3_7h_1

treatment_protocol: Confluent monolayers of polarized Calu-3 achieving stable transepithelial resistance were infected apically at a MOI of 1. After a 1-hour incubation, monolayers were washed to remove nonadherent virus and 2 ml of MEM-BSA was added to both apical and basolateral reservoirs of cells and left for the duration of the experiment.


title: CHI5

description: MicroRNA profile of monocytes


title: Toxoplasma monoclonal Toxoplasma_1

description:
Alexa-647 conjugated Streptavidin tertiary
Toxoplasma_1


title: Hu_Anhui01_pCalu3_7h_2


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_220

description: Group HSS

value: Male


title: TB monoclonal TB_1

description:
Alexa-647 conjugated Streptavidin tertiary
TB_1

source_name: TB

value: TB monoclonal


title: TB monoclonal TB_2

description:
Alexa-647 conjugated Streptavidin tertiary
TB_2


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_215

description: Group HSS


title: Hu_Anhui01_pCalu3_3h_1


title: LTNP3

description: MicroRNA profile of monocytes


title: CHI4

description: MicroRNA profile of monocytes


title: Smallpox monoclonal Smallpox_2

description:
Alexa-647 conjugated Streptavidin tertiary
Smallpox_2

source_name: Smallpox

value: Smallpox monoclonal


title: HC6

description: MicroRNA profile of monocytes

value: healthy control


title: ML RA 6_12d 0106011728(10)

city: Hannover

first: Juergen

last: Borlak

state: Lower Saxony

address: Feodor-Lynen-Str. 35

department: Centre for Pharmacology and Toxicology

country: Germany

institute: Hannover Medical School

description:
ML RA 6_12d 0106011728(10) 106011728(10)
Cy3-channel pictures and correspondig raw data are marked by an 1b at the end of the file name
Cy5-channel pictures and correspondig raw data are marked by an 2b at the end of the file name

hyb_protocol: signal quantification of hybridized PIQORTM cDNA arrays were performed with the ScanArray3000 (GSI Lumonics, Watertown, MA).

scan_protocol: images were quantified and analysed by ImaGene software version 4.1 (Bio Discovery, Los Angeles, CA)

data_processing: LOWESS normalization

organism: Rattus norvegicus

source_name: vehicle

label_protocol: 2 µl of FluoroLinkTM Cy3and Cy5-dCTP (Amersham Pharmacia Biotech, Freiburg, Germany), 4 µl of 0.1 M DTT and 1 µl of RNasin (20–40 U) (Promega), One µl (200 U) of Superscript TM II enzyme was added, incubated at 42°C for 30 min followed by the addition of a further 1 µl of SSII enzyme and again incubated in the same conditions.50 µl of  equal volume of 2x hybridization solution (MEMOREC) pre-warmed to 42°C was added to the cy3 and cy5 labelled samples. Hybridization was performed according to manufacturer's guidelines (MEMOREC) using a Gene TACTM hybridization station (Perkin Elmer, Langen, Germany).

growth_protocol: Pregnant female Wistar rats were dosed daily with either EMD 82571 (50 or 150 mg/kg/day, low and high dose of EMD, respectively) or retinoic acid (12 mg/kg/day) on gestational days 6-11 and 6-17, respectively.

extract_protocol: The mRNA was then reverse-transcribed by adding it to a mix consisting of 8 µl of 5x first-strand buffer (Invitrogen), 2 µl of Primer-Mix [oligo (dT) and randomeres] (MEMOREC, Köln, Germany), 2 µl of low C dNTPs (10 mM dATP, 10 mM dGTP, 10 mM dTTP, 4 mM dCTP).

treatment_protocol: One hundred µg of total RNA was combined with control RNA consisting of an in vitro-transcribed Escherichia coli genomic DNA fragment carrying a 30 nucleotide poly(A)+tail (CR1) and the resulting mRNA was subsequently isolated using Oligotex mRNA Mini Kit (Qiagen).

tag: tissue

value: Maternal Liver

tag: treatment

value: vehicle

tag: strain

value: Wistar

source_name: Maternal Liver 20mg RA 12day

value: 20mg RA


title: HC5

description: MicroRNA profile of monocytes


title: LTNP4

description: MicroRNA profile of monocytes


title: Smallpox monoclonal Smallpox_1

description:
Alexa-647 conjugated Streptavidin tertiary
Smallpox_1


title: EMD_EL_50_20d 2905010941(06)

description:
EMD_EL_50_20d 2905010941(06) 2905010941(06)
Cy3-channel pictures and correspondig raw data are marked by an 1b at the end of the file name
Cy5-channel pictures and correspondig raw data are marked by an 2b at the end of the file name

value: Embryo Liver

source_name: Embryo Liver 50mg EMD 20day

value: 50mg EMD


title: Hu_Anhui01_pCalu3_3h_4

value: polarized Calu3 cells


title: Hu_Anhui01_pCalu3_3h_2


title: Hu_Anhui01_pCalu3_24h_4


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_214

description: Group HSS


title: Hu_Anhui01_pCalu3_24h_2


title: SM1470P monoclonal SM1470P_2

description:
Alexa-647 conjugated Streptavidin tertiary
SM1470P_2

value: SM1470P monoclonal


title: HC4

description: MicroRNA profile of monocytes

value: Monocytes


title: Hu_Anhui01_pCalu3_3h_3


title: Hu_Anhui01_pCalu3_24h_3


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_211

description: Group HSS

value: Metagenomic DNA


title: Hu_Anhui01_pCalu3_24h_1


title: HC3

description: MicroRNA profile of monocytes


title: Rubella monoclonal Rubella_2

description:
Alexa-647 conjugated Streptavidin tertiary
Rubella_2

source_name: Rubella

value: Rubella monoclonal


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_210

description: Group HSS

value: Femal


title: HC2

description: MicroRNA profile of monocytes


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_212

description: Group HSS


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_213

description: Group HSS


title: Rubella monoclonal Rubella_1

description:
Alexa-647 conjugated Streptavidin tertiary
Rubella_1


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_203

description: Group HSS


title: CHI3

description: MicroRNA profile of monocytes

value: Chronic HIV patient


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_204

description: Group HSS


title: Hu_Anhui01_pCalu3_12h_3


title: SM1470P monoclonal SM1470P_1

description:
Alexa-647 conjugated Streptavidin tertiary
SM1470P_1


title: Rotovirus monoclonal Rotovirus_1

description:
Alexa-647 conjugated Streptavidin tertiary
Rotovirus_1

source_name: Rotovirus

value: Rotovirus monoclonal


title: Rotovirus monoclonal Rotovirus_2

description:
Alexa-647 conjugated Streptavidin tertiary
Rotovirus_2


title: LTNP2

description: MicroRNA profile of monocytes

value: Long-term nonprogressor


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_202

description: Group HSS

value: Male


title: Hu_Anhui01_pCalu3_12h_2


title: shCHD4#2631-DAY5 [MA55]

city: New York

first: Milan

middle: Girish

last: Chheda

state: NY

address: 408 E. 69th Street

department: Neurology

institute: Memorial Sloan-Kettering Cancer Center

description: Gene expression after TIC treated by shCHD4 #2632 for 5 days

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133plus 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The CEL files were preprocessed and normalized with the aroma package (http://aroma-project.org/) using CDF file (HG-U133_Plus_2) from The Cancer Genome Atlas (https://tcga-data.nci.nih.gov/tcga/tcgaPlatformDesign.jsp).

label: biotin

source_name: glioblastoma TICs

label_protocol: Complementary RNA synthesis and labeling/hybridization/scanning of U133 plus 2.0 microarrays using GeneChip products (Affymetrix) was done as described in the GeneChip manual (see below fields).

growth_protocol: Cells were grown in NBE media, as described in Lee, J., Kotliarova, S., Kotliarov, Y., Li, A., Su, Q., Donin, N.M., Pastorino, S., Purow, B.W., Christopher, N., Zhang, W., et al. (2006). Tumor stem cells derived from glioblastomas cultured in bFGF and EGF more closely mirror the phenotype and genotype of primary tumors than do serum-cultured cell lines. Cancer Cell 9, 391-403.

extract_protocol: We extracted total RNA at 3 days and 5 days after transduction of 0308 TICs with control, CHD4-, or ZFHX4-targeting shRNAs, from 3 (for CHD4) or 5 (ZFHX4) independent experiments. RNA was harvested using Trizol RNA isolation reagent (Life Technologies), DNase I digestion, and RNeasy MinElute Cleanup Kit (Qiagen) following manufacturer’s protocols. We performed synthesis of complementary RNA from total RNA and hybridization/scanning of U133 plus 2.0 microarrays using GeneChip products (Affymetrix) as described in the GeneChip manual.

treatment_protocol: Samples were transduced with shRNAs targeting control (shLACZ#1935), CHD4 (either shCHD4#716 or shCHD4#2631), or ZFHX4 (either shZFHX4#289 or ZFHX4#9674), selected with puromycin, and harvested at the indicated time point (day 3 or day 5)

value: glioblastoma tumor initiating cell


title: RMB14 monoclonal RMB14_2

description:
Alexa-647 conjugated Streptavidin tertiary
RMB14_2

value: RMB14 monoclonal


title: RBM14 monoclonal RBM14_1

description:
Alexa-647 conjugated Streptavidin tertiary
RBM14_1

value: RBM14 monoclonal


title: Hu_Anhui01_pCalu3_12h_4


title: LTNP1

description: MicroRNA profile of monocytes


title: CHI1

description: MicroRNA profile of monocytes


title: shCHD4#716-DAY5 [MA54]

description: Gene expression after TIC treated by shCHD4 #716 for 5 days


title: Rabies monoclonal Rabies_3

description:
Alexa-647 conjugated Streptavidin tertiary
Rabies_3

source_name: Rabies

value: Rabies monoclonal


title: CHI2

description: MicroRNA profile of monocytes


title: HC1

description: MicroRNA profile of monocytes

value: healthy control


title: Rabies monoclonal Rabies_2

description:
Alexa-647 conjugated Streptavidin tertiary
Rabies_2


title: Hu_Anhui01_pCalu3_12h_1


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_199

description: Group HSS


title: shLACZ#1935-DAY5 [MA53]

description: Gene expression after TIC treated by shLACZ #1935 for 5 days


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_200

description: Group HSS


title: Rabies monoclonal Rabies_1

description:
Alexa-647 conjugated Streptavidin tertiary
Rabies_1


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_198

description: Group HSS


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_201

description: Group HSS


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_197

description: Group HSS


title: shCHD4#2631-DAY5 [MA52]


title: Plasmodium monoclonal Plasmodium_2

description:
Alexa-647 conjugated Streptavidin tertiary
Plasmodium_2

source_name: Plasmodium

value: Plasmodium monoclonal


title: Plasmodium monoclonal Plasmodium_1

description:
Alexa-647 conjugated Streptavidin tertiary
Plasmodium_1


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_195

description: Group HSS


title: shLACZ-#1935-DAY5 [MA50]


title: PJNK monoclonal PJNK_2

description:
Alexa-647 conjugated Streptavidin tertiary
PJNK_2

source_name: PJNK

value: PJNK monoclonal


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_196

description: Group HSS

source_name: High School Students_Fecal


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_194

description: Group HSS


title: shCHD4#2631-DAY5 [MA49]


title: shCHD4#716-DAY5 [MA48]


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_192

description: Group HSS


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_193

description: Group HSS


title: shCHD4#716-DAY5 [MA51]


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_190

description: Group CH

source_name: pre-school Children_Fecal


title: PJNK monoclonal PJNK_1

description:
Alexa-647 conjugated Streptavidin tertiary
PJNK_1


title: HC8

description: MicroRNA profile of monocytes


title: PBEF monoclonal PBEF_2

description:
Alexa-647 conjugated Streptavidin tertiary
PBEF_2

source_name: PBEF

value: PBEF monoclonal


title: shLACZ#1935-DAY5 [MA47]


title: plasma＿healthy control7＿rep1

city: Nanjing

first: Lijuan

last: Chen

address: 300 Guangzhou Road

institute: the First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital

description: miRNA expression in plasma of healthy control

hyb_protocol: Each slide was hybridized with 100ng Cy3-labeled RNA using miRNA Complete Labeling and Hyb Kit(Cat#5190-0456, Agilent technologies, Santa Clara, CA, US)in hybridization Oven(Cat#G2545A, Agilent technologies, Santa Clara, CA, US)at 55℃，20rpm for 20 hours according to the manufacturer’s instructions, hybridization section. After hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US).

scan_protocol: Slides were scanned by Agilent Microarray Scanner(Cat#G2565BA，Agilent technologies, Santa Clara, CA, US)

data_processing: The scanned images were analyzed with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US)with default settings. Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0(Agilent technologies, Santa Clara, CA, US).

source_name: plasma, healthy control

label_protocol: miRNA molecular in total RNA was labeled by miRNA Complete Labeling and Hyb Kit(Cat#5190-0456, Agilent technologies, Santa Clara, CA, US)followed the manufacturer’s instructions, labeling section.

growth_protocol: Peripheral blood was collected into EDTA tubes

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

treatment_protocol: Plasma was obtained by centrifugation from the EDTA tubes at 1500rpm,for 5min.The plasma samples were stored at −80°C until analysis

tag: disease state

value: female

value: plasma


title: plasma＿healthy control6＿rep1


title: shZFHX4#9674-DAY5 [MA45]

description: Gene expression after TIC treated by shZFHX4 #9674 for 5 days


title: plasma＿healthy control5＿rep1


title: plasma＿healthy control4＿rep1

value: male


title: Parvo monoclonal Parvo_2

description:
Alexa-647 conjugated Streptavidin tertiary
Parvo_2

source_name: Parvo

value: Parvo monoclonal


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_188

description: Group CH

value: Femal

value: Metagenomic DNA


title: shZFHX4#9674-DAY3 [MA41]

description: Gene expression after TIC treated by shZFHX4 #9674 for 3 days


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_189

description: Group CH


title: shLACZ#1935-DAY5 [MA43]


title: PBEF monoclonal PBEF_1

description:
Alexa-647 conjugated Streptavidin tertiary
PBEF_1


title: Parvo monoclonal Parvo_1

description:
Alexa-647 conjugated Streptavidin tertiary
Parvo_1


title: plasma＿healthy control3＿rep1


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_187

description: Group CH


title: P. mallei monoclonal P. mallei_2

description:
Alexa-647 conjugated Streptavidin tertiary
P. mallei_2

source_name: P. mallei

value: P. mallei monoclonal


title: plasma＿healthy control2＿rep1


title: P. mallei monoclonal P. mallei_1

description:
Alexa-647 conjugated Streptavidin tertiary
P. mallei_1


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_186

description: Group CH


title: shZFHX4#289-DAY5 [MA44]

description: Gene expression after TIC treated by shZFHX4 #289 for 5 days


title: shZFHX4#289-DAY5 [MA36]


title: shZFHX4#9674-DAY5 [MA37]


title: shLACZ#1935-DAY3 [MA39]

description: Gene expression after TIC treated by shLACZ #1935 for 3 days


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_185

description: Group CH


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_221

description: Group HSS


title: shZFHX4#289-DAY3 [MA40]

description: Gene expression after TIC treated by shZFHX4 #289 for 3 days


title: P. aureginosa monoclonal P. aureginosa_2

description:
Alexa-647 conjugated Streptavidin tertiary
P. aureginosa_2

source_name: P. aureginosa

value: P. aureginosa monoclonal


title: P. aureginosa monoclonal P. aureginosa_1

description:
Alexa-647 conjugated Streptavidin tertiary
P. aureginosa_1


title: shLACZ#1935-DAY5 [MA35]

description: Gene expression after TIC treated by shLACZ #1935 for 5 days


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_183

description: Group CH

value: Male


title: plasma＿patient9＿rep1

description: miRNA expression in plasma of MM patient

source_name: plasma, MM patient

value: MM


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_182

description: Group CH


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_184

description: Group CH


title: plasma＿healthy control1＿rep1


title: O157 monoclonal O157_2

description:
Alexa-647 conjugated Streptavidin tertiary
O157_2

value: O157 monoclonal


title: plasma＿patient7＿rep1


title: O157 monoclonal O157_1

description:
Alexa-647 conjugated Streptavidin tertiary
O157_1


title: Nesseria monoclonal Nesseria_2

description:
Alexa-647 conjugated Streptavidin tertiary
Nesseria_2

source_name: Nesseria

value: Nesseria monoclonal


title: Nesseria monoclonal Nesseria_1

description:
Alexa-647 conjugated Streptavidin tertiary
Nesseria_1


title: Mumps monoclonal Mumps_2

description:
Alexa-647 conjugated Streptavidin tertiary
Mumps_2

source_name: Mumps

value: Mumps monoclonal


title: plasma＿patient5＿rep1


title: plasma＿patient3＿rep1


title: plasma＿patient4＿rep1


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_179

description: Group CH


title: shZFHX4#289-DAY3 [MA32]

value: glioblastoma tumor initiating cell


title: shCHD4#2631-DAY3 [MA30]

description: Gene expression after TIC treated by shCHD4 #2632 for 3 days


title: shLACZ#1935-DAY3 [MA31]


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_180

description: Group CH


title: shLACZ-#1935-DAY3 [MA28]


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_181

description: Group CH


title: shZFHX4#9674-DAY3 [MA33]

description: Gene expression after TIC treated by shZFHX4 #9674 for 3 days


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_178

description: Group CH


title: plasma＿patient6＿rep1


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_177

description: Group CH


title: plasma＿patient8＿rep1


title: shCHD4#716-DAY3 [MA29]

description: Gene expression after TIC treated by shCHD4 #716 for 3 days


title: Mumps monoclonal Mumps_1

description:
Alexa-647 conjugated Streptavidin tertiary
Mumps_1


title: LNKB2 monoclonal LNKB2_2

description:
Alexa-647 conjugated Streptavidin tertiary
LNKB2_2

value: LNKB2 monoclonal


title: plasma＿patient2＿rep1


title: plasma＿patient1＿rep1


title: LNKB2 monoclonal LNKB2_1

description:
Alexa-647 conjugated Streptavidin tertiary
LNKB2_1


title: shCHD4#716-DAY3 [MA26]


title: shLACZ#1935-DAY3 [MA25]

description: Gene expression after TIC treated by shLACZ #1935 for 3 days


title: shCHD4#2631-DAY3 [MA27]


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_174

description: Group CH


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_173

description: Group CH


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_176

description: Group CH


title: Listeria monoclonal Listeria_2

description:
Alexa-647 conjugated Streptavidin tertiary
Listeria_2

source_name: Listeria

value: Listeria monoclonal


title: Listeria monoclonal Listeria_1

description:
Alexa-647 conjugated Streptavidin tertiary
Listeria_1


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_175

description: Group CH


title: shCHD4#2631-DAY3 [MA24]


title: HSV monoclonal HSV_2

description:
Alexa-647 conjugated Streptavidin tertiary
HSV_2

source_name: HSV

value: HSV monoclonal


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_172

description: Group CH


title: ICAM1 monoclonal ICAM1_1

description:
Alexa-647 conjugated Streptavidin tertiary
ICAM1_1

value: ICAM1 monoclonal


title: HSV monoclonal HSV_1

description:
Alexa-647 conjugated Streptavidin tertiary
HSV_1


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_170

description: Group CH


title: shZFHX4#289-DAY5 [MA19]

description: Gene expression after TIC treated by shZFHX4 #289 for 5 days


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_171

description: Group CH


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_168

description: Group CH


title: shLACZ#1935-DAY5 [MA18]

description: Gene expression after TIC treated by shLACZ #1935 for 5 days


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_169

description: Group CH


title: HIS monoclonal HIS_2

description:
Alexa-647 conjugated Streptavidin tertiary
HIS_2

source_name: HIS

value: HIS monoclonal


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_164

description: Group AD


title: shLACZ#1935-DAY3 [MA22]

source_name: glioblastoma TICs


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_163

description: Group AD


title: ICAM1 monoclonal ICAM1_2

description:
Alexa-647 conjugated Streptavidin tertiary
ICAM1_2


title: HIS monoclonal HIS_1

description:
Alexa-647 conjugated Streptavidin tertiary
HIS_1


title: shZFHX4#9674-DAY5 [MA20]

description: Gene expression after TIC treated by shZFHX4 #9674 for 5 days


title: shZFHX4#9674-DAY3 [MA17]

description: Gene expression after TIC treated by shZFHX4 #9674 for 3 days


title: shZFHX4#289-DAY3 [MA16]

description: Gene expression after TIC treated by shZFHX4 #289 for 3 days


title: H1V1 monoclonal H1V1_2

description:
Alexa-647 conjugated Streptavidin tertiary
H1V1_2

value: H1V1 monoclonal


title: shCHD4#716-DAY3 [MA23]

description: Gene expression after TIC treated by shCHD4 #716 for 3 days


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_162

description: Group AD


title: H1V1 monoclonal H1V1_1

description:
Alexa-647 conjugated Streptavidin tertiary
H1V1_1


title: shLACZ#1935-DAY3 [MA15]

description: Gene expression after TIC treated by shLACZ #1935 for 3 days


title: Ebola monoclonal Ebola_2

description:
Alexa-647 conjugated Streptavidin tertiary
Ebola_2

source_name: Ebola

value: Ebola monoclonal


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_137

description: Group AD

value: Femal


title: Ebola monoclonal Ebola_1

description:
Alexa-647 conjugated Streptavidin tertiary
Ebola_1


title: shZFHX4#9674-DAY5 [MA13]


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_142

description: Group AD

value: Metagenomic DNA


title: EB monoclonal EB_1

description:
Alexa-647 conjugated Streptavidin tertiary
EB_1

source_name: EB

value: EB monoclonal


title: DM1A monoclonal DM1A_2

description:
Alexa-647 conjugated Streptavidin tertiary
DM1A_2

value: DM1A monoclonal


title: DM1A monoclonal DM1A_1

description:
Alexa-647 conjugated Streptavidin tertiary
DM1A_1


title: shZFHX4#289-DAY5 [MA12]

description: Gene expression after TIC treated by shZFHX4 #289 for 5 days


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_134

description: Group AD


title: Diphtheria monoclonal Diphtheria_2

description:
Alexa-647 conjugated Streptavidin tertiary
Diphtheria_2

source_name: Diphtheria

value: Diphtheria monoclonal


title: EB monoclonal EB_2

description:
Alexa-647 conjugated Streptavidin tertiary
EB_2


title: shLACZ#1935-DAY5 [MA11]

description: Gene expression after TIC treated by shLACZ #1935 for 5 days


title: shZFHX4#289-DAY3 [MA9]


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_130

description: Group AD

value: Male


title: shZFHX4#9674-DAY5 [MA6]


title: shZFHX4#9674-DAY3 [MA10]


title: Dengue monoclonal Dengue_2

description:
Alexa-647 conjugated Streptavidin tertiary
Dengue_2

source_name: Dengue

value: Dengue monoclonal


title: Diphtheria monoclonal Diphtheria_1

description:
Alexa-647 conjugated Streptavidin tertiary
Diphtheria_1


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_129

description: Group AD


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_125

description: Group AD


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_126

description: Group AD


title: shLACZ#1935-DAY3 [MA8]


title: shLACZ#1935-DAY5 [MA4]


title: shZFHX4#289-DAY5 [MA5]


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_123

description: Group AD


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_133

description: Group AD


title: shZFHX4#9674-DAY3 [MA3]

description: Gene expression after TIC treated by shZFHX4 #9674 for 3 days


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_122

description: Group AD


title: Dengue monoclonal Dengue_1

description:
Alexa-647 conjugated Streptavidin tertiary
Dengue_1


title: Cyclin G1 monoclonal Cyclin G1_2

description:
Alexa-647 conjugated Streptavidin tertiary
Cyclin G1_2

source_name: Cyclin G1

value: Cyclin G1 monoclonal


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_120

description: Group AD


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_121

description: Group AD


title: Cyclin G1 monoclonal Cyclin G1_1

description:
Alexa-647 conjugated Streptavidin tertiary
Cyclin G1_1


title: Coronavirus monoclonal Coronavirus_2

description:
Alexa-647 conjugated Streptavidin tertiary
Coronavirus_2

source_name: Coronavirus

value: Coronavirus monoclonal


title: Coronavirus monoclonal Coronavirus_1

description:
Alexa-647 conjugated Streptavidin tertiary
Coronavirus_1


title: shZFHX4#289-DAY3 [MA2]

description: Gene expression after TIC treated by shZFHX4 #289 for 3 days

value: glioblastoma tumor initiating cell


title: Patient 9 Tumor

city: Heidelberg

first: Mohammed

last: Abba

address: Im Neuenheimer Feld 280

department: Molecular Oncology of Solid Tumors

institute: German Cancer Research Center (DKFZ)

hyb_protocol: Illumina Sentrix Universal Array Matrices  hybridization protocol

scan_protocol: Beadstation array scanner

data_processing: Data extraction was done for beads individually, and outliers with greater than 2.5 median absolute deviation (MAD) were removed. The data was normalised as following using Microsoft Excel 2010;  1) Index the values; 2) sort the values according to size from the lowest to the highest; 3) Obtain the average of the values and 4) replace the original values with the averages based on their indices.

source_name: Tumor tissue

label_protocol: Standard Illumina label protocol

extract_protocol: miRNeasy  kit (Qiagen, Germany)

tag: patient id

value: Patient 9

value: Resected tissue

tag: tissue subtype

value: Tumor tissue


title: Patient 9 Normal colon

source_name: Normal colorectal mucosa

value: Normal colorectal mucosa


title: CDK2 monoclonal CDK2_2

description:
Alexa-647 conjugated Streptavidin tertiary
CDK2_2

value: CDK2 monoclonal


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_115

description: Group AD


title: CLX160AP monoclonal CLX160AP_2

description:
Alexa-647 conjugated Streptavidin tertiary
CLX160AP_2

value: CLX160AP monoclonal


title: CLX160AP monoclonal CLX160AP_1

description:
Alexa-647 conjugated Streptavidin tertiary
CLX160AP_1


title: Patient 9 Liver

source_name: Liver

value: Liver


title: Patient 9 Metastasis

source_name: Liver Metastasis

value: Liver Metastasis


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_113

description: Group AD

value: Metagenomic DNA


title: Patient 8 rectal Tumor

value: Patient 8


title: CDK2 monoclonal CDK2_1

description:
Alexa-647 conjugated Streptavidin tertiary
CDK2_1


title: shLACZ#1935-DAY3 [MA1]

description: Gene expression after TIC treated by shLACZ #1935 for 3 days


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_117

description: Group AD


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_118

description: Group AD


title: Patient 8 colonic Tumor


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_112

description: Group AD

value: Femal


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_98

description: Group AD


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_100

description: Group AD


title: Patient 8 Normal rectum


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_102

description: Group AD


title: Patient 8 Normal colon


title: Patient 8 Liver


title: CDC2 monoclonal CDC2_2

description:
Alexa-647 conjugated Streptavidin tertiary
CDC2_2

value: CDC2 monoclonal


title: Patient 8 Metastasis


title: CDC2 monoclonal CDC2_1

description:
Alexa-647 conjugated Streptavidin tertiary
CDC2_1


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_92

description: Group AD


title: Borrelia monoclonal Borrelia_1

description:
Alexa-647 conjugated Streptavidin tertiary
Borrelia_1

source_name: Borrelia

value: Borrelia monoclonal


title: C. trachomatis monoclonal C. trachomatis_1

description:
Alexa-647 conjugated Streptavidin tertiary
C. trachomatis_1

source_name: C. trachomatis

value: C. trachomatis monoclonal


title: Borrelia monoclonal Borrelia_2

description:
Alexa-647 conjugated Streptavidin tertiary
Borrelia_2


title: Patient 7 Normal rectum

value: Patient 7


title: FLAG monoclonal

description: Alexa-647 conjugated Streptavidin tertiary

source_name: FLAG

value: FLAG monoclonal


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_95

description: Group AD


title: C. trachomatis monoclonal C. trachomatis_2

description:
Alexa-647 conjugated Streptavidin tertiary
C. trachomatis_2


title: Bordetella monoclonal Bordetella_2

description:
Alexa-647 conjugated Streptavidin tertiary
Bordetella_2

source_name: Bordetella

value: Bordetella monoclonal


title: HA monoclonal

source_name: HA

value: HA monoclonal


title: A10 monoclonal

value: A10 monoclonal


title: 4C1 monoclonal

value: 4C1 monoclonal


title: DM1A monoclonal

value: DM1A monoclonal


title: Patient 7 Tumor

value: Resected tissue

value: Tumor tissue


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_91

description: Group AD

value: Male


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_80

description: Group AD


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_87

description: Group AD


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_81

description: Group AD


title: Patient 7 Metastasis

value: Liver Metastasis


title: p53Ab8 monoclonal

value: p53Ab8 monoclonal


title: p53Ab1 monoclonal

value: p53Ab1 monoclonal


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_77

description: Group AD

value: Metagenomic DNA


title: Patient 7 Liver

value: Liver


title: Bordetella monoclonal Bordetella_1

description:
Alexa-647 conjugated Streptavidin tertiary
Bordetella_1


title: Anthrax monoclonal Anthrax_2

description:
Alexa-647 conjugated Streptavidin tertiary
Anthrax_2

source_name: Anthrax

value: Anthrax monoclonal


title: Patient  6 Normal colon

value: Patient 6

value: Normal colorectal mucosa


title: Patient 6 Metastasis


title: AKT2 monoclonal AKT2_2

description:
Alexa-647 conjugated Streptavidin tertiary
AKT2_2

value: AKT2 monoclonal


title: AKT2 monoclonal AKT2_1

description:
Alexa-647 conjugated Streptavidin tertiary
AKT2_1


title: 2C11 monoclonal

value: 2C11 monoclonal


title: Patient 4 Normal colon

value: Patient 4


title: Patient 4 Tumor


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_76

description: Group AD


title: AKT1(B1) monoclonal AKT1(B1)_2

description:
Alexa-647 conjugated Streptavidin tertiary
AKT1(B1)_2

value: AKT1(B1) monoclonal


title: Patient 4 Metastasis

source_name: Metastasis

value: Metastasis


title: AKT1(B1) monoclonal AKT1(B1)_1

description:
Alexa-647 conjugated Streptavidin tertiary
AKT1(B1)_1


title: Anthrax monoclonal Anthrax_1

description:
Alexa-647 conjugated Streptavidin tertiary
Anthrax_1


title: Patient 6 Liver


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_74

description: Group AD

value: Femal


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_75

description: Group AD


title: AKT1(7) monoclonal AKT1(7)_1

description:
Alexa-647 conjugated Streptavidin tertiary
AKT1(7)_1

value: AKT1(7) monoclonal


title: AKT1(7) monoclonal AKT1(7)_2

description:
Alexa-647 conjugated Streptavidin tertiary
AKT1(7)_2


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_71

description: Group AD


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_72

description: Group AD


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_73

description: Group AD


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_70

description: Group AD


title: Ab6160 monoclonal Ab6160_2

description:
Alexa-647 conjugated Streptavidin tertiary
Ab6160_2

value: Ab6160 monoclonal


title: Patient 2 Normal

value: Patient 2

value: Resected tissue


title: Patient 2 Tumor

value: Tumor tissue


title: Patient 12 Tumor

value: Patient 12


title: Patient 2 Liver


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_68

description: Group AD

value: Male

value: Metagenomic DNA


title: Ab6160 monoclonal Ab6160_1

description:
Alexa-647 conjugated Streptavidin tertiary
Ab6160_1


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_66

description: Group AD


title: Patient 12 Normal rectum


title: Ab2033 monoclonal Ab2033_1

description:
Alexa-647 conjugated Streptavidin tertiary
Ab2033_1

value: Ab2033 monoclonal


title: Ab2033 monoclonal Ab2033_2

description:
Alexa-647 conjugated Streptavidin tertiary
Ab2033_2


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_63

description: Group AD


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_67

description: Group AD


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_65

description: Group AD


title: AAT monoclonal AAT_2

description:
Alexa-647 conjugated Streptavidin tertiary
AAT_2

source_name: AAT

value: AAT monoclonal


title: Patient 11 Tumor

value: Patient 11


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_61

description: Group AD


title: Patient 11 Normal rectum

value: Normal colorectal mucosa


title: Patient 12 Liver

value: Liver


title: A10 monoclonal A10_2

description:
Alexa-647 conjugated Streptavidin tertiary
A10_2

value: A10 monoclonal


title: Patient 11 Metastasis

value: Liver Metastasis


title: genomic DNA from cultured cells_HFF_p23

city: Toronto

first: Daniel

last: De Carvalho

state: ON

address: 101 College Street, room 9-302

country: Canada

institute: Ontario Cancer Institute

description: parental fibroblast

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

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

data_processing: BeadStudio software; the non_normalized.txt contains unmethylated and methylated signal intensities.

label: Cy5 and Cy3

source_name: parental fibroblasts

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from cultured cells using Qiagen DNeasy Kit according to standard instructions

value: normal

value: parental fibroblasts


title: AAT monoclonal AAT_1

description:
Alexa-647 conjugated Streptavidin tertiary
AAT_1


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_58

description: Group AD


title: A10 monoclonal A10_1

description:
Alexa-647 conjugated Streptavidin tertiary
A10_1


title: genomic DNA from cultured cells_iPS OSLN6

description: induced pluripotent stem cell by OSLN cocktail

source_name: iPS cells derived using Thompson factors (OSLN)

value: Induced pluripotent stem (iPS) cells

tag: reprogramming factors used

value: Thomson factors (OCT4, SOX2, NANOG and LIN28)


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_59

description: Group AD


title: genomic DNA from cultured cells_iPS OSLN5


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_56

description: Group AD


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_57

description: Group AD


title: 8A1 monoclonal 8A1_2

description:
Alexa-647 conjugated Streptavidin tertiary
8A1_2

value: 8A1 monoclonal


title: Patient 10 Tumor

value: Patient 10

value: Resected tissue


title: Patient 11 Liver


title: Patient 10 Normal rectum


title: genomic DNA from cultured cells_iPS OSLN3


title: 8A1 monoclonal 8A1_1

description:
Alexa-647 conjugated Streptavidin tertiary
8A1_1


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_55

description: Group AD

value: Femal


title: genomic DNA from cultured cells_iPS OSLN2


title: genomic DNA from cultured cells_iPS OSLN1


title: genomic DNA from cultured cells_iPS OSLN4


title: 3A1 monoclonal 3A1_2

description:
Alexa-647 conjugated Streptavidin tertiary
3A1_2

value: 3A1 monoclonal


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_54

description: Group AD

value: Male

value: Metagenomic DNA


title: genomic DNA from cultured cells_hES2

description: human embrionic stem cell

source_name: embrionic ES cells

value: embrionic ES cells


title: genomic DNA from cultured cells_HFF_p17

description: parental fibroblast


title: Patient 10 Metastasis


title: Patient 10 Liver


title: 3A1 monoclonal 3A1_1

description:
Alexa-647 conjugated Streptavidin tertiary
3A1_1


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_53

description: Group AD


title: genomic DNA from cultured cells_iPS OSKM9

description: induced pluripotent stem cell by OSKM cocktail

source_name: iPS cells derived using Yamanaka factors (OSKM)

value: Yamanaka factors (OCT4, SOX2, KLF4 and MYC)


title: genomic DNA from cultured cells_iPS OSKM8


title: hydG_ech_none 20

status: Public on Jan 15 2014

city: Oak Ridge

first: Dawn

middle: Marie

last: Klingeman

state: TN

address: 1 Bethel Valley Rd building 15056 Rm 366  MS 6038

department: Biosciences Division

institute: Oak Ridge National Lab

hyb_protocol: The hybridization was performed following NimbleGen company's protocols.

scan_protocol: The scanning was performed following NimbleGen company's protocols.

data_processing: Statistical analysis was done with JMP Genomics 6.0 software (SAS Institute, Cary, NC). The data were subsequently normalized using the Loess normalization algorithm within JMP Genomics. An analysis of variance (ANOVA) was performed to determine differential expression levels between conditions and time points using the FDR testing method (p < 0.05).

organism: Acetivibrio thermocellus DSM 1313

source_name: hydG_ech, untreated

label_protocol: The labeling was performed following NimbleGen company's protocols.

growth_protocol: Clostridium thermocellum DSM1313 and mutant strains were grown at 55 deg C in the 100 ml volume in 250 ml anaerobic bottles in rich medium as described by Tripathi et al., 2010, which is based on DSM122 medium.

extract_protocol: Briefly, samples were harvested by centrifugation and the TRIzol reagent (Invitrogen, Carlsbad, CA) was used to extract total cellular RNA. Each total RNA preparation was treated with RNase-free DNase I (Ambion, Austin, TX) to digest residual chromosomal DNA and subsequently purified with the Qiagen RNeasy Mini kit in accordance with the instructions from the manufacturer. Total cellular RNA was quantified at OD260 and OD280 with a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE) and the RNA quality was checked with Agilent Bioanalyzer (Agilent, CA). The purified RNA with good quality from each sample was used as the template to generate ds-cDNA using Invitrogen ds-cDNA synthesis kit (Invitrogen, CA).

treatment_protocol: The wild type and mutants were grown in rich medium with 5 mM added acetate and controls were grown without acetate. The cells were grown to an OD of 0.3-0.4 in rich medium and centrifuged at 4 deg C for 5 min; immediately flash frozen in liquid N2. Total RNA was isolated for comparison of acetate treatment.

tag: strain/background

tag: genotype/variation

value: ∆hydG∆ech


title: hydG_ech_acetate 21

source_name: hydG_ech, acetate

value: acetate


title: WT 1313_acetate 23

source_name: WT 1313, acetate

value: wild type


title: WT 1313_acetate 15


title: WT 1313_none 22

source_name: WT 1313, untreated


title: hydG_none 12

source_name: hydG, untreated

value: ∆hydG


title: genomic DNA from cultured cells_iPS OSKM6

value: normal


title: hydG_none 19


title: genomic DNA from cultured cells_iPS OSKM3


title: hydG_acetate 18

source_name: hydG, acetate


title: Runx1 iTG, sorted bulge cells, biological rep1

city: Ithaca

first: Tudorita

last: Tumbar

address: 260 Biotechnology Building

department: Molecular Biology & Genetics

institute: Cornell University

description: Expression data from Runx1 iTG bulge cells

hyb_protocol: The labeled cDNA was hybridized to Mouse Genome 430 2.0 genechips (Affymetrix) in the Cornell microarray core facility (Ithaca, NY), according to the protocol indicated in the Encore Biotin Module kit.

scan_protocol: The arrays were scanned on the Affymetrix GeneChip Scanner 7G.

data_processing: The scanned images were then imported and normalized with GeneSpring software 12.1 (Agilent Technologies). Exclude the probes with a signal value <100 or celled absent.

source_name: Tet-on Runx1 transgenic mouse skin after 1day Doxycycline chase

label_protocol: Five nanogram of total RNA was processed with the “Ovation Pico WTA System (NuGEN)” for cDNA amplification, followed by “Encore Biotin Module (NuGEN)” for labeling and fragmentation of cDNA.

growth_protocol: Mice are housed in the Biotechnology Building mouse facility of Cornell University approved by Cornell IACUC.

extract_protocol: Total RNA was extracted using Rnease micro kit (QIAGEN) according to the manufacturer's instructions.

treatment_protocol: Mice were fed doxy at 1g/KG of food (Bio-serv) to repress H2BGFP expression.

value: Skin

value: Bulge

tag: genotype

value: Runx1 iTG

tag: protocol

value: 1day Doxycycline chase


title: [CAM.04]-[T2]-[rep2]

type: mixed

city: Porto

first: Tiago

last: Beites

address: rua do campo alegre, 823

country: Portugal

institute: IBMC

description: Streptomyces natalensis CAM.04 (ΔahpCD::aac(3)IV-oriT)

hyb_protocol: Hybridization was carried out as previously described [Rodriguez-Garcia, A, et al. (2007) Proteomics 7(14)]

scan_protocol: Microarray chips were scanned in Agilent G2565BA and using the software "Feature Extraction v8.1".

data_processing: Processed signal was obtained using the "subtract method". Normalization was carried out combining a within-array normalization (median) with an inter-array normalization (cyclic loess)

organism: Streptomyces natalensis ATCC 27448

source_name: mycelium, stationary phase

label_protocol: cDNA and genomic DNA were labeled with Cy3 and Cy5 as previously described [Rodriguez-Garcia, A, et al. (2007) Proteomics 7(14)].

growth_protocol: Baffled flasks; YEME medium; 30 ºC; 250 rpm

extract_protocol: Total RNA was extracted using the commercial kit "Rneasy Mini Kit" (Qiagen). cDNA was synthesized using iScript™ Reverse Transcription Supermix (Bio-Rad).

tag: sample type

value: mycelium

tag: growth phase

value: stationary phase

extract_protocol: Genomic DNA was extracted using the Kirby mix procedure [Kieser, T, et al. (2000) John Innes Center, Norwich, United Kingdom].

value: WT


title: Runx1 iTG, sorted hair germ cells, biological rep1

description: Expression data from Runx1 iTG hair germ cells

tag: cell type

value: Hair germ


title: WT 1313_none 14


title: [CAM.04]-[T2]-[rep3]


title: WT, sorted hair germ cells, biological rep2

description: Expression data from WT hair germ cells

source_name: Control mouse skin after 1day Doxycycline chase


title: WT, sorted hair germ cells, biological rep1

description: Expression data from WT hair germ cells


title: Runx1 iTG, sorted hair germ cells, biological rep2


title: genomic DNA from cultured cells_iPS OSKM5

value: Induced pluripotent stem (iPS) cells


title: Runx1 iTG, sorted bulge cells, biological rep2


title: genomic DNA from cultured cells_iPS OSKM7


title: hydG_ech_acetate 13


title: hydG_acetate 11


title: [CAM.04]-[T2]-[rep1]


title: WT 1313_none 7


title: genomic DNA from cultured cells_iPS OSKM1


title: genomic DNA from cultured cells_iPS OSKM4


title: WT 1313_acetate 8


title: genomic DNA from cultured cells_iPS OSKM2


title: hydG_ech_acetate 6


title: hydG_ech_none 5


title: [CAM.02]-[T2]-[rep3]

description: Streptomyces natalensis CAM.02 (ΔsodF::aac(3)IV-oriT)


title: [CAM.02]-[T2]-[rep2]


title: TRKO_WT_004

city: Washington

first: Dongmei

last: Li

state: DC

address: 3900 Reservoir Rd Med dent SE318

description: Total of 6101 genes including 12 mitochondrial genes was spotted on arry and gene expression profile of C. albicans null mutant rbf1Δ was compared with the wild type strain

hyb_protocol: Purified 600ng of Cy3-labbled cDNA was denatured at 95°C for 2 min. The hybridization was carried out in 8X15K Agilent array with Agilent gene expression hybridization kit in Agilent's Surehyb Chambers at 65°C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers.

scan_protocol: scanned using the Agilent Microarry Scanner G2505C at 5 micron resolution

data_processing: Data extraction from images was done using Agilent Feature Extraction software v 10.7.3.1 and 75th percentile shift normalization of the data was doen in GeneSpring GX v 11

organism: Candida albicans

source_name: WT log phase

label_protocol: One-color microarray based gene expression was performed. 100ng of total RNA of each samples were incubated with reverse transcripton mix (Agilent Quick-Amp Labling Kit) at 40°C and converted into cDNA by  oligodT with a T7 polymerase promter. 2 nM Cy3-dCTP was added into the mixture according to  the manufacturer's instructions. 50μg/ml RNase A and 0.05U RNase H were added and incubated for 30 min at 37°C

growth_protocol: Overnight cultures of a C. albicans null mutants and parental strain SN250 were diluted to a A 600 of 0.2 in 20 ml of SD medium containing 2% glucose and incubated at 200 rpm at 30°C for 5 hours

extract_protocol: The total RNAs were extracted by the pheno/chloroform method and RNA integrity was assess using an Agilent 2100 bioanalyzer

treatment_protocol: Culture were collected at 10,000rpm for 5 min, washed with DEPC-water and proceeded for RNA extraction


title: 64 rep3

city: Madison

first: Dan

last: Cullen

state: WI

address: One Gifford Pinchot Dr

institute: UW/FPL

hyb_protocol: Hybridization was carried out with 6ug of labeled cDNA suspended in NimbleGen hybridization solution for 17 hours at 42°C

scan_protocol: Arrays were scanned on the Axon4000B Scanner (Molecular Dynamics) and data was extracted from the scanned image using NimbleScan v2.4.

data_processing: Quantile normalization and robust multi-array averaging (RMA) applied

organism: Phanerodontia chrysosporium

label_protocol: One ug of each cDNA sample was amplified and labeled with 1 unit per ul of Klenow Fragment (New England BioLabs) and 1 O.D unit of Cy3 fluorophore (TriLink Biotechnologies, Inc.) for 2 hours at 37°C

growth_protocol: Five days growth in shaking flasks at room temperature.

extract_protocol: RNA was converted to double-strand cDNA and labeled with the Cy3 fluorophore sample for hybridization to the array by Roche NimbleGen (Iceland).  In brief, 10ug of total RNA was incubated with 1X first strand buffer, 10 mM DTT, 0.5mM dNTPs, 100 pM oligo T7 d(T)24  primer, and 200 units of SuperScript II (Invitrogen) for 60 min at 42°C. Second strand cDNA was synthesized by incubation with 1X second strand buffer, 0.2mM dNTPs, 0.07 units per ul DNA ligase (Invitrogen), 0.27 units per ul DNA polymerase I (Invitrogen), 0.013 units per ul RNase H (Invitrogen), at 16°C for 2 hours.  Immediately following, 10 units T4 DNA polymerase (Invitrogen) was added for additional 5 minute incubation at 16°C.  Double-stranded cDNA was treated with 27ng/ul of RNase A (EpiCenter Technologies)  for 10 minutes at 37°C.  Treated cDNA was purified using an equal volume of phenol:chloroform:isoamyl alcohol (Ambion), ethanol precipitated, washed with 80% ethanol, and resuspended in 20ul water.

value: RP-B

tag: wood substrate line

value: transgenic line 64


title: TRKO_hfl1Δ _002

source_name: hfl1Δ log phase


title: R-28C rep3

city: New Delhi

first: Gurudutta

last: Panda

address: New Mehrauli Road

department: School of Biotechnology

country: India

institute: Jawaharlal Nehru University

hyb_protocol: Fragmentation of labeled cRNA and hybridization to the custom designed B. anthracis microarrays were carried out using standard Agilent protocols. Appropriate quality checks were carried out to ensure that the above steps have occurred properly as per standard protocol.

scan_protocol: Hybridized arrays were scanned at 3μm resolution on an Agilent Microarray Scanner (G2505B, Agilent Technologies, USA). Data extraction from images was done using Feature Extraction Software. Once the raw data files were obtained, further bioinformatics and statistical analysis were carried out as described below.

data_processing: Normalization and statistical analyses were performed using the Partek Genome Suite 6.0. The data set containing 12 single color microarrays, with each condition measured in biological triplicate,was analyzed together. The background corrected probe intensities were normalized between arrays using Quantile normalization method and were log2 transformed. The probe intensities corresponding to a particular gene were averaged to obtain a single value for each gene

organism: Bacillus anthracis

label_protocol: RNA samples were then reverse transcribed using random hexamers tagged with a T7 polymerase promoter. Synthesized double stranded cDNA were then used as template for generation of Cy3 labeled cRNA using Agilent One-Color Microarray-Based labeling Kit (Agilent Technologies, USA).

growth_protocol: The strain was grown in a chemically defined media called R medium  36 in the presence of 5%CO2 at 37°C to simulate host like conditions and induce toxin production (referred as ‘R-Full’).

extract_protocol: RNA isolated from exponentially growing cells. Samples to be processed for transcriptomics were treated with RNAprotect bacterial reagent (QIAGEN) as per manufactures instruction before harvesting to avoid changes in the RNA levels during the handling procedure.Bacterial culture samples were thawed and incubated with 10mg/ml lysozyme for 30min at 37°C followed by homogenization in a MagNA Lyser instrument with glass beads (Roche Applied Sciences) for six 30 sec cycles at 5000 rpm with 1min incubation on ice in between the cycles. Total RNA was isolated using Tri-reagent (Sigma, USA) as per the manufacturer’s instructions. Post DNAse treatment (QIAGEN), the yield and RNA purity was determined using NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Inc.). Integrity of the RNA was checked using Agilent Bioanalyzer (Agilent Technologies, USA).

treatment_protocol: To investigate the effect of factors that affect toxin production i.e. glucose, bicarbonate and growth temperature, sequential environmental perturbations were carried out in R media, wherein glucose was replaced by glycerol (0.25%) or no bicarbonate was added or the growth temperature was 28°C instead of 37°C. Bacillus anthracis was grown under the above described conditions (one toxin inducing and three toxin non-inducing ) in biological replicates and were harvested at exponential phase of growth (OD600 = 0.6-0.8) by centrifugation

value: virulent strain

tag: environmental condition

value: growth temperature 28°C


title: R(-)Bicarbonate rep3

source_name: R(-)Bicarbonate

value: no bicarbonate


title: R-28C rep2


title: 64 rep2


title: 82 rep3

value: transgenic line 82


title: 64 rep1


title: [WT]-[T2]-[rep1]

description: Streptomyces natalensis ATCC 27448

value: wild type


title: [WT]-[T2]-[rep3]

description: Streptomyces natalensis ATCC 27448


title: [CAM.02]-[T2]-[rep1]


title: R-28C rep1


title: hydG_none 4

value: ∆hydG


title: [WT]-[T2]-[rep2]

description: Streptomyces natalensis ATCC 27448


title: TRKO_rbf1Δ _001

source_name: rbf1Δ log phase


title: WT, sorted bulge cells, biological rep2

description: Expression data from WT bulge cells

value: Skin

tag: age


title: hydG_acetate 3

value: acetate


title: XJH_2

first: Xiaohui

last: Wang

address: 15 beisanhuan east road, chaoyang district, beijing, 100029

institute: Beijing University of Chemical Technology

description: GeoChip data for activated sludge sample collected at System XJH, replicate 2

hyb_protocol: All labeled DNA was resuspended in 10 μl hybridization solution as previously described (Wu et al. 2006) and was hybridized with GeoChip 4.2 on a MAUI hybridization station (BioMicro, Salt Lake City, UT, USA) at 42℃ with 40% formamide for 16h.

scan_protocol: Microarrays were scanned by a ScanArray 5000 Microarray Analysis System (PerkinElmer, Wellesley, MA, USA) at 100% laser power.

data_processing: Signal intensities of the spots were measured with ImaGene 6.0 (Biodiscovery Inc., El Segundo, CA, USA). Low quality spots with a signal to noise ratio (SNR) of less than 2.0 or with signal intensity less than 1000 were removed before further data analysis. The genes detected in only one out of three samples from the same system were removed. Then the intensities of replicates were transformed to the natural logarithmic form and divided by mean signal intensity.

organism: activated sludge metagenome

source_name: Microbes in activated sludge of full-scale wastewater treatment plants

label_protocol: As previously described (Lu et al. 2012), 1000 ng of each DNA sample was labeled were labeled with the fluorescent dye Cy-5 using a random priming method and purified using the QIA quick purification kit (Qiagen, Valencia, CA, USA) and then dried.

growth_protocol: On July 24, 2011, mixed-liquor suspended sludge samples were taken from the aerobic zones of the four full-scale wastewater treatment systems. At each site, three 50 ml samples were collected. All samples were kept on ice when transporting to laboratory. Each sample was dispensed into a 50 ml sterile Eppendorf tube and centrifuged at 14,000 g for 10min. The pellets were stored at -80℃ for analysis.

extract_protocol: Microbial genomic DNA was extracted from the pellets of activated sludge samples through joint use of freezing and sodium dodecyl sulfate (SDS) for cell lysis (Zhou et al. 1996). The extracted products were then purified employing the Wizard® SV Genomic DNA Purification Kit (Promega, Madison WI). DNA quality and quantity were measured using NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies Inc., Wilmington, DE, USA) and with PicoGreen using a FLUOstar Optima (BMG Labtech, Jena, Germany), respectively.

tag: wastewater treatment plant

value: XJH


title: WT, sorted bulge cells, biological rep1

description: Expression data from WT bulge cells

tag: tissue

value: Bulge

value: 1day Doxycycline chase


title: XJH_3

description: GeoChip data for activated sludge sample collected at System XJH, replicate 3


title: XJH_1

description: GeoChip data for activated sludge sample collected at System XJH, replicate 1


title: XHM_3

description: GeoChip data for activated sludge sample collected at System XHM, replicate 3

value: XHM


title: [CAM.04]-[T1]-[rep3]

source_name: mycelium, exponential phase

value: mycelium

value: exponential phase

tag: strain

value: WT


title: TRKO_dpb4Δ _003

source_name: dpb4Δ log phase


title: [CAM.04]-[T1]-[rep2]


title: R(-)Bicarbonate rep2


title: R(-)Glucose rep3

source_name: R(-)Glucose

value: glucose was replaced by glycerol (0.25%)


title: 82 rep2

value: RP-B


title: P717 rep3

value: hybrid line P717


title: 82 rep1


title: [CAM.04]-[T1]-[rep1]


title: R(-)Bicarbonate rep1

value: virulent strain


title: R-Full rep3

value: defined media R in the presence of 5%CO2 at 37°C


title: XHM_1

description: GeoChip data for activated sludge sample collected at System XHM, replicate 1


title: QH_3

description: GeoChip data for activated sludge sample collected at System QH, replicate 3

value: QH


title: P717 rep1


title: [CAM.02]-[T1]-[rep3]


title: [CAM.02]-[T1]-[rep1]


title: P717 rep2


title: R-Full rep2


title: QH_2

description: GeoChip data for activated sludge sample collected at System QH, replicate 2


title: R(-)Glucose rep2


title: XHM_2

description: GeoChip data for activated sludge sample collected at System XHM, replicate 2


title: HL60_shSYK_1_Replicate2

city: Cambridge

first: Gabriela

last: Alexe

state: MA

address: 415 Main St.

department: Computational Biology and Bioinformatics

institute: Broad Institute

description: The samples were profiled using the HT U133A Gene Expression Arrays (Affymetrix) at the Broad Institute of MIT and Harvard (Cambridge, MA, USA).

hyb_protocol: GeneChip® Hybridization Control Kit (Affymetrix, P/N 900454)

scan_protocol: Affymetrix GeneChip Scanner 7G

data_processing: Data were extracted from the  CEL files and preprocessed through  the ExpressionFileCreator module implemented  in  GenePattern 3.5.0  software platform (Broad Institute, http://www.broadinstitute.org/cancer/software/genepattern/),  by applying  RMA and the quantile normalization procedures.  The computational analysis of the gene expression data was performed through the Genome Space bioinformatics platform (http://www.genomespace.org).

source_name: HL-60 cell line, transduced with shSYK_1 and selected with  1 µg/ml puromycin 48 hours post-infection

label_protocol: Biotin

growth_protocol: HL-60, MOLM-14, and U937 were maintained in RPMI 1640 (Cellgro) supplemented with 1% penicillin-streptomycin and 10% fetal bovine serum (FBS, Sigma-Aldrich) at 37 °C with 5% CO2

extract_protocol: RNA was extracted using Qiagen Rneasy Mini Kit (74104) at 5 days post infection.

treatment_protocol: HL-60, MOLM-14, and U937 cell lines were transduced in triplicate with a control luciferase-directed shRNA (target sequence CCTAAGGTTAAGTCGCCCTCG), and in duplicate with two SYK-directed shRNAs:  shSYK_1 (clone ID TRCN0000197257,  target sequence  GCAGCAGAACAGACATGTCAA)   and shSYK_2  (clone ID TRCN0000003163 , target sequence  GCAGGCCATCATCAGTCAGAA),  and were then selected with 1 µg/ml puromycin 48 hours post-infection.

tag: cell line

tag: replicate

tag: treatment


title: [WT]-[T1]-[rep2]

description: Streptomyces natalensis ATCC 27448

value: wild type


title: R-Full rep1


title: R(-)Glucose rep1


title: QH_1

description: GeoChip data for activated sludge sample collected at System QH, replicate 1


title: [WT]-[T1]-[rep1]

description: Streptomyces natalensis ATCC 27448


title: GBD_2

description: GeoChip data for activated sludge sample collected at System GBD, replicate 2

value: GBD


title: [WT]-[T1]-[rep3]

description: Streptomyces natalensis ATCC 27448


title: GBD_3

description: GeoChip data for activated sludge sample collected at System GBD, replicate 3


title: HL60_shSYK_2_Replicate2

source_name: HL-60 cell line, transduced with shSYK_2 and selected with  1 µg/ml puromycin 48 hours post-infection


title: [CAM.02]-[T1]-[rep2]


title: HL60_shSYK_1_Replicate1


title: U937_shSYK_1_Replicate2

source_name: U937 cell line, transduced with shSYK_1 and selected with  1 µg/ml puromycin 48 hours post-infection


title: HL60_luc_Replicate1

source_name: HL-60 cell line, transduced with a control luciferase and selected with  1 µg/ml puromycin 48 hours post-infection

value: shLuciferase


title: U937_shSYK_1_Replicate1


title: GBD_1

description: GeoChip data for activated sludge sample collected at System GBD, replicate 1


title: HL60_luc_Replicate3


title: SKOV3 treated with DMSO 60hr rep 2

city: NANCAHNG

first: Shiwen

last: Luo

state: JiangXi

address: 17 Yong Wai street

department: Center for experimental medicine

institute: The Frist Affiliated Hospital of Nanchang University

description: replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

source_name: SK-OV-3 cell line

label_protocol: Each biotinylated cRNA (750 ng) was hybridized to an Illumina Human HT expression BeadChip V4 (Illumina Inc., San Diego, CA). Following standard washing steps and staining with Streotavidin-Cy3, the arrays were scanned using an Illumina BeadArray Reader.

growth_protocol: Cells were cultured in RPMI-1640 medium supplemented with 10% FBS, penicillin (100 U/ml), and streptomycin (100 μg/ml).

extract_protocol: Total RNA from each sample was isolated by TRIzol (Invitrogen) according to the manufacturer's instructions. Double-stranded cDNA and biotin-labeled cRNA were synthesized from RNA (300 ng) using an Illumina TotalPrep RNA Amplification Kit (Ambion Inc., Austin, TX) according to the manufacturer’s protocol.

treatment_protocol: SKOV3 cells were treated with GANT61 (20 μM for 60 hr) and control vehicle DMSO, respectively.

value: ovary derived from metastatic site:ascites

tag: disease state

value: adenocarcinoma

tag: morphology

value: epithelial

tag: growth properties

value: adherent

value: DMSO 60hr


title: SKOV3 treated with DMSO 60hr rep 1

description: replicate 1


title: SKOV3 treated with GANT61 60hr rep 2

description: replicate 2

value: GANT61 60hr


title: U937_shSYK_2_Replicate2

source_name: U937 cell line, transduced with shSYK_2 and selected with  1 µg/ml puromycin 48 hours post-infection


title: SKOV3 treated with GANT61 60hr rep 1

description: replicate 1


title: U937_luc_Replicate3

source_name: U937 cell line, transduced with a control luciferase and selected with  1 µg/ml puromycin 48 hours post-infection


title: HL60_luc_Replicate2


title: U937_shSYK_2_Replicate1


title: U937_luc_Replicate2


title: MOLM14_shSYK_2_Replicate2

source_name: MOLM-14 cell line, transduced with shSYK_2 and selected with  1 µg/ml puromycin 48 hours post-infection


title: U937_luc_Replicate1


title: MOLM14_shSYK_2_Replicate1


title: HBsAg Oil Tumor, biological replicate 1

city: Singapore

first: Kanaga

last: Sabapathy

state: Singapore

address: 11 Hospital Drive

country: Singapore

institute: National Cancer Centre Singapore

description: AH 276T1.CEL

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials as per manufactorere's instructions  Samples were hybridized using Affymetrix hybridization kit materials as per manufactorere's instructions

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using Partek software (v.6.5).
Quantile normalization using GC-RMS method, gene level expression were summarized from the quantile normalized data

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (WT PLUS Reagent Kit User Manual, 2013, Affymetrix).

growth_protocol: fresh liver were harvested from mouse and snap frozen in liquid nitrogen

extract_protocol: All samples were snap frozen in liquid N2. Total RNA was extracted from all samples using Trizol and further purified by RNeasy RNA extraction kit (Qiagen).

treatment_protocol: mice were treated with AFB 6 µg/g body weight (19 nmol/g) in trioctanoin containing 6% DMSO or corn oil on day 7 (D7) after birth

tag: strain background

tag: genotype/variation

value: Hepatitis B surface antigen (HBsAg) transgenic

tag: injected with

value: corn oil on day7 (D7) after birth

tag: age at tissue collection

value: 15 months

value: liver

tag: tissue subtype

value: Tumor


title: MOLM14_shSYK_1_Replicate2

source_name: MOLM-14 cell line, transduced with shSYK_1 and selected with  1 µg/ml puromycin 48 hours post-infection


title: MOLM14_luc_Replicate3

source_name: MOLM-14 cell line, transduced with a control luciferase and selected with  1 µg/ml puromycin 48 hours post-infection


title: MOLM14_luc_Replicate2


title: 12 months Mouse hipocampus 039

city: Suita, Osaka

first: Noriyuki

last: Hayashi

address: G9, 2-2, Yamadaoka,

department: Complementary and Alternative Medicine

country: Japan

institute: Osaka University Graduate School of Medicine

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

source_name: 12 months Mouse hipocampus

label_protocol: Biotinylated cRNA were prepared with the Illumina® TotalPrep™ RNA Amplification Kit

extract_protocol: Total RNA was isolated from mouse and human powdered hippocampi using RNeasy Lipid Tissue Mini kit (Qiagen). cDNA was prepared using High Capacity RNA-to-cDNA Master Mix (#4390775 Applied Biosystems) following the manufacturer’s standard protocol. Quality of RNA was assessed for each sample using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

tag: strain b6(%)

tag: strain sjl(%)

tag: strain dba2(%)

tag: log10(guhcl fractionation a-beta1-40)

tag: transgenic(tg)

value: non Tg

value: 12 months

value: hippocampus


title: WT AFB Tumor, biological replicate 2

description: AH 32 T2.CEL

value: wild type

value: aflatoxin B1 (AFB1) on day7 (D7) after birth

tag: tissue


title: MOLM14_luc_Replicate1

tag: cell line

value: shLuciferase


title: HBsAg Oil Tumor, biological replicate 2

description: AH 276T2.CEL


title: WT AFB Tumor, biological replicate 1

description: AH 32 T1.CEL


title: 12 months Mouse hipocampus 040

tag: age


title: MOLM14_shSYK_1_Replicate1

tag: replicate

tag: treatment


title: 12 months Mouse hipocampus 037


title: WT AFB Tumor, biological replicate 3

description: AH 52 T1.CEL


title: HBsAg AFB Tumor, biological replicate 3

description: AH 88 T1.CEL


title: 12 months Mouse hipocampus 038


title: HBsAg AFB Tumor, biological replicate 4

description: AH 113 T1.CEL


title: 12 months Mouse hipocampus 035


title: 12 months Mouse hipocampus 036


title: 12 months Mouse hipocampus 031


title: HBsAg AFB Tumor, biological replicate 2

description: AH 31 T1.CEL


title: P4M4-2

city: Uppsala

first: Paolo

last: Innocenti

address: Norbyvägen 18D

department: Dept. of Animal Ecology

country: Sweden

institute: Uppsala university

hyb_protocol: Affymetrix Eukaryotic Target Hybridization protocol

scan_protocol: Affymetrix GeneChip Scanner 3000 with GCOS software

data_processing: Probesets pre-processed with RMA, as implemented in R/Bioconductor package affy. Data are log2 transformed.

organism: Drosophila melanogaster

source_name: Adult LHM, whole fly

label_protocol: Affymetrix GeneChip IVT Labeling Kit, standard manufacturer's protocol

extract_protocol: Trizol (Invitrogen) extraction and RNeasy (Qiagen) purification

tag: Sex

value: F

value: Prom

value: Mono

tag: interaction

tag: label

tag: batch


title: 12 months Mouse hipocampus 030


title: 12 months Mouse hipocampus 034


title: 12 months Mouse hipocampus 033


title: HBsAg AFB Adjacent normal, biological replicate 3

description: AH 113M.CEL

tag: strain background

tag: genotype/variation

tag: injected with

value: Adjacent normal


title: P3P3-1


title: P3P3-2


title: HBsAg AFB Adjacent normal, biological replicate 2

description: AH 88M.CEL

tag: age at tissue collection

tag: tissue subtype


title: P4P4-2


title: P4M4-1


title: P4P4-1


title: 12 months Mouse hipocampus 032

tag: strain b6(%)

tag: strain sjl(%)

tag: strain dba2(%)


title: 12 months Mouse hipocampus 029

tag: log10(guhcl fractionation a-beta1-40)

tag: transgenic(tg)

tag: tissue


title: HBsAg AFB Tumor, biological replicate 1

description: AH 29 T1.CEL


title: P3M3-2


title: HBsAg AFB Adjacent normal, biological replicate 1

description: AH 29M.CEL


title: 12 months Mouse hipocampus 028

value: APP Tg

tag: age


title: WT Oil Normal, biological replicate 3

description: AH 436.CEL

value: Normal


title: P3M3-1


title: WT Oil Normal, biological replicate 2

description: AH 273.CEL


title: P2P2-1


title: 12 months Mouse hipocampus 026


title: 12 months Mouse hipocampus 025


title: 12 months Mouse hipocampus 027


title: P2M2-2


title: P2M2-1


title: 12 months Mouse hipocampus 022


title: HBsAg Oil Normal, biological replicate 3

description: AH 372.CEL

value: Hepatitis B surface antigen (HBsAg) transgenic


title: 12 months Mouse hipocampus 024


title: HBsAg Oil Normal, biological replicate 2

description: AH 366.CEL

value: corn oil on day7 (D7) after birth


title: P1P1-2


title: P1M1-1


title: 12 months Mouse hipocampus 023


title: WT AFB Normal, biological replicate 2

description: AH 96.CEL

value: 15 months


title: HBsAg Oil Normal, biological replicate 1

description: AH 275.CEL

value: liver


title: P1M1-2


title: WT AFB Normal, biological replicate 1

description: AH 58.CEL


title: 12 months Mouse hipocampus 020


title: P2P2-2


title: Bach2KO Lung alveolar macrophage rep2

city: Sendai

first: ari

last: itoh

state: Miyagi

address: 2-1 Seiryo-machi, Aobaku

institute: Tohoku univ.

description: Gene expression in alveolar macrophage of Bach2KO

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity > 5.0 pmol (WT_AM1, WT_AM2, and Bach2KO AM1),  3.7 pmol (Bach2KO_AM2) Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Labeled samples were incubated with Whole Mouse Genome Array (4 × 44 K, G4846F) slides for 17 h. The slides were scanned, and the gene expression analysis was performed using the Genespring GX software program version 11.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Bach2KO Lung alveolar macrophage

label_protocol: One RNA sample of WT AM or Bach2-/- AM was split into two samples and amplified and labeled with cyanine-3 (Cy3) dye. Agilent Low RNA Input Fluorescent Linear Amplification Kits were used to amplify RNA samples following the manufacturer’s protocol. After amplification and labeling, cRNA yields and dye incorporation efficiencies were determined using a Nanodrop  spectrophotometer.

extract_protocol: RNA was prepared using the RNeasy Plus Micro kit (QIAGEN) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: The RNA samples of AMs cells was gerthered on eight WT or four Bach2KO mouse. Then they were sorted by FACSAria II (BD) into 3% FBS/PBS.


title: Bach2KO Lung alveolar macrophage rep1


title: P1P1-1


title: WT Lung alveolar macrophage rep2

description: Gene expression in alveolar macrophage of WT

source_name: WT Lung alveolar macrophage

value: WT


title: 12 months Mouse hipocampus 021


title: M4P4-1


title: 12 months Mouse hipocampus 019


title: M4M4-2


title: M3P3-2


title: M4P4-2


title: M3P3-1


title: 12 months Mouse hipocampus 016


title: WT Lung alveolar macrophage rep1


title: M4M4-1


title: 12 months Mouse hipocampus 017


title: 12 months Mouse hipocampus 018


title: M3M3-2


title: 12 months Mouse hipocampus 011


title: BJEL cells CMS 8 hours treatment

city: Illkirch; Strasbourg

first: Marco Antonio

last: Mendoza-Parra

address: 1, rue Laurent Fries

country: France

institute: IGBMC

description: gene expression data from pre-transformed BJEL cells treated with CMS

hyb_protocol: biotin-labeled-cDNAs were hybridized on Affymetrix Human Gene 1.0 ST Arrays (Affymetrix, Santa Clara, CA, USA). The arrays were further washed and stained with streptavidine-phycoerythrin in an Affymetrix GeneChip® Fluidics station 450 using the script protocol F450-0007.

scan_protocol: The arrays were scanned with an Affymetrix Gene Chip Scanner 3000 7G.

data_processing: Expression values were generated with Affymetrix software Expression Console version 1.1, using sketch quantile normalization and median polish summarization as in Robust Multiarray Analysis (RMA).

source_name: pre-transformed BJEL cells incubated with conditioned medium from senescent cells (CMS)

label_protocol: biotin-labelled cDNA (GeneChip® WT Terminal labeling kit; Affymetrix)

growth_protocol: Pre-transformed BJEL cells were incubated with CMS for 0, 1, 3, 6, 8, 16 or 24 h and prior RNA extraction

extract_protocol: Total RNA was extracted using the GENEElute(TM) RNA extraction kit (SIGMA)

treatment_protocol: Cells were incubated with conditioned media from senescent cells (CMS)

tag: cell line

value: pre-transformed BJEL cells

tag: treatment

tag: time

value: 8 hours


title: M2P2-1

tag: Sex

tag: interaction

tag: label


title: M2M2-2

tag: batch


title: 12 months Mouse hipocampus 015

value: 12 months

value: hippocampus


title: BJEL cells CMS 3 hours treatment

value: conditioned media from senescent cells (CMS)

value: 3 hours


title: 12 months Mouse hipocampus 012


title: M2M2-1

value: F


title: 252800515178-7

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

hyb_protocol: Agilent : 200.0 ng at 65 degree_C during 17 hours

scan_protocol: Arrays were scanned using the Agilent SureScan High Resolution Scanner.

data_processing: Feature extraction data processing. Between-array normalization using the quantile normalization  in R, using the limma package

source_name: B220+ splenic B cells

label_protocol: Agilent - Low RNA input QuickAmp

extract_protocol: Chomzynski

value: B220+ splenic B cells

tag: amount in (µg)

tag: genotype/variation

value: wild type

tag: strain

tag: rin number


title: 12 months Mouse hipocampus 013

tag: strain b6(%)

tag: strain sjl(%)


title: BJEL cells CMS 6 hours treatment

value: 6 hours


title: 12 months Mouse hipocampus 014

tag: strain dba2(%)

tag: log10(guhcl fractionation a-beta1-40)

value: APP Tg


title: BJEL cells CMS 24 hours treatment

value: 24 hours


title: M2P2-2

value: Mono

value: Prom


title: 12 months Mouse hipocampus 010

tag: transgenic(tg)

tag: tissue


title: 12 months Mouse hipocampus 009

tag: age


title: 252800515178-6


title: M1P1-2


title: BJEL cells CMS 16 hours treatment

tag: cell line

tag: treatment

value: 16 hours


title: BJEL cells no treatment

description: gene expression data from pre-transformed BJEL cells

source_name: human foreskin BJ fibroblasts pretransformed by the introduction of telomerase subunit and inactivation of pRb and p53 tumor suppresors (pre-transformed BJEL cells)

value: untreated


title: 252800515178-5


title: M1P1-1

tag: Sex


title: 12 months Mouse hipocampus 007


title: BJEL cells CMS 1 hours treatment

tag: time

value: 1 hours


title: 12 months Mouse hipocampus 008


title: 252800515178-4

value: 3'RR-deficient mice (KO of the 129 IgH allele in a BALBC background)

value: BALBC


title: 252800515178-3


title: 252800515178-8


title: 12 months Mouse hipocampus 006

value: 12 months


title: 12 months Mouse hipocampus 005

value: hippocampus


title: M1M1-2

tag: interaction

tag: label


title: M1M1-1

tag: batch


title: 12 months Mouse hipocampus 004


title: 12 months Mouse hipocampus 003


title: 252800515178-2

tag: amount in (µg)

tag: genotype/variation


title: Elicitor 2h, biological rep2

city: Bellaterra (Cerdanyola del Vallés)

first: Sonia

last: Campo

state: Barcelona

address: Parc de Recerca UAB Edifici CRAG, Campus UAB

country: Spain

institute: Center for Research in Agricultural Genomics (CRAG)

description: treatment was performed spraying plant with an elicitor suspension (300 µg/mL of sterile water containing 0.02% Tween-20 (v/v))

hyb_protocol: Three biological replicates for each condition were independently hybridized.  If the quality control was correct, then 10 µg of fragmented cRNA were hybridized to the GeneChip Rice Genome Array (Affymetrix, Santa Clara, CA), containing probes to query 51279 transcripts representing two rice cultivars. Each sample was added to a hybridization solution containing 100mM 2-(N-morpholino) ethanesulfonic acid (MES), 1 M Na+, and 20mM of EDTA in the presence of 0.01% of Tween-20 to a final cRNA concentration of 0.05 µg/ml. Hybridization was performed for 16 h at 45C . Each microarray was washed and stained with streptavidin-phycoerythrin in a Fluidics station 450 (Affymetrix)

scan_protocol: GeneChips were scanned at 2.5 µm resolution in a GeneChip® Scanner 3000 7G System (Affymetrix)

data_processing:
CEL files obtained using GeneChip Operating Software (GCOS).
Robust Muti-Array Analysis (RMA) algorithm was used for background correction, normalization and expression levels summarization [Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, Scherf U, Speed TP. (2003) “Exploration, normalization, and summaries of high density oligonucleotide array probe level data”. Biostatistics 4:249-264]. Differential expression analysis was performed with the Bayes t-statistics from the linear models for Microarray data (LIMMA). To control the false-discovery rate, P-values were corrected for multiple-testing using the Benjamini-Hochberg’s method [Benjamini Y and Hochberg Y. (1995). “Controling the false discovery rate: a practical and powerful approach to multiple testing”. J. Roy. Stat. Soc. B. 57:289-300 -and- Reiner A, Yekutieli D, Benjamini Y. (2003).“Identifying differentially expressed genes using false discovery rate controlling procedures”. Bioinformatics 19:368-375.]. Statistical analysis and graphical visualization of data were performed with the interactive tool FIESTA (http://bioinfogp.cnb.csic.es/tools/FIESTA)

organism: Oryza sativa Japonica Group

source_name: Elicitor treated Leaves

label_protocol: Each RNA preparation was tested for degradation using the Agilent 2100 Bioanalyzer (Agilent technologies, Palo Alto, CA). cDNA was synthesized from 4 µg of total RNA using One-Cycle Target Labeling and Control Reagents (Affymetrix, Santa Clara, CA) to produce biotin labeled cRNA. The cRNA preparation (15 µg) were fragmented at 94ºC for 35 min into 35-200 bases in length.

growth_protocol:
15 day-old Nipponbare rice plants, grown at 28º±2ºC using a 16-h/8-h light/dark cycles, were used.
Elicitors from the Magnaporthe oryzae strain 18.1 were prepared as previously described (Casacuberta JM, Raventos D, Puigdomenech P and Segundo BS. (1992). Expression of the Gene Encoding the PR-Like Protein PRms in Germinating Maize Embryos. Mol Gen Genet 234(1): 97-104.)

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

treatment_protocol: Elicitor treatment was performed by spraying the rice plants with 100 mL of a Magnaporthe oryzae 18.1 suspension (300 µg elicitor/mL) of sterile water containing 0.02% Tween-20 (v/v)

value: 15-days old plants

tag: cultivar

value: Nipponbare

tag: elicitors

value: Magnaporthe oryzae 18.1


title: 252800515178-1

value: B220+ splenic B cells

tag: strain

tag: rin number


title: Elicitor 2h, biological rep3


title: 12 months Mouse hipocampus 002

tag: strain b6(%)

tag: strain sjl(%)

tag: strain dba2(%)

tag: log10(guhcl fractionation a-beta1-40)


title: Control 2h, biological rep2

description: treatment was performed spraying plants with sterile water containing 0.02% Tween-20 (v/v)

source_name: Control Leaves

tag: age

value: Water


title: 252800515187-1

data_processing: Feature extraction data processing. Quantile Normalization within R bioconductor.

tag: tissue

value: wild type


title: Elicitor 2h, biological rep1


title: Control 2h, biological rep3


title: SKW batch 3 at day 8 ABF-1-GFP

city: Taipei

first: Yikai

last: Chiu

address: 128 Academia Road, Section 2, Nankang

country: Taiwan

institute: Genomics Research Center, Academia Sinica

description: Gene expression data from SKW cells transduced with lentiviral vector expressing ABF-1-GFP

hyb_protocol: Following fragmentation, 30 mg of cRNA were hybridized for 16 hr at 45°C on GeneChip human Genome U133 plus Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip scanner 3000.

data_processing: The data were analyzed by RMA with GeneSpring version 7.3 or 10 software.

source_name: SKW lymphoblastoid cells with enforced ABF-1-GFP expression

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol using 3-5 mg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: SKW cells were cultured in RPMI1640 supplemented with 10% FBS. The cell denity was maiteined in 5´10^5-2´10^6.

extract_protocol: Total RNA was isolated by RNeasay mini kit (Qiagen).

treatment_protocol: SKW cells were transduced with ABF-1-GFP lentiviral vector or control GFP vector.

tag: cell type

value: SKW lymphoblastoid cells


title: SKW batch 2 at day 8 GFP

description: Gene expression data from SKW cells transduced with lentiviral vector expressing GFP

source_name: SKW lymphoblastoid cells with enforced GFP expression


title: 252800515187-2


title: SKW batch 2 at day 8 ABF-1-GFP


title: 12 months Mouse hipocampus 001

tag: transgenic(tg)

value: APP Tg


title: SKW batch 3 at day 8 GFP


title: WT Oil Normal, biological replicate 1

description: AH 272.CEL

tag: strain background

tag: injected with

value: corn oil on day7 (D7) after birth

tag: age at tissue collection

value: 15 months

value: liver

tag: tissue subtype

value: Normal


title: 103-AHRR-b2

city: Woods Hole

first: Neelakanteswar

last: Aluru

address: 45 Water Street

department: Biology

institute: Woods Hole Oceanographic Institution

description: Sample 6

hyb_protocol: Equal amount of Cy3 (Universal Reference RNA) and Cy5 (individual samples) labeled cRNA probes were mixed and hybridized

scan_protocol: Genepix 4100A scanner

data_processing: Feature Extraction software and data processing using Limma, bioconductor package

organism: Danio rerio

source_name: embryos_72 hpf_AHRRb morpholino

label_protocol: Labeling was done using Agilent Low Input Quick Amp Labeling kit

extract_protocol: Total RNA was isolated using STAT60 protocol

treatment_protocol: Morpholino oligonucleotides(Control, AHRRa or AHRRb) were injected into 1-2 cell stage zebrafish embryos and sampled at 72 hpf for microarray analysis

value: TL

tag: genotype/variation

tag: developmental stage

value: 72 hpf embryo

value: AHRRb morpholino oligonucleotides

source_name: universal reference RNA

tag: sample type

value: universal reference RNA


title: Elicitor 30', biological rep3

tag: cultivar

tag: elicitors

tag: time


title: SKW batch 1 at day 8 ABF1-GFP


title: Control 2h, biological rep1


title: 103-AHRR-b1

description: Sample 5

tag: strain


title: Elicitor 30', biological rep2


title: SKW batch 1 at day 8 GFP


title: Control 30', biological rep2


title: 252800515187-5

tag: amount in (µg)

value: 3'RR-deficient mice (KO of the 129 IgH allele in a BALBC background)

value: BALBC

tag: rin number


title: Elicitor 30', biological rep1

tag: age

value: 15-days old plants

value: Nipponbare


title: 252800515187-8

tag: tissue

value: B220+ splenic B cells


title: M3M3-1

tag: Sex

value: F

value: Mono

tag: interaction

tag: label

tag: batch


title: Control 30', biological rep3

value: Water


title: 252800515187-7


title: 103-AHRR-a1

description: Sample 3

source_name: embryos_72 hpf_AHRRa morpholino

value: wild type

tag: injected with

value: AHRRa morpholino oligonucleotides


title: 102-CONT-1

description: Sample 1

source_name: embryos_72 hpf_control morpholino

value: control morpholino oligonucleotides


title: 102-CONT-2

description: Sample 2


title: 103-AHRR-a2

description: Sample 4


title: 252800515187-6


title: 252800515187-3


title: Control 30', biological rep1


title: Normal_Control_Pirc_rat23

status: Public on Jan 14 2014

first: Amy

last: Irving

address: 1400 University Avenue

department: McArdle Laboratory for Cancer Research

institute: University of Wisconsin-Madison

hyb_protocol: Agilent One-Color Microarray-Based Gene Expression Analysis 17hrs 65 deg celcius Surehyb chamber

scan_protocol: Agilent Technologies Scanner G2505B US22502567 5um 16bit

data_processing: Agilent Feature extraction versions 9.1 and 9.5 for background subtraction - localbackground and normalization Linear LOWESS.  No quantile normalization was deemed necessary by Partek software.

source_name: normal distal colon

label_protocol: Total RNA was amplified and labeled according to manufacturer instructions. Agilent One-Color Microarray-Based Gene Expression Analysis Agilent low RNA input linear amplification kit, PLUS

growth_protocol: Ad lib feeding and drinking.  12hours light:12hours dark.

extract_protocol: Qiagen Qiashredder columns followed by Qiagen Allprep DNA/RNA Extraction Kit with optional on-the-column Dnase treatment

treatment_protocol: Indicated animals given 4% DSS (500,000 MW) in drinking water from 40-47 and 54-61 days of age.  Sacrificed and dissected at 97 days, samples homogenized in RLTplus and stored at -80C

tag: genotype

value: Pirc/+

tag: treatment

value: Control

value: 97 days


title: Normal_DSS_Pirc_rat20

value: DSS


title: Normal_Control_WT_rat21

value: Apc wild type


title: Normal_DSS_WT_rat22


title: Normal_DSS_WT_rat18


title: Normal_DSS_Pirc_rat16


title: Normal_DSS_Pirc_rat24


title: Normal_DSS_WT_rat14


title: Normal_Control_Pirc_rat11


title: Normal_Control_WT_rat17


title: Normal_DSS_WT_rat26


title: Normal_Control_Pirc_rat15


title: Normal_Control_WT_rat25


title: 4M_PPARa-null_Alcohol 4

first: Henghong

address: 3970 Reservoir Rd., NW

department: Biochemistry

institute: Georgetown University

hyb_protocol: follow Agilent's two-color expression array hybridization protocol

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version 9.1).

data_processing: GeneSpring version11 was used to filter, normalize, and calculate the signal intensities.

source_name: liver RNA

label_protocol: Invitrogen SuperScript indirect cDNA labeling system

growth_protocol: Mice were 6-8 weeks old when the treatment started

extract_protocol: Total RNA extracted using Trizol followed by RNeasy Midi kit

treatment_protocol: Alcohol-treated mice were fed ad libitum a liquid diet containing 4% ethanol. Control animals were fed an isocaloric diet supplemented with maltose dextran

value: liver

value: Alcohol

value: PPARa-null


title: Normal_Control_WT_rat13


title: Normal_Control_Pirc_rat19


title: 4M_PPARa-null_Control 4


title: 4M_PPARa-null_Alcohol 1


title: 4M_PPARa-null_Control 1


title: 4M_PPARa-null_Alcohol 2


title: 4M_PPARa-null_Control 2


title: 4M_WildType_Alcohol 2

value: Wild Type


title: Normal_DSS_Pirc_rat12


title: 4M_WildType_Alcohol 1


title: 4M_PPARa-null_Control 3


title: 4M_WildType_Alcohol 3


title: 4M_WildType_Alcohol 4


title: 4M_PPARa-null_Alcohol 3


title: 4M_WildType_Control 4


title: 2M_PPARa-null_Control 1


title: 4M_WildType_Control 1


title: 2M_PPARa-null_Alcohol 3


title: 2M_PPARa-null_Control 4


title: 2M_PPARa-null_Alcohol 1


title: 2M_WildType_Alcohol 1


title: 2M_PPARa-null_Control 2


title: 2M_PPARa-null_Alcohol 4


title: 4M_WildType_Control 2


title: 2M_PPARa-null_Control 3


title: 4M_WildType_Control 3


title: 2M_WildType_Control 2


title: 2M_WildType_Control 4


title: 2M_WildType_Control 3


title: 1M_PPARa-null_Control 4


title: 2M_WildType_Control 1


title: 2M_WildType_Alcohol 2


title: 2M_WildType_Alcohol 3


title: 2M_WildType_Alcohol 4


title: 1M_PPARa-null_Control 2


title: 1M_PPARa-null_Control 5


title: 2M_PPARa-null_Alcohol 2


title: 1M_PPARa-null_Alcohol 2


title: 1M_PPARa-null_Control 3


title: 1M_PPARa-null_Alcohol 3


title: 1M_PPARa-null_Control 1


title: BC4885 resting B cells

city: Cologne

first: Alexander

last: Shimabukuro-Vornhagen

address: Kerpener Str. 62

department: Department I of Internal Medicine

institute: University Hospital of Cologne

hyb_protocol: Hybridization and washing was performed following standard procedures for Affymetrix HG-U133A arrays (www.affymetrix.com) on a GeneChip Fluidic station 400, using the EukGe-WS2v4 protocol.

scan_protocol: Scanning was performed twice with filter set at 570 nm on an Agilent gene array scanner (Affymetrix).

data_processing: MAS5.0 (Affymetrix) was used for raw data measurement and quality control. dChip 2006 was used for data normalization, quality control and data analysis.

label: Biotin

source_name: peripheral blood

label_protocol: Synthesis of biotin labeled cRNA was performed with BioArray HighYield RNA TranscriptLabeling Kit (ENZO) following standard procedures.

growth_protocol: For CD40-activation the purified CD19-positive B cells were stimulated via CD40 by means of  NIH3T3 cells transfected with CD40L in 6-well plates in medium containing 45% Dulbecco modified Eagle medium supplemented with 10% fetal calf serum, 2 mM glutamine, and 15 ug/mL gentamicin.

extract_protocol: Immature monocyte-derived DC were harvested on day 7, lyzed in TRIzol and stored at 80°C until further processing. RNA was extracted from cell lyzates with chloroform/isopropanol method, and was clean-uped in silica columns (Qiagen). The quality of the isolated RNA was determined by measuring the A260/280 ratio and the integrity of the ribosomal 28s and 18s bands were determined by agarose-gel electrophoresis.

treatment_protocol: Human B cells were purified from buffy coats using CD19 MACS.

tag: donor id

value: peripheral blood

tag: cell type

value: CD19-positive B cells

tag: cell status

value: Resting


title: 252800515187-4

value: B220+ splenic B cells

tag: genotype/variation


title: 1M_WildType_Alcohol 4

last: Li

tag: time


title: 1M_WildType_Alcohol 3

tag: strain


title: 1M_WildType_Control 4


title: 1M_WildType_Alcohol 2


title: 1M_WildType_Alcohol 1